From bc99dc593933f81bd5d9ddae7a1ee24ea8bbf814 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 07:09:59 -0500 Subject: [PATCH 001/191] feat(rust): scaffold Rust rewrite workspace + redesigned schema Foundation milestone for the Play/Scala 3 -> Rust rewrite (plan: clean-slate, full parity, Axum + SQLx + Askama, JSONB document columns, noodles for genomics, Apple `container` PostGIS for Docker-less local testing). - 8-crate Cargo workspace (du-domain/db/bio/atproto/external/web/jobs/migrate); compiles and tests green. du-web boots Axum with the /health endpoint. - du-domain: typed IDs, Postgres-mirroring enums, and the variant JSONB contract (Coordinates/Aliases/Annotations) with round-trip tests. - Redesigned schema (migrations 0001-0009) across 10 namespaces, verified applying to live PostGIS. De-sprawl: 3 biosample tables -> 1 unified core.biosample; ~7 deprecated child tables folded into JSONB on parents; metadata DB collapsed into `fed`; scattered at_uri/at_cid -> one `atproto` JSONB column; GIN/GiST/expression indexes on queried JSONB paths. - du-db: PgPool + run_migrations; live-DB integration test (gated on DATABASE_URL) covering all schemas + JSONB variant round-trip. build.rs watches migrations/ so sqlx::migrate! re-embeds on change. - scripts/test-db.sh: Apple `container` PostGIS harness (IP-aware, since Apple containers have no localhost port forwarding), native DATABASE_URL fallback. - Multi-stage Dockerfile (slim runtime, single binary, no JRE), compose.yaml, .env.example. Coexists with the Scala app under rust/ during the transition. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/.env.example | 17 + rust/.gitignore | 3 + rust/Cargo.lock | 3101 +++++++++++++++++ rust/Cargo.toml | 77 + rust/Dockerfile | 44 + rust/compose.yaml | 43 + rust/crates/du-atproto/Cargo.toml | 14 + rust/crates/du-atproto/src/lib.rs | 5 + rust/crates/du-bio/Cargo.toml | 12 + rust/crates/du-bio/src/lib.rs | 5 + rust/crates/du-db/Cargo.toml | 20 + rust/crates/du-db/build.rs | 7 + rust/crates/du-db/src/lib.rs | 33 + rust/crates/du-db/tests/migrations.rs | 125 + rust/crates/du-domain/Cargo.toml | 15 + rust/crates/du-domain/src/enums.rs | 143 + rust/crates/du-domain/src/error.rs | 15 + rust/crates/du-domain/src/ids.rs | 54 + rust/crates/du-domain/src/lib.rs | 15 + rust/crates/du-domain/src/variant.rs | 109 + rust/crates/du-external/Cargo.toml | 14 + rust/crates/du-external/src/lib.rs | 4 + rust/crates/du-jobs/Cargo.toml | 19 + rust/crates/du-jobs/src/main.rs | 14 + rust/crates/du-migrate/Cargo.toml | 23 + rust/crates/du-migrate/src/main.rs | 17 + rust/crates/du-web/Cargo.toml | 25 + rust/crates/du-web/src/main.rs | 36 + rust/crates/du-web/src/routes.rs | 27 + rust/migrations/0001_foundation.sql | 33 + rust/migrations/0002_core.sql | 80 + rust/migrations/0003_tree.sql | 214 ++ rust/migrations/0004_genomics.sql | 220 ++ rust/migrations/0005_ident.sql | 121 + rust/migrations/0006_pubs.sql | 81 + rust/migrations/0007_ibd.sql | 126 + rust/migrations/0008_fed.sql | 75 + .../0009_social_support_billing.sql | 130 + rust/scripts/test-db.sh | 130 + 39 files changed, 5246 insertions(+) create mode 100644 rust/.env.example create mode 100644 rust/.gitignore create mode 100644 rust/Cargo.lock create mode 100644 rust/Cargo.toml create mode 100644 rust/Dockerfile create mode 100644 rust/compose.yaml create mode 100644 rust/crates/du-atproto/Cargo.toml create mode 100644 rust/crates/du-atproto/src/lib.rs create mode 100644 rust/crates/du-bio/Cargo.toml create mode 100644 rust/crates/du-bio/src/lib.rs create mode 100644 rust/crates/du-db/Cargo.toml create mode 100644 rust/crates/du-db/build.rs create mode 100644 rust/crates/du-db/src/lib.rs create mode 100644 rust/crates/du-db/tests/migrations.rs create mode 100644 rust/crates/du-domain/Cargo.toml create mode 100644 rust/crates/du-domain/src/enums.rs create mode 100644 rust/crates/du-domain/src/error.rs create mode 100644 rust/crates/du-domain/src/ids.rs create mode 100644 rust/crates/du-domain/src/lib.rs create mode 100644 rust/crates/du-domain/src/variant.rs create mode 100644 rust/crates/du-external/Cargo.toml create mode 100644 rust/crates/du-external/src/lib.rs create mode 100644 rust/crates/du-jobs/Cargo.toml create mode 100644 rust/crates/du-jobs/src/main.rs create mode 100644 rust/crates/du-migrate/Cargo.toml create mode 100644 rust/crates/du-migrate/src/main.rs create mode 100644 rust/crates/du-web/Cargo.toml create mode 100644 rust/crates/du-web/src/main.rs create mode 100644 rust/crates/du-web/src/routes.rs create mode 100644 rust/migrations/0001_foundation.sql create mode 100644 rust/migrations/0002_core.sql create mode 100644 rust/migrations/0003_tree.sql create mode 100644 rust/migrations/0004_genomics.sql create mode 100644 rust/migrations/0005_ident.sql create mode 100644 rust/migrations/0006_pubs.sql create mode 100644 rust/migrations/0007_ibd.sql create mode 100644 rust/migrations/0008_fed.sql create mode 100644 rust/migrations/0009_social_support_billing.sql create mode 100755 rust/scripts/test-db.sh diff --git a/rust/.env.example b/rust/.env.example new file mode 100644 index 0000000..ef42429 --- /dev/null +++ b/rust/.env.example @@ -0,0 +1,17 @@ +# Copy to rust/.env and adjust. 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b/rust/Cargo.toml new file mode 100644 index 0000000..7612440 --- /dev/null +++ b/rust/Cargo.toml @@ -0,0 +1,77 @@ +# DecodingUs — Rust workspace (rewrite of the Play/Scala 3 app) +# See /Users/jkane/.claude/plans/robust-knitting-lampson.md +[workspace] +resolver = "2" +members = [ + "crates/du-domain", + "crates/du-db", + "crates/du-bio", + "crates/du-atproto", + "crates/du-external", + "crates/du-web", + "crates/du-jobs", + "crates/du-migrate", +] + +[workspace.package] +version = "0.1.0" +edition = "2021" +rust-version = "1.80" +license = "BSD-3-Clause" +repository = "https://github.com/decodingus/decodingus" + +[workspace.dependencies] +# Internal crates +du-domain = { path = "crates/du-domain" } +du-db = { path = "crates/du-db" } +du-bio = { path = "crates/du-bio" } +du-atproto = { path = "crates/du-atproto" } +du-external = { path = "crates/du-external" } + +# Async runtime + web +tokio = { version = "1", features = ["full"] } +axum = { version = "0.7", features = ["macros"] } +tower = "0.5" +tower-http = { version = "0.6", features = ["fs", "trace", "compression-gzip", "catch-panic"] } +tower-cookies = "0.10" + +# Database (runtime-checked queries for now; switch to compile-time macros + .sqlx +# offline cache once a dev DB is reachable — see plan §3 / §9) +sqlx = { version = "0.8", default-features = false, features = [ + "runtime-tokio-rustls", "postgres", "uuid", "chrono", "json", "macros", "migrate", +] } + +# Templating (typed, compile-time — Twirl analog) +askama = "0.12" + +# Serialization / JSONB payloads +serde = { version = "1", features = ["derive"] } +serde_json = "1" + +# Common types +uuid = { version = "1", features = ["v4", "serde"] } +chrono = { version = "0.4", features = ["serde"] } +rust_decimal = "1" + +# HTTP client (external APIs) +reqwest = { version = "0.12", default-features = false, features = ["json", "rustls-tls"] } + +# Errors / logging / config +thiserror = "2" +anyhow = "1" +tracing = "0.1" +tracing-subscriber = { version = "0.3", features = ["env-filter"] } + +# Crypto +argon2 = "0.5" +bcrypt = "0.16" +ed25519-dalek = "2" +aes-gcm = "0.10" + +# Genomics (pure Rust — replaces htsjdk) +noodles = { version = "0.85", features = ["vcf", "gff", "fasta", "bed"] } + +[profile.release] +lto = "thin" +codegen-units = 1 +strip = true diff --git a/rust/Dockerfile b/rust/Dockerfile new file mode 100644 index 0000000..75d9f58 --- /dev/null +++ b/rust/Dockerfile @@ -0,0 +1,44 @@ +# DecodingUs (Rust) — multi-stage build to a single static-ish binary. +# No JRE, no htslib system lib (genomics is pure-Rust via noodles). +# +# docker build -t decodingus -f rust/Dockerfile rust +# (or via compose.yaml) + +# ── builder ────────────────────────────────────────────────────────────────── +FROM rust:1-bookworm AS builder +WORKDIR /build + +# Cache dependencies: copy manifests first, then sources. +COPY Cargo.toml Cargo.lock ./ +COPY crates ./crates +COPY migrations ./migrations +# SQLx is built in offline mode in CI/Docker (no DB at build time). Once a dev DB +# exists, commit the `.sqlx/` cache and this picks it up automatically. +ENV SQLX_OFFLINE=true +RUN cargo build --release --bin decodingus --bin decodingus-jobs --bin decodingus-migrate + +# ── runtime ────────────────────────────────────────────────────────────────── +FROM debian:bookworm-slim AS runtime +# curl for the healthcheck; ca-certificates for outbound TLS (OpenAlex/ENA/AWS). +RUN apt-get update \ + && apt-get install -y --no-install-recommends ca-certificates curl \ + && rm -rf /var/lib/apt/lists/* + +RUN groupadd -r decodingus && useradd -r -g decodingus decodingus +WORKDIR /app + +COPY --from=builder /build/target/release/decodingus /usr/local/bin/decodingus +COPY --from=builder /build/target/release/decodingus-jobs /usr/local/bin/decodingus-jobs +COPY --from=builder /build/target/release/decodingus-migrate /usr/local/bin/decodingus-migrate +# Static assets + migrations shipped alongside the binary. +COPY --chown=decodingus:decodingus assets ./assets +COPY --chown=decodingus:decodingus migrations ./migrations + +USER decodingus +EXPOSE 9000 +ENV PORT=9000 + +HEALTHCHECK --interval=30s --timeout=10s --start-period=20s --retries=3 \ + CMD curl -fsS http://localhost:9000/health || exit 1 + +CMD ["decodingus"] diff --git a/rust/compose.yaml b/rust/compose.yaml new file mode 100644 index 0000000..d66ba57 --- /dev/null +++ b/rust/compose.yaml @@ -0,0 +1,43 @@ +# DecodingUs (Rust) — production-ish compose. Works with Docker or Apple +# `container compose`. Mirrors the deployment intent of the legacy compose. +# +# docker compose up --build (or: container compose up --build) + +services: + db: + image: postgis/postgis:16-3.4 + environment: + POSTGRES_PASSWORD: ${DU_PG_PASSWORD:-dev} + POSTGRES_DB: ${DU_PG_DB:-decodingus} + ports: + - "5432:5432" + volumes: + - du-pgdata:/var/lib/postgresql/data + healthcheck: + test: ["CMD-SHELL", "pg_isready -U postgres -d ${DU_PG_DB:-decodingus}"] + interval: 10s + timeout: 5s + retries: 10 + + app: + build: + context: . + dockerfile: Dockerfile + environment: + DATABASE_URL: postgres://postgres:${DU_PG_PASSWORD:-dev}@db:5432/${DU_PG_DB:-decodingus}?sslmode=disable + APP_SECRET: ${APP_SECRET:-changeme} + RUST_LOG: ${RUST_LOG:-info,du_web=debug} + ports: + - "9000:9000" + depends_on: + db: + condition: service_healthy + restart: unless-stopped + healthcheck: + test: ["CMD", "curl", "-fsS", "http://localhost:9000/health"] + interval: 30s + timeout: 10s + retries: 3 + +volumes: + du-pgdata: diff --git a/rust/crates/du-atproto/Cargo.toml b/rust/crates/du-atproto/Cargo.toml new file mode 100644 index 0000000..16757f3 --- /dev/null +++ b/rust/crates/du-atproto/Cargo.toml @@ -0,0 +1,14 @@ +[package] +name = "du-atproto" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +# AT Protocol: DID/handle resolution, Ed25519 signature verification, firehose +# decode, PDS client/fleet. Crypto + HTTP deps added during implementation. +[dependencies] +du-domain = { workspace = true } +serde = { workspace = true } +serde_json = { workspace = true } +thiserror = { workspace = true } diff --git a/rust/crates/du-atproto/src/lib.rs b/rust/crates/du-atproto/src/lib.rs new file mode 100644 index 0000000..0c3939b --- /dev/null +++ b/rust/crates/du-atproto/src/lib.rs @@ -0,0 +1,5 @@ +//! AT Protocol / PDS federation (plan §7). Scaffold only. +//! +//! Planned: `did` (PLC directory + handle resolution), `signature` (Ed25519 +//! multibase verification against AT Protocol spec test vectors), `firehose` +//! (Atmosphere lexicon event decode), `pds` (client + fleet heartbeat/submission). diff --git a/rust/crates/du-bio/Cargo.toml b/rust/crates/du-bio/Cargo.toml new file mode 100644 index 0000000..19a5fb6 --- /dev/null +++ b/rust/crates/du-bio/Cargo.toml @@ -0,0 +1,12 @@ +[package] +name = "du-bio" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +# Genomics file I/O (pure Rust, replaces htsjdk). noodles + a ported liftover +# module are added when the genomics ingestion subsystem is implemented. +[dependencies] +du-domain = { workspace = true } +thiserror = { workspace = true } diff --git a/rust/crates/du-bio/src/lib.rs b/rust/crates/du-bio/src/lib.rs new file mode 100644 index 0000000..584dd43 --- /dev/null +++ b/rust/crates/du-bio/src/lib.rs @@ -0,0 +1,5 @@ +//! Genomics file I/O for DecodingUs — pure Rust, replacing the JVM `htsjdk`. +//! +//! Planned modules (plan §6): `vcf`/`gff`/`fasta` (noodles wrappers), `liftover` +//! (ported UCSC chain-file interval mapping — no drop-in crate exists), and +//! `callable_loci` (BED interval math). Scaffold only for now. diff --git a/rust/crates/du-db/Cargo.toml b/rust/crates/du-db/Cargo.toml new file mode 100644 index 0000000..dc9b31f --- /dev/null +++ b/rust/crates/du-db/Cargo.toml @@ -0,0 +1,20 @@ +[package] +name = "du-db" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +# Data-access layer: SQLx pool + per-aggregate query modules. Runtime-checked +# queries for now (no live DB in this environment); migrate to compile-time +# `query_as!` + committed `.sqlx` offline cache once a dev DB is reachable. +[dependencies] +du-domain = { workspace = true } +sqlx = { workspace = true } +tokio = { workspace = true } +serde = { workspace = true } +serde_json = { workspace = true } +uuid = { workspace = true } +chrono = { workspace = true } +thiserror = { workspace = true } +tracing = { workspace = true } diff --git a/rust/crates/du-db/build.rs b/rust/crates/du-db/build.rs new file mode 100644 index 0000000..9271537 --- /dev/null +++ b/rust/crates/du-db/build.rs @@ -0,0 +1,7 @@ +// `sqlx::migrate!` embeds the migrations directory at COMPILE time. Without this +// hint, adding/editing a .sql file does not rebuild du-db, so the embedded set +// goes stale and migrations silently fail to apply. Watch the directory so any +// change forces a recompile. +fn main() { + println!("cargo:rerun-if-changed=../../migrations"); +} diff --git a/rust/crates/du-db/src/lib.rs b/rust/crates/du-db/src/lib.rs new file mode 100644 index 0000000..f242e66 --- /dev/null +++ b/rust/crates/du-db/src/lib.rs @@ -0,0 +1,33 @@ +//! Data-access layer. Owns the `PgPool` and exposes per-aggregate query modules. +//! +//! Status: scaffold. The pool + error type are wired; query modules +//! (`biosample`, `variant`, `haplogroup`, …) land as each subsystem is ported. + +use sqlx::postgres::{PgPool, PgPoolOptions}; +use std::time::Duration; +use thiserror::Error; + +#[derive(Debug, Error)] +pub enum DbError { + #[error("database error: {0}")] + Sqlx(#[from] sqlx::Error), + #[error("migration error: {0}")] + Migrate(#[from] sqlx::migrate::MigrateError), +} + +/// Connect and return a pool. `database_url` is the standard `postgres://` DSN +/// (driven by `DATABASE_URL`; see `scripts/test-db.sh` and plan §9). +pub async fn connect(database_url: &str, max_connections: u32) -> Result { + let pool = PgPoolOptions::new() + .max_connections(max_connections) + .acquire_timeout(Duration::from_secs(10)) + .connect(database_url) + .await?; + Ok(pool) +} + +/// Apply the workspace migrations (the redesigned schema) to the given pool. +pub async fn run_migrations(pool: &PgPool) -> Result<(), DbError> { + sqlx::migrate!("../../migrations").run(pool).await?; + Ok(()) +} diff --git a/rust/crates/du-db/tests/migrations.rs b/rust/crates/du-db/tests/migrations.rs new file mode 100644 index 0000000..669619e --- /dev/null +++ b/rust/crates/du-db/tests/migrations.rs @@ -0,0 +1,125 @@ +//! Integration test: applies the redesigned schema to a live Postgres and +//! exercises the JSONB variant contract end-to-end. +//! +//! Skips (passes) when DATABASE_URL is unset so `cargo test` stays green without +//! a database. To run for real: +//! eval "$(./scripts/test-db.sh up)" && cargo test -p du-db -- --nocapture + +use du_domain::variant::{BuildCoordinate, Coordinates}; +use du_domain::ReferenceBuild; + +fn database_url() -> Option { + std::env::var("DATABASE_URL").ok().filter(|s| !s.is_empty()) +} + +#[tokio::test] +async fn migrations_apply_and_variant_jsonb_roundtrips() { + let Some(url) = database_url() else { + eprintln!("DATABASE_URL unset — skipping live-DB test"); + return; + }; + + let pool = du_db::connect(&url, 4).await.expect("connect"); + du_db::run_migrations(&pool).await.expect("run migrations"); + + // A representative table from every schema in the redesign exists — proves + // the full migration sequence (0001..0009) applies as a unit. + for obj in [ + "core.variant", + "core.biosample", + "core.specimen_donor", + "core.genome_region", + "tree.haplogroup", + "tree.change_set", + "tree.biosample_private_variant", + "genomics.sequence_file", + "genomics.alignment_metadata", + "genomics.test_type_definition", + "pubs.publication", + "pubs.publication_biosample", + "ident.users", + "ident.roles", + "ibd.ibd_discovery_index", + "ibd.population_breakdown", + "fed.pds_node", + "fed.pds_submission", + "social.reputation_event", + "social.group_project", + "support.contact_message", + "billing.patron_subscription", + ] { + let exists: Option = sqlx::query_scalar("SELECT to_regclass($1)::text") + .bind(obj) + .fetch_one(&pool) + .await + .expect("to_regclass"); + assert_eq!(exists.as_deref(), Some(obj), "{obj} should exist"); + } + + // The base RBAC roles are seeded. + let roles: i64 = + sqlx::query_scalar("SELECT count(*) FROM ident.roles WHERE name IN ('Admin','Curator','TreeCurator')") + .fetch_one(&pool) + .await + .expect("count roles"); + assert_eq!(roles, 3, "base roles should be seeded"); + + // PostGIS / citext extensions are installed. + let postgis: i64 = sqlx::query_scalar( + "SELECT count(*) FROM pg_extension WHERE extname IN ('postgis','citext','pgcrypto')", + ) + .fetch_one(&pool) + .await + .expect("pg_extension"); + assert_eq!(postgis, 3, "postgis, citext, pgcrypto should be installed"); + + // Insert a variant whose coordinates JSONB is the du-domain shape, then read + // it back and confirm it deserializes and is queryable by JSONB path. + let mut coords = Coordinates::default(); + coords.set( + ReferenceBuild::GRCh38, + BuildCoordinate { + contig: "chrY".into(), + position: 2_787_319, + reference_allele: Some("C".into()), + alternate_allele: Some("T".into()), + }, + ); + let coords_json = serde_json::to_value(&coords).unwrap(); + + let id: i64 = sqlx::query_scalar( + "INSERT INTO core.variant (canonical_name, mutation_type, coordinates) + VALUES ($1, 'SNP', $2) RETURNING id", + ) + .bind("M269") + .bind(&coords_json) + .fetch_one(&pool) + .await + .expect("insert variant"); + + // Read the JSONB back as a serde_json::Value and decode into the typed shape. + let stored: serde_json::Value = + sqlx::query_scalar("SELECT coordinates FROM core.variant WHERE id = $1") + .bind(id) + .fetch_one(&pool) + .await + .expect("select coordinates"); + let decoded: Coordinates = serde_json::from_value(stored).unwrap(); + assert_eq!(decoded.get(ReferenceBuild::GRCh38).unwrap().position, 2_787_319); + + // JSONB-path query (the kind the GIN index accelerates) finds it by build. + let by_path: i64 = sqlx::query_scalar( + "SELECT count(*) FROM core.variant WHERE coordinates -> 'GRCh38' ->> 'contig' = 'chrY'", + ) + .fetch_one(&pool) + .await + .expect("jsonb path query"); + assert!(by_path >= 1, "variant should be found by JSONB path"); + + // Clean up so the test is re-runnable against a persistent DB. + sqlx::query("DELETE FROM core.variant WHERE id = $1") + .bind(id) + .execute(&pool) + .await + .expect("cleanup"); +} diff --git a/rust/crates/du-domain/Cargo.toml b/rust/crates/du-domain/Cargo.toml new file mode 100644 index 0000000..6656d62 --- /dev/null +++ b/rust/crates/du-domain/Cargo.toml @@ -0,0 +1,15 @@ +[package] +name = "du-domain" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +# Pure domain layer: types + algorithms, NO IO. Keep dependencies minimal. +[dependencies] +serde = { workspace = true } +serde_json = { workspace = true } +uuid = { workspace = true } +chrono = { workspace = true } +rust_decimal = { workspace = true } +thiserror = { workspace = true } diff --git a/rust/crates/du-domain/src/enums.rs b/rust/crates/du-domain/src/enums.rs new file mode 100644 index 0000000..a53ab8d --- /dev/null +++ b/rust/crates/du-domain/src/enums.rs @@ -0,0 +1,143 @@ +//! Domain enums mirroring the Postgres native enums in the redesigned schema. +//! +//! `serde(rename_all = "SCREAMING_SNAKE_CASE")` keeps the wire/JSONB form equal +//! to the Postgres enum labels so `du-db` can map these directly with +//! `#[derive(sqlx::Type)]` and JSONB round-trips are stable. + +use serde::{Deserialize, Serialize}; + +/// Y-DNA vs mtDNA. (legacy `dna_type` / `HaplogroupType`) +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum DnaType { + YDna, + MtDna, +} + +/// Origin of a biosample. Replaces the three separate legacy tables +/// (`biosample`, `citizen_biosample`, `pgp_biosample`) — see plan §2. +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum BiosampleSource { + Standard, + Citizen, + Pgp, + External, + Ancient, +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum BiologicalSex { + Male, + Female, + Intersex, +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum DataGenerationMethod { + Sequencing, + Genotyping, +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum TargetType { + WholeGenome, + YChromosome, + MtDna, + Autosomal, + XChromosome, + Mixed, +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum MutationType { + Snp, + Indel, + Str, + Del, + Ins, + Mnp, +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum NamingStatus { + Unnamed, + PendingReview, + Named, +} + +/// Reference genome builds tracked across the platform. The redesigned variant +/// `coordinates` JSONB is keyed by these. +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)] +pub enum ReferenceBuild { + #[serde(rename = "GRCh37")] + GRCh37, + #[serde(rename = "GRCh38")] + GRCh38, + /// T2T-CHM13 / hs1. + #[serde(rename = "hs1")] + Hs1, +} + +impl ReferenceBuild { + pub fn as_str(&self) -> &'static str { + match self { + ReferenceBuild::GRCh37 => "GRCh37", + ReferenceBuild::GRCh38 => "GRCh38", + ReferenceBuild::Hs1 => "hs1", + } + } + + pub fn parse(s: &str) -> Result { + match s { + "GRCh37" => Ok(ReferenceBuild::GRCh37), + "GRCh38" => Ok(ReferenceBuild::GRCh38), + "hs1" | "CHM13" | "T2T-CHM13" => Ok(ReferenceBuild::Hs1), + other => Err(crate::DomainError::InvalidBuild(other.to_string())), + } + } +} + +/// Tree change-set lifecycle (legacy `tree.change_set_status`). +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "SCREAMING_SNAKE_CASE")] +pub enum ChangeSetStatus { + Draft, + ReadyForReview, + UnderReview, + Applied, + Discarded, +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn reference_build_roundtrips_through_json() { + for b in [ReferenceBuild::GRCh37, ReferenceBuild::GRCh38, ReferenceBuild::Hs1] { + let s = serde_json::to_string(&b).unwrap(); + let back: ReferenceBuild = serde_json::from_str(&s).unwrap(); + assert_eq!(b, back); + assert_eq!(format!("\"{}\"", b.as_str()), s); + } + } + + #[test] + fn enum_labels_match_screaming_snake_case() { + assert_eq!(serde_json::to_string(&DnaType::YDna).unwrap(), "\"Y_DNA\""); + assert_eq!( + serde_json::to_string(&BiosampleSource::External).unwrap(), + "\"EXTERNAL\"" + ); + assert_eq!( + serde_json::to_string(&NamingStatus::PendingReview).unwrap(), + "\"PENDING_REVIEW\"" + ); + } +} diff --git a/rust/crates/du-domain/src/error.rs b/rust/crates/du-domain/src/error.rs new file mode 100644 index 0000000..76b6dfa --- /dev/null +++ b/rust/crates/du-domain/src/error.rs @@ -0,0 +1,15 @@ +use thiserror::Error; + +/// Errors raised by pure domain logic (validation, invariant violations, +/// algorithm preconditions). IO/database errors live in their own crates. +#[derive(Debug, Error)] +pub enum DomainError { + #[error("validation failed: {0}")] + Validation(String), + + #[error("invalid reference build: {0}")] + InvalidBuild(String), + + #[error("invariant violated: {0}")] + Invariant(String), +} diff --git a/rust/crates/du-domain/src/ids.rs b/rust/crates/du-domain/src/ids.rs new file mode 100644 index 0000000..5cfbbf3 --- /dev/null +++ b/rust/crates/du-domain/src/ids.rs @@ -0,0 +1,54 @@ +//! Strongly-typed identifiers. Prevents mixing up the many integer/UUID keys +//! that flow through the genomics domain (a frequent source of bugs in the +//! legacy code where everything was a bare `Int`/`UUID`). + +use serde::{Deserialize, Serialize}; +use uuid::Uuid; + +macro_rules! int_id { + ($(#[$m:meta])* $name:ident) => { + $(#[$m])* + #[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, PartialOrd, Ord, Serialize, Deserialize)] + #[serde(transparent)] + pub struct $name(pub i64); + + impl std::fmt::Display for $name { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + write!(f, "{}", self.0) + } + } + impl From for $name { + fn from(v: i64) -> Self { $name(v) } + } + }; +} + +int_id!(/// Primary key of `core.variant`. + VariantId); +int_id!(/// Primary key of `tree.haplogroup`. + HaplogroupId); +int_id!(/// Primary key of `pub.publication`. + PublicationId); + +/// A biosample's stable cross-system identity (UUID), shared by all sources +/// (standard/citizen/pgp/external/ancient) in the unified `core.biosample`. +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)] +#[serde(transparent)] +pub struct SampleGuid(pub Uuid); + +impl std::fmt::Display for SampleGuid { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + write!(f, "{}", self.0) + } +} + +/// A user's stable identity (UUID). +#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)] +#[serde(transparent)] +pub struct UserId(pub Uuid); + +impl std::fmt::Display for UserId { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + write!(f, "{}", self.0) + } +} diff --git a/rust/crates/du-domain/src/lib.rs b/rust/crates/du-domain/src/lib.rs new file mode 100644 index 0000000..3d4d61f --- /dev/null +++ b/rust/crates/du-domain/src/lib.rs @@ -0,0 +1,15 @@ +//! Pure domain layer for DecodingUs: types and algorithms with no IO. +//! +//! This crate intentionally has no database, web, or async dependencies. JSONB +//! payload shapes (the redesigned "document columns") live here as `serde` +//! structs so both `du-db` (persistence) and `du-web` (presentation) share one +//! source of truth. + +pub mod enums; +pub mod error; +pub mod ids; +pub mod variant; + +pub use enums::*; +pub use error::DomainError; +pub use ids::*; diff --git a/rust/crates/du-domain/src/variant.rs b/rust/crates/du-domain/src/variant.rs new file mode 100644 index 0000000..8d8dbd7 --- /dev/null +++ b/rust/crates/du-domain/src/variant.rs @@ -0,0 +1,109 @@ +//! Variant domain model and its JSONB payload shapes. +//! +//! This is the canonical example of the schema redesign: the legacy `variant` + +//! `variant_alias` tables (and per-build coordinate rows) collapse into one +//! `core.variant` row whose `aliases`, `coordinates`, and `annotations` columns +//! are JSONB. These structs ARE that JSONB contract. + +use crate::enums::{MutationType, NamingStatus, ReferenceBuild}; +use crate::ids::VariantId; +use serde::{Deserialize, Serialize}; +use std::collections::BTreeMap; + +/// A coordinate of a variant on one reference build. +#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +pub struct BuildCoordinate { + /// Contig/accession on this build (e.g. "chrY", "CM000686.2"). + pub contig: String, + pub position: i64, + #[serde(skip_serializing_if = "Option::is_none")] + pub reference_allele: Option, + #[serde(skip_serializing_if = "Option::is_none")] + pub alternate_allele: Option, +} + +/// `core.variant.coordinates` JSONB — keyed by reference build. +/// Stored as `{ "GRCh38": {...}, "hs1": {...} }`. +#[derive(Debug, Clone, Default, PartialEq, Eq, Serialize, Deserialize)] +#[serde(transparent)] +pub struct Coordinates(pub BTreeMap); + +impl Coordinates { + pub fn get(&self, build: ReferenceBuild) -> Option<&BuildCoordinate> { + self.0.get(build.as_str()) + } + + pub fn set(&mut self, build: ReferenceBuild, coord: BuildCoordinate) { + self.0.insert(build.as_str().to_string(), coord); + } +} + +/// `core.variant.aliases` JSONB — consolidates the old `variant_alias` rows. +#[derive(Debug, Clone, Default, PartialEq, Eq, Serialize, Deserialize)] +pub struct Aliases { + #[serde(default, skip_serializing_if = "Vec::is_empty")] + pub common_names: Vec, + #[serde(default, skip_serializing_if = "Vec::is_empty")] + pub rs_ids: Vec, + /// alias -> source attribution (e.g. "M269" -> "ISOGG"). + #[serde(default, skip_serializing_if = "BTreeMap::is_empty")] + pub sources: BTreeMap, +} + +/// `core.variant.annotations` JSONB. +#[derive(Debug, Clone, Default, PartialEq, Eq, Serialize, Deserialize)] +pub struct Annotations { + #[serde(default, skip_serializing_if = "Vec::is_empty")] + pub cytobands: Vec, + #[serde(default, skip_serializing_if = "Vec::is_empty")] + pub str_overlaps: Vec, +} + +/// A fully-hydrated variant (scalar columns + decoded JSONB payloads). +#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +pub struct Variant { + pub id: VariantId, + pub canonical_name: String, + pub mutation_type: MutationType, + pub naming_status: NamingStatus, + pub aliases: Aliases, + pub coordinates: Coordinates, + pub annotations: Annotations, +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn coordinates_json_is_keyed_by_build_label() { + let mut c = Coordinates::default(); + c.set( + ReferenceBuild::GRCh38, + BuildCoordinate { + contig: "chrY".into(), + position: 2_787_319, + reference_allele: Some("C".into()), + alternate_allele: Some("T".into()), + }, + ); + let json = serde_json::to_value(&c).unwrap(); + assert!(json.get("GRCh38").is_some(), "keyed by build label: {json}"); + assert_eq!(json["GRCh38"]["position"], 2_787_319); + + // round-trips and is queryable by typed build. + let back: Coordinates = serde_json::from_value(json).unwrap(); + assert_eq!(back.get(ReferenceBuild::GRCh38).unwrap().contig, "chrY"); + assert!(back.get(ReferenceBuild::Hs1).is_none()); + } + + #[test] + fn empty_alias_fields_are_omitted_from_json() { + let a = Aliases { + common_names: vec!["M269".into()], + ..Default::default() + }; + let json = serde_json::to_string(&a).unwrap(); + assert_eq!(json, r#"{"common_names":["M269"]}"#); + } +} diff --git a/rust/crates/du-external/Cargo.toml b/rust/crates/du-external/Cargo.toml new file mode 100644 index 0000000..be829d3 --- /dev/null +++ b/rust/crates/du-external/Cargo.toml @@ -0,0 +1,14 @@ +[package] +name = "du-external" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +# External integrations: OpenAlex + ENA (reqwest), AWS SES + Secrets Manager, +# reCAPTCHA. HTTP + AWS SDK deps added during implementation. +[dependencies] +du-domain = { workspace = true } +serde = { workspace = true } +serde_json = { workspace = true } +thiserror = { workspace = true } diff --git a/rust/crates/du-external/src/lib.rs b/rust/crates/du-external/src/lib.rs new file mode 100644 index 0000000..b97cd6b --- /dev/null +++ b/rust/crates/du-external/src/lib.rs @@ -0,0 +1,4 @@ +//! External service clients (plan §7). Scaffold only. +//! +//! Planned: `openalex`, `ena`, `ses` (AWS SES email), `secrets` (AWS Secrets +//! Manager with a 1h TTL cache), `recaptcha` (with a mock impl behind a config flag). diff --git a/rust/crates/du-jobs/Cargo.toml b/rust/crates/du-jobs/Cargo.toml new file mode 100644 index 0000000..5154936 --- /dev/null +++ b/rust/crates/du-jobs/Cargo.toml @@ -0,0 +1,19 @@ +[package] +name = "du-jobs" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +[[bin]] +name = "decodingus-jobs" +path = "src/main.rs" + +# Scheduled background workers (plan §7): publication update/discovery, YBrowse +# ingest, variant export, match discovery. Scheduler + job deps added on impl. +[dependencies] +du-db = { workspace = true } +tokio = { workspace = true } +tracing = { workspace = true } +tracing-subscriber = { workspace = true } +anyhow = { workspace = true } diff --git a/rust/crates/du-jobs/src/main.rs b/rust/crates/du-jobs/src/main.rs new file mode 100644 index 0000000..5871525 --- /dev/null +++ b/rust/crates/du-jobs/src/main.rs @@ -0,0 +1,14 @@ +//! Background job runner (replaces Pekko Quartz scheduler). Scaffold only — +//! the five scheduled jobs are wired in during the genomics/external milestone. + +#[tokio::main] +async fn main() -> anyhow::Result<()> { + tracing_subscriber::fmt() + .with_env_filter( + tracing_subscriber::EnvFilter::try_from_default_env() + .unwrap_or_else(|_| "info".into()), + ) + .init(); + tracing::info!("decodingus-jobs scaffold — no jobs scheduled yet"); + Ok(()) +} diff --git a/rust/crates/du-migrate/Cargo.toml b/rust/crates/du-migrate/Cargo.toml new file mode 100644 index 0000000..394f318 --- /dev/null +++ b/rust/crates/du-migrate/Cargo.toml @@ -0,0 +1,23 @@ +[package] +name = "du-migrate" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +[[bin]] +name = "decodingus-migrate" +path = "src/main.rs" + +# One-time ETL: legacy Postgres -> redesigned schema (plan §8). Idempotent, +# resumable, with a `--verify` reconciliation pass. +[dependencies] +du-domain = { workspace = true } +du-db = { workspace = true } +sqlx = { workspace = true } +tokio = { workspace = true } +serde = { workspace = true } +serde_json = { workspace = true } +tracing = { workspace = true } +tracing-subscriber = { workspace = true } +anyhow = { workspace = true } diff --git a/rust/crates/du-migrate/src/main.rs b/rust/crates/du-migrate/src/main.rs new file mode 100644 index 0000000..c37a475 --- /dev/null +++ b/rust/crates/du-migrate/src/main.rs @@ -0,0 +1,17 @@ +//! Legacy -> new schema ETL binary (plan §8). Scaffold only. +//! +//! Usage (planned): +//! decodingus-migrate --legacy --target run the ETL +//! decodingus-migrate --legacy --target --verify reconcile counts + +#[tokio::main] +async fn main() -> anyhow::Result<()> { + tracing_subscriber::fmt() + .with_env_filter( + tracing_subscriber::EnvFilter::try_from_default_env() + .unwrap_or_else(|_| "info".into()), + ) + .init(); + tracing::info!("decodingus-migrate scaffold — ETL transformers not yet implemented"); + Ok(()) +} diff --git a/rust/crates/du-web/Cargo.toml b/rust/crates/du-web/Cargo.toml new file mode 100644 index 0000000..8184fc9 --- /dev/null +++ b/rust/crates/du-web/Cargo.toml @@ -0,0 +1,25 @@ +[package] +name = "du-web" +version.workspace = true +edition.workspace = true +rust-version.workspace = true +license.workspace = true + +[[bin]] +name = "decodingus" +path = "src/main.rs" + +# Axum web app: routers, extractors, Askama templates, i18n, HTMX fragments. +[dependencies] +du-domain = { workspace = true } +du-db = { workspace = true } +axum = { workspace = true } +tokio = { workspace = true } +tower = { workspace = true } +tower-http = { workspace = true } +askama = { workspace = true } +serde = { workspace = true } +serde_json = { workspace = true } +tracing = { workspace = true } +tracing-subscriber = { workspace = true } +anyhow = { workspace = true } diff --git a/rust/crates/du-web/src/main.rs b/rust/crates/du-web/src/main.rs new file mode 100644 index 0000000..f827a2e --- /dev/null +++ b/rust/crates/du-web/src/main.rs @@ -0,0 +1,36 @@ +//! DecodingUs web binary (Axum). HTML + JSON API + static assets + firehose. +//! +//! Scaffold: boots tracing, builds the router, serves `/health` (carried over +//! from the Play app's load-balancer check). Subsystem routers are mounted as +//! they are ported (plan §4, §10). + +use axum::{routing::get, Router}; +use std::net::SocketAddr; + +mod routes; + +#[tokio::main] +async fn main() -> anyhow::Result<()> { + tracing_subscriber::fmt() + .with_env_filter( + tracing_subscriber::EnvFilter::try_from_default_env() + .unwrap_or_else(|_| "info,du_web=debug".into()), + ) + .init(); + + let app = build_router(); + + let port: u16 = std::env::var("PORT").ok().and_then(|p| p.parse().ok()).unwrap_or(9000); + let addr = SocketAddr::from(([0, 0, 0, 0], port)); + tracing::info!(%addr, "decodingus web starting"); + + let listener = tokio::net::TcpListener::bind(addr).await?; + axum::serve(listener, app).await?; + Ok(()) +} + +/// Builds the application router. Split out so handler tests can exercise it +/// without binding a socket. +pub fn build_router() -> Router { + Router::new().route("/health", get(routes::health)) +} diff --git a/rust/crates/du-web/src/routes.rs b/rust/crates/du-web/src/routes.rs new file mode 100644 index 0000000..994a870 --- /dev/null +++ b/rust/crates/du-web/src/routes.rs @@ -0,0 +1,27 @@ +//! HTTP handlers. Grows into submodules (public, curator, api, federation) as +//! subsystems are ported. For now: the health check. + +use axum::http::StatusCode; + +/// Load-balancer / container health check. Mirrors the Play `/health` route. +pub async fn health() -> (StatusCode, &'static str) { + (StatusCode::OK, "ok") +} + +#[cfg(test)] +mod tests { + use crate::build_router; + use axum::body::Body; + use axum::http::{Request, StatusCode}; + use tower::ServiceExt; // for `oneshot` + + #[tokio::test] + async fn health_returns_ok() { + let app = build_router(); + let resp = app + .oneshot(Request::builder().uri("/health").body(Body::empty()).unwrap()) + .await + .unwrap(); + assert_eq!(resp.status(), StatusCode::OK); + } +} diff --git a/rust/migrations/0001_foundation.sql b/rust/migrations/0001_foundation.sql new file mode 100644 index 0000000..f07c2b6 --- /dev/null +++ b/rust/migrations/0001_foundation.sql @@ -0,0 +1,33 @@ +-- DecodingUs redesigned schema — foundation. +-- Namespaces, extensions, and native enums. See plan §2. +-- +-- The legacy app spread tables across public/auth/tree/social/support/genomics/ +-- billing + a second "metadata" database. We keep logical grouping via schemas +-- but in ONE database (the metadata DB collapses into `fed`). + +CREATE EXTENSION IF NOT EXISTS postgis; -- biosample/donor geometry(Point,4326) +CREATE EXTENSION IF NOT EXISTS citext; -- case-insensitive user email +CREATE EXTENSION IF NOT EXISTS pgcrypto; -- gen_random_uuid() + +CREATE SCHEMA IF NOT EXISTS core; -- samples, donors, variants, regions +CREATE SCHEMA IF NOT EXISTS tree; -- haplogroups + versioning +CREATE SCHEMA IF NOT EXISTS genomics; -- sequencing, coverage, callable loci +CREATE SCHEMA IF NOT EXISTS pubs; -- publications/studies (`pub` is reserved-ish; use pubs) +CREATE SCHEMA IF NOT EXISTS ident; -- users/auth/roles/atproto +CREATE SCHEMA IF NOT EXISTS ibd; -- match discovery +CREATE SCHEMA IF NOT EXISTS fed; -- PDS fleet/firehose (was the metadata DB) +CREATE SCHEMA IF NOT EXISTS social; -- reputation/messaging +CREATE SCHEMA IF NOT EXISTS support; -- contact messages +CREATE SCHEMA IF NOT EXISTS billing; -- subscriptions + +-- Native enums. Labels match du-domain serde forms (SCREAMING_SNAKE_CASE) so +-- Rust maps them directly via #[derive(sqlx::Type)] and JSONB round-trips align. +CREATE TYPE core.dna_type AS ENUM ('Y_DNA', 'MT_DNA'); +CREATE TYPE core.biological_sex AS ENUM ('MALE', 'FEMALE', 'INTERSEX'); +CREATE TYPE core.biosample_source AS ENUM ('STANDARD', 'CITIZEN', 'PGP', 'EXTERNAL', 'ANCIENT'); +CREATE TYPE core.data_generation_method AS ENUM ('SEQUENCING', 'GENOTYPING'); +CREATE TYPE core.target_type AS ENUM ('WHOLE_GENOME', 'Y_CHROMOSOME', 'MT_DNA', 'AUTOSOMAL', 'X_CHROMOSOME', 'MIXED'); +CREATE TYPE core.mutation_type AS ENUM ('SNP', 'INDEL', 'STR', 'DEL', 'INS', 'MNP'); +CREATE TYPE core.naming_status AS ENUM ('UNNAMED', 'PENDING_REVIEW', 'NAMED'); +CREATE TYPE tree.change_set_status AS ENUM ('DRAFT', 'READY_FOR_REVIEW', 'UNDER_REVIEW', 'APPLIED', 'DISCARDED'); +CREATE TYPE tree.tree_change_type AS ENUM ('CREATE', 'UPDATE', 'DELETE', 'REPARENT', 'VARIANT_EDIT'); diff --git a/rust/migrations/0002_core.sql b/rust/migrations/0002_core.sql new file mode 100644 index 0000000..470848d --- /dev/null +++ b/rust/migrations/0002_core.sql @@ -0,0 +1,80 @@ +-- core schema: variants, specimen donors, the UNIFIED biosample, genome regions. +-- This migration realizes the central de-sprawl moves from plan §2. + +-- ── Variants ────────────────────────────────────────────────────────────── +-- One row per variant. Replaces legacy `variant` + `variant_alias` + per-build +-- coordinate rows. JSONB payload shapes are defined in du-domain::variant. +CREATE TABLE core.variant ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + canonical_name TEXT NOT NULL, + mutation_type core.mutation_type NOT NULL, + naming_status core.naming_status NOT NULL DEFAULT 'UNNAMED', + aliases JSONB NOT NULL DEFAULT '{}'::jsonb, -- {common_names, rs_ids, sources} + coordinates JSONB NOT NULL DEFAULT '{}'::jsonb, -- {GRCh38:{...}, hs1:{...}, ...} + annotations JSONB NOT NULL DEFAULT '{}'::jsonb, -- {cytobands, str_overlaps} + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE UNIQUE INDEX variant_canonical_name_key ON core.variant (canonical_name); +-- GIN indexes on the queried JSONB paths (alias lookup, build-coordinate search). +CREATE INDEX variant_aliases_gin ON core.variant USING gin (aliases jsonb_path_ops); +CREATE INDEX variant_coordinates_gin ON core.variant USING gin (coordinates jsonb_path_ops); + +-- ── Specimen donors ─────────────────────────────────────────────────────── +-- Owns demographic data (consolidated from legacy biosample in evolutions 16/18). +CREATE TABLE core.specimen_donor ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + donor_identifier TEXT, + origin_biobank TEXT, + sex core.biological_sex, + donor_type core.biosample_source NOT NULL DEFAULT 'STANDARD', + geocoord geometry(Point, 4326), + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX specimen_donor_geocoord_gist ON core.specimen_donor USING gist (geocoord); + +-- ── Unified biosample ─────────────────────────────────────────────────────── +-- Replaces three legacy tables (biosample, citizen_biosample, pgp_biosample). +-- `source` discriminates; `source_attrs` JSONB holds source-specific fields +-- (at_uri/at_cid, pgp_participant_id, ena accession, …). `atproto` is the single +-- consistent federation reference replacing scattered at_uri/at_cid columns. +CREATE TABLE core.biosample ( + sample_guid UUID PRIMARY KEY DEFAULT gen_random_uuid(), + donor_id BIGINT REFERENCES core.specimen_donor(id), + source core.biosample_source NOT NULL, + accession TEXT, + alias TEXT, + description TEXT, + center_name TEXT, + locked BOOLEAN NOT NULL DEFAULT false, + deleted BOOLEAN NOT NULL DEFAULT false, + source_attrs JSONB NOT NULL DEFAULT '{}'::jsonb, + -- original haplogroup calls per publication (folded in from the dropped + -- biosample_original_haplogroup / citizen_* tables). + original_haplogroups JSONB NOT NULL DEFAULT '[]'::jsonb, + atproto JSONB, -- {uri, cid, repo_did} or NULL when not federated + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE UNIQUE INDEX biosample_accession_key ON core.biosample (accession) WHERE accession IS NOT NULL; +CREATE INDEX biosample_source_idx ON core.biosample (source); +CREATE INDEX biosample_source_attrs_gin ON core.biosample USING gin (source_attrs jsonb_path_ops); +-- Unique federation URI when present (citizen samples carry an at:// URI). +CREATE UNIQUE INDEX biosample_atproto_uri_key + ON core.biosample ((atproto->>'uri')) WHERE atproto IS NOT NULL; + +-- ── Genome regions ────────────────────────────────────────────────────────── +-- Multi-build structural regions (centromere/telomere/PAR/…). Coordinates as +-- JSONB keyed by build (legacy genome_region_v2 shape). +CREATE TABLE core.genome_region ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + region_type TEXT NOT NULL, + name TEXT NOT NULL, + coordinates JSONB NOT NULL DEFAULT '{}'::jsonb, -- {GRCh38:{contig,start,end}, hs1:{...}} + properties JSONB NOT NULL DEFAULT '{}'::jsonb, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE UNIQUE INDEX genome_region_type_name_key ON core.genome_region (region_type, name); +CREATE INDEX genome_region_coordinates_gin ON core.genome_region USING gin (coordinates jsonb_path_ops); diff --git a/rust/migrations/0003_tree.sql b/rust/migrations/0003_tree.sql new file mode 100644 index 0000000..8be9542 --- /dev/null +++ b/rust/migrations/0003_tree.sql @@ -0,0 +1,214 @@ +-- tree schema: haplogroup phylogeny, temporal versioning, bulk-merge staging, +-- and the discovery pipeline. De-sprawl moves (plan §2): +-- * per-revision metadata tables (relationship_revision_metadata, +-- haplogroup_variant_metadata) fold into a `revision` JSONB column. +-- * discovery's polymorphic (sample_type, sample_id) collapses to one +-- core.biosample(sample_guid) FK. + +-- ── Phylogeny ──────────────────────────────────────────────────────────────── +CREATE TABLE tree.haplogroup ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + name TEXT NOT NULL, + haplogroup_type core.dna_type NOT NULL, + lineage TEXT, + source TEXT, + confidence_level TEXT, + formed_ybp INTEGER, + tmrca_ybp INTEGER, + -- multi-source attribution + age-estimate detail, formerly scattered columns. + provenance JSONB NOT NULL DEFAULT '{}'::jsonb, + valid_from TIMESTAMPTZ NOT NULL DEFAULT now(), + valid_until TIMESTAMPTZ +); +CREATE UNIQUE INDEX haplogroup_name_type_key ON tree.haplogroup (name, haplogroup_type); +CREATE INDEX haplogroup_provenance_gin ON tree.haplogroup USING gin (provenance jsonb_path_ops); + +-- Temporal parent/child edges. `revision` JSONB folds the old +-- relationship_revision_metadata (author/timestamp/comment/change_type). +CREATE TABLE tree.haplogroup_relationship ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + child_haplogroup_id BIGINT NOT NULL REFERENCES tree.haplogroup(id), + parent_haplogroup_id BIGINT REFERENCES tree.haplogroup(id), + revision_id INTEGER NOT NULL DEFAULT 1, + source TEXT, + revision JSONB NOT NULL DEFAULT '{}'::jsonb, + valid_from TIMESTAMPTZ NOT NULL DEFAULT now(), + valid_until TIMESTAMPTZ +); +CREATE INDEX haplogroup_rel_child_idx ON tree.haplogroup_relationship (child_haplogroup_id); +CREATE INDEX haplogroup_rel_parent_idx ON tree.haplogroup_relationship (parent_haplogroup_id); +-- One currently-valid parent per child. +CREATE UNIQUE INDEX haplogroup_rel_current_child_key + ON tree.haplogroup_relationship (child_haplogroup_id) WHERE valid_until IS NULL; + +-- Defining variants per haplogroup. `revision` JSONB folds haplogroup_variant_metadata. +CREATE TABLE tree.haplogroup_variant ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + haplogroup_id BIGINT NOT NULL REFERENCES tree.haplogroup(id), + variant_id BIGINT NOT NULL REFERENCES core.variant(id), + revision JSONB NOT NULL DEFAULT '{}'::jsonb, + valid_from TIMESTAMPTZ NOT NULL DEFAULT now(), + valid_until TIMESTAMPTZ +); +CREATE UNIQUE INDEX haplogroup_variant_current_key + ON tree.haplogroup_variant (haplogroup_id, variant_id) WHERE valid_until IS NULL; + +-- Historical/archaeological date constraints for age estimation. +CREATE TABLE tree.genealogical_anchor ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + haplogroup_id BIGINT NOT NULL REFERENCES tree.haplogroup(id), + anchor_type TEXT NOT NULL, -- KNOWN_MRCA / MDKA / ANCIENT_DNA + date_ce INTEGER, + carbon_date_bp INTEGER, + confidence NUMERIC(4,3), + details JSONB NOT NULL DEFAULT '{}'::jsonb +); +CREATE INDEX genealogical_anchor_hg_idx ON tree.genealogical_anchor (haplogroup_id); + +-- Modal STR haplotypes for STR-based age estimation. +CREATE TABLE tree.haplogroup_ancestral_str ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + haplogroup_id BIGINT NOT NULL REFERENCES tree.haplogroup(id), + marker_name TEXT NOT NULL, + ancestral_value INTEGER NOT NULL, + confidence NUMERIC(4,3), + method TEXT -- MODAL / PHYLOGENETIC / MANUAL +); +CREATE INDEX haplogroup_ancestral_str_hg_idx ON tree.haplogroup_ancestral_str (haplogroup_id); + +-- ── Versioning / bulk merge staging ────────────────────────────────────────── +CREATE TABLE tree.change_set ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + source TEXT NOT NULL, -- ISOGG, ytree.net, ... + haplogroup_type core.dna_type, + status tree.change_set_status NOT NULL DEFAULT 'DRAFT', + description TEXT, + change_count INTEGER NOT NULL DEFAULT 0, + created_by TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + promoted_by TEXT, + promoted_at TIMESTAMPTZ +); +CREATE INDEX change_set_status_idx ON tree.change_set (status); + +CREATE TABLE tree.tree_change ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + change_type tree.tree_change_type NOT NULL, + haplogroup_id BIGINT REFERENCES tree.haplogroup(id), + old_values JSONB, + new_values JSONB, + status TEXT NOT NULL DEFAULT 'PENDING' -- PENDING/APPROVED/REJECTED +); +CREATE INDEX tree_change_set_idx ON tree.tree_change (change_set_id, status); + +CREATE TABLE tree.change_set_comment ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + commented_by TEXT NOT NULL, + comment TEXT NOT NULL, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- WIP shadow tables hold proposed structure before it is applied to production. +CREATE TABLE tree.wip_haplogroup ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + placeholder_id INTEGER NOT NULL, -- negative temp id within the change set + name TEXT NOT NULL, + source TEXT, + formed_ybp INTEGER, + provenance JSONB NOT NULL DEFAULT '{}'::jsonb +); +CREATE INDEX wip_haplogroup_cs_idx ON tree.wip_haplogroup (change_set_id); + +CREATE TABLE tree.wip_relationship ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + child_placeholder_id INTEGER NOT NULL, + parent_placeholder_id INTEGER, + parent_production_id BIGINT REFERENCES tree.haplogroup(id) +); + +CREATE TABLE tree.wip_haplogroup_variant ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + wip_haplogroup_id BIGINT NOT NULL REFERENCES tree.wip_haplogroup(id) ON DELETE CASCADE, + variant_id BIGINT NOT NULL REFERENCES core.variant(id) +); + +CREATE TABLE tree.wip_reparent ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + haplogroup_id BIGINT NOT NULL REFERENCES tree.haplogroup(id), + old_parent_id BIGINT REFERENCES tree.haplogroup(id), + new_parent_id BIGINT REFERENCES tree.haplogroup(id) +); + +CREATE TABLE tree.wip_resolution ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + change_set_id BIGINT NOT NULL REFERENCES tree.change_set(id) ON DELETE CASCADE, + wip_haplogroup_id BIGINT REFERENCES tree.wip_haplogroup(id) ON DELETE CASCADE, + wip_reparent_id BIGINT REFERENCES tree.wip_reparent(id) ON DELETE CASCADE, + resolution_type TEXT NOT NULL, -- REPARENT/EDIT_VARIANTS/MERGE_EXISTING/DEFER + new_parent_id BIGINT REFERENCES tree.haplogroup(id), + merge_target_id BIGINT REFERENCES tree.haplogroup(id), + details JSONB NOT NULL DEFAULT '{}'::jsonb +); + +-- ── Discovery pipeline ─────────────────────────────────────────────────────── +-- Private variants found in a sample. Was polymorphic (sample_type, sample_id); +-- now one core.biosample(sample_guid) FK. +CREATE TABLE tree.biosample_private_variant ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid), + variant_id BIGINT NOT NULL REFERENCES core.variant(id), + haplogroup_type core.dna_type NOT NULL, + terminal_haplogroup_id BIGINT REFERENCES tree.haplogroup(id), + status TEXT NOT NULL DEFAULT 'ACTIVE', -- ACTIVE/PROMOTED/INVALIDATED + discovered_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX bpv_sample_idx ON tree.biosample_private_variant (sample_guid); +CREATE INDEX bpv_variant_idx ON tree.biosample_private_variant (variant_id); + +CREATE TABLE tree.proposed_branch ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + proposed_name TEXT, + parent_haplogroup_id BIGINT REFERENCES tree.haplogroup(id), + discovery_sample_guids UUID[] NOT NULL DEFAULT '{}', + evidence_count INTEGER NOT NULL DEFAULT 0, + confidence NUMERIC(4,3), + proposed_by TEXT, + status TEXT NOT NULL DEFAULT 'PROPOSED' -- PROPOSED/UNDER_REVIEW/REJECTED/ACCEPTED +); + +CREATE TABLE tree.proposed_branch_variant ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + proposed_branch_id BIGINT NOT NULL REFERENCES tree.proposed_branch(id) ON DELETE CASCADE, + variant_id BIGINT NOT NULL REFERENCES core.variant(id), + supporting_sample_count INTEGER NOT NULL DEFAULT 0 +); + +CREATE TABLE tree.proposed_branch_evidence ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + proposed_branch_id BIGINT NOT NULL REFERENCES tree.proposed_branch(id) ON DELETE CASCADE, + evidence_type TEXT NOT NULL, -- PRIVATE_VARIANT/SHARED_DERIVED/STRVAL_SIMILARITY/PUBLICATION + evidence_detail JSONB NOT NULL DEFAULT '{}'::jsonb, + confidence NUMERIC(4,3) +); + +CREATE TABLE tree.curator_action ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + proposed_branch_id BIGINT REFERENCES tree.proposed_branch(id) ON DELETE CASCADE, + action TEXT NOT NULL, -- APPROVE/DEFER/REJECT + notes TEXT, + action_by TEXT, + action_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE tree.discovery_config ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + config_key TEXT NOT NULL UNIQUE, + config_value JSONB NOT NULL DEFAULT '{}'::jsonb, + description TEXT +); diff --git a/rust/migrations/0004_genomics.sql b/rust/migrations/0004_genomics.sql new file mode 100644 index 0000000..5a173ff --- /dev/null +++ b/rust/migrations/0004_genomics.sql @@ -0,0 +1,220 @@ +-- genomics schema: sequencing runs/files, coverage, callable loci, labs & +-- instruments, pangenome. De-sprawl (plan §2): +-- * sequence_file_checksum / _http_location / _atp_location -> JSONB on sequence_file +-- * alignment_coverage / pangenome_alignment_coverage -> coverage JSONB on metadata +-- * biosample_callable_loci polymorphic (sample_type, sample_id) -> sample_guid FK +-- * scattered at_uri/at_cid -> single `atproto` JSONB + +-- ── Reference contigs ──────────────────────────────────────────────────────── +CREATE TABLE genomics.genbank_contig ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + accession TEXT NOT NULL UNIQUE, + common_name TEXT, + reference_genome TEXT NOT NULL, -- GRCh37/GRCh38/hs1 + seq_length BIGINT +); + +-- ── Labs & instruments ─────────────────────────────────────────────────────── +CREATE TABLE genomics.sequencing_lab ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + name TEXT NOT NULL UNIQUE, + is_d2c BOOLEAN NOT NULL DEFAULT false, + website_url TEXT, + description_markdown TEXT +); + +CREATE TABLE genomics.sequencer_instrument ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + instrument_id TEXT NOT NULL UNIQUE, -- e.g. 'A00123' + model_name TEXT, + manufacturer TEXT, + year_introduced INTEGER, + estimated_max_throughput BIGINT +); + +CREATE TABLE genomics.instrument_observation ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + instrument_id BIGINT REFERENCES genomics.sequencer_instrument(id), + lab_name TEXT, + biosample_ref TEXT, + platform TEXT, + instrument_model TEXT, + flowcell_id TEXT, + run_date DATE, + confidence TEXT, -- KNOWN/INFERRED/GUESSED + atproto JSONB -- {uri, cid, repo_did} +); +CREATE UNIQUE INDEX instrument_observation_atproto_uri_key + ON genomics.instrument_observation ((atproto->>'uri')) WHERE atproto IS NOT NULL; + +CREATE TABLE genomics.instrument_association_proposal ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + instrument_id BIGINT REFERENCES genomics.sequencer_instrument(id), + proposed_lab_name TEXT, + proposed_model TEXT, + observation_count INTEGER NOT NULL DEFAULT 0, + distinct_citizen_count INTEGER NOT NULL DEFAULT 0, + confidence_score NUMERIC(5,4), + status TEXT NOT NULL DEFAULT 'PENDING', + accepted_lab_id BIGINT REFERENCES genomics.sequencing_lab(id), + accepted_instrument_id BIGINT REFERENCES genomics.sequencer_instrument(id) +); + +-- ── Test types & coverage expectations ────────────────────────────────────── +CREATE TABLE genomics.test_type_definition ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + code TEXT NOT NULL UNIQUE, + display_name TEXT NOT NULL, + category core.data_generation_method NOT NULL, + vendor TEXT, + target_type core.target_type, + expected_min_depth DOUBLE PRECISION, + supports_haplogroup_y BOOLEAN NOT NULL DEFAULT false, + supports_haplogroup_mt BOOLEAN NOT NULL DEFAULT false, + supports_autosomal_ibd BOOLEAN NOT NULL DEFAULT false, + supports_ancestry BOOLEAN NOT NULL DEFAULT false, + typical_file_formats TEXT[] NOT NULL DEFAULT '{}', + description TEXT +); + +CREATE TABLE genomics.coverage_expectation_profile ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + test_type_id BIGINT NOT NULL REFERENCES genomics.test_type_definition(id) ON DELETE CASCADE, + contig_name TEXT, + variant_class TEXT, -- SNP/STR/INDEL + min_depth_high DOUBLE PRECISION, + min_depth_medium DOUBLE PRECISION, + min_depth_low DOUBLE PRECISION, + min_coverage_pct DOUBLE PRECISION, + min_mapping_quality DOUBLE PRECISION +); + +-- ── Pangenome ─────────────────────────────────────────────────────────────── +CREATE TABLE genomics.pangenome_graph ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + graph_name TEXT NOT NULL UNIQUE, + source_gfa_file TEXT, + description TEXT, + creation_date TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE genomics.pangenome_path ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + graph_id BIGINT NOT NULL REFERENCES genomics.pangenome_graph(id) ON DELETE CASCADE, + path_name TEXT NOT NULL, + is_reference BOOLEAN NOT NULL DEFAULT false, + length_bp BIGINT, + UNIQUE (graph_id, path_name) +); + +CREATE TABLE genomics.canonical_pangenome_variant ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + pangenome_graph_id BIGINT NOT NULL REFERENCES genomics.pangenome_graph(id) ON DELETE CASCADE, + variant_type TEXT, + variant_nodes INTEGER[] NOT NULL DEFAULT '{}', + variant_edges INTEGER[] NOT NULL DEFAULT '{}', + reference_path_id BIGINT REFERENCES genomics.pangenome_path(id), + reference_allele_sequence TEXT, + canonical_hash TEXT NOT NULL UNIQUE +); + +-- ── Sequencing runs & files ───────────────────────────────────────────────── +CREATE TABLE genomics.sequence_library ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid), + test_type_id BIGINT REFERENCES genomics.test_type_definition(id), + lab_id BIGINT REFERENCES genomics.sequencing_lab(id), + run_date DATE, + instrument TEXT, + reads BIGINT, + read_length INTEGER, + paired_end BOOLEAN, + insert_size INTEGER, + atproto JSONB, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX sequence_library_sample_idx ON genomics.sequence_library (sample_guid); + +CREATE TABLE genomics.sequence_file ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + library_id BIGINT NOT NULL REFERENCES genomics.sequence_library(id) ON DELETE CASCADE, + file_name TEXT NOT NULL, + file_size_bytes BIGINT, + file_format TEXT, -- BAM/CRAM/VCF/... + aligner TEXT, + target_reference TEXT, + pangenome_graph_id BIGINT REFERENCES genomics.pangenome_graph(id), + checksums JSONB NOT NULL DEFAULT '[]'::jsonb, -- [{algorithm, checksum, verified_at}] + http_locations JSONB NOT NULL DEFAULT '[]'::jsonb, -- [{file_url, file_index_url}] + atp_location JSONB, -- {repo_did, record_cid, record_path} + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX sequence_file_library_idx ON genomics.sequence_file (library_id); + +-- Linear-reference alignment stats. coverage JSONB replaces alignment_coverage; +-- expression indexes target the hot aggregation paths. +CREATE TABLE genomics.alignment_metadata ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sequence_file_id BIGINT NOT NULL REFERENCES genomics.sequence_file(id) ON DELETE CASCADE, + genbank_contig_id BIGINT REFERENCES genomics.genbank_contig(id), + metric_level TEXT NOT NULL, -- CONTIG_OVERALL/REGION + region_name TEXT, + region_start_pos BIGINT, + region_end_pos BIGINT, + reference_build TEXT, + variant_caller TEXT, + coverage JSONB NOT NULL DEFAULT '{}'::jsonb -- {meanDepth, medianDepth, percent_coverage_at_*x} +); +CREATE INDEX alignment_metadata_file_idx ON genomics.alignment_metadata (sequence_file_id); +CREATE INDEX alignment_metadata_meandepth_idx + ON genomics.alignment_metadata (((coverage->>'meanDepth')::double precision)); + +CREATE TABLE genomics.pangenome_alignment_metadata ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sequence_file_id BIGINT NOT NULL REFERENCES genomics.sequence_file(id) ON DELETE CASCADE, + pangenome_graph_id BIGINT NOT NULL REFERENCES genomics.pangenome_graph(id), + metric_level TEXT NOT NULL, -- GRAPH_OVERALL/PATH/NODE/REGION + metadata JSONB NOT NULL DEFAULT '{}'::jsonb -- includes coverage +); + +CREATE TABLE genomics.reported_variant_pangenome ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid), + graph_id BIGINT NOT NULL REFERENCES genomics.pangenome_graph(id), + variant_type TEXT, + variant_nodes INTEGER[] NOT NULL DEFAULT '{}', + variant_edges INTEGER[] NOT NULL DEFAULT '{}', + allele_fraction DOUBLE PRECISION, + depth INTEGER, + zygosity TEXT, -- HOM_REF/HET/HOM_ALT + haplotype_information JSONB NOT NULL DEFAULT '{}'::jsonb +); +CREATE INDEX reported_variant_pangenome_sample_idx ON genomics.reported_variant_pangenome (sample_guid); + +-- ── Chip genotype data ─────────────────────────────────────────────────────── +CREATE TABLE genomics.genotype_data ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid), + test_type_id BIGINT REFERENCES genomics.test_type_definition(id), + provider TEXT, + metrics JSONB NOT NULL DEFAULT '{}'::jsonb, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX genotype_data_sample_idx ON genomics.genotype_data (sample_guid); + +-- ── Callable loci (was polymorphic; now sample_guid FK) ────────────────────── +CREATE TABLE genomics.biosample_callable_loci ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid), + chromosome TEXT NOT NULL, + total_callable_bp BIGINT NOT NULL DEFAULT 0, + region_count INTEGER NOT NULL DEFAULT 0, + bed_file_hash TEXT, + source_test_type_id BIGINT REFERENCES genomics.test_type_definition(id), + y_xdegen_callable_bp BIGINT, + y_ampliconic_callable_bp BIGINT, + y_palindromic_callable_bp BIGINT, + computed_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX callable_loci_sample_idx ON genomics.biosample_callable_loci (sample_guid); diff --git a/rust/migrations/0005_ident.sql b/rust/migrations/0005_ident.sql new file mode 100644 index 0000000..7766d0c --- /dev/null +++ b/rust/migrations/0005_ident.sql @@ -0,0 +1,121 @@ +-- ident schema: users, RBAC, AT Protocol identity/OAuth, consent. + +CREATE TABLE ident.users ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + email CITEXT UNIQUE, -- case-insensitive + did TEXT UNIQUE, -- AT Protocol DID + handle TEXT UNIQUE, + display_name TEXT, + is_active BOOLEAN NOT NULL DEFAULT true, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- ── RBAC ───────────────────────────────────────────────────────────────────── +CREATE TABLE ident.roles ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + name TEXT NOT NULL UNIQUE, + description TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE ident.permissions ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + name TEXT NOT NULL UNIQUE, + description TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE ident.role_permissions ( + role_id UUID NOT NULL REFERENCES ident.roles(id) ON DELETE CASCADE, + permission_id UUID NOT NULL REFERENCES ident.permissions(id) ON DELETE CASCADE, + PRIMARY KEY (role_id, permission_id) +); + +CREATE TABLE ident.user_roles ( + user_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + role_id UUID NOT NULL REFERENCES ident.roles(id) ON DELETE CASCADE, + PRIMARY KEY (user_id, role_id) +); + +-- Base roles the app expects to exist (Admin, Curator, TreeCurator). +INSERT INTO ident.roles (name, description) VALUES + ('Admin', 'Full administrative access'), + ('Curator', 'Content curation'), + ('TreeCurator', 'Haplogroup tree curation') +ON CONFLICT (name) DO NOTHING; + +-- ── AT Protocol identity / OAuth ──────────────────────────────────────────── +CREATE TABLE ident.user_pds_info ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + user_id UUID NOT NULL UNIQUE REFERENCES ident.users(id) ON DELETE CASCADE, + pds_url VARCHAR(512) NOT NULL, + did TEXT UNIQUE, + handle TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE ident.user_login_info ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + user_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + provider_id TEXT NOT NULL, + provider_key TEXT NOT NULL, + -- bcrypt for legacy verification, argon2 for new hashes (NULL for OAuth-only). + password_hash TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now(), + UNIQUE (provider_id, provider_key) +); + +CREATE TABLE ident.user_oauth2_info ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + login_info_id UUID NOT NULL UNIQUE REFERENCES ident.user_login_info(id) ON DELETE CASCADE, + access_token TEXT NOT NULL, + token_type TEXT, + expires_in BIGINT, + refresh_token TEXT, + scope TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE ident.atprotocol_authorization_servers ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + issuer_url TEXT NOT NULL UNIQUE, + authorization_endpoint TEXT, + token_endpoint TEXT, + pushed_authorization_request_endpoint TEXT, + dpop_signing_alg_values_supported TEXT, + scopes_supported TEXT, + metadata_fetched_at TIMESTAMPTZ, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE ident.atprotocol_client_metadata ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + client_id_url TEXT NOT NULL UNIQUE, + client_name TEXT, + logo_uri TEXT, + tos_uri TEXT, + policy_uri TEXT, + redirect_uris TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- ── GDPR cookie consent (authenticated or anonymous) ───────────────────────── +CREATE TABLE ident.cookie_consents ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + user_id UUID REFERENCES ident.users(id) ON DELETE SET NULL, + session_id TEXT, + ip_address_hash VARCHAR(64), + consent_given BOOLEAN NOT NULL DEFAULT false, + consent_timestamp TIMESTAMPTZ NOT NULL DEFAULT now(), + policy_version TEXT, + user_agent TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); diff --git a/rust/migrations/0006_pubs.sql b/rust/migrations/0006_pubs.sql new file mode 100644 index 0000000..643fe83 --- /dev/null +++ b/rust/migrations/0006_pubs.sql @@ -0,0 +1,81 @@ +-- pubs schema: publications, genomic studies, and their links to samples. +-- De-sprawl: publication_biosample + publication_citizen_biosample collapse into +-- one link table now that biosamples are unified under core.biosample. + +CREATE TYPE pubs.study_source AS ENUM ('ENA', 'NCBI_BIOPROJECT', 'NCBI_GENBANK'); + +CREATE TABLE pubs.genomic_study ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + accession TEXT NOT NULL UNIQUE, + title TEXT, + center_name TEXT, + study_name TEXT, + source pubs.study_source NOT NULL DEFAULT 'ENA', + bio_project_id TEXT, + molecule TEXT, + topology TEXT, + taxonomy_id INTEGER, + version INTEGER, + submission_date DATE, + details JSONB NOT NULL DEFAULT '{}'::jsonb +); + +CREATE TABLE pubs.publication ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + pubmed_id TEXT UNIQUE, + doi TEXT UNIQUE, + open_alex_id TEXT UNIQUE, + title TEXT NOT NULL, + journal TEXT, + publication_date DATE, + url TEXT, + authors TEXT, + abstract_summary TEXT, + citation_normalized_percentile NUMERIC, + cited_by_count INTEGER, + open_access_status TEXT, + open_access_url TEXT, + primary_topic TEXT, + publication_type TEXT, + publisher TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- Unified publication<->biosample link (both standard and citizen samples). +CREATE TABLE pubs.publication_biosample ( + publication_id BIGINT NOT NULL REFERENCES pubs.publication(id) ON DELETE CASCADE, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + PRIMARY KEY (publication_id, sample_guid) +); + +CREATE TABLE pubs.publication_study ( + publication_id BIGINT NOT NULL REFERENCES pubs.publication(id) ON DELETE CASCADE, + study_id BIGINT NOT NULL REFERENCES pubs.genomic_study(id) ON DELETE CASCADE, + PRIMARY KEY (publication_id, study_id) +); + +-- Editorial review queue from OpenAlex discovery. +CREATE TABLE pubs.publication_candidate ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + openalex_id TEXT NOT NULL UNIQUE, + doi TEXT, + title TEXT, + abstract TEXT, + publication_date DATE, + journal_name TEXT, + relevance_score NUMERIC, + status TEXT NOT NULL DEFAULT 'pending', -- pending/accepted/rejected/deferred + reviewed_by UUID REFERENCES ident.users(id), + raw_metadata JSONB NOT NULL DEFAULT '{}'::jsonb, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX publication_candidate_status_idx ON pubs.publication_candidate (status); + +CREATE TABLE pubs.publication_search_config ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + name TEXT NOT NULL UNIQUE, + search_query TEXT, + concepts JSONB NOT NULL DEFAULT '[]'::jsonb, + enabled BOOLEAN NOT NULL DEFAULT true +); diff --git a/rust/migrations/0007_ibd.sql b/rust/migrations/0007_ibd.sql new file mode 100644 index 0000000..82cdab2 --- /dev/null +++ b/rust/migrations/0007_ibd.sql @@ -0,0 +1,126 @@ +-- ibd schema: population/ancestry analysis + privacy-preserving IBD matching, +-- attestations, suggestions, and match request/consent tracking. + +-- ── Population & ancestry ──────────────────────────────────────────────────── +CREATE TABLE ibd.population ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + population_name TEXT NOT NULL UNIQUE +); + +CREATE TABLE ibd.analysis_method ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + method_name TEXT NOT NULL UNIQUE +); + +CREATE TABLE ibd.ancestry_analysis ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + analysis_method_id BIGINT NOT NULL REFERENCES ibd.analysis_method(id), + population_id BIGINT NOT NULL REFERENCES ibd.population(id), + probability NUMERIC(5,4) NOT NULL, + UNIQUE (sample_guid, analysis_method_id, population_id) +); + +-- Full ADMIXTURE/PCA breakdown per sample (pca_coordinates as JSONB). +CREATE TABLE ibd.population_breakdown ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + analysis_method TEXT, + panel_type TEXT, + pca_coordinates JSONB NOT NULL DEFAULT '{}'::jsonb, + analysis_date TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX population_breakdown_sample_idx ON ibd.population_breakdown (sample_guid); + +CREATE TABLE ibd.population_breakdown_cache ( + sample_guid UUID PRIMARY KEY REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + breakdown JSONB NOT NULL DEFAULT '{}'::jsonb, + breakdown_hash VARCHAR(64), + cached_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- Cached O(N^2) pairwise overlap scores (order-independent pair key). +CREATE TABLE ibd.population_overlap_score ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid_1 UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + sample_guid_2 UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + score DOUBLE PRECISION NOT NULL, + computed_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE UNIQUE INDEX population_overlap_pair_key + ON ibd.population_overlap_score (LEAST(sample_guid_1, sample_guid_2), GREATEST(sample_guid_1, sample_guid_2)); + +-- ── IBD matching ───────────────────────────────────────────────────────────── +CREATE TABLE ibd.validation_service ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + guid UUID NOT NULL UNIQUE DEFAULT gen_random_uuid(), + name TEXT NOT NULL UNIQUE, + description TEXT, + trust_level INTEGER NOT NULL DEFAULT 0 +); + +CREATE TABLE ibd.ibd_discovery_index ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + sample_guid_1 UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + sample_guid_2 UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + pangenome_graph_id BIGINT REFERENCES genomics.pangenome_graph(id), + match_region_type TEXT NOT NULL, -- AUTOSOMAL/X/Y/MT + total_shared_cm_approx DOUBLE PRECISION, + num_shared_segments_approx INTEGER, + is_publicly_discoverable BOOLEAN NOT NULL DEFAULT false, + consensus_status TEXT, + validation_service_id BIGINT REFERENCES ibd.validation_service(id), + indexed_date TIMESTAMPTZ NOT NULL DEFAULT now() +); +-- Order-independent pair uniqueness per region type. +CREATE UNIQUE INDEX ibd_discovery_pair_key + ON ibd.ibd_discovery_index (LEAST(sample_guid_1, sample_guid_2), GREATEST(sample_guid_1, sample_guid_2), match_region_type); + +CREATE TABLE ibd.ibd_pds_attestation ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + ibd_discovery_index_id BIGINT NOT NULL REFERENCES ibd.ibd_discovery_index(id) ON DELETE CASCADE, + attesting_pds_guid UUID NOT NULL, + attestation_timestamp TIMESTAMPTZ NOT NULL DEFAULT now(), + attestation_signature TEXT NOT NULL, + attestation_type TEXT NOT NULL, -- INITIAL_REPORT/CONFIRMATION/DISPUTE/REVOCATION + attestation_notes TEXT +); +CREATE INDEX ibd_attestation_index_idx ON ibd.ibd_pds_attestation (ibd_discovery_index_id); + +CREATE TABLE ibd.match_suggestion ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + target_sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + suggested_sample_guid UUID NOT NULL REFERENCES core.biosample(sample_guid) ON DELETE CASCADE, + suggestion_type TEXT NOT NULL, -- SHARED_MATCH/POPULATION_OVERLAP/HAPLOGROUP + score DOUBLE PRECISION, + metadata JSONB NOT NULL DEFAULT '{}'::jsonb, + status TEXT NOT NULL DEFAULT 'ACTIVE', -- ACTIVE/DISMISSED/EXPIRED/CONVERTED + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + expires_at TIMESTAMPTZ +); +CREATE INDEX match_suggestion_target_idx ON ibd.match_suggestion (target_sample_guid, status); + +-- ── Match request & consent (AT Protocol records keyed by at:// URI) ───────── +CREATE TABLE ibd.match_request ( + request_uri TEXT PRIMARY KEY, + requester_did TEXT NOT NULL, + target_did TEXT NOT NULL, + requester_sample_guid UUID REFERENCES core.biosample(sample_guid), + target_sample_guid UUID REFERENCES core.biosample(sample_guid), + status TEXT NOT NULL DEFAULT 'PENDING', -- PENDING/CANCELLED/CONSENTED/DECLINED/EXPIRED + details JSONB NOT NULL DEFAULT '{}'::jsonb, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX match_request_target_did_idx ON ibd.match_request (target_did, status); +CREATE INDEX match_request_requester_did_idx ON ibd.match_request (requester_did, status); + +CREATE TABLE ibd.match_consent ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + request_uri TEXT NOT NULL REFERENCES ibd.match_request(request_uri) ON DELETE CASCADE, + consenting_did TEXT NOT NULL, + consent_given BOOLEAN NOT NULL, + consent_uri TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX match_consent_request_idx ON ibd.match_consent (request_uri); diff --git a/rust/migrations/0008_fed.sql b/rust/migrations/0008_fed.sql new file mode 100644 index 0000000..f4e0e75 --- /dev/null +++ b/rust/migrations/0008_fed.sql @@ -0,0 +1,75 @@ +-- fed schema: PDS fleet + firehose. This collapses the legacy second "metadata" +-- database into the single DB (plan §2) — one database, one pool. + +-- Firehose cursor/lease tracking per registered PDS (distributed consumers). +CREATE TABLE fed.pds_registration ( + did TEXT PRIMARY KEY, + pds_url TEXT NOT NULL, + handle TEXT, + last_commit_cid TEXT, + cursor BIGINT, + leased_by_instance_id TEXT, + lease_expires_at TIMESTAMPTZ, + processing_status TEXT NOT NULL DEFAULT 'IDLE', + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX pds_registration_lease_idx ON fed.pds_registration (lease_expires_at); + +CREATE TABLE fed.pds_node ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + did TEXT NOT NULL UNIQUE, + pds_url TEXT, + handle TEXT, + node_name TEXT, + software_version TEXT, + status TEXT NOT NULL DEFAULT 'UNKNOWN', -- ONLINE/OFFLINE/BUSY/ERROR/UNKNOWN + capabilities JSONB NOT NULL DEFAULT '{}'::jsonb, + last_heartbeat TIMESTAMPTZ, + last_commit_cid TEXT, + ip_address TEXT, + os_info TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX pds_node_status_idx ON fed.pds_node (status); + +CREATE TABLE fed.pds_heartbeat_log ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + pds_node_id BIGINT NOT NULL REFERENCES fed.pds_node(id) ON DELETE CASCADE, + status TEXT, + software_version TEXT, + load_metrics JSONB NOT NULL DEFAULT '{}'::jsonb, + processing_queue_size INTEGER, + error_message TEXT, + recorded_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX pds_heartbeat_node_time_idx ON fed.pds_heartbeat_log (pds_node_id, recorded_at DESC); + +CREATE TABLE fed.pds_fleet_config ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + config_key TEXT NOT NULL UNIQUE, + config_value TEXT, + description TEXT, + updated_by TEXT, + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- Distributed variant/haplogroup/STR proposals submitted by edge nodes. +CREATE TABLE fed.pds_submission ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + pds_node_id BIGINT REFERENCES fed.pds_node(id) ON DELETE SET NULL, + submission_type TEXT NOT NULL, -- HAPLOGROUP_CALL/VARIANT_CALL/BRANCH_PROPOSAL/PRIVATE_VARIANT/STR_PROFILE + biosample_guid UUID REFERENCES core.biosample(sample_guid), + proposed_value TEXT, + confidence_score NUMERIC(5,4), + algorithm_version TEXT, + software_version TEXT, + payload JSONB NOT NULL DEFAULT '{}'::jsonb, + status TEXT NOT NULL DEFAULT 'PENDING', -- PENDING/ACCEPTED/REJECTED/SUPERSEDED + reviewed_by TEXT, + reviewed_at TIMESTAMPTZ, + atproto JSONB, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX pds_submission_status_type_idx ON fed.pds_submission (status, submission_type); diff --git a/rust/migrations/0009_social_support_billing.sql b/rust/migrations/0009_social_support_billing.sql new file mode 100644 index 0000000..061a78a --- /dev/null +++ b/rust/migrations/0009_social_support_billing.sql @@ -0,0 +1,130 @@ +-- social / support / billing schemas. + +-- ── social: reputation ────────────────────────────────────────────────────── +CREATE TABLE social.reputation_event_type ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + name TEXT NOT NULL UNIQUE, + description TEXT, + default_points_change INTEGER NOT NULL DEFAULT 0, + is_positive BOOLEAN NOT NULL DEFAULT true, + is_system_generated BOOLEAN NOT NULL DEFAULT false, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +CREATE TABLE social.reputation_event ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + user_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + event_type_id UUID NOT NULL REFERENCES social.reputation_event_type(id), + actual_points_change INTEGER NOT NULL, + source_user_id UUID REFERENCES ident.users(id) ON DELETE SET NULL, + related_entity_type TEXT, + related_entity_id UUID, + notes TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX reputation_event_user_idx ON social.reputation_event (user_id, created_at DESC); + +CREATE TABLE social.user_reputation_score ( + user_id UUID PRIMARY KEY REFERENCES ident.users(id) ON DELETE CASCADE, + score BIGINT NOT NULL DEFAULT 0, + last_calculated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- ── social: messaging & feed ───────────────────────────────────────────────── +CREATE TABLE social.user_block ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + blocker_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + blocked_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + reason TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + UNIQUE (blocker_id, blocked_id) +); + +CREATE TABLE social.conversation ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + participant_ids UUID[] NOT NULL DEFAULT '{}', + subject TEXT, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + last_message_at TIMESTAMPTZ, + deleted_at TIMESTAMPTZ +); +CREATE INDEX conversation_participants_gin ON social.conversation USING gin (participant_ids); + +CREATE TABLE social.message ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + conversation_id UUID NOT NULL REFERENCES social.conversation(id) ON DELETE CASCADE, + sender_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + body TEXT NOT NULL, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + read_at TIMESTAMPTZ +); +CREATE INDEX message_conversation_idx ON social.message (conversation_id, created_at); + +CREATE TABLE social.feed_post ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + author_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + content TEXT NOT NULL, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now(), + deleted_at TIMESTAMPTZ +); + +-- ── social: group projects (legacy public.group_project) ───────────────────── +-- Rich access-control policies kept as TEXT (flexible) + atproto JSONB. +CREATE TABLE social.group_project ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + project_guid UUID NOT NULL UNIQUE DEFAULT gen_random_uuid(), + project_name TEXT NOT NULL, + project_type TEXT NOT NULL, -- HAPLOGROUP/SURNAME/GEOGRAPHIC/ETHNIC/RESEARCH/CUSTOM + target_haplogroup TEXT, + target_lineage TEXT, -- Y_DNA/MT_DNA/BOTH + description TEXT, + join_policy TEXT NOT NULL DEFAULT 'OPEN', + member_list_visibility TEXT NOT NULL DEFAULT 'MEMBERS_ONLY', + str_policy TEXT, + snp_policy TEXT, + public_tree_view BOOLEAN NOT NULL DEFAULT false, + succession_policy TEXT, + owner_did TEXT, + atproto JSONB, + deleted BOOLEAN NOT NULL DEFAULT false, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); + +-- ── support: contact messages (authenticated or anonymous) ─────────────────── +CREATE TABLE support.contact_message ( + id UUID PRIMARY KEY DEFAULT gen_random_uuid(), + user_id UUID REFERENCES ident.users(id) ON DELETE SET NULL, + sender_name TEXT, + sender_email TEXT, + subject TEXT, + message TEXT NOT NULL, + status TEXT NOT NULL DEFAULT 'new', -- new/read/replied/closed + ip_address_hash VARCHAR(64), + user_last_viewed_at TIMESTAMPTZ, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX contact_message_status_idx ON support.contact_message (status, created_at DESC); +CREATE INDEX contact_message_user_idx ON support.contact_message (user_id); + +-- ── billing: subscriptions ─────────────────────────────────────────────────── +CREATE TABLE billing.patron_subscription ( + id BIGINT GENERATED ALWAYS AS IDENTITY PRIMARY KEY, + user_id UUID NOT NULL REFERENCES ident.users(id) ON DELETE CASCADE, + patron_tier TEXT NOT NULL, -- SUPPORTER/CONTRIBUTOR/SUSTAINER/FOUNDING_PATRON + status TEXT NOT NULL DEFAULT 'ACTIVE', -- ACTIVE/CANCELLED/PAST_DUE/EXPIRED + payment_provider TEXT, -- STRIPE/PAYPAL + provider_subscription_id TEXT, + amount_cents INTEGER, + currency TEXT NOT NULL DEFAULT 'USD', + billing_interval TEXT, -- MONTHLY/YEARLY + current_period_start TIMESTAMPTZ, + current_period_end TIMESTAMPTZ, + cancelled_at TIMESTAMPTZ, + created_at TIMESTAMPTZ NOT NULL DEFAULT now(), + updated_at TIMESTAMPTZ NOT NULL DEFAULT now() +); +CREATE INDEX patron_subscription_user_idx ON billing.patron_subscription (user_id, status); diff --git a/rust/scripts/test-db.sh b/rust/scripts/test-db.sh new file mode 100755 index 0000000..d609578 --- /dev/null +++ b/rust/scripts/test-db.sh @@ -0,0 +1,130 @@ +#!/usr/bin/env bash +# Local Postgres (PostGIS) for tests/dev on a Docker-less Apple-Silicon Mac. +# +# Uses Apple's `container` CLI by default (this Mac Studio has no Docker). Apple +# `container` gives each container its own routable IP (no localhost port +# forwarding), so `up` discovers that IP and prints the matching DATABASE_URL. +# The same PostGIS image is used in production via compose.yaml. +# +# eval "$(./scripts/test-db.sh up)" start, wait, migrate, export DATABASE_URL +# ./scripts/test-db.sh down stop and remove the container +# ./scripts/test-db.sh reset down then up +# ./scripts/test-db.sh url print DATABASE_URL for the running container +# +# If $DATABASE_URL is already set, `up`/`url` use it as-is and DO NOT start a +# container (native-Postgres fallback — see plan §9). +set -euo pipefail + +NAME="${DU_PG_NAME:-du-pg}" +# imresamu/postgis publishes linux/arm64 (the official postgis/postgis is amd64-only +# and Apple `container` runs arm64 VMs without emulation). +IMAGE="${DU_PG_IMAGE:-docker.io/imresamu/postgis:16-3.4}" +PASSWORD="${DU_PG_PASSWORD:-dev}" +DB="${DU_PG_DB:-decodingus}" +USER="${DU_PG_USER:-postgres}" +HERE="$(cd "$(dirname "$0")" && pwd)" + +runtime() { + if command -v container >/dev/null 2>&1; then echo "container" + elif command -v docker >/dev/null 2>&1; then echo "docker" + else echo ""; fi +} + +require_runtime() { + local rt; rt="$(runtime)" + if [ -z "$rt" ]; then + cat >&2 <<'EOF' +ERROR: neither `container` (Apple) nor `docker` is installed. + Apple container: https://github.com/apple/container/releases + Or set DATABASE_URL to an existing Postgres and skip the container entirely. +EOF + exit 1 + fi + echo "$rt" +} + +# Resolve host:port for the running container under the given runtime. +container_host() { + local rt="$1" + if [ "$rt" = "container" ]; then + # Each container has its own IP; read it from `container ls`. + container ls 2>/dev/null | awk -v n="$NAME" '$1==n {print $6}' | cut -d/ -f1 + else + echo "localhost" + fi +} + +build_url() { echo "postgres://${USER}:${PASSWORD}@${1}:5432/${DB}?sslmode=disable"; } + +wait_ready() { + local host="$1" + echo "waiting for postgres on ${host}:5432 ..." >&2 + for _ in $(seq 1 60); do + if timeout 2 bash -c "(exec 3<>/dev/tcp/${host}/5432)" 2>/dev/null; then + sleep 1 + echo "postgres is accepting connections." >&2 + return 0 + fi + sleep 1 + done + echo "ERROR: postgres did not become ready in time" >&2 + exit 1 +} + +apply_migrations() { + local url="$1" + if command -v sqlx >/dev/null 2>&1; then + echo "applying migrations via sqlx-cli ..." >&2 + DATABASE_URL="$url" sqlx migrate run --source "${HERE}/../migrations" >&2 + else + echo "NOTE: sqlx-cli not found — migrations not auto-applied." >&2 + echo " \`cargo test\` applies them via du_db::run_migrations, or install sqlx-cli." >&2 + fi +} + +cmd="${1:-up}" +case "$cmd" in + up) + if [ -n "${DATABASE_URL:-}" ]; then + wait_ready "$(echo "$DATABASE_URL" | sed -E 's#.*@([^:/]+).*#\1#')" + apply_migrations "$DATABASE_URL" + echo "export DATABASE_URL=\"$DATABASE_URL\"" + exit 0 + fi + rt="$(require_runtime)" + echo "starting $NAME ($IMAGE) via $rt ..." >&2 + if [ "$rt" = "container" ]; then + container run -d --name "$NAME" \ + -e POSTGRES_PASSWORD="$PASSWORD" -e POSTGRES_DB="$DB" "$IMAGE" >/dev/null + else + docker run -d --name "$NAME" -p 5432:5432 \ + -e POSTGRES_PASSWORD="$PASSWORD" -e POSTGRES_DB="$DB" "$IMAGE" >/dev/null + fi + # Give Apple `container` a moment to assign an IP. + host=""; for _ in $(seq 1 20); do host="$(container_host "$rt")"; [ -n "$host" ] && break; sleep 1; done + [ -n "$host" ] || { echo "ERROR: could not resolve container IP" >&2; exit 1; } + url="$(build_url "$host")" + wait_ready "$host" + apply_migrations "$url" + echo "export DATABASE_URL=\"$url\"" + ;; + down) + rt="$(require_runtime)" + "$rt" rm -f "$NAME" >/dev/null 2>&1 || true + echo "removed $NAME" >&2 + ;; + reset) + "$0" down || true + "$0" up + ;; + url) + if [ -n "${DATABASE_URL:-}" ]; then echo "$DATABASE_URL"; exit 0; fi + rt="$(require_runtime)"; host="$(container_host "$rt")" + [ -n "$host" ] || { echo "ERROR: container '$NAME' not running" >&2; exit 1; } + build_url "$host" + ;; + *) + echo "usage: $0 {up|down|reset|url}" >&2 + exit 2 + ;; +esac From 0eeb394dc1c7ac11d340c781ff412ecb3b4e0d8e Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 07:22:40 -0500 Subject: [PATCH 002/191] feat(rust): du-db query modules + read-side domain types Data-access layer for the public read surface, with a reusable mapping pattern: JSONB columns decode into du-domain payload structs via sqlx Json; Postgres enums are read as ::text and parsed through serde (parse_pg_enum / pg_enum_label), keeping du-domain free of any sqlx dependency. - du-domain: Haplogroup, Publication, Biosample read-side types. - du-db modules: * variant - get_by_id, paginated search (canonical name + common_names/rs_ids JSONB alias arrays) * haplogroup- get_by_id/by_name, children, roots (current edges, valid_until IS NULL) * publication - get_by_id, paginated search (title/journal/doi, newest-first) * biosample - get_by_guid, find_by_alias_or_accession * pagination - generic Page - tests/queries.rs: seeds sentinel rows, exercises every module against live PostGIS, cleans up. Full workspace 7/7 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/crates/du-db/src/biosample.rs | 61 ++++++++++ rust/crates/du-db/src/haplogroup.rs | 101 ++++++++++++++++ rust/crates/du-db/src/lib.rs | 31 +++++ rust/crates/du-db/src/pagination.rs | 27 +++++ rust/crates/du-db/src/publication.rs | 98 +++++++++++++++ rust/crates/du-db/src/variant.rs | 96 +++++++++++++++ rust/crates/du-db/tests/queries.rs | 145 +++++++++++++++++++++++ rust/crates/du-domain/src/biosample.rs | 22 ++++ rust/crates/du-domain/src/haplogroup.rs | 19 +++ rust/crates/du-domain/src/lib.rs | 3 + rust/crates/du-domain/src/publication.rs | 19 +++ 11 files changed, 622 insertions(+) create mode 100644 rust/crates/du-db/src/biosample.rs create mode 100644 rust/crates/du-db/src/haplogroup.rs create mode 100644 rust/crates/du-db/src/pagination.rs create mode 100644 rust/crates/du-db/src/publication.rs create mode 100644 rust/crates/du-db/src/variant.rs create mode 100644 rust/crates/du-db/tests/queries.rs create mode 100644 rust/crates/du-domain/src/biosample.rs create mode 100644 rust/crates/du-domain/src/haplogroup.rs create mode 100644 rust/crates/du-domain/src/publication.rs diff --git a/rust/crates/du-db/src/biosample.rs b/rust/crates/du-db/src/biosample.rs new file mode 100644 index 0000000..2d1f7cb --- /dev/null +++ b/rust/crates/du-db/src/biosample.rs @@ -0,0 +1,61 @@ +//! Queries for the unified `core.biosample`. + +use crate::{parse_pg_enum, DbError}; +use du_domain::biosample::Biosample; +use du_domain::ids::SampleGuid; +use sqlx::PgPool; +use uuid::Uuid; + +#[derive(sqlx::FromRow)] +struct BiosampleRow { + sample_guid: Uuid, + source: String, + accession: Option, + alias: Option, + description: Option, + center_name: Option, + locked: bool, + source_attrs: serde_json::Value, + atproto: Option, +} + +impl BiosampleRow { + fn into_domain(self) -> Result { + Ok(Biosample { + sample_guid: SampleGuid(self.sample_guid), + source: parse_pg_enum(&self.source, "source")?, + accession: self.accession, + alias: self.alias, + description: self.description, + center_name: self.center_name, + locked: self.locked, + source_attrs: self.source_attrs, + atproto: self.atproto, + }) + } +} + +const SELECT: &str = "SELECT sample_guid, source::text AS source, accession, alias, description, \ + center_name, locked, source_attrs, atproto FROM core.biosample WHERE deleted = false"; + +pub async fn get_by_guid(pool: &PgPool, guid: SampleGuid) -> Result, DbError> { + let row: Option = sqlx::query_as(&format!("{SELECT} AND sample_guid = $1")) + .bind(guid.0) + .fetch_optional(pool) + .await?; + row.map(BiosampleRow::into_domain).transpose() +} + +/// Lookup by accession or alias (the private biosample search). +pub async fn find_by_alias_or_accession( + pool: &PgPool, + query: &str, +) -> Result, DbError> { + let like = format!("%{}%", query.trim()); + let rows: Vec = + sqlx::query_as(&format!("{SELECT} AND (accession ILIKE $1 OR alias ILIKE $1) ORDER BY accession LIMIT 50")) + .bind(&like) + .fetch_all(pool) + .await?; + rows.into_iter().map(BiosampleRow::into_domain).collect() +} diff --git a/rust/crates/du-db/src/haplogroup.rs b/rust/crates/du-db/src/haplogroup.rs new file mode 100644 index 0000000..c126dd2 --- /dev/null +++ b/rust/crates/du-db/src/haplogroup.rs @@ -0,0 +1,101 @@ +//! Queries for `tree.haplogroup` + current parent/child edges. These back the +//! Y/MT tree views. "Current" edges are those with `valid_until IS NULL`. + +use crate::{parse_pg_enum, pg_enum_label, DbError}; +use du_domain::enums::DnaType; +use du_domain::haplogroup::Haplogroup; +use du_domain::ids::HaplogroupId; +use sqlx::PgPool; + +#[derive(sqlx::FromRow)] +struct HaplogroupRow { + id: i64, + name: String, + haplogroup_type: String, + lineage: Option, + source: Option, + confidence_level: Option, + formed_ybp: Option, + tmrca_ybp: Option, + provenance: serde_json::Value, +} + +impl HaplogroupRow { + fn into_domain(self) -> Result { + Ok(Haplogroup { + id: HaplogroupId(self.id), + name: self.name, + haplogroup_type: parse_pg_enum(&self.haplogroup_type, "haplogroup_type")?, + lineage: self.lineage, + source: self.source, + confidence_level: self.confidence_level, + formed_ybp: self.formed_ybp, + tmrca_ybp: self.tmrca_ybp, + provenance: self.provenance, + }) + } +} + +// Columns qualified with alias `h` so joins (which also carry an `id`) stay +// unambiguous; output column names still match HaplogroupRow's fields. +const COLS: &str = "h.id, h.name, h.haplogroup_type::text AS haplogroup_type, h.lineage, h.source, \ + h.confidence_level, h.formed_ybp, h.tmrca_ybp, h.provenance"; + +fn collect(rows: Vec) -> Result, DbError> { + rows.into_iter().map(HaplogroupRow::into_domain).collect() +} + +pub async fn get_by_id(pool: &PgPool, id: HaplogroupId) -> Result, DbError> { + let row: Option = + sqlx::query_as(&format!("SELECT {COLS} FROM tree.haplogroup h WHERE h.id = $1")) + .bind(id.0) + .fetch_optional(pool) + .await?; + row.map(HaplogroupRow::into_domain).transpose() +} + +pub async fn get_by_name( + pool: &PgPool, + name: &str, + dna_type: DnaType, +) -> Result, DbError> { + let row: Option = sqlx::query_as(&format!( + "SELECT {COLS} FROM tree.haplogroup h WHERE h.name = $1 AND h.haplogroup_type::text = $2" + )) + .bind(name) + .bind(pg_enum_label(&dna_type)?) + .fetch_optional(pool) + .await?; + row.map(HaplogroupRow::into_domain).transpose() +} + +/// Direct children of a haplogroup (current edges), ordered by name. +pub async fn children(pool: &PgPool, parent: HaplogroupId) -> Result, DbError> { + let rows: Vec = sqlx::query_as(&format!( + "SELECT {COLS} FROM tree.haplogroup h \ + JOIN tree.haplogroup_relationship r ON r.child_haplogroup_id = h.id \ + WHERE r.parent_haplogroup_id = $1 AND r.valid_until IS NULL \ + ORDER BY h.name" + )) + .bind(parent.0) + .fetch_all(pool) + .await?; + collect(rows) +} + +/// Root haplogroups of a lineage: no current edge to a parent. +pub async fn roots(pool: &PgPool, dna_type: DnaType) -> Result, DbError> { + let rows: Vec = sqlx::query_as(&format!( + "SELECT {COLS} FROM tree.haplogroup h \ + WHERE h.haplogroup_type::text = $1 \ + AND NOT EXISTS ( \ + SELECT 1 FROM tree.haplogroup_relationship r \ + WHERE r.child_haplogroup_id = h.id AND r.parent_haplogroup_id IS NOT NULL \ + AND r.valid_until IS NULL) \ + ORDER BY h.name" + )) + .bind(pg_enum_label(&dna_type)?) + .fetch_all(pool) + .await?; + collect(rows) +} diff --git a/rust/crates/du-db/src/lib.rs b/rust/crates/du-db/src/lib.rs index f242e66..fd44f8a 100644 --- a/rust/crates/du-db/src/lib.rs +++ b/rust/crates/du-db/src/lib.rs @@ -7,12 +7,43 @@ use sqlx::postgres::{PgPool, PgPoolOptions}; use std::time::Duration; use thiserror::Error; +pub mod biosample; +pub mod haplogroup; +pub mod pagination; +pub mod publication; +pub mod variant; + +pub use pagination::Page; + #[derive(Debug, Error)] pub enum DbError { #[error("database error: {0}")] Sqlx(#[from] sqlx::Error), #[error("migration error: {0}")] Migrate(#[from] sqlx::migrate::MigrateError), + /// A row's text/JSONB column failed to decode into a domain type. + #[error("decode error: {0}")] + Decode(String), +} + +/// Decode a Postgres enum label (fetched as `::text`) into a domain enum that +/// derives `Deserialize` with matching SCREAMING_SNAKE_CASE variants. Keeps +/// du-domain free of any sqlx dependency. +pub(crate) fn parse_pg_enum( + label: &str, + what: &str, +) -> Result { + serde_json::from_value(serde_json::Value::String(label.to_string())) + .map_err(|e| DbError::Decode(format!("{what} = {label:?}: {e}"))) +} + +/// Inverse of `parse_pg_enum`: a domain enum's SCREAMING_SNAKE_CASE label for +/// binding against a `::text`-cast enum column. +pub(crate) fn pg_enum_label(value: &T) -> Result { + match serde_json::to_value(value).map_err(|e| DbError::Decode(e.to_string()))? { + serde_json::Value::String(s) => Ok(s), + other => Err(DbError::Decode(format!("expected enum string, got {other}"))), + } } /// Connect and return a pool. `database_url` is the standard `postgres://` DSN diff --git a/rust/crates/du-db/src/pagination.rs b/rust/crates/du-db/src/pagination.rs new file mode 100644 index 0000000..d24d889 --- /dev/null +++ b/rust/crates/du-db/src/pagination.rs @@ -0,0 +1,27 @@ +//! Pagination helper shared by list/search queries. + +use serde::Serialize; + +/// A page of results plus the totals the UI needs to render pagination controls. +#[derive(Debug, Clone, Serialize)] +pub struct Page { + pub items: Vec, + pub total: i64, + pub page: i64, + pub page_size: i64, +} + +impl Page { + pub fn total_pages(&self) -> i64 { + if self.page_size <= 0 { + 0 + } else { + (self.total + self.page_size - 1) / self.page_size + } + } + + /// Clamp page/page_size to sane bounds and return the SQL OFFSET. + pub fn offset(page: i64, page_size: i64) -> i64 { + (page.max(1) - 1) * page_size.clamp(1, 200) + } +} diff --git a/rust/crates/du-db/src/publication.rs b/rust/crates/du-db/src/publication.rs new file mode 100644 index 0000000..7fbdc86 --- /dev/null +++ b/rust/crates/du-db/src/publication.rs @@ -0,0 +1,98 @@ +//! Queries for `pubs.publication` (the references listing). + +use crate::{DbError, Page}; +use du_domain::ids::PublicationId; +use du_domain::publication::Publication; +use sqlx::PgPool; + +#[derive(sqlx::FromRow)] +struct PublicationRow { + id: i64, + title: String, + doi: Option, + pubmed_id: Option, + journal: Option, + publication_date: Option, + authors: Option, + abstract_summary: Option, + url: Option, + cited_by_count: Option, + open_access_status: Option, +} + +impl From for Publication { + fn from(r: PublicationRow) -> Self { + Publication { + id: PublicationId(r.id), + title: r.title, + doi: r.doi, + pubmed_id: r.pubmed_id, + journal: r.journal, + publication_date: r.publication_date, + authors: r.authors, + abstract_summary: r.abstract_summary, + url: r.url, + cited_by_count: r.cited_by_count, + open_access_status: r.open_access_status, + } + } +} + +const SELECT: &str = "SELECT id, title, doi, pubmed_id, journal, publication_date, authors, \ + abstract_summary, url, cited_by_count, open_access_status FROM pubs.publication"; + +pub async fn get_by_id(pool: &PgPool, id: PublicationId) -> Result, DbError> { + let row: Option = sqlx::query_as(&format!("{SELECT} WHERE id = $1")) + .bind(id.0) + .fetch_optional(pool) + .await?; + Ok(row.map(Into::into)) +} + +/// Paginated list, optionally filtered by title/journal/DOI substring, newest first. +pub async fn search( + pool: &PgPool, + query: Option<&str>, + page: i64, + page_size: i64, +) -> Result, DbError> { + let offset = Page::<()>::offset(page, page_size); + let limit = page_size.clamp(1, 200); + let term = query.map(str::trim).filter(|q| !q.is_empty()); + + const FILTER: &str = "WHERE title ILIKE $1 OR journal ILIKE $1 OR doi ILIKE $1"; + const ORDER: &str = "ORDER BY publication_date DESC NULLS LAST, id DESC"; + + let (total, rows): (i64, Vec) = if let Some(t) = term { + let like = format!("%{t}%"); + let total: i64 = + sqlx::query_scalar(&format!("SELECT count(*) FROM pubs.publication {FILTER}")) + .bind(&like) + .fetch_one(pool) + .await?; + let rows = sqlx::query_as(&format!("{SELECT} {FILTER} {ORDER} LIMIT $2 OFFSET $3")) + .bind(&like) + .bind(limit) + .bind(offset) + .fetch_all(pool) + .await?; + (total, rows) + } else { + let total: i64 = sqlx::query_scalar("SELECT count(*) FROM pubs.publication") + .fetch_one(pool) + .await?; + let rows = sqlx::query_as(&format!("{SELECT} {ORDER} LIMIT $1 OFFSET $2")) + .bind(limit) + .bind(offset) + .fetch_all(pool) + .await?; + (total, rows) + }; + + Ok(Page { + items: rows.into_iter().map(Into::into).collect(), + total, + page: page.max(1), + page_size: limit, + }) +} diff --git a/rust/crates/du-db/src/variant.rs b/rust/crates/du-db/src/variant.rs new file mode 100644 index 0000000..529ba24 --- /dev/null +++ b/rust/crates/du-db/src/variant.rs @@ -0,0 +1,96 @@ +//! Queries for `core.variant`. Demonstrates the du-db mapping pattern: +//! enum columns are fetched as `::text` and parsed via serde; JSONB columns are +//! read through `sqlx::types::Json` into the du-domain payload structs. + +use crate::{parse_pg_enum, DbError, Page}; +use du_domain::ids::VariantId; +use du_domain::variant::{Aliases, Annotations, Coordinates, Variant}; +use sqlx::types::Json; +use sqlx::PgPool; + +#[derive(sqlx::FromRow)] +struct VariantRow { + id: i64, + canonical_name: String, + mutation_type: String, + naming_status: String, + aliases: Json, + coordinates: Json, + annotations: Json, +} + +impl VariantRow { + fn into_domain(self) -> Result { + Ok(Variant { + id: VariantId(self.id), + canonical_name: self.canonical_name, + mutation_type: parse_pg_enum(&self.mutation_type, "mutation_type")?, + naming_status: parse_pg_enum(&self.naming_status, "naming_status")?, + aliases: self.aliases.0, + coordinates: self.coordinates.0, + annotations: self.annotations.0, + }) + } +} + +const SELECT: &str = "SELECT id, canonical_name, mutation_type::text AS mutation_type, \ + naming_status::text AS naming_status, aliases, coordinates, annotations FROM core.variant"; + +pub async fn get_by_id(pool: &PgPool, id: VariantId) -> Result, DbError> { + let row: Option = sqlx::query_as(&format!("{SELECT} WHERE id = $1")) + .bind(id.0) + .fetch_optional(pool) + .await?; + row.map(VariantRow::into_domain).transpose() +} + +/// Paginated search by canonical name OR any alias in the `common_names`/`rs_ids` +/// JSONB arrays (the public variant browser). `query = None`/empty lists all. +pub async fn search( + pool: &PgPool, + query: Option<&str>, + page: i64, + page_size: i64, +) -> Result, DbError> { + let offset = Page::<()>::offset(page, page_size); + let limit = page_size.clamp(1, 200); + let term = query.map(str::trim).filter(|q| !q.is_empty()); + + // Matches canonical_name or any element of the alias arrays, case-insensitive. + const FILTER: &str = "WHERE canonical_name ILIKE $1 \ + OR EXISTS (SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') a WHERE a ILIKE $1) \ + OR EXISTS (SELECT 1 FROM jsonb_array_elements_text(aliases->'rs_ids') r WHERE r ILIKE $1)"; + + let (total, rows): (i64, Vec) = if let Some(t) = term { + let like = format!("%{t}%"); + let total: i64 = sqlx::query_scalar(&format!("SELECT count(*) FROM core.variant {FILTER}")) + .bind(&like) + .fetch_one(pool) + .await?; + let rows = sqlx::query_as(&format!( + "{SELECT} {FILTER} ORDER BY canonical_name LIMIT $2 OFFSET $3" + )) + .bind(&like) + .bind(limit) + .bind(offset) + .fetch_all(pool) + .await?; + (total, rows) + } else { + let total: i64 = sqlx::query_scalar("SELECT count(*) FROM core.variant") + .fetch_one(pool) + .await?; + let rows = sqlx::query_as(&format!("{SELECT} ORDER BY canonical_name LIMIT $1 OFFSET $2")) + .bind(limit) + .bind(offset) + .fetch_all(pool) + .await?; + (total, rows) + }; + + let items = rows + .into_iter() + .map(VariantRow::into_domain) + .collect::, _>>()?; + Ok(Page { items, total, page: page.max(1), page_size: limit }) +} diff --git a/rust/crates/du-db/tests/queries.rs b/rust/crates/du-db/tests/queries.rs new file mode 100644 index 0000000..f3c33b1 --- /dev/null +++ b/rust/crates/du-db/tests/queries.rs @@ -0,0 +1,145 @@ +//! Live-DB tests for the du-db query modules. Seeds sentinel rows (prefixed +//! `TESTQ-`), exercises each module, then cleans up so it is re-runnable against +//! a persistent database. Skips (passes) when DATABASE_URL is unset. +//! +//! eval "$(./scripts/test-db.sh up)" && cargo test -p du-db --test queries + +use du_domain::enums::DnaType; +use du_domain::ids::{PublicationId, SampleGuid}; +use serde_json::json; +use sqlx::PgPool; +use uuid::Uuid; + +fn database_url() -> Option { + std::env::var("DATABASE_URL").ok().filter(|s| !s.is_empty()) +} + +async fn cleanup(pool: &PgPool) { + // Order respects FKs: edges -> haplogroups; the rest are independent. + let _ = sqlx::query( + "DELETE FROM tree.haplogroup_relationship r USING tree.haplogroup h \ + WHERE (r.child_haplogroup_id = h.id OR r.parent_haplogroup_id = h.id) AND h.name LIKE 'TESTQ-%'", + ) + .execute(pool) + .await; + let _ = sqlx::query("DELETE FROM tree.haplogroup WHERE name LIKE 'TESTQ-%'").execute(pool).await; + let _ = sqlx::query("DELETE FROM core.variant WHERE canonical_name LIKE 'TESTQ-%'").execute(pool).await; + let _ = sqlx::query("DELETE FROM pubs.publication WHERE title LIKE 'TESTQ-%'").execute(pool).await; + let _ = sqlx::query("DELETE FROM core.biosample WHERE accession LIKE 'TESTQ-%'").execute(pool).await; +} + +#[tokio::test] +async fn query_modules_against_live_db() { + let Some(url) = database_url() else { + eprintln!("DATABASE_URL unset — skipping live-DB query test"); + return; + }; + let pool = du_db::connect(&url, 4).await.expect("connect"); + du_db::run_migrations(&pool).await.expect("migrate"); + cleanup(&pool).await; // in case a prior run left sentinels behind + + // ── seed ────────────────────────────────────────────────────────────── + let v1: i64 = sqlx::query_scalar( + "INSERT INTO core.variant (canonical_name, mutation_type, aliases, coordinates) \ + VALUES ('TESTQ-M269', 'SNP'::core.mutation_type, $1, $2) RETURNING id", + ) + .bind(json!({"common_names": ["TESTQ-RM269"]})) + .bind(json!({"GRCh38": {"contig": "chrY", "position": 2787319}})) + .fetch_one(&pool) + .await + .expect("insert v1"); + + sqlx::query( + "INSERT INTO core.variant (canonical_name, mutation_type, aliases) \ + VALUES ('TESTQ-L21', 'SNP'::core.mutation_type, $1)", + ) + .bind(json!({"rs_ids": ["rsTESTQ999"]})) + .execute(&pool) + .await + .expect("insert v2"); + + let root: i64 = sqlx::query_scalar( + "INSERT INTO tree.haplogroup (name, haplogroup_type) \ + VALUES ('TESTQ-ROOT', 'Y_DNA'::core.dna_type) RETURNING id", + ) + .fetch_one(&pool) + .await + .expect("insert root"); + let child: i64 = sqlx::query_scalar( + "INSERT INTO tree.haplogroup (name, haplogroup_type) \ + VALUES ('TESTQ-CHILD', 'Y_DNA'::core.dna_type) RETURNING id", + ) + .fetch_one(&pool) + .await + .expect("insert child"); + sqlx::query( + "INSERT INTO tree.haplogroup_relationship (child_haplogroup_id, parent_haplogroup_id) \ + VALUES ($1, $2)", + ) + .bind(child) + .bind(root) + .execute(&pool) + .await + .expect("insert edge"); + + let pub_id: i64 = sqlx::query_scalar( + "INSERT INTO pubs.publication (title, doi) VALUES ('TESTQ-Ancient DNA', '10.testq/1') RETURNING id", + ) + .fetch_one(&pool) + .await + .expect("insert pub"); + + let sample = Uuid::new_v4(); + sqlx::query( + "INSERT INTO core.biosample (sample_guid, source, accession) \ + VALUES ($1, 'EXTERNAL'::core.biosample_source, 'TESTQ-ACC1')", + ) + .bind(sample) + .execute(&pool) + .await + .expect("insert biosample"); + + // ── variant ─────────────────────────────────────────────────────────── + let by_name = du_db::variant::search(&pool, Some("TESTQ-M269"), 1, 25).await.expect("variant search"); + assert_eq!(by_name.total, 1); + assert_eq!(by_name.items[0].canonical_name, "TESTQ-M269"); + assert_eq!(by_name.items[0].coordinates.get(du_domain::ReferenceBuild::GRCh38).unwrap().contig, "chrY"); + + let got = du_db::variant::get_by_id(&pool, by_name.items[0].id).await.expect("get variant"); + assert_eq!(got.unwrap().canonical_name, "TESTQ-M269"); + + // found by rs_id alias (JSONB array search) + let by_rsid = du_db::variant::search(&pool, Some("rsTESTQ999"), 1, 25).await.expect("variant rsid search"); + assert_eq!(by_rsid.total, 1); + assert_eq!(by_rsid.items[0].canonical_name, "TESTQ-L21"); + + // ── haplogroup / tree ─────────────────────────────────────────────────── + let root_hg = du_db::haplogroup::get_by_name(&pool, "TESTQ-ROOT", DnaType::YDna) + .await + .expect("get root") + .expect("root exists"); + let roots = du_db::haplogroup::roots(&pool, DnaType::YDna).await.expect("roots"); + assert!(roots.iter().any(|h| h.name == "TESTQ-ROOT"), "root listed as a root"); + assert!(!roots.iter().any(|h| h.name == "TESTQ-CHILD"), "child is not a root"); + + let kids = du_db::haplogroup::children(&pool, root_hg.id).await.expect("children"); + assert_eq!(kids.len(), 1); + assert_eq!(kids[0].name, "TESTQ-CHILD"); + + // ── publication ────────────────────────────────────────────────────────── + let pubs = du_db::publication::search(&pool, Some("TESTQ"), 1, 25).await.expect("pub search"); + assert!(pubs.items.iter().any(|p| p.title == "TESTQ-Ancient DNA")); + let one = du_db::publication::get_by_id(&pool, PublicationId(pub_id)).await.expect("get pub"); + assert_eq!(one.unwrap().doi.as_deref(), Some("10.testq/1")); + + // ── biosample ───────────────────────────────────────────────────────────── + let bs = du_db::biosample::get_by_guid(&pool, SampleGuid(sample)).await.expect("get biosample"); + assert_eq!(bs.unwrap().accession.as_deref(), Some("TESTQ-ACC1")); + let found = du_db::biosample::find_by_alias_or_accession(&pool, "TESTQ-ACC1").await.expect("find biosample"); + assert_eq!(found.len(), 1); + + // ensure the unused binding is acknowledged + let _ = v1; + + cleanup(&pool).await; +} diff --git a/rust/crates/du-domain/src/biosample.rs b/rust/crates/du-domain/src/biosample.rs new file mode 100644 index 0000000..0e5a227 --- /dev/null +++ b/rust/crates/du-domain/src/biosample.rs @@ -0,0 +1,22 @@ +//! Biosample domain type — the unified sample (standard/citizen/pgp/external/ +//! ancient) discriminated by `source`, with source-specific fields and the +//! AT Protocol reference carried in JSONB (plan §2). + +use crate::enums::BiosampleSource; +use crate::ids::SampleGuid; +use serde::{Deserialize, Serialize}; + +#[derive(Debug, Clone, Serialize, Deserialize)] +pub struct Biosample { + pub sample_guid: SampleGuid, + pub source: BiosampleSource, + pub accession: Option, + pub alias: Option, + pub description: Option, + pub center_name: Option, + pub locked: bool, + /// `core.biosample.source_attrs` JSONB (source-specific fields). + pub source_attrs: serde_json::Value, + /// `core.biosample.atproto` JSONB ({uri, cid, repo_did}) or None. + pub atproto: Option, +} diff --git a/rust/crates/du-domain/src/haplogroup.rs b/rust/crates/du-domain/src/haplogroup.rs new file mode 100644 index 0000000..b8876f4 --- /dev/null +++ b/rust/crates/du-domain/src/haplogroup.rs @@ -0,0 +1,19 @@ +//! Haplogroup (phylogenetic tree node) domain type. + +use crate::enums::DnaType; +use crate::ids::HaplogroupId; +use serde::{Deserialize, Serialize}; + +#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)] +pub struct Haplogroup { + pub id: HaplogroupId, + pub name: String, + pub haplogroup_type: DnaType, + pub lineage: Option, + pub source: Option, + pub confidence_level: Option, + pub formed_ybp: Option, + pub tmrca_ybp: Option, + /// `tree.haplogroup.provenance` JSONB (multi-source attribution / age detail). + pub provenance: serde_json::Value, +} diff --git a/rust/crates/du-domain/src/lib.rs b/rust/crates/du-domain/src/lib.rs index 3d4d61f..4ea54b6 100644 --- a/rust/crates/du-domain/src/lib.rs +++ b/rust/crates/du-domain/src/lib.rs @@ -5,9 +5,12 @@ //! structs so both `du-db` (persistence) and `du-web` (presentation) share one //! source of truth. +pub mod biosample; pub mod enums; pub mod error; +pub mod haplogroup; pub mod ids; +pub mod publication; pub mod variant; pub use enums::*; diff --git a/rust/crates/du-domain/src/publication.rs b/rust/crates/du-domain/src/publication.rs new file mode 100644 index 0000000..19978bd --- /dev/null +++ b/rust/crates/du-domain/src/publication.rs @@ -0,0 +1,19 @@ +//! Publication domain type (research papers, enriched via OpenAlex). + +use crate::ids::PublicationId; +use serde::{Deserialize, Serialize}; + +#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)] +pub struct Publication { + pub id: PublicationId, + pub title: String, + pub doi: Option, + pub pubmed_id: Option, + pub journal: Option, + pub publication_date: Option, + pub authors: Option, + pub abstract_summary: Option, + pub url: Option, + pub cited_by_count: Option, + pub open_access_status: Option, +} From 8e2b06ed641739e803f87d87c331ec1e997f132b Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 07:45:21 -0500 Subject: [PATCH 003/191] feat(rust): public read-only vertical slice (variant browser + Y/MT tree) First user-visible slice through Axum + Askama + HTMX, server-rendered with HATEOAS fragment navigation, verified end-to-end against the live PostGIS: - du-web restructured: AppState (PgPool), AppError -> HTTP mapping, explicit Askama render helper, routes/ module. main() connects+migrates when DATABASE_URL is set, else serves /health only. - Variant browser: /variants page lazy-loads /variants/list fragment (search by name + common_names/rs_ids JSONB aliases, paginated); rows load /variants/detail/:id panel rendering multi-build coordinates. - Tree: /ytree & /mtree pages lazy-load /{y,m}tree/fragment; clicking a node swaps #tree-container and pushes the URL (hx-get + href + hx-push-url) so browser back/forward walks the tree. Graceful empty states + 404s. - du-domain: Display/label() for DnaType/MutationType/NamingStatus (templates). - du-db: re-export PgPool so du-web needn't depend on sqlx; migrations test uses a sentinel variant name to avoid colliding with real data. - Askama templates (base/index/variants/tree) on Bootstrap 5 + htmx 2. Workspace 7/7 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/crates/du-db/src/lib.rs | 4 +- rust/crates/du-db/tests/migrations.rs | 4 +- rust/crates/du-domain/src/enums.rs | 47 ++++++ rust/crates/du-web/src/error.rs | 27 ++++ rust/crates/du-web/src/main.rs | 34 +++-- rust/crates/du-web/src/render.rs | 20 +++ rust/crates/du-web/src/routes.rs | 27 ---- rust/crates/du-web/src/routes/mod.rs | 55 +++++++ rust/crates/du-web/src/routes/tree.rs | 92 ++++++++++++ rust/crates/du-web/src/routes/variants.rs | 138 ++++++++++++++++++ rust/crates/du-web/src/state.rs | 8 + rust/crates/du-web/templates/base.html | 31 ++++ rust/crates/du-web/templates/index.html | 16 ++ .../du-web/templates/tree/fragment.html | 29 ++++ rust/crates/du-web/templates/tree/page.html | 10 ++ .../du-web/templates/variants/browser.html | 26 ++++ .../du-web/templates/variants/detail.html | 40 +++++ .../du-web/templates/variants/list.html | 35 +++++ 18 files changed, 602 insertions(+), 41 deletions(-) create mode 100644 rust/crates/du-web/src/error.rs create mode 100644 rust/crates/du-web/src/render.rs delete mode 100644 rust/crates/du-web/src/routes.rs create mode 100644 rust/crates/du-web/src/routes/mod.rs create mode 100644 rust/crates/du-web/src/routes/tree.rs create mode 100644 rust/crates/du-web/src/routes/variants.rs create mode 100644 rust/crates/du-web/src/state.rs create mode 100644 rust/crates/du-web/templates/base.html create mode 100644 rust/crates/du-web/templates/index.html create mode 100644 rust/crates/du-web/templates/tree/fragment.html create mode 100644 rust/crates/du-web/templates/tree/page.html create mode 100644 rust/crates/du-web/templates/variants/browser.html create mode 100644 rust/crates/du-web/templates/variants/detail.html create mode 100644 rust/crates/du-web/templates/variants/list.html diff --git a/rust/crates/du-db/src/lib.rs b/rust/crates/du-db/src/lib.rs index fd44f8a..47f5333 100644 --- a/rust/crates/du-db/src/lib.rs +++ b/rust/crates/du-db/src/lib.rs @@ -3,7 +3,9 @@ //! Status: scaffold. The pool + error type are wired; query modules //! (`biosample`, `variant`, `haplogroup`, …) land as each subsystem is ported. -use sqlx::postgres::{PgPool, PgPoolOptions}; +/// Re-exported so downstream crates can hold a pool without depending on sqlx. +pub use sqlx::postgres::PgPool; +use sqlx::postgres::PgPoolOptions; use std::time::Duration; use thiserror::Error; diff --git a/rust/crates/du-db/tests/migrations.rs b/rust/crates/du-db/tests/migrations.rs index 669619e..5b27315 100644 --- a/rust/crates/du-db/tests/migrations.rs +++ b/rust/crates/du-db/tests/migrations.rs @@ -91,7 +91,9 @@ async fn migrations_apply_and_variant_jsonb_roundtrips() { "INSERT INTO core.variant (canonical_name, mutation_type, coordinates) VALUES ($1, 'SNP', $2) RETURNING id", ) - .bind("M269") + // Sentinel name so this never collides with seeded/real data (canonical_name + // is unique). + .bind("TESTMIG-M269") .bind(&coords_json) .fetch_one(&pool) .await diff --git a/rust/crates/du-domain/src/enums.rs b/rust/crates/du-domain/src/enums.rs index a53ab8d..c2710c5 100644 --- a/rust/crates/du-domain/src/enums.rs +++ b/rust/crates/du-domain/src/enums.rs @@ -103,6 +103,53 @@ impl ReferenceBuild { } } +impl DnaType { + pub fn label(&self) -> &'static str { + match self { + DnaType::YDna => "Y_DNA", + DnaType::MtDna => "MT_DNA", + } + } +} +impl std::fmt::Display for DnaType { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + f.write_str(self.label()) + } +} + +impl MutationType { + pub fn label(&self) -> &'static str { + match self { + MutationType::Snp => "SNP", + MutationType::Indel => "INDEL", + MutationType::Str => "STR", + MutationType::Del => "DEL", + MutationType::Ins => "INS", + MutationType::Mnp => "MNP", + } + } +} +impl std::fmt::Display for MutationType { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + f.write_str(self.label()) + } +} + +impl NamingStatus { + pub fn label(&self) -> &'static str { + match self { + NamingStatus::Unnamed => "UNNAMED", + NamingStatus::PendingReview => "PENDING_REVIEW", + NamingStatus::Named => "NAMED", + } + } +} +impl std::fmt::Display for NamingStatus { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + f.write_str(self.label()) + } +} + /// Tree change-set lifecycle (legacy `tree.change_set_status`). #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] #[serde(rename_all = "SCREAMING_SNAKE_CASE")] diff --git a/rust/crates/du-web/src/error.rs b/rust/crates/du-web/src/error.rs new file mode 100644 index 0000000..45cfeeb --- /dev/null +++ b/rust/crates/du-web/src/error.rs @@ -0,0 +1,27 @@ +//! Handler error type. Maps data-layer failures to HTTP responses. + +use axum::http::StatusCode; +use axum::response::{IntoResponse, Response}; + +pub enum AppError { + Db(du_db::DbError), + NotFound(String), +} + +impl From for AppError { + fn from(e: du_db::DbError) -> Self { + AppError::Db(e) + } +} + +impl IntoResponse for AppError { + fn into_response(self) -> Response { + match self { + AppError::Db(e) => { + tracing::error!(error = %e, "database error"); + (StatusCode::INTERNAL_SERVER_ERROR, "internal server error").into_response() + } + AppError::NotFound(what) => (StatusCode::NOT_FOUND, format!("not found: {what}")).into_response(), + } + } +} diff --git a/rust/crates/du-web/src/main.rs b/rust/crates/du-web/src/main.rs index f827a2e..9a221da 100644 --- a/rust/crates/du-web/src/main.rs +++ b/rust/crates/du-web/src/main.rs @@ -1,13 +1,16 @@ -//! DecodingUs web binary (Axum). HTML + JSON API + static assets + firehose. +//! DecodingUs web binary (Axum). HTML + (later) JSON API + firehose. //! -//! Scaffold: boots tracing, builds the router, serves `/health` (carried over -//! from the Play app's load-balancer check). Subsystem routers are mounted as -//! they are ported (plan §4, §10). +//! Public vertical slice: home, variant browser, and Y/MT tree navigation, +//! server-rendered with Askama and driven by HTMX fragments (plan §4). -use axum::{routing::get, Router}; use std::net::SocketAddr; +mod error; +mod render; mod routes; +mod state; + +use state::AppState; #[tokio::main] async fn main() -> anyhow::Result<()> { @@ -18,7 +21,20 @@ async fn main() -> anyhow::Result<()> { ) .init(); - let app = build_router(); + // Build the app. With a DATABASE_URL we connect, migrate, and serve the full + // site; without one we serve only /health (keeps the binary runnable bare). + let app = match std::env::var("DATABASE_URL").ok().filter(|s| !s.is_empty()) { + Some(url) => { + let pool = du_db::connect(&url, 8).await?; + du_db::run_migrations(&pool).await?; + tracing::info!("connected to database; migrations applied"); + routes::app(AppState { pool }) + } + None => { + tracing::warn!("DATABASE_URL not set — serving /health only"); + routes::health_only() + } + }; let port: u16 = std::env::var("PORT").ok().and_then(|p| p.parse().ok()).unwrap_or(9000); let addr = SocketAddr::from(([0, 0, 0, 0], port)); @@ -28,9 +44,3 @@ async fn main() -> anyhow::Result<()> { axum::serve(listener, app).await?; Ok(()) } - -/// Builds the application router. Split out so handler tests can exercise it -/// without binding a socket. -pub fn build_router() -> Router { - Router::new().route("/health", get(routes::health)) -} diff --git a/rust/crates/du-web/src/render.rs b/rust/crates/du-web/src/render.rs new file mode 100644 index 0000000..8104ea6 --- /dev/null +++ b/rust/crates/du-web/src/render.rs @@ -0,0 +1,20 @@ +//! Renders an Askama template into an HTML response. Used instead of the +//! `askama_axum` IntoResponse integration to keep the rendering path explicit +//! and version-independent. + +use axum::http::{header, StatusCode}; +use axum::response::{IntoResponse, Response}; + +pub fn html(t: &T) -> Response { + match t.render() { + Ok(body) => ( + [(header::CONTENT_TYPE, "text/html; charset=utf-8")], + body, + ) + .into_response(), + Err(e) => { + tracing::error!(error = %e, "template render failed"); + (StatusCode::INTERNAL_SERVER_ERROR, "template error").into_response() + } + } +} diff --git a/rust/crates/du-web/src/routes.rs b/rust/crates/du-web/src/routes.rs deleted file mode 100644 index 994a870..0000000 --- a/rust/crates/du-web/src/routes.rs +++ /dev/null @@ -1,27 +0,0 @@ -//! HTTP handlers. Grows into submodules (public, curator, api, federation) as -//! subsystems are ported. For now: the health check. - -use axum::http::StatusCode; - -/// Load-balancer / container health check. Mirrors the Play `/health` route. -pub async fn health() -> (StatusCode, &'static str) { - (StatusCode::OK, "ok") -} - -#[cfg(test)] -mod tests { - use crate::build_router; - use axum::body::Body; - use axum::http::{Request, StatusCode}; - use tower::ServiceExt; // for `oneshot` - - #[tokio::test] - async fn health_returns_ok() { - let app = build_router(); - let resp = app - .oneshot(Request::builder().uri("/health").body(Body::empty()).unwrap()) - .await - .unwrap(); - assert_eq!(resp.status(), StatusCode::OK); - } -} diff --git a/rust/crates/du-web/src/routes/mod.rs b/rust/crates/du-web/src/routes/mod.rs new file mode 100644 index 0000000..025b176 --- /dev/null +++ b/rust/crates/du-web/src/routes/mod.rs @@ -0,0 +1,55 @@ +//! Router assembly + top-level pages. + +use crate::render::html; +use crate::state::AppState; +use axum::http::StatusCode; +use axum::response::Response; +use axum::routing::get; +use axum::Router; + +pub mod tree; +pub mod variants; + +/// Full application router (requires a DB-backed AppState). +pub fn app(state: AppState) -> Router { + Router::new() + .route("/health", get(health)) + .route("/", get(index)) + .merge(variants::router()) + .merge(tree::router()) + .with_state(state) +} + +/// Health-only router for environments without a database (and for tests). +pub fn health_only() -> Router { + Router::new().route("/health", get(health)) +} + +async fn health() -> (StatusCode, &'static str) { + (StatusCode::OK, "ok") +} + +#[derive(askama::Template)] +#[template(path = "index.html")] +struct IndexTemplate; + +async fn index() -> Response { + html(&IndexTemplate) +} + +#[cfg(test)] +mod tests { + use super::*; + use axum::body::Body; + use axum::http::{Request, StatusCode}; + use tower::ServiceExt; + + #[tokio::test] + async fn health_returns_ok() { + let resp = health_only() + .oneshot(Request::builder().uri("/health").body(Body::empty()).unwrap()) + .await + .unwrap(); + assert_eq!(resp.status(), StatusCode::OK); + } +} diff --git a/rust/crates/du-web/src/routes/tree.rs b/rust/crates/du-web/src/routes/tree.rs new file mode 100644 index 0000000..be24d72 --- /dev/null +++ b/rust/crates/du-web/src/routes/tree.rs @@ -0,0 +1,92 @@ +//! Public Y/MT haplogroup tree navigation. `/ytree` and `/mtree` are full pages +//! whose `#tree-container` lazy-loads a fragment; clicking a node swaps the +//! fragment and pushes the URL (HATEOAS navigation, no client routing). + +use crate::error::AppError; +use crate::render::html; +use crate::state::AppState; +use axum::extract::{Query, State}; +use axum::response::Response; +use axum::routing::get; +use axum::Router; +use du_domain::enums::DnaType; +use serde::Deserialize; + +pub fn router() -> Router { + Router::new() + .route("/ytree", get(ytree_page)) + .route("/mtree", get(mtree_page)) + .route("/ytree/fragment", get(ytree_fragment)) + .route("/mtree/fragment", get(mtree_fragment)) +} + +#[derive(Deserialize)] +struct RootQuery { + root: Option, +} + +#[derive(askama::Template)] +#[template(path = "tree/page.html")] +struct TreePageTemplate { + title: &'static str, + base_path: &'static str, + root: Option, +} + +struct NodeView { + name: String, + formed_ybp: Option, +} + +#[derive(askama::Template)] +#[template(path = "tree/fragment.html")] +struct FragmentTemplate { + base_path: &'static str, + current: Option, + nodes: Vec, +} + +async fn ytree_page(Query(q): Query) -> Response { + html(&TreePageTemplate { title: "Y-DNA Tree", base_path: "/ytree", root: q.root }) +} + +async fn mtree_page(Query(q): Query) -> Response { + html(&TreePageTemplate { title: "mtDNA Tree", base_path: "/mtree", root: q.root }) +} + +async fn ytree_fragment(st: State, q: Query) -> Result { + fragment(st, q, DnaType::YDna, "/ytree").await +} + +async fn mtree_fragment(st: State, q: Query) -> Result { + fragment(st, q, DnaType::MtDna, "/mtree").await +} + +async fn fragment( + State(st): State, + Query(q): Query, + dna_type: DnaType, + base_path: &'static str, +) -> Result { + let to_view = |h: du_domain::haplogroup::Haplogroup| NodeView { + name: h.name, + formed_ybp: h.formed_ybp, + }; + + let (current, nodes) = match q.root.as_deref().filter(|s| !s.is_empty()) { + None => (None, du_db::haplogroup::roots(&st.pool, dna_type).await?), + Some(name) => { + let cur = du_db::haplogroup::get_by_name(&st.pool, name, dna_type) + .await? + .ok_or_else(|| AppError::NotFound(format!("haplogroup {name}")))?; + let kids = du_db::haplogroup::children(&st.pool, cur.id).await?; + (Some(cur), kids) + } + }; + + Ok(html(&FragmentTemplate { + base_path, + current: current.map(to_view), + nodes: nodes.into_iter().map(to_view).collect(), + })) +} diff --git a/rust/crates/du-web/src/routes/variants.rs b/rust/crates/du-web/src/routes/variants.rs new file mode 100644 index 0000000..13c64b8 --- /dev/null +++ b/rust/crates/du-web/src/routes/variants.rs @@ -0,0 +1,138 @@ +//! Public variant browser. Demonstrates the HTMX two-panel + fragment pattern: +//! a full page (`/variants`) that lazy-loads a list fragment (`/variants/list`), +//! whose rows load a detail panel fragment (`/variants/detail/:id`). + +use crate::error::AppError; +use crate::render::html; +use crate::state::AppState; +use axum::extract::{Path, Query, State}; +use axum::response::Response; +use axum::routing::get; +use axum::Router; +use du_db::Page; +use du_domain::ids::VariantId; +use du_domain::variant::Variant; +use serde::Deserialize; + +pub fn router() -> Router { + Router::new() + .route("/variants", get(browser)) + .route("/variants/list", get(list)) + .route("/variants/detail/:id", get(detail)) +} + +#[derive(Deserialize)] +struct ListQuery { + query: Option, + page: Option, + page_size: Option, +} + +/// A flattened variant for the list table (templates stay logic-free). +struct RowView { + id: i64, + name: String, + mutation_type: String, + naming_status: String, + builds: String, +} + +impl RowView { + fn from(v: &Variant) -> Self { + let mut builds: Vec<&str> = v.coordinates.0.keys().map(String::as_str).collect(); + builds.sort_unstable(); + RowView { + id: v.id.0, + name: v.canonical_name.clone(), + mutation_type: v.mutation_type.label().to_string(), + naming_status: v.naming_status.label().to_string(), + builds: builds.join(", "), + } + } +} + +#[derive(askama::Template)] +#[template(path = "variants/browser.html")] +struct BrowserTemplate { + query: String, +} + +#[derive(askama::Template)] +#[template(path = "variants/list.html")] +struct ListTemplate { + query: String, + rows: Vec, + page: i64, + page_size: i64, + total: i64, + total_pages: i64, +} + +struct CoordView { + build: String, + contig: String, + position: i64, + change: Option, +} + +#[derive(askama::Template)] +#[template(path = "variants/detail.html")] +struct DetailTemplate { + name: String, + mutation_type: String, + naming_status: String, + common_names: Vec, + rs_ids: Vec, + coords: Vec, +} + +async fn browser(Query(q): Query) -> Response { + html(&BrowserTemplate { query: q.query.unwrap_or_default() }) +} + +async fn list(State(st): State, Query(q): Query) -> Result { + let page_num = q.page.unwrap_or(1); + let page_size = q.page_size.unwrap_or(25); + let result: Page = + du_db::variant::search(&st.pool, q.query.as_deref(), page_num, page_size).await?; + let rows = result.items.iter().map(RowView::from).collect(); + Ok(html(&ListTemplate { + query: q.query.unwrap_or_default(), + rows, + page: result.page, + page_size: result.page_size, + total: result.total, + total_pages: result.total_pages(), + })) +} + +async fn detail(State(st): State, Path(id): Path) -> Result { + let v = du_db::variant::get_by_id(&st.pool, VariantId(id)) + .await? + .ok_or_else(|| AppError::NotFound(format!("variant {id}")))?; + + let mut coords: Vec = v + .coordinates + .0 + .iter() + .map(|(build, c)| CoordView { + build: build.clone(), + contig: c.contig.clone(), + position: c.position, + change: match (&c.reference_allele, &c.alternate_allele) { + (Some(r), Some(a)) => Some(format!("{r}>{a}")), + _ => None, + }, + }) + .collect(); + coords.sort_by(|a, b| a.build.cmp(&b.build)); + + Ok(html(&DetailTemplate { + name: v.canonical_name, + mutation_type: v.mutation_type.label().to_string(), + naming_status: v.naming_status.label().to_string(), + common_names: v.aliases.common_names, + rs_ids: v.aliases.rs_ids, + coords, + })) +} diff --git a/rust/crates/du-web/src/state.rs b/rust/crates/du-web/src/state.rs new file mode 100644 index 0000000..546c93c --- /dev/null +++ b/rust/crates/du-web/src/state.rs @@ -0,0 +1,8 @@ +//! Shared application state injected into handlers via `State`. + +use du_db::PgPool; + +#[derive(Clone)] +pub struct AppState { + pub pool: PgPool, +} diff --git a/rust/crates/du-web/templates/base.html b/rust/crates/du-web/templates/base.html new file mode 100644 index 0000000..c6c9e26 --- /dev/null +++ b/rust/crates/du-web/templates/base.html @@ -0,0 +1,31 @@ + + + + + + {% block title %}Decoding Us{% endblock %} + + + + + + + +
+ {% block content %}{% endblock %} +
+ + diff --git a/rust/crates/du-web/templates/index.html b/rust/crates/du-web/templates/index.html new file mode 100644 index 0000000..f0a1bc3 --- /dev/null +++ b/rust/crates/du-web/templates/index.html @@ -0,0 +1,16 @@ +{% extends "base.html" %} +{% block title %}Decoding Us — genetic genealogy & population research{% endblock %} +{% block content %} +
+

Decoding Us

+

+ A collaborative platform for genetic genealogy and population research — + Y/mtDNA haplogroup trees, a public variant browser, and privacy-preserving + relative discovery. +

+
+ Browse the Y-DNA tree + Search variants +
+
+{% endblock %} diff --git a/rust/crates/du-web/templates/tree/fragment.html b/rust/crates/du-web/templates/tree/fragment.html new file mode 100644 index 0000000..f4ceb9d --- /dev/null +++ b/rust/crates/du-web/templates/tree/fragment.html @@ -0,0 +1,29 @@ +{# Fragment: one tree level. Clicking a node swaps this container and pushes the + URL so browser back/forward navigates the tree (HATEOAS). #} +{% if let Some(cur) = current %} + +

+ {{ cur.name }} + {% if let Some(ybp) = cur.formed_ybp %}· formed ~{{ ybp }} ybp{% endif %} +

+{% else %} +

Root lineages

+{% endif %} + +
+ {% for n in nodes %} + + {{ n.name }} + {% if let Some(ybp) = n.formed_ybp %}~{{ ybp }} ybp{% endif %} + + {% else %} +
No child haplogroups.
+ {% endfor %} +
diff --git a/rust/crates/du-web/templates/tree/page.html b/rust/crates/du-web/templates/tree/page.html new file mode 100644 index 0000000..b5d78af --- /dev/null +++ b/rust/crates/du-web/templates/tree/page.html @@ -0,0 +1,10 @@ +{% extends "base.html" %} +{% block title %}{{ title }} — Decoding Us{% endblock %} +{% block content %} +

{{ title }}

+
+ Loading tree… +
+{% endblock %} diff --git a/rust/crates/du-web/templates/variants/browser.html b/rust/crates/du-web/templates/variants/browser.html new file mode 100644 index 0000000..dc36d38 --- /dev/null +++ b/rust/crates/du-web/templates/variants/browser.html @@ -0,0 +1,26 @@ +{% extends "base.html" %} +{% block title %}Variant Browser — Decoding Us{% endblock %} +{% block content %} +

Variant Browser

+
+
+ + +
+
+
+
+
+

Select a variant to see details.

+
+
+
+{% endblock %} diff --git a/rust/crates/du-web/templates/variants/detail.html b/rust/crates/du-web/templates/variants/detail.html new file mode 100644 index 0000000..8a19ace --- /dev/null +++ b/rust/crates/du-web/templates/variants/detail.html @@ -0,0 +1,40 @@ +{# Fragment: variant detail card. Target of #detail-panel. #} +
+
+ {{ name }} + {{ mutation_type }} +
+
+

Naming status: {{ naming_status }}

+ + {% if !common_names.is_empty() %} +

Also known as: + {% for n in common_names %}{{ n }} {% endfor %} +

+ {% endif %} + {% if !rs_ids.is_empty() %} +

rs IDs: + {% for r in rs_ids %}{{ r }} {% endfor %} +

+ {% endif %} + +
Coordinates
+ {% if coords.is_empty() %} +

No mapped coordinates.

+ {% else %} + + + + {% for c in coords %} + + + + + + + {% endfor %} + +
BuildContigPositionChange
{{ c.build }}{{ c.contig }}{{ c.position }}{% if let Some(ch) = c.change %}{{ ch }}{% else %}—{% endif %}
+ {% endif %} +
+
diff --git a/rust/crates/du-web/templates/variants/list.html b/rust/crates/du-web/templates/variants/list.html new file mode 100644 index 0000000..fd42f17 --- /dev/null +++ b/rust/crates/du-web/templates/variants/list.html @@ -0,0 +1,35 @@ +{# Fragment: the variant results table + pager. Target of #variants-table. #} + + + + + + {% for r in rows %} + + + + + + + {% else %} + + {% endfor %} + +
NameTypeStatusBuilds
{{ r.name }}{{ r.mutation_type }}{{ r.naming_status }}{{ r.builds }}
No variants match.
+ +{% if total_pages > 1 %} + +{% else %} +{{ total }} total +{% endif %} From faf04e249bc39d3cd7d9c41e28138a33cc7b3467 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 08:09:23 -0500 Subject: [PATCH 004/191] feat(rust): harden public slice to plan spec (assets, i18n, HX negotiation) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bring the read-only slice up to plan §4: Vendored assets: bootstrap 5.3.3 (css + bundle js) and htmx 2.0.4 under crates/du-web/assets/vendor, served via tower-http ServeDir at /assets (DU_ASSETS_DIR env, compile-time crate-dir fallback). Custom main.css replaces inline styles. CDN links removed; Dockerfile copies assets + sets DU_ASSETS_DIR. i18n (en/es/fr): Play-style key=value catalogs embedded via include_str; Lang+T translator with en/key fallback; Locale extractor resolves lang from the `lang` cookie then Accept-Language (default en); navbar language switcher with percent-encoded `next`; GET /language/:lang sets the cookie + redirects with an open-redirect guard. Templates fully localized. Unit tests assert the fallback chain and that es/fr cover every English key. HX-Request unification: HxRequest extractor (htmx + history-restore + target). Tree collapses to one handler per lineage (/ytree, /mtree) — full page embeds the current level inline; an HTMX swap of #tree-container returns just the fragment with a server-driven HX-Push-Url; history-restore and boosted navigations get the full page (target-aware negotiation). HxHeaders builder for HX-* response headers. Variant browser embeds its first results page inline (no load round-trip). Verified live against the container PostGIS; workspace 9/9 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/Cargo.lock | 1 + rust/Cargo.toml | 3 + rust/Dockerfile | 6 +- rust/crates/du-web/Cargo.toml | 1 + rust/crates/du-web/assets/main.css | 4 + .../assets/vendor/bootstrap.bundle.min.js | 7 + .../du-web/assets/vendor/bootstrap.min.css | 6 + rust/crates/du-web/assets/vendor/htmx.min.js | 1 + rust/crates/du-web/src/htmx.rs | 110 ++++++++++ rust/crates/du-web/src/i18n.rs | 188 ++++++++++++++++++ rust/crates/du-web/src/main.rs | 2 + rust/crates/du-web/src/routes/mod.rs | 50 ++++- rust/crates/du-web/src/routes/tree.rs | 95 ++++++--- rust/crates/du-web/src/routes/variants.rs | 82 +++++--- rust/crates/du-web/templates/base.html | 38 ++-- rust/crates/du-web/templates/index.html | 14 +- .../du-web/templates/tree/fragment.html | 19 +- rust/crates/du-web/templates/tree/page.html | 9 +- .../du-web/templates/variants/browser.html | 16 +- .../du-web/templates/variants/detail.html | 17 +- .../du-web/templates/variants/list.html | 35 ++-- rust/locales/en.txt | 48 +++++ rust/locales/es.txt | 48 +++++ rust/locales/fr.txt | 48 +++++ 24 files changed, 716 insertions(+), 132 deletions(-) create mode 100644 rust/crates/du-web/assets/main.css create mode 100644 rust/crates/du-web/assets/vendor/bootstrap.bundle.min.js create mode 100644 rust/crates/du-web/assets/vendor/bootstrap.min.css create mode 100644 rust/crates/du-web/assets/vendor/htmx.min.js create mode 100644 rust/crates/du-web/src/htmx.rs create mode 100644 rust/crates/du-web/src/i18n.rs create mode 100644 rust/locales/en.txt create mode 100644 rust/locales/es.txt create mode 100644 rust/locales/fr.txt diff --git a/rust/Cargo.lock b/rust/Cargo.lock index b9a4033..958913b 100644 --- a/rust/Cargo.lock +++ b/rust/Cargo.lock @@ -587,6 +587,7 @@ dependencies = [ "axum", "du-db", "du-domain", + "percent-encoding", "serde", "serde_json", "tokio", diff --git a/rust/Cargo.toml b/rust/Cargo.toml index 7612440..a7200e7 100644 --- a/rust/Cargo.toml +++ b/rust/Cargo.toml @@ -56,6 +56,9 @@ rust_decimal = "1" # HTTP client (external APIs) reqwest = { version = "0.12", default-features = false, features = ["json", "rustls-tls"] } +# URL/query encoding (language-switcher `next` param) +percent-encoding = "2" + # Errors / logging / config thiserror = "2" anyhow = "1" diff --git a/rust/Dockerfile b/rust/Dockerfile index 75d9f58..3791804 100644 --- a/rust/Dockerfile +++ b/rust/Dockerfile @@ -30,13 +30,15 @@ WORKDIR /app COPY --from=builder /build/target/release/decodingus /usr/local/bin/decodingus COPY --from=builder /build/target/release/decodingus-jobs /usr/local/bin/decodingus-jobs COPY --from=builder /build/target/release/decodingus-migrate /usr/local/bin/decodingus-migrate -# Static assets + migrations shipped alongside the binary. -COPY --chown=decodingus:decodingus assets ./assets +# Vendored static assets + migrations shipped alongside the binary. (Askama +# templates and locale catalogs are embedded into the binary at compile time.) +COPY --chown=decodingus:decodingus crates/du-web/assets ./assets COPY --chown=decodingus:decodingus migrations ./migrations USER decodingus EXPOSE 9000 ENV PORT=9000 +ENV DU_ASSETS_DIR=/app/assets HEALTHCHECK --interval=30s --timeout=10s --start-period=20s --retries=3 \ CMD curl -fsS http://localhost:9000/health || exit 1 diff --git a/rust/crates/du-web/Cargo.toml b/rust/crates/du-web/Cargo.toml index 8184fc9..35bf30d 100644 --- a/rust/crates/du-web/Cargo.toml +++ b/rust/crates/du-web/Cargo.toml @@ -18,6 +18,7 @@ tokio = { workspace = true } tower = { workspace = true } tower-http = { workspace = true } askama = { workspace = true } +percent-encoding = { workspace = true } serde = { workspace = true } serde_json = { workspace = true } tracing = { workspace = true } diff --git a/rust/crates/du-web/assets/main.css b/rust/crates/du-web/assets/main.css new file mode 100644 index 0000000..571513e --- /dev/null +++ b/rust/crates/du-web/assets/main.css @@ -0,0 +1,4 @@ +/* DecodingUs custom styles (vendored bootstrap handles the rest). */ +body { padding-top: 4.5rem; } +.detail-empty { color: var(--bs-secondary-color); } +.tree-node { cursor: pointer; } diff --git a/rust/crates/du-web/assets/vendor/bootstrap.bundle.min.js b/rust/crates/du-web/assets/vendor/bootstrap.bundle.min.js new file mode 100644 index 0000000..04e9185 --- /dev/null +++ b/rust/crates/du-web/assets/vendor/bootstrap.bundle.min.js @@ -0,0 +1,7 @@ +/*! + * Bootstrap v5.3.3 (https://getbootstrap.com/) + * Copyright 2011-2024 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors) + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE) + */ +!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?module.exports=e():"function"==typeof define&&define.amd?define(e):(t="undefined"!=typeof globalThis?globalThis:t||self).bootstrap=e()}(this,(function(){"use strict";const t=new Map,e={set(e,i,n){t.has(e)||t.set(e,new Map);const s=t.get(e);s.has(i)||0===s.size?s.set(i,n):console.error(`Bootstrap doesn't allow more than one instance per element. 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st(this._element,t)}_keydown(t){if(/input|textarea/i.test(t.target.tagName))return;const e=Tt[t.key];e&&(t.preventDefault(),this._slide(this._directionToOrder(e)))}_getItemIndex(t){return this._getItems().indexOf(t)}_setActiveIndicatorElement(t){if(!this._indicatorsElement)return;const e=z.findOne(wt,this._indicatorsElement);e.classList.remove(yt),e.removeAttribute("aria-current");const i=z.findOne(`[data-bs-slide-to="${t}"]`,this._indicatorsElement);i&&(i.classList.add(yt),i.setAttribute("aria-current","true"))}_updateInterval(){const t=this._activeElement||this._getActive();if(!t)return;const e=Number.parseInt(t.getAttribute("data-bs-interval"),10);this._config.interval=e||this._config.defaultInterval}_slide(t,e=null){if(this._isSliding)return;const i=this._getActive(),n=t===at,s=e||b(this._getItems(),i,n,this._config.wrap);if(s===i)return;const 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H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,jn=`hide${xn}`,Mn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,jn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,Mn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,Mn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],dd:[],div:[],dl:[],dt:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
"},Un={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Gn={entry:"(string|element|function|null)",selector:"(string|element)"};class Jn extends H{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Yn}static get DefaultType(){return Un}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,i]of Object.entries(this._config.content))this._setContent(t,i,e);const e=t.children[0],i=this._resolvePossibleFunction(this._config.extraClass);return i&&e.classList.add(...i.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t 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var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color:#dee2e6;--bs-dropdown-bg:#343a40;--bs-dropdown-border-color:var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color:#dee2e6;--bs-dropdown-link-hover-color:#fff;--bs-dropdown-divider-bg:var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg:rgba(255, 255, 255, 0.15);--bs-dropdown-link-active-color:#fff;--bs-dropdown-link-active-bg:#0d6efd;--bs-dropdown-link-disabled-color:#adb5bd;--bs-dropdown-header-color:#adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group-vertical>.btn,.btn-group>.btn{position:relative;flex:1 1 auto}.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn.active,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:hover,.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn.active,.btn-group>.btn:active,.btn-group>.btn:focus,.btn-group>.btn:hover{z-index:1}.btn-toolbar{display:flex;flex-wrap:wrap;justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>.btn-group:not(:first-child),.btn-group>:not(.btn-check:first-child)+.btn{margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn-group:not(:last-child)>.btn,.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn:not(:last-child):not(.dropdown-toggle){border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn-group:not(:first-child)>.btn,.btn-group>.btn:nth-child(n+3),.btn-group>:not(.btn-check)+.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-group-sm>.btn+.dropdown-toggle-split,.btn-sm+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-group-lg>.btn+.dropdown-toggle-split,.btn-lg+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;align-items:flex-start;justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn-group:not(:first-child),.btn-group-vertical>.btn:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn-group:not(:last-child)>.btn,.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle){border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn-group:not(:first-child)>.btn,.btn-group-vertical>.btn~.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x:1rem;--bs-nav-link-padding-y:0.5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color:var(--bs-link-color);--bs-nav-link-hover-color:var(--bs-link-hover-color);--bs-nav-link-disabled-color:var(--bs-secondary-color);display:flex;flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;background:0 0;border:0;transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out}@media (prefers-reduced-motion:reduce){.nav-link{transition:none}}.nav-link:focus,.nav-link:hover{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem 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.nav-link:hover{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-item.show .nav-link,.nav-tabs .nav-link.active{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius:var(--bs-border-radius);--bs-nav-pills-link-active-color:#fff;--bs-nav-pills-link-active-bg:#0d6efd}.nav-pills .nav-link{border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap:1rem;--bs-nav-underline-border-width:0.125rem;--bs-nav-underline-link-active-color:var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:focus,.nav-underline .nav-link:hover{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill .nav-item,.nav-fill>.nav-link{flex:1 1 auto;text-align:center}.nav-justified .nav-item,.nav-justified>.nav-link{flex-basis:0;flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x:0;--bs-navbar-padding-y:0.5rem;--bs-navbar-color:rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color:rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color:rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color:rgba(var(--bs-emphasis-color-rgb), 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var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion:reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type>.accordion-header .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type>.accordion-header 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0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon:url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x:0;--bs-breadcrumb-padding-y:0;--bs-breadcrumb-margin-bottom:1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color:var(--bs-secondary-color);--bs-breadcrumb-item-padding-x:0.5rem;--bs-breadcrumb-item-active-color:var(--bs-secondary-color);display:flex;flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/")}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x:0.75rem;--bs-pagination-padding-y:0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color:var(--bs-link-color);--bs-pagination-bg:var(--bs-body-bg);--bs-pagination-border-width:var(--bs-border-width);--bs-pagination-border-color:var(--bs-border-color);--bs-pagination-border-radius:var(--bs-border-radius);--bs-pagination-hover-color:var(--bs-link-hover-color);--bs-pagination-hover-bg:var(--bs-tertiary-bg);--bs-pagination-hover-border-color:var(--bs-border-color);--bs-pagination-focus-color:var(--bs-link-hover-color);--bs-pagination-focus-bg:var(--bs-secondary-bg);--bs-pagination-focus-box-shadow:0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-pagination-active-color:#fff;--bs-pagination-active-bg:#0d6efd;--bs-pagination-active-border-color:#0d6efd;--bs-pagination-disabled-color:var(--bs-secondary-color);--bs-pagination-disabled-bg:var(--bs-secondary-bg);--bs-pagination-disabled-border-color:var(--bs-border-color);display:flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media (prefers-reduced-motion:reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.active>.page-link,.page-link.active{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.disabled>.page-link,.page-link.disabled{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x:1.5rem;--bs-pagination-padding-y:0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius:var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x:0.5rem;--bs-pagination-padding-y:0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius:var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x:0.65em;--bs-badge-padding-y:0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight:700;--bs-badge-color:#fff;--bs-badge-border-radius:var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg:transparent;--bs-alert-padding-x:1rem;--bs-alert-padding-y:1rem;--bs-alert-margin-bottom:1rem;--bs-alert-color:inherit;--bs-alert-border-color:transparent;--bs-alert-border:var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius:var(--bs-border-radius);--bs-alert-link-color:inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-primary{--bs-alert-color:var(--bs-primary-text-emphasis);--bs-alert-bg:var(--bs-primary-bg-subtle);--bs-alert-border-color:var(--bs-primary-border-subtle);--bs-alert-link-color:var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color:var(--bs-secondary-text-emphasis);--bs-alert-bg:var(--bs-secondary-bg-subtle);--bs-alert-border-color:var(--bs-secondary-border-subtle);--bs-alert-link-color:var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color:var(--bs-success-text-emphasis);--bs-alert-bg:var(--bs-success-bg-subtle);--bs-alert-border-color:var(--bs-success-border-subtle);--bs-alert-link-color:var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color:var(--bs-info-text-emphasis);--bs-alert-bg:var(--bs-info-bg-subtle);--bs-alert-border-color:var(--bs-info-border-subtle);--bs-alert-link-color:var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color:var(--bs-warning-text-emphasis);--bs-alert-bg:var(--bs-warning-bg-subtle);--bs-alert-border-color:var(--bs-warning-border-subtle);--bs-alert-link-color:var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color:var(--bs-danger-text-emphasis);--bs-alert-bg:var(--bs-danger-bg-subtle);--bs-alert-border-color:var(--bs-danger-border-subtle);--bs-alert-link-color:var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color:var(--bs-light-text-emphasis);--bs-alert-bg:var(--bs-light-bg-subtle);--bs-alert-border-color:var(--bs-light-border-subtle);--bs-alert-link-color:var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color:var(--bs-dark-text-emphasis);--bs-alert-bg:var(--bs-dark-bg-subtle);--bs-alert-border-color:var(--bs-dark-border-subtle);--bs-alert-link-color:var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height:1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg:var(--bs-secondary-bg);--bs-progress-border-radius:var(--bs-border-radius);--bs-progress-box-shadow:var(--bs-box-shadow-inset);--bs-progress-bar-color:#fff;--bs-progress-bar-bg:#0d6efd;--bs-progress-bar-transition:width 0.6s ease;display:flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;flex-direction:column;justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion:reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg,rgba(255,255,255,.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,.15) 50%,rgba(255,255,255,.15) 75%,transparent 75%,transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion:reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color:var(--bs-body-color);--bs-list-group-bg:var(--bs-body-bg);--bs-list-group-border-color:var(--bs-border-color);--bs-list-group-border-width:var(--bs-border-width);--bs-list-group-border-radius:var(--bs-border-radius);--bs-list-group-item-padding-x:1rem;--bs-list-group-item-padding-y:0.5rem;--bs-list-group-action-color:var(--bs-secondary-color);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-tertiary-bg);--bs-list-group-action-active-color:var(--bs-body-color);--bs-list-group-action-active-bg:var(--bs-secondary-bg);--bs-list-group-disabled-color:var(--bs-secondary-color);--bs-list-group-disabled-bg:var(--bs-body-bg);--bs-list-group-active-color:#fff;--bs-list-group-active-bg:#0d6efd;--bs-list-group-active-border-color:#0d6efd;display:flex;flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:focus,.list-group-item-action:hover{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width:576px){.list-group-horizontal-sm{flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:768px){.list-group-horizontal-md{flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:992px){.list-group-horizontal-lg{flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:1200px){.list-group-horizontal-xl{flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:1400px){.list-group-horizontal-xxl{flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-primary{--bs-list-group-color:var(--bs-primary-text-emphasis);--bs-list-group-bg:var(--bs-primary-bg-subtle);--bs-list-group-border-color:var(--bs-primary-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-primary-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-primary-border-subtle);--bs-list-group-active-color:var(--bs-primary-bg-subtle);--bs-list-group-active-bg:var(--bs-primary-text-emphasis);--bs-list-group-active-border-color:var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color:var(--bs-secondary-text-emphasis);--bs-list-group-bg:var(--bs-secondary-bg-subtle);--bs-list-group-border-color:var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-secondary-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-secondary-border-subtle);--bs-list-group-active-color:var(--bs-secondary-bg-subtle);--bs-list-group-active-bg:var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color:var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color:var(--bs-success-text-emphasis);--bs-list-group-bg:var(--bs-success-bg-subtle);--bs-list-group-border-color:var(--bs-success-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-success-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-success-border-subtle);--bs-list-group-active-color:var(--bs-success-bg-subtle);--bs-list-group-active-bg:var(--bs-success-text-emphasis);--bs-list-group-active-border-color:var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color:var(--bs-info-text-emphasis);--bs-list-group-bg:var(--bs-info-bg-subtle);--bs-list-group-border-color:var(--bs-info-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-info-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-info-border-subtle);--bs-list-group-active-color:var(--bs-info-bg-subtle);--bs-list-group-active-bg:var(--bs-info-text-emphasis);--bs-list-group-active-border-color:var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color:var(--bs-warning-text-emphasis);--bs-list-group-bg:var(--bs-warning-bg-subtle);--bs-list-group-border-color:var(--bs-warning-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-warning-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-warning-border-subtle);--bs-list-group-active-color:var(--bs-warning-bg-subtle);--bs-list-group-active-bg:var(--bs-warning-text-emphasis);--bs-list-group-active-border-color:var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color:var(--bs-danger-text-emphasis);--bs-list-group-bg:var(--bs-danger-bg-subtle);--bs-list-group-border-color:var(--bs-danger-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-danger-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-danger-border-subtle);--bs-list-group-active-color:var(--bs-danger-bg-subtle);--bs-list-group-active-bg:var(--bs-danger-text-emphasis);--bs-list-group-active-border-color:var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color:var(--bs-light-text-emphasis);--bs-list-group-bg:var(--bs-light-bg-subtle);--bs-list-group-border-color:var(--bs-light-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-light-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-light-border-subtle);--bs-list-group-active-color:var(--bs-light-bg-subtle);--bs-list-group-active-bg:var(--bs-light-text-emphasis);--bs-list-group-active-border-color:var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color:var(--bs-dark-text-emphasis);--bs-list-group-bg:var(--bs-dark-bg-subtle);--bs-list-group-border-color:var(--bs-dark-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-dark-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-dark-border-subtle);--bs-list-group-active-color:var(--bs-dark-bg-subtle);--bs-list-group-active-bg:var(--bs-dark-text-emphasis);--bs-list-group-active-border-color:var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color:#000;--bs-btn-close-bg:url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity:0.5;--bs-btn-close-hover-opacity:0.75;--bs-btn-close-focus-shadow:0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-btn-close-focus-opacity:1;--bs-btn-close-disabled-opacity:0.25;--bs-btn-close-white-filter:invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close.disabled,.btn-close:disabled{pointer-events:none;-webkit-user-select:none;-moz-user-select:none;user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex:1090;--bs-toast-padding-x:0.75rem;--bs-toast-padding-y:0.5rem;--bs-toast-spacing:1.5rem;--bs-toast-max-width:350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg:rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width:var(--bs-border-width);--bs-toast-border-color:var(--bs-border-color-translucent);--bs-toast-border-radius:var(--bs-border-radius);--bs-toast-box-shadow:var(--bs-box-shadow);--bs-toast-header-color:var(--bs-secondary-color);--bs-toast-header-bg:rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color:var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex:1090;position:absolute;z-index:var(--bs-toast-zindex);width:-webkit-max-content;width:-moz-max-content;width:max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex:1055;--bs-modal-width:500px;--bs-modal-padding:1rem;--bs-modal-margin:0.5rem;--bs-modal-color: ;--bs-modal-bg:var(--bs-body-bg);--bs-modal-border-color:var(--bs-border-color-translucent);--bs-modal-border-width:var(--bs-border-width);--bs-modal-border-radius:var(--bs-border-radius-lg);--bs-modal-box-shadow:var(--bs-box-shadow-sm);--bs-modal-inner-border-radius:calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x:1rem;--bs-modal-header-padding-y:1rem;--bs-modal-header-padding:1rem 1rem;--bs-modal-header-border-color:var(--bs-border-color);--bs-modal-header-border-width:var(--bs-border-width);--bs-modal-title-line-height:1.5;--bs-modal-footer-gap:0.5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color:var(--bs-border-color);--bs-modal-footer-border-width:var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform .3s ease-out;transform:translate(0,-50px)}@media (prefers-reduced-motion:reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex:1050;--bs-backdrop-bg:#000;--bs-backdrop-opacity:0.5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;flex-shrink:0;align-items:center;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header 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(min-width:576px){.modal{--bs-modal-margin:1.75rem;--bs-modal-box-shadow:var(--bs-box-shadow)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width:300px}}@media (min-width:992px){.modal-lg,.modal-xl{--bs-modal-width:800px}}@media (min-width:1200px){.modal-xl{--bs-modal-width:1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-footer,.modal-fullscreen .modal-header{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media (max-width:575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-footer,.modal-fullscreen-sm-down .modal-header{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media (max-width:767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-footer,.modal-fullscreen-md-down .modal-header{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media (max-width:991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-footer,.modal-fullscreen-lg-down .modal-header{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media (max-width:1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-footer,.modal-fullscreen-xl-down .modal-header{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media (max-width:1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-footer,.modal-fullscreen-xxl-down .modal-header{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex:1080;--bs-tooltip-max-width:200px;--bs-tooltip-padding-x:0.5rem;--bs-tooltip-padding-y:0.25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:0.875rem;--bs-tooltip-color:var(--bs-body-bg);--bs-tooltip-bg:var(--bs-emphasis-color);--bs-tooltip-border-radius:var(--bs-border-radius);--bs-tooltip-opacity:0.9;--bs-tooltip-arrow-width:0.8rem;--bs-tooltip-arrow-height:0.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-auto[data-popper-placement^=top] 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var(--bs-tooltip-arrow-height))}.bs-tooltip-auto[data-popper-placement^=bottom] .tooltip-arrow::before,.bs-tooltip-bottom .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-auto[data-popper-placement^=left] .tooltip-arrow,.bs-tooltip-start .tooltip-arrow{right:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-auto[data-popper-placement^=left] .tooltip-arrow::before,.bs-tooltip-start .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) 0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) 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HTMX request/response plumbing for server-driven hypermedia (plan §4). + +use axum::extract::FromRequestParts; +use axum::http::header::{HeaderName, HeaderValue}; +use axum::http::request::Parts; +use axum::response::{IntoResponseParts, ResponseParts}; +use std::convert::Infallible; + +/// Whether the request came from HTMX, and whether it is a history-restore. +/// +/// `wants_fragment()` is the negotiation rule: serve just the inner fragment for +/// HTMX-driven swaps, but serve the FULL page for normal navigations AND for +/// htmx history restoration (back/forward), which expects the whole document. +pub struct HxRequest { + pub is_htmx: bool, + pub is_history_restore: bool, + /// The `HX-Target` element id, if the swap names one. + pub target: Option, +} + +impl HxRequest { + /// Serve the inner fragment only when this is an HTMX swap aimed at the + /// given target id — NOT for boosted full-page navigations (which target the + /// body and expect a whole document) nor history restoration. + pub fn wants_fragment_for(&self, target_id: &str) -> bool { + self.is_htmx + && !self.is_history_restore + && self.target.as_deref() == Some(target_id) + } +} + +#[axum::async_trait] +impl FromRequestParts for HxRequest { + type Rejection = Infallible; + + async fn from_request_parts(parts: &mut Parts, _: &S) -> Result { + let has = |name: &str| parts.headers.get(name).is_some_and(|v| v == "true"); + let target = parts + .headers + .get("hx-target") + .and_then(|v| v.to_str().ok()) + .map(str::to_owned); + Ok(HxRequest { + is_htmx: has("hx-request"), + is_history_restore: has("hx-history-restore-request"), + target, + }) + } +} + +/// Builder for HTMX response headers, so state transitions are server-driven +/// (HX-Push-Url / HX-Trigger / HX-Redirect / HX-Location / HX-Reswap). +#[derive(Default)] +pub struct HxHeaders { + push_url: Option, + trigger: Option, + redirect: Option, + location: Option, + reswap: Option, +} + +// Builder surface kept complete for upcoming write flows (curator CRUD, forms); +// only push_url is exercised by the read-only slice so far. +#[allow(dead_code)] +impl HxHeaders { + pub fn new() -> Self { + Self::default() + } + pub fn push_url(mut self, url: impl Into) -> Self { + self.push_url = Some(url.into()); + self + } + pub fn trigger(mut self, event: impl Into) -> Self { + self.trigger = Some(event.into()); + self + } + pub fn redirect(mut self, url: impl Into) -> Self { + self.redirect = Some(url.into()); + self + } + pub fn location(mut self, url: impl Into) -> Self { + self.location = Some(url.into()); + self + } + pub fn reswap(mut self, spec: impl Into) -> Self { + self.reswap = Some(spec.into()); + self + } +} + +impl IntoResponseParts for HxHeaders { + type Error = Infallible; + + fn into_response_parts(self, mut res: ResponseParts) -> Result { + let headers = res.headers_mut(); + let mut set = |name: &'static str, val: Option| { + if let Some(v) = val { + if let Ok(hv) = HeaderValue::from_str(&v) { + headers.insert(HeaderName::from_static(name), hv); + } + } + }; + set("hx-push-url", self.push_url); + set("hx-trigger", self.trigger); + set("hx-redirect", self.redirect); + set("hx-location", self.location); + set("hx-reswap", self.reswap); + Ok(res) + } +} diff --git a/rust/crates/du-web/src/i18n.rs b/rust/crates/du-web/src/i18n.rs new file mode 100644 index 0000000..5bb33ca --- /dev/null +++ b/rust/crates/du-web/src/i18n.rs @@ -0,0 +1,188 @@ +//! Lightweight i18n: Play-style `key=value` catalogs embedded at compile time, +//! a `Lang` + `T` translator, and a `Locale` extractor that resolves the active +//! language from the `lang` cookie then `Accept-Language` (default English). +//! +//! Replaces Play's `messages`/`Messages`. Keeping it dependency-free (no fluent) +//! matches the catalog format the project already used. + +use axum::extract::FromRequestParts; +use axum::http::header::{ACCEPT_LANGUAGE, COOKIE}; +use axum::http::request::Parts; +use std::collections::HashMap; +use std::convert::Infallible; +use std::sync::OnceLock; + +#[derive(Clone, Copy, PartialEq, Eq, Debug)] +pub enum Lang { + En, + Es, + Fr, +} + +impl Lang { + pub fn code(self) -> &'static str { + match self { + Lang::En => "en", + Lang::Es => "es", + Lang::Fr => "fr", + } + } + + pub fn parse(s: &str) -> Option { + match s.get(0..2).map(str::to_ascii_lowercase).as_deref() { + Some("en") => Some(Lang::En), + Some("es") => Some(Lang::Es), + Some("fr") => Some(Lang::Fr), + _ => None, + } + } + + /// All languages, for rendering the switcher. + pub fn all() -> [Lang; 3] { + [Lang::En, Lang::Es, Lang::Fr] + } +} + +const EN_SRC: &str = include_str!("../../../locales/en.txt"); +const ES_SRC: &str = include_str!("../../../locales/es.txt"); +const FR_SRC: &str = include_str!("../../../locales/fr.txt"); + +fn parse_catalog(src: &'static str) -> HashMap<&'static str, &'static str> { + src.lines() + .filter_map(|line| { + let line = line.trim(); + if line.is_empty() || line.starts_with('#') { + return None; + } + line.split_once('=').map(|(k, v)| (k.trim(), v.trim())) + }) + .collect() +} + +fn catalog(lang: Lang) -> &'static HashMap<&'static str, &'static str> { + static EN: OnceLock> = OnceLock::new(); + static ES: OnceLock> = OnceLock::new(); + static FR: OnceLock> = OnceLock::new(); + match lang { + Lang::En => EN.get_or_init(|| parse_catalog(EN_SRC)), + Lang::Es => ES.get_or_init(|| parse_catalog(ES_SRC)), + Lang::Fr => FR.get_or_init(|| parse_catalog(FR_SRC)), + } +} + +/// Translator for one language. Cheap to copy. +#[derive(Clone, Copy)] +pub struct T { + pub lang: Lang, +} + +impl T { + pub fn new(lang: Lang) -> Self { + T { lang } + } + + /// Look up a key in the active language, falling back to English, then to + /// the key itself. Returned slices are `'static` (from the embedded catalogs) + /// or the borrowed key, so no allocation. + pub fn get<'a>(&self, key: &'a str) -> &'a str { + catalog(self.lang) + .get(key) + .or_else(|| catalog(Lang::En).get(key)) + .copied() + .unwrap_or(key) + } + + /// True when `lang` is the active language (for highlighting the switcher). + pub fn is(&self, lang: Lang) -> bool { + self.lang == lang + } + + /// Options for the language switcher: (code, localized label, active). + pub fn languages(&self) -> Vec { + Lang::all() + .into_iter() + .map(|l| LangOption { + code: l.code(), + label: self.get(match l { + Lang::En => "lang.en", + Lang::Es => "lang.es", + Lang::Fr => "lang.fr", + }), + active: self.is(l), + }) + .collect() + } +} + +pub struct LangOption { + pub code: &'static str, + pub label: &'static str, + pub active: bool, +} + +/// Per-request locale: the translator plus the current path (percent-encoded) +/// so the language switcher can return the user to the same page. +pub struct Locale { + pub t: T, + /// Current path+query, percent-encoded for use as a `?next=` value. + pub next: String, +} + +fn lang_from_cookie(parts: &Parts) -> Option { + let raw = parts.headers.get(COOKIE)?.to_str().ok()?; + raw.split(';') + .filter_map(|kv| kv.trim().split_once('=')) + .find(|(k, _)| *k == "lang") + .and_then(|(_, v)| Lang::parse(v)) +} + +fn lang_from_accept(parts: &Parts) -> Option { + let raw = parts.headers.get(ACCEPT_LANGUAGE)?.to_str().ok()?; + // First tag wins (ignore q-weights for our small set). + raw.split(',').next().and_then(|tag| Lang::parse(tag.trim())) +} + +#[axum::async_trait] +impl FromRequestParts for Locale { + type Rejection = Infallible; + + async fn from_request_parts(parts: &mut Parts, _: &S) -> Result { + let lang = lang_from_cookie(parts) + .or_else(|| lang_from_accept(parts)) + .unwrap_or(Lang::En); + let path_q = parts + .uri + .path_and_query() + .map(|pq| pq.as_str()) + .unwrap_or("/"); + let next = percent_encoding::utf8_percent_encode( + path_q, + percent_encoding::NON_ALPHANUMERIC, + ) + .to_string(); + Ok(Locale { t: T::new(lang), next }) + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn fallback_chain_en_then_key() { + let es = T::new(Lang::Es); + assert_eq!(es.get("nav.home"), "Inicio"); + // a key only present implicitly falls back to English, then the key. + assert_eq!(es.get("does.not.exist"), "does.not.exist"); + } + + #[test] + fn catalogs_share_keys_with_english() { + let en = catalog(Lang::En); + for lang in [Lang::Es, Lang::Fr] { + for k in en.keys() { + assert!(catalog(lang).contains_key(k), "{} missing key {k}", lang.code()); + } + } + } +} diff --git a/rust/crates/du-web/src/main.rs b/rust/crates/du-web/src/main.rs index 9a221da..e433e2f 100644 --- a/rust/crates/du-web/src/main.rs +++ b/rust/crates/du-web/src/main.rs @@ -6,6 +6,8 @@ use std::net::SocketAddr; mod error; +mod htmx; +mod i18n; mod render; mod routes; mod state; diff --git a/rust/crates/du-web/src/routes/mod.rs b/rust/crates/du-web/src/routes/mod.rs index 025b176..56bcbb0 100644 --- a/rust/crates/du-web/src/routes/mod.rs +++ b/rust/crates/du-web/src/routes/mod.rs @@ -1,22 +1,37 @@ //! Router assembly + top-level pages. +use crate::i18n::{Lang, Locale, T}; use crate::render::html; use crate::state::AppState; +use axum::extract::{Path, Query}; +use axum::http::header::{LOCATION, SET_COOKIE}; use axum::http::StatusCode; -use axum::response::Response; +use axum::response::{IntoResponse, Response}; use axum::routing::get; use axum::Router; +use serde::Deserialize; +use tower_http::services::ServeDir; pub mod tree; pub mod variants; +/// Directory holding vendored static assets. Settable for deployment +/// (Dockerfile sets DU_ASSETS_DIR=/app/assets); falls back to the crate's +/// assets dir for local `cargo run`. +fn assets_dir() -> String { + std::env::var("DU_ASSETS_DIR") + .unwrap_or_else(|_| concat!(env!("CARGO_MANIFEST_DIR"), "/assets").to_string()) +} + /// Full application router (requires a DB-backed AppState). pub fn app(state: AppState) -> Router { Router::new() .route("/health", get(health)) .route("/", get(index)) + .route("/language/:lang", get(switch_language)) .merge(variants::router()) .merge(tree::router()) + .nest_service("/assets", ServeDir::new(assets_dir())) .with_state(state) } @@ -31,10 +46,37 @@ async fn health() -> (StatusCode, &'static str) { #[derive(askama::Template)] #[template(path = "index.html")] -struct IndexTemplate; +struct IndexTemplate { + t: T, + next: String, +} + +async fn index(locale: Locale) -> Response { + html(&IndexTemplate { t: locale.t, next: locale.next }) +} + +#[derive(Deserialize)] +struct NextQuery { + next: Option, +} -async fn index() -> Response { - html(&IndexTemplate) +/// Set the `lang` cookie and redirect back. Only same-site relative paths are +/// honored as the redirect target (open-redirect guard, like the legacy app). +async fn switch_language(Path(lang): Path, Query(q): Query) -> Response { + let chosen = Lang::parse(&lang).unwrap_or(Lang::En); + let next = q + .next + .filter(|n| n.starts_with('/') && !n.starts_with("//")) + .unwrap_or_else(|| "/".to_string()); + let cookie = format!( + "lang={}; Path=/; Max-Age=31536000; SameSite=Lax", + chosen.code() + ); + ( + StatusCode::SEE_OTHER, + [(SET_COOKIE, cookie), (LOCATION, next)], + ) + .into_response() } #[cfg(test)] diff --git a/rust/crates/du-web/src/routes/tree.rs b/rust/crates/du-web/src/routes/tree.rs index be24d72..92f92e7 100644 --- a/rust/crates/du-web/src/routes/tree.rs +++ b/rust/crates/du-web/src/routes/tree.rs @@ -1,23 +1,27 @@ -//! Public Y/MT haplogroup tree navigation. `/ytree` and `/mtree` are full pages -//! whose `#tree-container` lazy-loads a fragment; clicking a node swaps the -//! fragment and pushes the URL (HATEOAS navigation, no client routing). +//! Public Y/MT haplogroup tree navigation, unified into ONE handler per lineage +//! (plan §4): a normal request returns the full page with the current level +//! embedded inline; an HTMX swap of `#tree-container` returns just the fragment +//! and sets `HX-Push-Url` server-side. History-restore and boosted navigations +//! get the full page. use crate::error::AppError; +use crate::htmx::{HxHeaders, HxRequest}; +use crate::i18n::{Locale, T}; use crate::render::html; use crate::state::AppState; use axum::extract::{Query, State}; -use axum::response::Response; +use axum::response::{IntoResponse, Response}; use axum::routing::get; use axum::Router; use du_domain::enums::DnaType; use serde::Deserialize; +const TARGET: &str = "tree-container"; + pub fn router() -> Router { Router::new() - .route("/ytree", get(ytree_page)) - .route("/mtree", get(mtree_page)) - .route("/ytree/fragment", get(ytree_fragment)) - .route("/mtree/fragment", get(mtree_fragment)) + .route("/ytree", get(ytree)) + .route("/mtree", get(mtree)) } #[derive(Deserialize)] @@ -25,48 +29,57 @@ struct RootQuery { root: Option, } +struct NodeView { + name: String, + formed_ybp: Option, +} + #[derive(askama::Template)] #[template(path = "tree/page.html")] struct TreePageTemplate { - title: &'static str, + t: T, + next: String, + title: String, base_path: &'static str, - root: Option, -} - -struct NodeView { - name: String, - formed_ybp: Option, + current: Option, + nodes: Vec, } #[derive(askama::Template)] #[template(path = "tree/fragment.html")] struct FragmentTemplate { + t: T, base_path: &'static str, current: Option, nodes: Vec, } -async fn ytree_page(Query(q): Query) -> Response { - html(&TreePageTemplate { title: "Y-DNA Tree", base_path: "/ytree", root: q.root }) -} - -async fn mtree_page(Query(q): Query) -> Response { - html(&TreePageTemplate { title: "mtDNA Tree", base_path: "/mtree", root: q.root }) -} - -async fn ytree_fragment(st: State, q: Query) -> Result { - fragment(st, q, DnaType::YDna, "/ytree").await +async fn ytree( + st: State, + hx: HxRequest, + locale: Locale, + q: Query, +) -> Result { + render_tree(st, hx, locale, q, DnaType::YDna, "/ytree", "tree.title.y").await } -async fn mtree_fragment(st: State, q: Query) -> Result { - fragment(st, q, DnaType::MtDna, "/mtree").await +async fn mtree( + st: State, + hx: HxRequest, + locale: Locale, + q: Query, +) -> Result { + render_tree(st, hx, locale, q, DnaType::MtDna, "/mtree", "tree.title.mt").await } -async fn fragment( +async fn render_tree( State(st): State, + hx: HxRequest, + locale: Locale, Query(q): Query, dna_type: DnaType, base_path: &'static str, + title_key: &str, ) -> Result { let to_view = |h: du_domain::haplogroup::Haplogroup| NodeView { name: h.name, @@ -83,10 +96,26 @@ async fn fragment( (Some(cur), kids) } }; + let current = current.map(to_view); + let nodes: Vec = nodes.into_iter().map(to_view).collect(); - Ok(html(&FragmentTemplate { - base_path, - current: current.map(to_view), - nodes: nodes.into_iter().map(to_view).collect(), - })) + if hx.wants_fragment_for(TARGET) { + // Server drives the URL bar for the swap. + let push = match ¤t { + Some(n) => format!("{base_path}?root={}", n.name), + None => base_path.to_string(), + }; + let frag = FragmentTemplate { t: locale.t, base_path, current, nodes }; + Ok((HxHeaders::new().push_url(push), html(&frag)).into_response()) + } else { + let page = TreePageTemplate { + t: locale.t, + next: locale.next, + title: locale.t.get(title_key).to_string(), + base_path, + current, + nodes, + }; + Ok(html(&page)) + } } diff --git a/rust/crates/du-web/src/routes/variants.rs b/rust/crates/du-web/src/routes/variants.rs index 13c64b8..72073eb 100644 --- a/rust/crates/du-web/src/routes/variants.rs +++ b/rust/crates/du-web/src/routes/variants.rs @@ -1,8 +1,9 @@ -//! Public variant browser. Demonstrates the HTMX two-panel + fragment pattern: -//! a full page (`/variants`) that lazy-loads a list fragment (`/variants/list`), -//! whose rows load a detail panel fragment (`/variants/detail/:id`). +//! Public variant browser. The browser page embeds the first results page inline +//! (no load round-trip); search/pagination and the detail panel are HTMX +//! fragments targeting `#variants-table` / `#detail-panel`. use crate::error::AppError; +use crate::i18n::{Locale, T}; use crate::render::html; use crate::state::AppState; use axum::extract::{Path, Query, State}; @@ -51,21 +52,44 @@ impl RowView { } } +/// Shared list-fragment view data (also embedded by the browser page). +struct ListView { + query: String, + rows: Vec, + page: i64, + page_size: i64, + total: i64, + total_pages: i64, +} + +async fn load_list(st: &AppState, q: &ListQuery) -> Result { + let page_num = q.page.unwrap_or(1); + let page_size = q.page_size.unwrap_or(25); + let result: Page = + du_db::variant::search(&st.pool, q.query.as_deref(), page_num, page_size).await?; + Ok(ListView { + query: q.query.clone().unwrap_or_default(), + rows: result.items.iter().map(RowView::from).collect(), + page: result.page, + page_size: result.page_size, + total: result.total, + total_pages: result.total_pages(), + }) +} + #[derive(askama::Template)] #[template(path = "variants/browser.html")] struct BrowserTemplate { - query: String, + t: T, + next: String, + list: ListView, } #[derive(askama::Template)] #[template(path = "variants/list.html")] struct ListTemplate { - query: String, - rows: Vec, - page: i64, - page_size: i64, - total: i64, - total_pages: i64, + t: T, + list: ListView, } struct CoordView { @@ -78,6 +102,7 @@ struct CoordView { #[derive(askama::Template)] #[template(path = "variants/detail.html")] struct DetailTemplate { + t: T, name: String, mutation_type: String, naming_status: String, @@ -86,27 +111,29 @@ struct DetailTemplate { coords: Vec, } -async fn browser(Query(q): Query) -> Response { - html(&BrowserTemplate { query: q.query.unwrap_or_default() }) +async fn browser( + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&BrowserTemplate { t: locale.t, next: locale.next, list })) } -async fn list(State(st): State, Query(q): Query) -> Result { - let page_num = q.page.unwrap_or(1); - let page_size = q.page_size.unwrap_or(25); - let result: Page = - du_db::variant::search(&st.pool, q.query.as_deref(), page_num, page_size).await?; - let rows = result.items.iter().map(RowView::from).collect(); - Ok(html(&ListTemplate { - query: q.query.unwrap_or_default(), - rows, - page: result.page, - page_size: result.page_size, - total: result.total, - total_pages: result.total_pages(), - })) +async fn list( + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&ListTemplate { t: locale.t, list })) } -async fn detail(State(st): State, Path(id): Path) -> Result { +async fn detail( + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { let v = du_db::variant::get_by_id(&st.pool, VariantId(id)) .await? .ok_or_else(|| AppError::NotFound(format!("variant {id}")))?; @@ -128,6 +155,7 @@ async fn detail(State(st): State, Path(id): Path) -> Result - + - {% block title %}Decoding Us{% endblock %} - - - - + {% block title %}{{ t.get("app.name") }}{% endblock %} + + +
{% block content %}{% endblock %}
+ diff --git a/rust/crates/du-web/templates/index.html b/rust/crates/du-web/templates/index.html index f0a1bc3..73b3766 100644 --- a/rust/crates/du-web/templates/index.html +++ b/rust/crates/du-web/templates/index.html @@ -1,16 +1,12 @@ {% extends "base.html" %} -{% block title %}Decoding Us — genetic genealogy & population research{% endblock %} +{% block title %}{{ t.get("home.title") }}{% endblock %} {% block content %}
-

Decoding Us

-

- A collaborative platform for genetic genealogy and population research — - Y/mtDNA haplogroup trees, a public variant browser, and privacy-preserving - relative discovery. -

+

{{ t.get("home.heading") }}

+

{{ t.get("home.lead") }}

- Browse the Y-DNA tree - Search variants + {{ t.get("home.cta.tree") }} + {{ t.get("home.cta.variants") }}
{% endblock %} diff --git a/rust/crates/du-web/templates/tree/fragment.html b/rust/crates/du-web/templates/tree/fragment.html index f4ceb9d..d1e2a09 100644 --- a/rust/crates/du-web/templates/tree/fragment.html +++ b/rust/crates/du-web/templates/tree/fragment.html @@ -1,29 +1,28 @@ -{# Fragment: one tree level. Clicking a node swaps this container and pushes the - URL so browser back/forward navigates the tree (HATEOAS). #} +{# Fragment: one tree level. Links hit the unified {base_path} endpoint targeting + #tree-container; the server returns this fragment and sets HX-Push-Url. The + href is the no-JS fallback. References `t`, `base_path`, `current`, `nodes`. #} {% if let Some(cur) = current %}

{{ cur.name }} - {% if let Some(ybp) = cur.formed_ybp %}· formed ~{{ ybp }} ybp{% endif %} + {% if let Some(ybp) = cur.formed_ybp %}· {{ t.get("tree.formed") }} ~{{ ybp }} ybp{% endif %}

{% else %} -

Root lineages

+

{{ t.get("tree.rootLineages") }}

{% endif %}
{% for n in nodes %} + hx-get="{{ base_path }}?root={{ n.name }}" + hx-target="#tree-container"> {{ n.name }} {% if let Some(ybp) = n.formed_ybp %}~{{ ybp }} ybp{% endif %} {% else %} -
No child haplogroups.
+
{{ t.get("tree.noChildren") }}
{% endfor %}
diff --git a/rust/crates/du-web/templates/tree/page.html b/rust/crates/du-web/templates/tree/page.html index b5d78af..1f9d72b 100644 --- a/rust/crates/du-web/templates/tree/page.html +++ b/rust/crates/du-web/templates/tree/page.html @@ -1,10 +1,9 @@ {% extends "base.html" %} -{% block title %}{{ title }} — Decoding Us{% endblock %} +{% block title %}{{ title }} — {{ t.get("app.name") }}{% endblock %} {% block content %}

{{ title }}

-
- Loading tree… +{# Current level embedded inline; HTMX swaps just this container thereafter. #} +
+ {% include "tree/fragment.html" %}
{% endblock %} diff --git a/rust/crates/du-web/templates/variants/browser.html b/rust/crates/du-web/templates/variants/browser.html index dc36d38..42781d4 100644 --- a/rust/crates/du-web/templates/variants/browser.html +++ b/rust/crates/du-web/templates/variants/browser.html @@ -1,25 +1,25 @@ {% extends "base.html" %} -{% block title %}Variant Browser — Decoding Us{% endblock %} +{% block title %}{{ t.get("variants.title") }} — {{ t.get("app.name") }}{% endblock %} {% block content %} -

Variant Browser

+

{{ t.get("variants.title") }}

-
+ {# First page embedded inline (no load round-trip); search/pager swap it. #} +
+ {% include "variants/list.html" %}
-

Select a variant to see details.

+

{{ t.get("variants.detail.select") }}

diff --git a/rust/crates/du-web/templates/variants/detail.html b/rust/crates/du-web/templates/variants/detail.html index 8a19ace..45c381c 100644 --- a/rust/crates/du-web/templates/variants/detail.html +++ b/rust/crates/du-web/templates/variants/detail.html @@ -5,25 +5,30 @@ {{ mutation_type }}
-

Naming status: {{ naming_status }}

+

{{ t.get("variants.detail.naming") }} {{ naming_status }}

{% if !common_names.is_empty() %} -

Also known as: +

{{ t.get("variants.detail.aka") }} {% for n in common_names %}{{ n }} {% endfor %}

{% endif %} {% if !rs_ids.is_empty() %} -

rs IDs: +

{{ t.get("variants.detail.rsids") }} {% for r in rs_ids %}{{ r }} {% endfor %}

{% endif %} -
Coordinates
+
{{ t.get("variants.detail.coordinates") }}
{% if coords.is_empty() %} -

No mapped coordinates.

+

{{ t.get("variants.detail.nocoords") }}

{% else %} - + + + + + + {% for c in coords %} diff --git a/rust/crates/du-web/templates/variants/list.html b/rust/crates/du-web/templates/variants/list.html index fd42f17..c28adef 100644 --- a/rust/crates/du-web/templates/variants/list.html +++ b/rust/crates/du-web/templates/variants/list.html @@ -1,10 +1,16 @@ -{# Fragment: the variant results table + pager. Target of #variants-table. #} +{# Fragment: results table + pager. Target of #variants-table; also included by + the browser page. References `t` and `list`. #}
BuildContigPositionChange
{{ t.get("variants.col.build") }}{{ t.get("variants.col.contig") }}{{ t.get("variants.col.position") }}{{ t.get("variants.col.change") }}
- + + + + + + - {% for r in rows %} + {% for r in list.rows %} {{ r.builds }} {% else %} - + {% endfor %}
NameTypeStatusBuilds
{{ t.get("variants.col.name") }}{{ t.get("variants.col.type") }}{{ t.get("variants.col.status") }}{{ t.get("variants.col.builds") }}
No variants match.
{{ t.get("variants.none") }}
-{% if total_pages > 1 %} +{% if list.total_pages > 1 %} {% else %} -{{ total }} total +{{ list.total }} {{ t.get("pagination.total") }} {% endif %} diff --git a/rust/locales/en.txt b/rust/locales/en.txt new file mode 100644 index 0000000..ebcebc1 --- /dev/null +++ b/rust/locales/en.txt @@ -0,0 +1,48 @@ +# English message catalog. key=value, '#' comments. Ported subset (slice scope). +app.name=Decoding Us +nav.home=Home +nav.ytree=Y-DNA Tree +nav.mtree=mtDNA Tree +nav.variants=Variants +lang.label=Language +lang.en=English +lang.es=Español +lang.fr=Français + +home.title=Decoding Us — genetic genealogy & population research +home.heading=Decoding Us +home.lead=A collaborative platform for genetic genealogy and population research — Y/mtDNA haplogroup trees, a public variant browser, and privacy-preserving relative discovery. +home.cta.tree=Browse the Y-DNA tree +home.cta.variants=Search variants + +variants.title=Variant Browser +variants.search.placeholder=Search by name or alias (e.g. M269, rs9786153)… +variants.col.name=Name +variants.col.type=Type +variants.col.status=Status +variants.col.builds=Builds +variants.none=No variants match. +variants.detail.select=Select a variant to see details. +variants.detail.naming=Naming status: +variants.detail.aka=Also known as: +variants.detail.rsids=rs IDs: +variants.detail.coordinates=Coordinates +variants.detail.nocoords=No mapped coordinates. +variants.col.build=Build +variants.col.contig=Contig +variants.col.position=Position +variants.col.change=Change + +pagination.previous=Previous +pagination.next=Next +pagination.page=Page +pagination.of=of +pagination.total=total + +tree.title.y=Y-DNA Tree +tree.title.mt=mtDNA Tree +tree.loading=Loading tree… +tree.allRoots=← All roots +tree.rootLineages=Root lineages +tree.noChildren=No child haplogroups. +tree.formed=formed diff --git a/rust/locales/es.txt b/rust/locales/es.txt new file mode 100644 index 0000000..e6d3bfc --- /dev/null +++ b/rust/locales/es.txt @@ -0,0 +1,48 @@ +# Spanish message catalog. +app.name=Decoding Us +nav.home=Inicio +nav.ytree=Árbol Y-ADN +nav.mtree=Árbol ADNmt +nav.variants=Variantes +lang.label=Idioma +lang.en=English +lang.es=Español +lang.fr=Français + +home.title=Decoding Us — genealogía genética e investigación de poblaciones +home.heading=Decoding Us +home.lead=Una plataforma colaborativa para la genealogía genética y la investigación de poblaciones: árboles de haplogrupos Y/ADNmt, un explorador público de variantes y descubrimiento de parientes que preserva la privacidad. +home.cta.tree=Explorar el árbol Y-ADN +home.cta.variants=Buscar variantes + +variants.title=Explorador de variantes +variants.search.placeholder=Buscar por nombre o alias (p. ej. M269, rs9786153)… +variants.col.name=Nombre +variants.col.type=Tipo +variants.col.status=Estado +variants.col.builds=Ensamblajes +variants.none=No hay variantes coincidentes. +variants.detail.select=Seleccione una variante para ver los detalles. +variants.detail.naming=Estado de nomenclatura: +variants.detail.aka=También conocido como: +variants.detail.rsids=Identificadores rs: +variants.detail.coordinates=Coordenadas +variants.detail.nocoords=Sin coordenadas asignadas. +variants.col.build=Ensamblaje +variants.col.contig=Contig +variants.col.position=Posición +variants.col.change=Cambio + +pagination.previous=Anterior +pagination.next=Siguiente +pagination.page=Página +pagination.of=de +pagination.total=en total + +tree.title.y=Árbol Y-ADN +tree.title.mt=Árbol ADNmt +tree.loading=Cargando el árbol… +tree.allRoots=← Todas las raíces +tree.rootLineages=Linajes raíz +tree.noChildren=Sin haplogrupos descendientes. +tree.formed=formado diff --git a/rust/locales/fr.txt b/rust/locales/fr.txt new file mode 100644 index 0000000..bd1c732 --- /dev/null +++ b/rust/locales/fr.txt @@ -0,0 +1,48 @@ +# French message catalog. +app.name=Decoding Us +nav.home=Accueil +nav.ytree=Arbre Y-ADN +nav.mtree=Arbre ADNmt +nav.variants=Variants +lang.label=Langue +lang.en=English +lang.es=Español +lang.fr=Français + +home.title=Decoding Us — généalogie génétique et recherche sur les populations +home.heading=Decoding Us +home.lead=Une plateforme collaborative pour la généalogie génétique et la recherche sur les populations : arbres d’haplogroupes Y/ADNmt, un explorateur public de variants et une découverte de parents respectueuse de la vie privée. +home.cta.tree=Explorer l’arbre Y-ADN +home.cta.variants=Rechercher des variants + +variants.title=Explorateur de variants +variants.search.placeholder=Rechercher par nom ou alias (p. ex. M269, rs9786153)… +variants.col.name=Nom +variants.col.type=Type +variants.col.status=Statut +variants.col.builds=Assemblages +variants.none=Aucun variant correspondant. +variants.detail.select=Sélectionnez un variant pour voir les détails. +variants.detail.naming=Statut de nomenclature : +variants.detail.aka=Aussi connu sous le nom de : +variants.detail.rsids=Identifiants rs : +variants.detail.coordinates=Coordonnées +variants.detail.nocoords=Aucune coordonnée cartographiée. +variants.col.build=Assemblage +variants.col.contig=Contig +variants.col.position=Position +variants.col.change=Changement + +pagination.previous=Précédent +pagination.next=Suivant +pagination.page=Page +pagination.of=sur +pagination.total=au total + +tree.title.y=Arbre Y-ADN +tree.title.mt=Arbre ADNmt +tree.loading=Chargement de l’arbre… +tree.allRoots=← Toutes les racines +tree.rootLineages=Lignées racines +tree.noChildren=Aucun haplogroupe descendant. +tree.formed=formé From ae1fba9208588c7510121fb0223cc0f278ccd671 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 08:22:39 -0500 Subject: [PATCH 005/191] feat(rust): public references + per-publication biosample report MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Broaden the public surface, reusing the publication/biosample query modules and the established HTMX two-panel + i18n patterns. - du-db: biosample::for_publication — paginated biosamples linked to a publication (join pubs.publication_biosample), returning Page. - du-domain: Display/label() for BiosampleSource. - du-web references routes: /references (page, first list embedded inline), /references/list (search + pagination fragment), /references/:id/biosamples (per-publication report fragment, paginated). Clicking a publication loads its samples into #reference-detail. 404 on missing publication. - i18n: references/* keys added across en/es/fr; nav "References" link. - Templates references/{page,list,biosamples}.html. Verified live against the container PostGIS (list, search, es localization, ancient/external sample reports with DOI link). Workspace 9/9 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/crates/du-db/src/biosample.rs | 44 ++++- rust/crates/du-domain/src/enums.rs | 17 ++ rust/crates/du-web/src/routes/mod.rs | 2 + rust/crates/du-web/src/routes/references.rs | 167 ++++++++++++++++++ rust/crates/du-web/templates/base.html | 1 + .../templates/references/biosamples.html | 45 +++++ .../du-web/templates/references/list.html | 35 ++++ .../du-web/templates/references/page.html | 25 +++ rust/locales/en.txt | 17 ++ rust/locales/es.txt | 17 ++ rust/locales/fr.txt | 17 ++ 11 files changed, 385 insertions(+), 2 deletions(-) create mode 100644 rust/crates/du-web/src/routes/references.rs create mode 100644 rust/crates/du-web/templates/references/biosamples.html create mode 100644 rust/crates/du-web/templates/references/list.html create mode 100644 rust/crates/du-web/templates/references/page.html diff --git a/rust/crates/du-db/src/biosample.rs b/rust/crates/du-db/src/biosample.rs index 2d1f7cb..de70c70 100644 --- a/rust/crates/du-db/src/biosample.rs +++ b/rust/crates/du-db/src/biosample.rs @@ -1,8 +1,8 @@ //! Queries for the unified `core.biosample`. -use crate::{parse_pg_enum, DbError}; +use crate::{parse_pg_enum, DbError, Page}; use du_domain::biosample::Biosample; -use du_domain::ids::SampleGuid; +use du_domain::ids::{PublicationId, SampleGuid}; use sqlx::PgPool; use uuid::Uuid; @@ -46,6 +46,46 @@ pub async fn get_by_guid(pool: &PgPool, guid: SampleGuid) -> Result Result, DbError> { + let offset = Page::<()>::offset(page, page_size); + let limit = page_size.clamp(1, 200); + + let total: i64 = sqlx::query_scalar( + "SELECT count(*) FROM pubs.publication_biosample pb \ + JOIN core.biosample b ON b.sample_guid = pb.sample_guid \ + WHERE pb.publication_id = $1 AND b.deleted = false", + ) + .bind(publication_id.0) + .fetch_one(pool) + .await?; + + let rows: Vec = sqlx::query_as( + "SELECT b.sample_guid, b.source::text AS source, b.accession, b.alias, b.description, \ + b.center_name, b.locked, b.source_attrs, b.atproto \ + FROM pubs.publication_biosample pb \ + JOIN core.biosample b ON b.sample_guid = pb.sample_guid \ + WHERE pb.publication_id = $1 AND b.deleted = false \ + ORDER BY b.accession NULLS LAST, b.sample_guid LIMIT $2 OFFSET $3", + ) + .bind(publication_id.0) + .bind(limit) + .bind(offset) + .fetch_all(pool) + .await?; + + let items = rows + .into_iter() + .map(BiosampleRow::into_domain) + .collect::, _>>()?; + Ok(Page { items, total, page: page.max(1), page_size: limit }) +} + /// Lookup by accession or alias (the private biosample search). pub async fn find_by_alias_or_accession( pool: &PgPool, diff --git a/rust/crates/du-domain/src/enums.rs b/rust/crates/du-domain/src/enums.rs index c2710c5..69c9148 100644 --- a/rust/crates/du-domain/src/enums.rs +++ b/rust/crates/du-domain/src/enums.rs @@ -117,6 +117,23 @@ impl std::fmt::Display for DnaType { } } +impl BiosampleSource { + pub fn label(&self) -> &'static str { + match self { + BiosampleSource::Standard => "STANDARD", + BiosampleSource::Citizen => "CITIZEN", + BiosampleSource::Pgp => "PGP", + BiosampleSource::External => "EXTERNAL", + BiosampleSource::Ancient => "ANCIENT", + } + } +} +impl std::fmt::Display for BiosampleSource { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + f.write_str(self.label()) + } +} + impl MutationType { pub fn label(&self) -> &'static str { match self { diff --git a/rust/crates/du-web/src/routes/mod.rs b/rust/crates/du-web/src/routes/mod.rs index 56bcbb0..5aeb73d 100644 --- a/rust/crates/du-web/src/routes/mod.rs +++ b/rust/crates/du-web/src/routes/mod.rs @@ -12,6 +12,7 @@ use axum::Router; use serde::Deserialize; use tower_http::services::ServeDir; +pub mod references; pub mod tree; pub mod variants; @@ -31,6 +32,7 @@ pub fn app(state: AppState) -> Router { .route("/language/:lang", get(switch_language)) .merge(variants::router()) .merge(tree::router()) + .merge(references::router()) .nest_service("/assets", ServeDir::new(assets_dir())) .with_state(state) } diff --git a/rust/crates/du-web/src/routes/references.rs b/rust/crates/du-web/src/routes/references.rs new file mode 100644 index 0000000..aa2111f --- /dev/null +++ b/rust/crates/du-web/src/routes/references.rs @@ -0,0 +1,167 @@ +//! Public references (publications) + per-publication biosample report. +//! Same two-panel HTMX pattern as the variant browser: a searchable/paginated +//! publication list on the left, the selected publication's samples on the right. + +use crate::error::AppError; +use crate::i18n::{Locale, T}; +use crate::render::html; +use crate::state::AppState; +use axum::extract::{Path, Query, State}; +use axum::response::Response; +use axum::routing::get; +use axum::Router; +use du_domain::ids::PublicationId; +use serde::Deserialize; + +pub fn router() -> Router { + Router::new() + .route("/references", get(page)) + .route("/references/list", get(list)) + .route("/references/:id/biosamples", get(biosamples)) +} + +#[derive(Deserialize)] +struct ListQuery { + query: Option, + page: Option, + page_size: Option, +} + +#[derive(Deserialize)] +struct PageQuery { + page: Option, + page_size: Option, +} + +struct PubRow { + id: i64, + title: String, + journal: String, + year: String, + citations: Option, +} + +struct PubListView { + query: String, + rows: Vec, + page: i64, + page_size: i64, + total: i64, + total_pages: i64, +} + +async fn load_list(st: &AppState, q: &ListQuery) -> Result { + let result = + du_db::publication::search(&st.pool, q.query.as_deref(), q.page.unwrap_or(1), q.page_size.unwrap_or(20)) + .await?; + let rows = result + .items + .iter() + .map(|p| PubRow { + id: p.id.0, + title: p.title.clone(), + journal: p.journal.clone().unwrap_or_default(), + year: p.publication_date.map(|d| d.format("%Y").to_string()).unwrap_or_default(), + citations: p.cited_by_count, + }) + .collect(); + Ok(PubListView { + query: q.query.clone().unwrap_or_default(), + rows, + page: result.page, + page_size: result.page_size, + total: result.total, + total_pages: result.total_pages(), + }) +} + +#[derive(askama::Template)] +#[template(path = "references/page.html")] +struct ReferencesPageTemplate { + t: T, + next: String, + list: PubListView, +} + +#[derive(askama::Template)] +#[template(path = "references/list.html")] +struct PubListTemplate { + t: T, + list: PubListView, +} + +struct BioRow { + source: String, + accession: String, + alias: String, + description: String, +} + +#[derive(askama::Template)] +#[template(path = "references/biosamples.html")] +struct BiosamplesTemplate { + t: T, + pub_id: i64, + pub_title: String, + pub_doi: Option, + rows: Vec, + page: i64, + page_size: i64, + total: i64, + total_pages: i64, +} + +async fn page( + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&ReferencesPageTemplate { t: locale.t, next: locale.next, list })) +} + +async fn list( + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&PubListTemplate { t: locale.t, list })) +} + +async fn biosamples( + State(st): State, + locale: Locale, + Path(id): Path, + Query(q): Query, +) -> Result { + let pub_id = PublicationId(id); + let publication = du_db::publication::get_by_id(&st.pool, pub_id) + .await? + .ok_or_else(|| AppError::NotFound(format!("publication {id}")))?; + let result = + du_db::biosample::for_publication(&st.pool, pub_id, q.page.unwrap_or(1), q.page_size.unwrap_or(25)) + .await?; + let rows = result + .items + .iter() + .map(|b| BioRow { + source: b.source.label().to_string(), + accession: b.accession.clone().unwrap_or_default(), + alias: b.alias.clone().unwrap_or_default(), + description: b.description.clone().unwrap_or_default(), + }) + .collect(); + + Ok(html(&BiosamplesTemplate { + t: locale.t, + pub_id: id, + pub_title: publication.title, + pub_doi: publication.doi, + rows, + page: result.page, + page_size: result.page_size, + total: result.total, + total_pages: result.total_pages(), + })) +} diff --git a/rust/crates/du-web/templates/base.html b/rust/crates/du-web/templates/base.html index 2953a38..a2b183f 100644 --- a/rust/crates/du-web/templates/base.html +++ b/rust/crates/du-web/templates/base.html @@ -16,6 +16,7 @@ {{ t.get("nav.ytree") }} {{ t.get("nav.mtree") }} {{ t.get("nav.variants") }} + {{ t.get("nav.references") }}
+ {{ t.get("pagination.page") }} {{ page }} {{ t.get("pagination.of") }} {{ total_pages }} + + + {% else %} + {{ total }} {{ t.get("pagination.total") }} + {% endif %} + {% endif %} +
+
diff --git a/rust/crates/du-web/templates/references/list.html b/rust/crates/du-web/templates/references/list.html new file mode 100644 index 0000000..f757df7 --- /dev/null +++ b/rust/crates/du-web/templates/references/list.html @@ -0,0 +1,35 @@ +{# Fragment: publication list + pager. Target of #references-table. #} +
+ {% for p in list.rows %} + +
{{ p.title }}
+ + {% if !p.journal.is_empty() %}{{ p.journal }}{% endif %} + {% if !p.year.is_empty() %} · {{ p.year }}{% endif %} + {% if let Some(c) = p.citations %} · {{ c }} {{ t.get("references.col.citations") }}{% endif %} + + + {% else %} +
{{ t.get("references.none") }}
+ {% endfor %} +
+ +{% if list.total_pages > 1 %} + +{% else %} +{{ list.total }} {{ t.get("pagination.total") }} +{% endif %} diff --git a/rust/crates/du-web/templates/references/page.html b/rust/crates/du-web/templates/references/page.html new file mode 100644 index 0000000..85c0a42 --- /dev/null +++ b/rust/crates/du-web/templates/references/page.html @@ -0,0 +1,25 @@ +{% extends "base.html" %} +{% block title %}{{ t.get("references.title") }} — {{ t.get("app.name") }}{% endblock %} +{% block content %} +

{{ t.get("references.title") }}

+
+
+ + +
+ {% include "references/list.html" %} +
+
+
+
+

{{ t.get("references.select") }}

+
+
+
+{% endblock %} diff --git a/rust/locales/en.txt b/rust/locales/en.txt index ebcebc1..9a9aa2d 100644 --- a/rust/locales/en.txt +++ b/rust/locales/en.txt @@ -4,6 +4,7 @@ nav.home=Home nav.ytree=Y-DNA Tree nav.mtree=mtDNA Tree nav.variants=Variants +nav.references=References lang.label=Language lang.en=English lang.es=Español @@ -46,3 +47,19 @@ tree.allRoots=← All roots tree.rootLineages=Root lineages tree.noChildren=No child haplogroups. tree.formed=formed + +references.title=References +references.search.placeholder=Search by title, journal, or DOI… +references.col.title=Title +references.col.journal=Journal +references.col.year=Year +references.col.citations=Citations +references.none=No publications match. +references.select=Select a publication to see its samples. +references.viewDoi=DOI +references.biosamples.title=Samples in this study +references.biosamples.none=No samples linked to this publication. +references.col.accession=Accession +references.col.alias=Alias +references.col.source=Source +references.col.description=Description diff --git a/rust/locales/es.txt b/rust/locales/es.txt index e6d3bfc..850bdb3 100644 --- a/rust/locales/es.txt +++ b/rust/locales/es.txt @@ -4,6 +4,7 @@ nav.home=Inicio nav.ytree=Árbol Y-ADN nav.mtree=Árbol ADNmt nav.variants=Variantes +nav.references=Referencias lang.label=Idioma lang.en=English lang.es=Español @@ -46,3 +47,19 @@ tree.allRoots=← Todas las raíces tree.rootLineages=Linajes raíz tree.noChildren=Sin haplogrupos descendientes. tree.formed=formado + +references.title=Referencias +references.search.placeholder=Buscar por título, revista o DOI… +references.col.title=Título +references.col.journal=Revista +references.col.year=Año +references.col.citations=Citas +references.none=No hay publicaciones coincidentes. +references.select=Seleccione una publicación para ver sus muestras. +references.viewDoi=DOI +references.biosamples.title=Muestras de este estudio +references.biosamples.none=No hay muestras vinculadas a esta publicación. +references.col.accession=Número de acceso +references.col.alias=Alias +references.col.source=Origen +references.col.description=Descripción diff --git a/rust/locales/fr.txt b/rust/locales/fr.txt index bd1c732..1ba3486 100644 --- a/rust/locales/fr.txt +++ b/rust/locales/fr.txt @@ -4,6 +4,7 @@ nav.home=Accueil nav.ytree=Arbre Y-ADN nav.mtree=Arbre ADNmt nav.variants=Variants +nav.references=Références lang.label=Langue lang.en=English lang.es=Español @@ -46,3 +47,19 @@ tree.allRoots=← Toutes les racines tree.rootLineages=Lignées racines tree.noChildren=Aucun haplogroupe descendant. tree.formed=formé + +references.title=Références +references.search.placeholder=Rechercher par titre, revue ou DOI… +references.col.title=Titre +references.col.journal=Revue +references.col.year=Année +references.col.citations=Citations +references.none=Aucune publication correspondante. +references.select=Sélectionnez une publication pour voir ses échantillons. +references.viewDoi=DOI +references.biosamples.title=Échantillons de cette étude +references.biosamples.none=Aucun échantillon lié à cette publication. +references.col.accession=Numéro d’accès +references.col.alias=Alias +references.col.source=Origine +references.col.description=Description From 089660940a5c933a13102f95301c3548add70dc5 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 08:34:33 -0500 Subject: [PATCH 006/191] feat(rust): biosample map (PostGIS + Leaflet) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds the geographic map and exercises the PostGIS spatial path end-to-end (de-risks plan §11's PostGIS-in-Rust concern). - du-db: biosample::geo_points — ST_X/ST_Y over the donor geocoord (geometry Point, 4326), joined to non-deleted biosamples. - du-domain: biosample::GeoPoint (serde). - du-web maps routes: /biosamples/map (page) and /biosamples/geo-data (GeoJSON FeatureCollection, [lon,lat] order). map_page is a full-page load (nav link hx-boost=false) so Leaflet initializes; base.html gains a head block for per-page assets. - Vendored Leaflet 1.9.4 (css + js); assets/map.js plots circle markers (no marker-image assets) with popups and fits bounds. OSM tiles at runtime. - i18n map.* keys + nav "Map" across en/es/fr. Verified live: GeoJSON has 3 features with correct [lon,lat] coords and accession/source props; assets served; es localization. Workspace 9/9 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/crates/du-db/src/biosample.rs | 32 +- rust/crates/du-domain/src/biosample.rs | 9 + rust/crates/du-web/assets/map.js | 34 + rust/crates/du-web/assets/vendor/leaflet.css | 661 ++++++++++++++++++ rust/crates/du-web/assets/vendor/leaflet.js | 6 + rust/crates/du-web/src/routes/maps.rs | 46 ++ rust/crates/du-web/src/routes/mod.rs | 2 + rust/crates/du-web/templates/base.html | 3 + .../du-web/templates/biosamples/map.html | 15 + rust/locales/en.txt | 5 + rust/locales/es.txt | 5 + rust/locales/fr.txt | 5 + 12 files changed, 822 insertions(+), 1 deletion(-) create mode 100644 rust/crates/du-web/assets/map.js create mode 100644 rust/crates/du-web/assets/vendor/leaflet.css create mode 100644 rust/crates/du-web/assets/vendor/leaflet.js create mode 100644 rust/crates/du-web/src/routes/maps.rs create mode 100644 rust/crates/du-web/templates/biosamples/map.html diff --git a/rust/crates/du-db/src/biosample.rs b/rust/crates/du-db/src/biosample.rs index de70c70..f65b18e 100644 --- a/rust/crates/du-db/src/biosample.rs +++ b/rust/crates/du-db/src/biosample.rs @@ -1,7 +1,7 @@ //! Queries for the unified `core.biosample`. use crate::{parse_pg_enum, DbError, Page}; -use du_domain::biosample::Biosample; +use du_domain::biosample::{Biosample, GeoPoint}; use du_domain::ids::{PublicationId, SampleGuid}; use sqlx::PgPool; use uuid::Uuid; @@ -46,6 +46,36 @@ pub async fn get_by_guid(pool: &PgPool, guid: SampleGuid) -> Result Result, DbError> { + #[derive(sqlx::FromRow)] + struct GeoRow { + lat: f64, + lon: f64, + accession: Option, + source: String, + } + let rows: Vec = sqlx::query_as( + "SELECT ST_Y(d.geocoord) AS lat, ST_X(d.geocoord) AS lon, b.accession, \ + b.source::text AS source \ + FROM core.biosample b JOIN core.specimen_donor d ON d.id = b.donor_id \ + WHERE d.geocoord IS NOT NULL AND b.deleted = false", + ) + .fetch_all(pool) + .await?; + rows.into_iter() + .map(|r| { + Ok(GeoPoint { + lat: r.lat, + lon: r.lon, + accession: r.accession, + source: parse_pg_enum(&r.source, "source")?, + }) + }) + .collect() +} + /// Paginated biosamples linked to a publication (the biosample report). pub async fn for_publication( pool: &PgPool, diff --git a/rust/crates/du-domain/src/biosample.rs b/rust/crates/du-domain/src/biosample.rs index 0e5a227..2778c40 100644 --- a/rust/crates/du-domain/src/biosample.rs +++ b/rust/crates/du-domain/src/biosample.rs @@ -6,6 +6,15 @@ use crate::enums::BiosampleSource; use crate::ids::SampleGuid; use serde::{Deserialize, Serialize}; +/// A mappable biosample location (from the donor's `geocoord`, WGS84). +#[derive(Debug, Clone, Serialize, Deserialize)] +pub struct GeoPoint { + pub lat: f64, + pub lon: f64, + pub accession: Option, + pub source: BiosampleSource, +} + #[derive(Debug, Clone, Serialize, Deserialize)] pub struct Biosample { pub sample_guid: SampleGuid, diff --git a/rust/crates/du-web/assets/map.js b/rust/crates/du-web/assets/map.js new file mode 100644 index 0000000..05b170c --- /dev/null +++ b/rust/crates/du-web/assets/map.js @@ -0,0 +1,34 @@ +// Biosample map: initialize Leaflet, load GeoJSON from the data-geo URL, and +// plot circle markers (no marker-image assets needed). +document.addEventListener("DOMContentLoaded", function () { + var el = document.getElementById("map"); + if (!el || typeof L === "undefined") return; + + var map = L.map("map").setView([20, 0], 2); + L.tileLayer("https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png", { + maxZoom: 18, + attribution: "© OpenStreetMap contributors", + }).addTo(map); + + fetch(el.dataset.geo) + .then(function (r) { return r.json(); }) + .then(function (fc) { + var layer = L.geoJSON(fc, { + pointToLayer: function (_f, latlng) { + return L.circleMarker(latlng, { + radius: 6, color: "#0d6efd", weight: 1, fillOpacity: 0.7, + }); + }, + onEachFeature: function (f, l) { + var p = f.properties || {}; + l.bindPopup((p.accession || "—") + " (" + (p.source || "") + ")"); + }, + }).addTo(map); + + var count = (fc.features || []).length; + var badge = document.getElementById("map-count"); + if (badge) badge.textContent = count; + if (count > 0) map.fitBounds(layer.getBounds().pad(0.2)); + }) + .catch(function (e) { console.error("geo-data load failed", e); }); +}); diff --git a/rust/crates/du-web/assets/vendor/leaflet.css b/rust/crates/du-web/assets/vendor/leaflet.css new file mode 100644 index 0000000..2961b76 --- /dev/null +++ b/rust/crates/du-web/assets/vendor/leaflet.css @@ -0,0 +1,661 @@ +/* required styles */ + +.leaflet-pane, +.leaflet-tile, +.leaflet-marker-icon, +.leaflet-marker-shadow, +.leaflet-tile-container, +.leaflet-pane > svg, +.leaflet-pane > canvas, +.leaflet-zoom-box, +.leaflet-image-layer, +.leaflet-layer { + position: absolute; + left: 0; + top: 0; + } +.leaflet-container { + overflow: hidden; + } +.leaflet-tile, +.leaflet-marker-icon, +.leaflet-marker-shadow { + -webkit-user-select: none; + -moz-user-select: none; + user-select: none; + -webkit-user-drag: none; + } +/* Prevents IE11 from highlighting tiles in blue */ +.leaflet-tile::selection { + background: transparent; +} +/* Safari renders non-retina tile on retina better with this, but Chrome is worse */ +.leaflet-safari .leaflet-tile { + image-rendering: -webkit-optimize-contrast; + } +/* hack that prevents hw layers "stretching" when loading new tiles */ +.leaflet-safari .leaflet-tile-container { + width: 1600px; + height: 1600px; + -webkit-transform-origin: 0 0; + } +.leaflet-marker-icon, +.leaflet-marker-shadow { + display: block; + } +/* .leaflet-container svg: reset svg max-width decleration shipped in Joomla! (joomla.org) 3.x */ +/* .leaflet-container img: map is broken in FF if you have max-width: 100% on tiles */ +.leaflet-container .leaflet-overlay-pane svg { + max-width: none !important; + max-height: none !important; + } +.leaflet-container .leaflet-marker-pane img, +.leaflet-container .leaflet-shadow-pane img, +.leaflet-container .leaflet-tile-pane img, +.leaflet-container img.leaflet-image-layer, +.leaflet-container .leaflet-tile { + max-width: none !important; + max-height: none !important; + width: auto; + padding: 0; + } + +.leaflet-container img.leaflet-tile { + /* See: https://bugs.chromium.org/p/chromium/issues/detail?id=600120 */ + mix-blend-mode: plus-lighter; +} + +.leaflet-container.leaflet-touch-zoom { + -ms-touch-action: pan-x pan-y; + touch-action: pan-x pan-y; + } +.leaflet-container.leaflet-touch-drag { + -ms-touch-action: pinch-zoom; + /* Fallback for FF which doesn't support pinch-zoom */ + touch-action: none; + touch-action: pinch-zoom; +} +.leaflet-container.leaflet-touch-drag.leaflet-touch-zoom { + -ms-touch-action: none; + touch-action: none; +} +.leaflet-container { + -webkit-tap-highlight-color: transparent; +} +.leaflet-container a { + -webkit-tap-highlight-color: rgba(51, 181, 229, 0.4); +} +.leaflet-tile { + filter: inherit; + visibility: hidden; + } +.leaflet-tile-loaded { + visibility: inherit; + } +.leaflet-zoom-box { + width: 0; + height: 0; + -moz-box-sizing: border-box; + box-sizing: border-box; + z-index: 800; + } +/* workaround for https://bugzilla.mozilla.org/show_bug.cgi?id=888319 */ +.leaflet-overlay-pane svg { + -moz-user-select: none; + } + +.leaflet-pane { z-index: 400; } + +.leaflet-tile-pane { z-index: 200; } +.leaflet-overlay-pane { z-index: 400; } +.leaflet-shadow-pane { z-index: 500; } +.leaflet-marker-pane { z-index: 600; } +.leaflet-tooltip-pane { z-index: 650; } +.leaflet-popup-pane { z-index: 700; } + +.leaflet-map-pane canvas { z-index: 100; } +.leaflet-map-pane svg { z-index: 200; } + +.leaflet-vml-shape { + width: 1px; + height: 1px; + } +.lvml { + behavior: url(#default#VML); + display: inline-block; + position: absolute; + } + + +/* control positioning */ + +.leaflet-control { + position: relative; + z-index: 800; + pointer-events: visiblePainted; /* IE 9-10 doesn't have auto */ + pointer-events: auto; + } +.leaflet-top, +.leaflet-bottom { + position: absolute; + z-index: 1000; + pointer-events: none; + } +.leaflet-top { + top: 0; + } +.leaflet-right { + right: 0; + } +.leaflet-bottom { + bottom: 0; + } +.leaflet-left { + left: 0; + } +.leaflet-control { + float: left; + clear: both; + } +.leaflet-right .leaflet-control { + float: right; + } +.leaflet-top .leaflet-control { + margin-top: 10px; + } +.leaflet-bottom .leaflet-control { + margin-bottom: 10px; + } +.leaflet-left .leaflet-control { + margin-left: 10px; + } +.leaflet-right .leaflet-control { + margin-right: 10px; + } + + +/* zoom and fade animations */ + +.leaflet-fade-anim .leaflet-popup { + opacity: 0; + -webkit-transition: opacity 0.2s linear; + -moz-transition: opacity 0.2s linear; + transition: opacity 0.2s linear; + } +.leaflet-fade-anim .leaflet-map-pane .leaflet-popup { + opacity: 1; + } +.leaflet-zoom-animated { + -webkit-transform-origin: 0 0; + -ms-transform-origin: 0 0; + transform-origin: 0 0; + } +svg.leaflet-zoom-animated { + will-change: transform; +} + +.leaflet-zoom-anim .leaflet-zoom-animated { + -webkit-transition: -webkit-transform 0.25s cubic-bezier(0,0,0.25,1); + -moz-transition: -moz-transform 0.25s cubic-bezier(0,0,0.25,1); + transition: transform 0.25s cubic-bezier(0,0,0.25,1); + } +.leaflet-zoom-anim .leaflet-tile, +.leaflet-pan-anim .leaflet-tile { + -webkit-transition: none; + -moz-transition: none; + transition: none; + } + +.leaflet-zoom-anim .leaflet-zoom-hide { + visibility: hidden; + } + + +/* cursors */ + +.leaflet-interactive { + cursor: pointer; + } +.leaflet-grab { + cursor: -webkit-grab; + cursor: -moz-grab; + cursor: grab; + } +.leaflet-crosshair, +.leaflet-crosshair .leaflet-interactive { + cursor: crosshair; + } +.leaflet-popup-pane, +.leaflet-control { + cursor: auto; + } +.leaflet-dragging .leaflet-grab, +.leaflet-dragging .leaflet-grab .leaflet-interactive, +.leaflet-dragging .leaflet-marker-draggable { + cursor: move; + cursor: -webkit-grabbing; + cursor: -moz-grabbing; + cursor: grabbing; + } + +/* marker & overlays interactivity */ +.leaflet-marker-icon, +.leaflet-marker-shadow, +.leaflet-image-layer, +.leaflet-pane > svg path, +.leaflet-tile-container { + pointer-events: none; + } + +.leaflet-marker-icon.leaflet-interactive, +.leaflet-image-layer.leaflet-interactive, +.leaflet-pane > svg path.leaflet-interactive, +svg.leaflet-image-layer.leaflet-interactive path { + pointer-events: visiblePainted; /* IE 9-10 doesn't have auto */ + pointer-events: auto; + } + +/* visual tweaks */ + +.leaflet-container { + background: #ddd; + outline-offset: 1px; + } +.leaflet-container a { + color: #0078A8; + } +.leaflet-zoom-box { + border: 2px dotted #38f; + background: rgba(255,255,255,0.5); + } + + +/* general typography */ +.leaflet-container { + font-family: "Helvetica Neue", Arial, Helvetica, sans-serif; + font-size: 12px; + font-size: 0.75rem; + line-height: 1.5; + } + + +/* general toolbar styles */ + +.leaflet-bar { + box-shadow: 0 1px 5px rgba(0,0,0,0.65); + border-radius: 4px; + } +.leaflet-bar a { + background-color: #fff; + border-bottom: 1px solid #ccc; + width: 26px; + height: 26px; + line-height: 26px; + display: block; + text-align: center; + text-decoration: none; + color: black; + } +.leaflet-bar a, +.leaflet-control-layers-toggle { + background-position: 50% 50%; + background-repeat: no-repeat; + display: block; + } +.leaflet-bar a:hover, +.leaflet-bar a:focus { + background-color: #f4f4f4; + } +.leaflet-bar a:first-child { + border-top-left-radius: 4px; + border-top-right-radius: 4px; + } +.leaflet-bar a:last-child { + border-bottom-left-radius: 4px; + border-bottom-right-radius: 4px; + border-bottom: none; + } +.leaflet-bar a.leaflet-disabled { + cursor: default; + background-color: #f4f4f4; + color: #bbb; + } + +.leaflet-touch .leaflet-bar a { + width: 30px; + height: 30px; + line-height: 30px; + } +.leaflet-touch .leaflet-bar a:first-child { + border-top-left-radius: 2px; + border-top-right-radius: 2px; + } +.leaflet-touch .leaflet-bar a:last-child { + border-bottom-left-radius: 2px; + border-bottom-right-radius: 2px; + } + +/* zoom control */ + +.leaflet-control-zoom-in, +.leaflet-control-zoom-out { + font: bold 18px 'Lucida Console', Monaco, monospace; + text-indent: 1px; + } + +.leaflet-touch .leaflet-control-zoom-in, .leaflet-touch .leaflet-control-zoom-out { + font-size: 22px; + } + + +/* layers control */ + +.leaflet-control-layers { + box-shadow: 0 1px 5px rgba(0,0,0,0.4); + background: #fff; + border-radius: 5px; + } +.leaflet-control-layers-toggle { + background-image: url(images/layers.png); + width: 36px; + height: 36px; + } +.leaflet-retina .leaflet-control-layers-toggle { + background-image: url(images/layers-2x.png); + background-size: 26px 26px; + } +.leaflet-touch .leaflet-control-layers-toggle { + width: 44px; + height: 44px; + } +.leaflet-control-layers .leaflet-control-layers-list, +.leaflet-control-layers-expanded .leaflet-control-layers-toggle { + display: none; + } +.leaflet-control-layers-expanded .leaflet-control-layers-list { + display: block; + position: relative; + } +.leaflet-control-layers-expanded { + padding: 6px 10px 6px 6px; + color: #333; + background: #fff; + } +.leaflet-control-layers-scrollbar { + overflow-y: scroll; + overflow-x: hidden; + padding-right: 5px; + } +.leaflet-control-layers-selector { + margin-top: 2px; + position: relative; + top: 1px; + } +.leaflet-control-layers label { + display: block; + font-size: 13px; + font-size: 1.08333em; + } +.leaflet-control-layers-separator { + height: 0; + border-top: 1px solid #ddd; + margin: 5px -10px 5px -6px; + } + +/* Default icon URLs */ +.leaflet-default-icon-path { /* used only in path-guessing heuristic, see L.Icon.Default */ + background-image: url(images/marker-icon.png); + } + + +/* attribution and scale controls */ + +.leaflet-container .leaflet-control-attribution { + background: #fff; + background: rgba(255, 255, 255, 0.8); + margin: 0; + } +.leaflet-control-attribution, +.leaflet-control-scale-line { + padding: 0 5px; + color: #333; + line-height: 1.4; + } +.leaflet-control-attribution a { + text-decoration: none; + } +.leaflet-control-attribution a:hover, +.leaflet-control-attribution a:focus { + text-decoration: underline; + } +.leaflet-attribution-flag { + display: inline !important; + vertical-align: baseline !important; + width: 1em; + height: 0.6669em; + } +.leaflet-left .leaflet-control-scale { + margin-left: 5px; + } +.leaflet-bottom .leaflet-control-scale { + margin-bottom: 5px; + } +.leaflet-control-scale-line { + border: 2px solid #777; + border-top: none; + line-height: 1.1; + padding: 2px 5px 1px; + white-space: nowrap; + -moz-box-sizing: border-box; + box-sizing: border-box; + background: rgba(255, 255, 255, 0.8); + text-shadow: 1px 1px #fff; + } +.leaflet-control-scale-line:not(:first-child) { + border-top: 2px solid #777; + border-bottom: none; + margin-top: -2px; + } +.leaflet-control-scale-line:not(:first-child):not(:last-child) { + border-bottom: 2px solid #777; + } + +.leaflet-touch .leaflet-control-attribution, +.leaflet-touch .leaflet-control-layers, +.leaflet-touch .leaflet-bar { + box-shadow: none; + } +.leaflet-touch .leaflet-control-layers, +.leaflet-touch .leaflet-bar { + border: 2px solid rgba(0,0,0,0.2); + background-clip: padding-box; + } + + +/* popup */ + +.leaflet-popup { + position: absolute; + text-align: center; + margin-bottom: 20px; + } +.leaflet-popup-content-wrapper { + padding: 1px; + text-align: left; + border-radius: 12px; + } +.leaflet-popup-content { + margin: 13px 24px 13px 20px; + line-height: 1.3; + font-size: 13px; + font-size: 1.08333em; + min-height: 1px; + } +.leaflet-popup-content p { + margin: 17px 0; + margin: 1.3em 0; + } +.leaflet-popup-tip-container { + width: 40px; + height: 20px; + position: absolute; + left: 50%; + margin-top: -1px; + margin-left: -20px; + overflow: hidden; + pointer-events: none; + } +.leaflet-popup-tip { + width: 17px; + height: 17px; + padding: 1px; + + margin: -10px auto 0; + pointer-events: auto; + + -webkit-transform: rotate(45deg); + -moz-transform: rotate(45deg); + -ms-transform: rotate(45deg); + transform: rotate(45deg); + } +.leaflet-popup-content-wrapper, +.leaflet-popup-tip { + background: white; + color: #333; + box-shadow: 0 3px 14px rgba(0,0,0,0.4); + } +.leaflet-container a.leaflet-popup-close-button { + position: absolute; + top: 0; + right: 0; + border: none; + text-align: center; + width: 24px; + height: 24px; + font: 16px/24px Tahoma, Verdana, sans-serif; + color: #757575; + text-decoration: none; + background: transparent; + } +.leaflet-container a.leaflet-popup-close-button:hover, +.leaflet-container a.leaflet-popup-close-button:focus { + color: #585858; + } +.leaflet-popup-scrolled { + overflow: auto; + } + +.leaflet-oldie .leaflet-popup-content-wrapper { + -ms-zoom: 1; + } +.leaflet-oldie .leaflet-popup-tip { + width: 24px; + margin: 0 auto; + + -ms-filter: "progid:DXImageTransform.Microsoft.Matrix(M11=0.70710678, M12=0.70710678, M21=-0.70710678, M22=0.70710678)"; + filter: progid:DXImageTransform.Microsoft.Matrix(M11=0.70710678, M12=0.70710678, M21=-0.70710678, M22=0.70710678); + } + +.leaflet-oldie .leaflet-control-zoom, +.leaflet-oldie .leaflet-control-layers, +.leaflet-oldie .leaflet-popup-content-wrapper, +.leaflet-oldie .leaflet-popup-tip { + border: 1px solid #999; + } + + +/* div icon */ + +.leaflet-div-icon { + background: #fff; + border: 1px solid #666; + } + + +/* Tooltip */ +/* Base styles for the element that has a tooltip */ +.leaflet-tooltip { + position: absolute; + padding: 6px; + background-color: #fff; + border: 1px solid #fff; + border-radius: 3px; + color: #222; + white-space: nowrap; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; + pointer-events: none; + box-shadow: 0 1px 3px rgba(0,0,0,0.4); + } +.leaflet-tooltip.leaflet-interactive { + cursor: pointer; + pointer-events: auto; + } +.leaflet-tooltip-top:before, +.leaflet-tooltip-bottom:before, +.leaflet-tooltip-left:before, +.leaflet-tooltip-right:before { + position: absolute; + pointer-events: none; + border: 6px solid transparent; + background: transparent; + content: ""; + } + +/* Directions */ + +.leaflet-tooltip-bottom { + margin-top: 6px; +} +.leaflet-tooltip-top { + margin-top: -6px; +} +.leaflet-tooltip-bottom:before, +.leaflet-tooltip-top:before { + left: 50%; + margin-left: -6px; + } +.leaflet-tooltip-top:before { + bottom: 0; + margin-bottom: -12px; + border-top-color: #fff; + } +.leaflet-tooltip-bottom:before { + top: 0; + margin-top: -12px; + margin-left: -6px; + border-bottom-color: #fff; + } +.leaflet-tooltip-left { + margin-left: -6px; +} +.leaflet-tooltip-right { + margin-left: 6px; +} +.leaflet-tooltip-left:before, +.leaflet-tooltip-right:before { + top: 50%; + margin-top: -6px; + } +.leaflet-tooltip-left:before { + right: 0; + margin-right: -12px; + border-left-color: #fff; + } +.leaflet-tooltip-right:before { + left: 0; + margin-left: -12px; + border-right-color: #fff; + } + +/* Printing */ + +@media print { + /* Prevent printers from removing background-images of controls. */ + .leaflet-control { + -webkit-print-color-adjust: exact; + print-color-adjust: exact; + } + } diff --git a/rust/crates/du-web/assets/vendor/leaflet.js b/rust/crates/du-web/assets/vendor/leaflet.js new file mode 100644 index 0000000..a3bf693 --- /dev/null +++ b/rust/crates/du-web/assets/vendor/leaflet.js @@ -0,0 +1,6 @@ +/* @preserve + * Leaflet 1.9.4, a JS library for interactive maps. https://leafletjs.com + * (c) 2010-2023 Vladimir Agafonkin, (c) 2010-2011 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e=this.getSize(),i=(this._sizeChanged=!0,this._lastCenter=null,this.getSize()),n=e.divideBy(2).round(),o=i.divideBy(2).round(),n=n.subtract(o);return n.x||n.y?(t.animate&&t.pan?this.panBy(n):(t.pan&&this._rawPanBy(n),this.fire("move"),t.debounceMoveend?(clearTimeout(this._sizeTimer),this._sizeTimer=setTimeout(a(this.fire,this,"moveend"),200)):this.fire("moveend")),this.fire("resize",{oldSize:e,newSize:i})):this},stop:function(){return this.setZoom(this._limitZoom(this._zoom)),this.options.zoomSnap||this.fire("viewreset"),this._stop()},locate:function(t){var e,i;return t=this._locateOptions=l({timeout:1e4,watch:!1},t),"geolocation"in navigator?(e=a(this._handleGeolocationResponse,this),i=a(this._handleGeolocationError,this),t.watch?this._locationWatchId=navigator.geolocation.watchPosition(e,i,t):navigator.geolocation.getCurrentPosition(e,i,t)):this._handleGeolocationError({code:0,message:"Geolocation not supported."}),this},stopLocate:function(){return navigator.geolocation&&navigator.geolocation.clearWatch&&navigator.geolocation.clearWatch(this._locationWatchId),this._locateOptions&&(this._locateOptions.setView=!1),this},_handleGeolocationError:function(t){var e;this._container._leaflet_id&&(e=t.code,t=t.message||(1===e?"permission denied":2===e?"position unavailable":"timeout"),this._locateOptions.setView&&!this._loaded&&this.fitWorld(),this.fire("locationerror",{code:e,message:"Geolocation error: "+t+"."}))},_handleGeolocationResponse:function(t){if(this._container._leaflet_id){var e,i,n=new v(t.coords.latitude,t.coords.longitude),o=n.toBounds(2*t.coords.accuracy),s=this._locateOptions,r=(s.setView&&(e=this.getBoundsZoom(o),this.setView(n,s.maxZoom?Math.min(e,s.maxZoom):e)),{latlng:n,bounds:o,timestamp:t.timestamp});for(i in t.coords)"number"==typeof t.coords[i]&&(r[i]=t.coords[i]);this.fire("locationfound",r)}},addHandler:function(t,e){return e&&(e=this[t]=new e(this),this._handlers.push(e),this.options[t]&&e.enable()),this},remove:function(){if(this._initEvents(!0),this.options.maxBounds&&this.off("moveend",this._panInsideMaxBounds),this._containerId!==this._container._leaflet_id)throw new Error("Map container is being reused by another instance");try{delete this._container._leaflet_id,delete this._containerId}catch(t){this._container._leaflet_id=void 0,this._containerId=void 0}for(var t in void 0!==this._locationWatchId&&this.stopLocate(),this._stop(),T(this._mapPane),this._clearControlPos&&this._clearControlPos(),this._resizeRequest&&(r(this._resizeRequest),this._resizeRequest=null),this._clearHandlers(),this._loaded&&this.fire("unload"),this._layers)this._layers[t].remove();for(t in this._panes)T(this._panes[t]);return this._layers=[],this._panes=[],delete this._mapPane,delete this._renderer,this},createPane:function(t,e){e=P("div","leaflet-pane"+(t?" leaflet-"+t.replace("Pane","")+"-pane":""),e||this._mapPane);return t&&(this._panes[t]=e),e},getCenter:function(){return this._checkIfLoaded(),this._lastCenter&&!this._moved()?this._lastCenter.clone():this.layerPointToLatLng(this._getCenterLayerPoint())},getZoom:function(){return this._zoom},getBounds:function(){var t=this.getPixelBounds();return new s(this.unproject(t.getBottomLeft()),this.unproject(t.getTopRight()))},getMinZoom:function(){return void 0===this.options.minZoom?this._layersMinZoom||0:this.options.minZoom},getMaxZoom:function(){return void 0===this.options.maxZoom?void 0===this._layersMaxZoom?1/0:this._layersMaxZoom:this.options.maxZoom},getBoundsZoom:function(t,e,i){t=g(t),i=m(i||[0,0]);var n=this.getZoom()||0,o=this.getMinZoom(),s=this.getMaxZoom(),r=t.getNorthWest(),t=t.getSouthEast(),i=this.getSize().subtract(i),t=_(this.project(t,n),this.project(r,n)).getSize(),r=b.any3d?this.options.zoomSnap:1,a=i.x/t.x,i=i.y/t.y,t=e?Math.max(a,i):Math.min(a,i),n=this.getScaleZoom(t,n);return r&&(n=Math.round(n/(r/100))*(r/100),n=e?Math.ceil(n/r)*r:Math.floor(n/r)*r),Math.max(o,Math.min(s,n))},getSize:function(){return this._size&&!this._sizeChanged||(this._size=new p(this._container.clientWidth||0,this._container.clientHeight||0),this._sizeChanged=!1),this._size.clone()},getPixelBounds:function(t,e){t=this._getTopLeftPoint(t,e);return new f(t,t.add(this.getSize()))},getPixelOrigin:function(){return this._checkIfLoaded(),this._pixelOrigin},getPixelWorldBounds:function(t){return this.options.crs.getProjectedBounds(void 0===t?this.getZoom():t)},getPane:function(t){return"string"==typeof t?this._panes[t]:t},getPanes:function(){return this._panes},getContainer:function(){return this._container},getZoomScale:function(t,e){var i=this.options.crs;return e=void 0===e?this._zoom:e,i.scale(t)/i.scale(e)},getScaleZoom:function(t,e){var i=this.options.crs,t=(e=void 0===e?this._zoom:e,i.zoom(t*i.scale(e)));return isNaN(t)?1/0:t},project:function(t,e){return e=void 0===e?this._zoom:e,this.options.crs.latLngToPoint(w(t),e)},unproject:function(t,e){return e=void 0===e?this._zoom:e,this.options.crs.pointToLatLng(m(t),e)},layerPointToLatLng:function(t){t=m(t).add(this.getPixelOrigin());return this.unproject(t)},latLngToLayerPoint:function(t){return this.project(w(t))._round()._subtract(this.getPixelOrigin())},wrapLatLng:function(t){return this.options.crs.wrapLatLng(w(t))},wrapLatLngBounds:function(t){return this.options.crs.wrapLatLngBounds(g(t))},distance:function(t,e){return this.options.crs.distance(w(t),w(e))},containerPointToLayerPoint:function(t){return m(t).subtract(this._getMapPanePos())},layerPointToContainerPoint:function(t){return m(t).add(this._getMapPanePos())},containerPointToLatLng:function(t){t=this.containerPointToLayerPoint(m(t));return this.layerPointToLatLng(t)},latLngToContainerPoint:function(t){return this.layerPointToContainerPoint(this.latLngToLayerPoint(w(t)))},mouseEventToContainerPoint:function(t){return De(t,this._container)},mouseEventToLayerPoint:function(t){return this.containerPointToLayerPoint(this.mouseEventToContainerPoint(t))},mouseEventToLatLng:function(t){return this.layerPointToLatLng(this.mouseEventToLayerPoint(t))},_initContainer:function(t){t=this._container=_e(t);if(!t)throw new Error("Map container not found.");if(t._leaflet_id)throw new Error("Map container is already initialized.");S(t,"scroll",this._onScroll,this),this._containerId=h(t)},_initLayout:function(){var t=this._container,e=(this._fadeAnimated=this.options.fadeAnimation&&b.any3d,M(t,"leaflet-container"+(b.touch?" leaflet-touch":"")+(b.retina?" leaflet-retina":"")+(b.ielt9?" leaflet-oldie":"")+(b.safari?" leaflet-safari":"")+(this._fadeAnimated?" leaflet-fade-anim":"")),pe(t,"position"));"absolute"!==e&&"relative"!==e&&"fixed"!==e&&"sticky"!==e&&(t.style.position="relative"),this._initPanes(),this._initControlPos&&this._initControlPos()},_initPanes:function(){var t=this._panes={};this._paneRenderers={},this._mapPane=this.createPane("mapPane",this._container),Z(this._mapPane,new p(0,0)),this.createPane("tilePane"),this.createPane("overlayPane"),this.createPane("shadowPane"),this.createPane("markerPane"),this.createPane("tooltipPane"),this.createPane("popupPane"),this.options.markerZoomAnimation||(M(t.markerPane,"leaflet-zoom-hide"),M(t.shadowPane,"leaflet-zoom-hide"))},_resetView:function(t,e,i){Z(this._mapPane,new p(0,0));var n=!this._loaded,o=(this._loaded=!0,e=this._limitZoom(e),this.fire("viewprereset"),this._zoom!==e);this._moveStart(o,i)._move(t,e)._moveEnd(o),this.fire("viewreset"),n&&this.fire("load")},_moveStart:function(t,e){return t&&this.fire("zoomstart"),e||this.fire("movestart"),this},_move:function(t,e,i,n){void 0===e&&(e=this._zoom);var o=this._zoom!==e;return this._zoom=e,this._lastCenter=t,this._pixelOrigin=this._getNewPixelOrigin(t),n?i&&i.pinch&&this.fire("zoom",i):((o||i&&i.pinch)&&this.fire("zoom",i),this.fire("move",i)),this},_moveEnd:function(t){return t&&this.fire("zoomend"),this.fire("moveend")},_stop:function(){return r(this._flyToFrame),this._panAnim&&this._panAnim.stop(),this},_rawPanBy:function(t){Z(this._mapPane,this._getMapPanePos().subtract(t))},_getZoomSpan:function(){return this.getMaxZoom()-this.getMinZoom()},_panInsideMaxBounds:function(){this._enforcingBounds||this.panInsideBounds(this.options.maxBounds)},_checkIfLoaded:function(){if(!this._loaded)throw new Error("Set map center and zoom first.")},_initEvents:function(t){this._targets={};var e=t?k:S;e((this._targets[h(this._container)]=this)._container,"click dblclick mousedown mouseup mouseover mouseout mousemove contextmenu keypress keydown keyup",this._handleDOMEvent,this),this.options.trackResize&&e(window,"resize",this._onResize,this),b.any3d&&this.options.transform3DLimit&&(t?this.off:this.on).call(this,"moveend",this._onMoveEnd)},_onResize:function(){r(this._resizeRequest),this._resizeRequest=x(function(){this.invalidateSize({debounceMoveend:!0})},this)},_onScroll:function(){this._container.scrollTop=0,this._container.scrollLeft=0},_onMoveEnd:function(){var t=this._getMapPanePos();Math.max(Math.abs(t.x),Math.abs(t.y))>=this.options.transform3DLimit&&this._resetView(this.getCenter(),this.getZoom())},_findEventTargets:function(t,e){for(var i,n=[],o="mouseout"===e||"mouseover"===e,s=t.target||t.srcElement,r=!1;s;){if((i=this._targets[h(s)])&&("click"===e||"preclick"===e)&&this._draggableMoved(i)){r=!0;break}if(i&&i.listens(e,!0)){if(o&&!We(s,t))break;if(n.push(i),o)break}if(s===this._container)break;s=s.parentNode}return n=n.length||r||o||!this.listens(e,!0)?n:[this]},_isClickDisabled:function(t){for(;t&&t!==this._container;){if(t._leaflet_disable_click)return!0;t=t.parentNode}},_handleDOMEvent:function(t){var e,i=t.target||t.srcElement;!this._loaded||i._leaflet_disable_events||"click"===t.type&&this._isClickDisabled(i)||("mousedown"===(e=t.type)&&Me(i),this._fireDOMEvent(t,e))},_mouseEvents:["click","dblclick","mouseover","mouseout","contextmenu"],_fireDOMEvent:function(t,e,i){"click"===t.type&&((a=l({},t)).type="preclick",this._fireDOMEvent(a,a.type,i));var n=this._findEventTargets(t,e);if(i){for(var o=[],s=0;sthis.options.zoomAnimationThreshold)return!1;var n=this.getZoomScale(e),n=this._getCenterOffset(t)._divideBy(1-1/n);if(!0!==i.animate&&!this.getSize().contains(n))return!1;x(function(){this._moveStart(!0,i.noMoveStart||!1)._animateZoom(t,e,!0)},this)}return!0},_animateZoom:function(t,e,i,n){this._mapPane&&(i&&(this._animatingZoom=!0,this._animateToCenter=t,this._animateToZoom=e,M(this._mapPane,"leaflet-zoom-anim")),this.fire("zoomanim",{center:t,zoom:e,noUpdate:n}),this._tempFireZoomEvent||(this._tempFireZoomEvent=this._zoom!==this._animateToZoom),this._move(this._animateToCenter,this._animateToZoom,void 0,!0),setTimeout(a(this._onZoomTransitionEnd,this),250))},_onZoomTransitionEnd:function(){this._animatingZoom&&(this._mapPane&&z(this._mapPane,"leaflet-zoom-anim"),this._animatingZoom=!1,this._move(this._animateToCenter,this._animateToZoom,void 0,!0),this._tempFireZoomEvent&&this.fire("zoom"),delete this._tempFireZoomEvent,this.fire("move"),this._moveEnd(!0))}});function Ue(t){return new B(t)}var B=et.extend({options:{position:"topright"},initialize:function(t){c(this,t)},getPosition:function(){return this.options.position},setPosition:function(t){var e=this._map;return e&&e.removeControl(this),this.options.position=t,e&&e.addControl(this),this},getContainer:function(){return this._container},addTo:function(t){this.remove(),this._map=t;var e=this._container=this.onAdd(t),i=this.getPosition(),t=t._controlCorners[i];return M(e,"leaflet-control"),-1!==i.indexOf("bottom")?t.insertBefore(e,t.firstChild):t.appendChild(e),this._map.on("unload",this.remove,this),this},remove:function(){return this._map&&(T(this._container),this.onRemove&&this.onRemove(this._map),this._map.off("unload",this.remove,this),this._map=null),this},_refocusOnMap:function(t){this._map&&t&&0",e=document.createElement("div");return e.innerHTML=t,e.firstChild},_addItem:function(t){var e,i=document.createElement("label"),n=this._map.hasLayer(t.layer),n=(t.overlay?((e=document.createElement("input")).type="checkbox",e.className="leaflet-control-layers-selector",e.defaultChecked=n):e=this._createRadioElement("leaflet-base-layers_"+h(this),n),this._layerControlInputs.push(e),e.layerId=h(t.layer),S(e,"click",this._onInputClick,this),document.createElement("span")),o=(n.innerHTML=" "+t.name,document.createElement("span"));return i.appendChild(o),o.appendChild(e),o.appendChild(n),(t.overlay?this._overlaysList:this._baseLayersList).appendChild(i),this._checkDisabledLayers(),i},_onInputClick:function(){if(!this._preventClick){var t,e,i=this._layerControlInputs,n=[],o=[];this._handlingClick=!0;for(var s=i.length-1;0<=s;s--)t=i[s],e=this._getLayer(t.layerId).layer,t.checked?n.push(e):t.checked||o.push(e);for(s=0;se.options.maxZoom},_expandIfNotCollapsed:function(){return this._map&&!this.options.collapsed&&this.expand(),this},_expandSafely:function(){var t=this._section,e=(this._preventClick=!0,S(t,"click",O),this.expand(),this);setTimeout(function(){k(t,"click",O),e._preventClick=!1})}})),qe=B.extend({options:{position:"topleft",zoomInText:'',zoomInTitle:"Zoom in",zoomOutText:'',zoomOutTitle:"Zoom out"},onAdd:function(t){var e="leaflet-control-zoom",i=P("div",e+" leaflet-bar"),n=this.options;return this._zoomInButton=this._createButton(n.zoomInText,n.zoomInTitle,e+"-in",i,this._zoomIn),this._zoomOutButton=this._createButton(n.zoomOutText,n.zoomOutTitle,e+"-out",i,this._zoomOut),this._updateDisabled(),t.on("zoomend zoomlevelschange",this._updateDisabled,this),i},onRemove:function(t){t.off("zoomend zoomlevelschange",this._updateDisabled,this)},disable:function(){return this._disabled=!0,this._updateDisabled(),this},enable:function(){return this._disabled=!1,this._updateDisabled(),this},_zoomIn:function(t){!this._disabled&&this._map._zoomthis._map.getMinZoom()&&this._map.zoomOut(this._map.options.zoomDelta*(t.shiftKey?3:1))},_createButton:function(t,e,i,n,o){i=P("a",i,n);return i.innerHTML=t,i.href="#",i.title=e,i.setAttribute("role","button"),i.setAttribute("aria-label",e),Ie(i),S(i,"click",Re),S(i,"click",o,this),S(i,"click",this._refocusOnMap,this),i},_updateDisabled:function(){var t=this._map,e="leaflet-disabled";z(this._zoomInButton,e),z(this._zoomOutButton,e),this._zoomInButton.setAttribute("aria-disabled","false"),this._zoomOutButton.setAttribute("aria-disabled","false"),!this._disabled&&t._zoom!==t.getMinZoom()||(M(this._zoomOutButton,e),this._zoomOutButton.setAttribute("aria-disabled","true")),!this._disabled&&t._zoom!==t.getMaxZoom()||(M(this._zoomInButton,e),this._zoomInButton.setAttribute("aria-disabled","true"))}}),Ge=(A.mergeOptions({zoomControl:!0}),A.addInitHook(function(){this.options.zoomControl&&(this.zoomControl=new qe,this.addControl(this.zoomControl))}),B.extend({options:{position:"bottomleft",maxWidth:100,metric:!0,imperial:!0},onAdd:function(t){var e="leaflet-control-scale",i=P("div",e),n=this.options;return this._addScales(n,e+"-line",i),t.on(n.updateWhenIdle?"moveend":"move",this._update,this),t.whenReady(this._update,this),i},onRemove:function(t){t.off(this.options.updateWhenIdle?"moveend":"move",this._update,this)},_addScales:function(t,e,i){t.metric&&(this._mScale=P("div",e,i)),t.imperial&&(this._iScale=P("div",e,i))},_update:function(){var t=this._map,e=t.getSize().y/2,t=t.distance(t.containerPointToLatLng([0,e]),t.containerPointToLatLng([this.options.maxWidth,e]));this._updateScales(t)},_updateScales:function(t){this.options.metric&&t&&this._updateMetric(t),this.options.imperial&&t&&this._updateImperial(t)},_updateMetric:function(t){var e=this._getRoundNum(t);this._updateScale(this._mScale,e<1e3?e+" m":e/1e3+" km",e/t)},_updateImperial:function(t){var e,i,t=3.2808399*t;5280'+(b.inlineSvg?' ':"")+"Leaflet"},initialize:function(t){c(this,t),this._attributions={}},onAdd:function(t){for(var e in(t.attributionControl=this)._container=P("div","leaflet-control-attribution"),Ie(this._container),t._layers)t._layers[e].getAttribution&&this.addAttribution(t._layers[e].getAttribution());return this._update(),t.on("layeradd",this._addAttribution,this),this._container},onRemove:function(t){t.off("layeradd",this._addAttribution,this)},_addAttribution:function(t){t.layer.getAttribution&&(this.addAttribution(t.layer.getAttribution()),t.layer.once("remove",function(){this.removeAttribution(t.layer.getAttribution())},this))},setPrefix:function(t){return this.options.prefix=t,this._update(),this},addAttribution:function(t){return t&&(this._attributions[t]||(this._attributions[t]=0),this._attributions[t]++,this._update()),this},removeAttribution:function(t){return t&&this._attributions[t]&&(this._attributions[t]--,this._update()),this},_update:function(){if(this._map){var t,e=[];for(t in this._attributions)this._attributions[t]&&e.push(t);var i=[];this.options.prefix&&i.push(this.options.prefix),e.length&&i.push(e.join(", ")),this._container.innerHTML=i.join(' ')}}}),n=(A.mergeOptions({attributionControl:!0}),A.addInitHook(function(){this.options.attributionControl&&(new Ke).addTo(this)}),B.Layers=Ve,B.Zoom=qe,B.Scale=Ge,B.Attribution=Ke,Ue.layers=function(t,e,i){return new Ve(t,e,i)},Ue.zoom=function(t){return new qe(t)},Ue.scale=function(t){return new Ge(t)},Ue.attribution=function(t){return new Ke(t)},et.extend({initialize:function(t){this._map=t},enable:function(){return this._enabled||(this._enabled=!0,this.addHooks()),this},disable:function(){return this._enabled&&(this._enabled=!1,this.removeHooks()),this},enabled:function(){return!!this._enabled}})),ft=(n.addTo=function(t,e){return t.addHandler(e,this),this},{Events:e}),Ye=b.touch?"touchstart mousedown":"mousedown",Xe=it.extend({options:{clickTolerance:3},initialize:function(t,e,i,n){c(this,n),this._element=t,this._dragStartTarget=e||t,this._preventOutline=i},enable:function(){this._enabled||(S(this._dragStartTarget,Ye,this._onDown,this),this._enabled=!0)},disable:function(){this._enabled&&(Xe._dragging===this&&this.finishDrag(!0),k(this._dragStartTarget,Ye,this._onDown,this),this._enabled=!1,this._moved=!1)},_onDown:function(t){var e,i;this._enabled&&(this._moved=!1,ve(this._element,"leaflet-zoom-anim")||(t.touches&&1!==t.touches.length?Xe._dragging===this&&this.finishDrag():Xe._dragging||t.shiftKey||1!==t.which&&1!==t.button&&!t.touches||((Xe._dragging=this)._preventOutline&&Me(this._element),Le(),re(),this._moving||(this.fire("down"),i=t.touches?t.touches[0]:t,e=Ce(this._element),this._startPoint=new p(i.clientX,i.clientY),this._startPos=Pe(this._element),this._parentScale=Ze(e),i="mousedown"===t.type,S(document,i?"mousemove":"touchmove",this._onMove,this),S(document,i?"mouseup":"touchend touchcancel",this._onUp,this)))))},_onMove:function(t){var e;this._enabled&&(t.touches&&1e&&(i.push(t[n]),o=n);oe.max.x&&(i|=2),t.ye.max.y&&(i|=8),i}function ri(t,e,i,n){var o=e.x,e=e.y,s=i.x-o,r=i.y-e,a=s*s+r*r;return 0this._layersMaxZoom&&this.setZoom(this._layersMaxZoom),void 0===this.options.minZoom&&this._layersMinZoom&&this.getZoom()t.y!=n.y>t.y&&t.x<(n.x-i.x)*(t.y-i.y)/(n.y-i.y)+i.x&&(l=!l);return l||yi.prototype._containsPoint.call(this,t,!0)}});var wi=ci.extend({initialize:function(t,e){c(this,e),this._layers={},t&&this.addData(t)},addData:function(t){var e,i,n,o=d(t)?t:t.features;if(o){for(e=0,i=o.length;es.x&&(r=i.x+a-s.x+o.x),i.x-r-n.x<(a=0)&&(r=i.x-n.x),i.y+e+o.y>s.y&&(a=i.y+e-s.y+o.y),i.y-a-n.y<0&&(a=i.y-n.y),(r||a)&&(this.options.keepInView&&(this._autopanning=!0),t.fire("autopanstart").panBy([r,a]))))},_getAnchor:function(){return m(this._source&&this._source._getPopupAnchor?this._source._getPopupAnchor():[0,0])}})),Ii=(A.mergeOptions({closePopupOnClick:!0}),A.include({openPopup:function(t,e,i){return this._initOverlay(Bi,t,e,i).openOn(this),this},closePopup:function(t){return(t=arguments.length?t:this._popup)&&t.close(),this}}),o.include({bindPopup:function(t,e){return this._popup=this._initOverlay(Bi,this._popup,t,e),this._popupHandlersAdded||(this.on({click:this._openPopup,keypress:this._onKeyPress,remove:this.closePopup,move:this._movePopup}),this._popupHandlersAdded=!0),this},unbindPopup:function(){return this._popup&&(this.off({click:this._openPopup,keypress:this._onKeyPress,remove:this.closePopup,move:this._movePopup}),this._popupHandlersAdded=!1,this._popup=null),this},openPopup:function(t){return this._popup&&(this instanceof ci||(this._popup._source=this),this._popup._prepareOpen(t||this._latlng)&&this._popup.openOn(this._map)),this},closePopup:function(){return this._popup&&this._popup.close(),this},togglePopup:function(){return this._popup&&this._popup.toggle(this),this},isPopupOpen:function(){return!!this._popup&&this._popup.isOpen()},setPopupContent:function(t){return this._popup&&this._popup.setContent(t),this},getPopup:function(){return this._popup},_openPopup:function(t){var e;this._popup&&this._map&&(Re(t),e=t.layer||t.target,this._popup._source!==e||e instanceof fi?(this._popup._source=e,this.openPopup(t.latlng)):this._map.hasLayer(this._popup)?this.closePopup():this.openPopup(t.latlng))},_movePopup:function(t){this._popup.setLatLng(t.latlng)},_onKeyPress:function(t){13===t.originalEvent.keyCode&&this._openPopup(t)}}),Ai.extend({options:{pane:"tooltipPane",offset:[0,0],direction:"auto",permanent:!1,sticky:!1,opacity:.9},onAdd:function(t){Ai.prototype.onAdd.call(this,t),this.setOpacity(this.options.opacity),t.fire("tooltipopen",{tooltip:this}),this._source&&(this.addEventParent(this._source),this._source.fire("tooltipopen",{tooltip:this},!0))},onRemove:function(t){Ai.prototype.onRemove.call(this,t),t.fire("tooltipclose",{tooltip:this}),this._source&&(this.removeEventParent(this._source),this._source.fire("tooltipclose",{tooltip:this},!0))},getEvents:function(){var t=Ai.prototype.getEvents.call(this);return this.options.permanent||(t.preclick=this.close),t},_initLayout:function(){var t="leaflet-tooltip "+(this.options.className||"")+" leaflet-zoom-"+(this._zoomAnimated?"animated":"hide");this._contentNode=this._container=P("div",t),this._container.setAttribute("role","tooltip"),this._container.setAttribute("id","leaflet-tooltip-"+h(this))},_updateLayout:function(){},_adjustPan:function(){},_setPosition:function(t){var e,i=this._map,n=this._container,o=i.latLngToContainerPoint(i.getCenter()),i=i.layerPointToContainerPoint(t),s=this.options.direction,r=n.offsetWidth,a=n.offsetHeight,h=m(this.options.offset),l=this._getAnchor(),i="top"===s?(e=r/2,a):"bottom"===s?(e=r/2,0):(e="center"===s?r/2:"right"===s?0:"left"===s?r:i.xthis.options.maxZoom||nthis.options.maxZoom||void 0!==this.options.minZoom&&oi.max.x)||!e.wrapLat&&(t.yi.max.y))return!1}return!this.options.bounds||(e=this._tileCoordsToBounds(t),g(this.options.bounds).overlaps(e))},_keyToBounds:function(t){return this._tileCoordsToBounds(this._keyToTileCoords(t))},_tileCoordsToNwSe:function(t){var e=this._map,i=this.getTileSize(),n=t.scaleBy(i),i=n.add(i);return[e.unproject(n,t.z),e.unproject(i,t.z)]},_tileCoordsToBounds:function(t){t=this._tileCoordsToNwSe(t),t=new s(t[0],t[1]);return t=this.options.noWrap?t:this._map.wrapLatLngBounds(t)},_tileCoordsToKey:function(t){return t.x+":"+t.y+":"+t.z},_keyToTileCoords:function(t){var t=t.split(":"),e=new p(+t[0],+t[1]);return e.z=+t[2],e},_removeTile:function(t){var e=this._tiles[t];e&&(T(e.el),delete this._tiles[t],this.fire("tileunload",{tile:e.el,coords:this._keyToTileCoords(t)}))},_initTile:function(t){M(t,"leaflet-tile");var e=this.getTileSize();t.style.width=e.x+"px",t.style.height=e.y+"px",t.onselectstart=u,t.onmousemove=u,b.ielt9&&this.options.opacity<1&&C(t,this.options.opacity)},_addTile:function(t,e){var i=this._getTilePos(t),n=this._tileCoordsToKey(t),o=this.createTile(this._wrapCoords(t),a(this._tileReady,this,t));this._initTile(o),this.createTile.length<2&&x(a(this._tileReady,this,t,null,o)),Z(o,i),this._tiles[n]={el:o,coords:t,current:!0},e.appendChild(o),this.fire("tileloadstart",{tile:o,coords:t})},_tileReady:function(t,e,i){e&&this.fire("tileerror",{error:e,tile:i,coords:t});var n=this._tileCoordsToKey(t);(i=this._tiles[n])&&(i.loaded=+new Date,this._map._fadeAnimated?(C(i.el,0),r(this._fadeFrame),this._fadeFrame=x(this._updateOpacity,this)):(i.active=!0,this._pruneTiles()),e||(M(i.el,"leaflet-tile-loaded"),this.fire("tileload",{tile:i.el,coords:t})),this._noTilesToLoad()&&(this._loading=!1,this.fire("load"),b.ielt9||!this._map._fadeAnimated?x(this._pruneTiles,this):setTimeout(a(this._pruneTiles,this),250)))},_getTilePos:function(t){return t.scaleBy(this.getTileSize()).subtract(this._level.origin)},_wrapCoords:function(t){var e=new p(this._wrapX?H(t.x,this._wrapX):t.x,this._wrapY?H(t.y,this._wrapY):t.y);return e.z=t.z,e},_pxBoundsToTileRange:function(t){var e=this.getTileSize();return new f(t.min.unscaleBy(e).floor(),t.max.unscaleBy(e).ceil().subtract([1,1]))},_noTilesToLoad:function(){for(var t in this._tiles)if(!this._tiles[t].loaded)return!1;return!0}});var Di=Ni.extend({options:{minZoom:0,maxZoom:18,subdomains:"abc",errorTileUrl:"",zoomOffset:0,tms:!1,zoomReverse:!1,detectRetina:!1,crossOrigin:!1,referrerPolicy:!1},initialize:function(t,e){this._url=t,(e=c(this,e)).detectRetina&&b.retina&&0')}}catch(t){}return function(t){return document.createElement("<"+t+' xmlns="urn:schemas-microsoft.com:vml" class="lvml">')}}(),zt={_initContainer:function(){this._container=P("div","leaflet-vml-container")},_update:function(){this._map._animatingZoom||(Wi.prototype._update.call(this),this.fire("update"))},_initPath:function(t){var e=t._container=Vi("shape");M(e,"leaflet-vml-shape "+(this.options.className||"")),e.coordsize="1 1",t._path=Vi("path"),e.appendChild(t._path),this._updateStyle(t),this._layers[h(t)]=t},_addPath:function(t){var e=t._container;this._container.appendChild(e),t.options.interactive&&t.addInteractiveTarget(e)},_removePath:function(t){var e=t._container;T(e),t.removeInteractiveTarget(e),delete this._layers[h(t)]},_updateStyle:function(t){var e=t._stroke,i=t._fill,n=t.options,o=t._container;o.stroked=!!n.stroke,o.filled=!!n.fill,n.stroke?(e=e||(t._stroke=Vi("stroke")),o.appendChild(e),e.weight=n.weight+"px",e.color=n.color,e.opacity=n.opacity,n.dashArray?e.dashStyle=d(n.dashArray)?n.dashArray.join(" "):n.dashArray.replace(/( *, *)/g," "):e.dashStyle="",e.endcap=n.lineCap.replace("butt","flat"),e.joinstyle=n.lineJoin):e&&(o.removeChild(e),t._stroke=null),n.fill?(i=i||(t._fill=Vi("fill")),o.appendChild(i),i.color=n.fillColor||n.color,i.opacity=n.fillOpacity):i&&(o.removeChild(i),t._fill=null)},_updateCircle:function(t){var e=t._point.round(),i=Math.round(t._radius),n=Math.round(t._radiusY||i);this._setPath(t,t._empty()?"M0 0":"AL "+e.x+","+e.y+" "+i+","+n+" 0,23592600")},_setPath:function(t,e){t._path.v=e},_bringToFront:function(t){fe(t._container)},_bringToBack:function(t){ge(t._container)}},qi=b.vml?Vi:ct,Gi=Wi.extend({_initContainer:function(){this._container=qi("svg"),this._container.setAttribute("pointer-events","none"),this._rootGroup=qi("g"),this._container.appendChild(this._rootGroup)},_destroyContainer:function(){T(this._container),k(this._container),delete this._container,delete this._rootGroup,delete this._svgSize},_update:function(){var t,e,i;this._map._animatingZoom&&this._bounds||(Wi.prototype._update.call(this),e=(t=this._bounds).getSize(),i=this._container,this._svgSize&&this._svgSize.equals(e)||(this._svgSize=e,i.setAttribute("width",e.x),i.setAttribute("height",e.y)),Z(i,t.min),i.setAttribute("viewBox",[t.min.x,t.min.y,e.x,e.y].join(" ")),this.fire("update"))},_initPath:function(t){var e=t._path=qi("path");t.options.className&&M(e,t.options.className),t.options.interactive&&M(e,"leaflet-interactive"),this._updateStyle(t),this._layers[h(t)]=t},_addPath:function(t){this._rootGroup||this._initContainer(),this._rootGroup.appendChild(t._path),t.addInteractiveTarget(t._path)},_removePath:function(t){T(t._path),t.removeInteractiveTarget(t._path),delete this._layers[h(t)]},_updatePath:function(t){t._project(),t._update()},_updateStyle:function(t){var e=t._path,t=t.options;e&&(t.stroke?(e.setAttribute("stroke",t.color),e.setAttribute("stroke-opacity",t.opacity),e.setAttribute("stroke-width",t.weight),e.setAttribute("stroke-linecap",t.lineCap),e.setAttribute("stroke-linejoin",t.lineJoin),t.dashArray?e.setAttribute("stroke-dasharray",t.dashArray):e.removeAttribute("stroke-dasharray"),t.dashOffset?e.setAttribute("stroke-dashoffset",t.dashOffset):e.removeAttribute("stroke-dashoffset")):e.setAttribute("stroke","none"),t.fill?(e.setAttribute("fill",t.fillColor||t.color),e.setAttribute("fill-opacity",t.fillOpacity),e.setAttribute("fill-rule",t.fillRule||"evenodd")):e.setAttribute("fill","none"))},_updatePoly:function(t,e){this._setPath(t,dt(t._parts,e))},_updateCircle:function(t){var e=t._point,i=Math.max(Math.round(t._radius),1),n="a"+i+","+(Math.max(Math.round(t._radiusY),1)||i)+" 0 1,0 ",e=t._empty()?"M0 0":"M"+(e.x-i)+","+e.y+n+2*i+",0 "+n+2*-i+",0 ";this._setPath(t,e)},_setPath:function(t,e){t._path.setAttribute("d",e)},_bringToFront:function(t){fe(t._path)},_bringToBack:function(t){ge(t._path)}});function Ki(t){return b.svg||b.vml?new Gi(t):null}b.vml&&Gi.include(zt),A.include({getRenderer:function(t){t=(t=t.options.renderer||this._getPaneRenderer(t.options.pane)||this.options.renderer||this._renderer)||(this._renderer=this._createRenderer());return this.hasLayer(t)||this.addLayer(t),t},_getPaneRenderer:function(t){var e;return"overlayPane"!==t&&void 0!==t&&(void 0===(e=this._paneRenderers[t])&&(e=this._createRenderer({pane:t}),this._paneRenderers[t]=e),e)},_createRenderer:function(t){return this.options.preferCanvas&&Ui(t)||Ki(t)}});var Yi=xi.extend({initialize:function(t,e){xi.prototype.initialize.call(this,this._boundsToLatLngs(t),e)},setBounds:function(t){return this.setLatLngs(this._boundsToLatLngs(t))},_boundsToLatLngs:function(t){return[(t=g(t)).getSouthWest(),t.getNorthWest(),t.getNorthEast(),t.getSouthEast()]}});Gi.create=qi,Gi.pointsToPath=dt,wi.geometryToLayer=bi,wi.coordsToLatLng=Li,wi.coordsToLatLngs=Ti,wi.latLngToCoords=Mi,wi.latLngsToCoords=zi,wi.getFeature=Ci,wi.asFeature=Zi,A.mergeOptions({boxZoom:!0});var _t=n.extend({initialize:function(t){this._map=t,this._container=t._container,this._pane=t._panes.overlayPane,this._resetStateTimeout=0,t.on("unload",this._destroy,this)},addHooks:function(){S(this._container,"mousedown",this._onMouseDown,this)},removeHooks:function(){k(this._container,"mousedown",this._onMouseDown,this)},moved:function(){return this._moved},_destroy:function(){T(this._pane),delete this._pane},_resetState:function(){this._resetStateTimeout=0,this._moved=!1},_clearDeferredResetState:function(){0!==this._resetStateTimeout&&(clearTimeout(this._resetStateTimeout),this._resetStateTimeout=0)},_onMouseDown:function(t){if(!t.shiftKey||1!==t.which&&1!==t.button)return!1;this._clearDeferredResetState(),this._resetState(),re(),Le(),this._startPoint=this._map.mouseEventToContainerPoint(t),S(document,{contextmenu:Re,mousemove:this._onMouseMove,mouseup:this._onMouseUp,keydown:this._onKeyDown},this)},_onMouseMove:function(t){this._moved||(this._moved=!0,this._box=P("div","leaflet-zoom-box",this._container),M(this._container,"leaflet-crosshair"),this._map.fire("boxzoomstart")),this._point=this._map.mouseEventToContainerPoint(t);var t=new f(this._point,this._startPoint),e=t.getSize();Z(this._box,t.min),this._box.style.width=e.x+"px",this._box.style.height=e.y+"px"},_finish:function(){this._moved&&(T(this._box),z(this._container,"leaflet-crosshair")),ae(),Te(),k(document,{contextmenu:Re,mousemove:this._onMouseMove,mouseup:this._onMouseUp,keydown:this._onKeyDown},this)},_onMouseUp:function(t){1!==t.which&&1!==t.button||(this._finish(),this._moved&&(this._clearDeferredResetState(),this._resetStateTimeout=setTimeout(a(this._resetState,this),0),t=new s(this._map.containerPointToLatLng(this._startPoint),this._map.containerPointToLatLng(this._point)),this._map.fitBounds(t).fire("boxzoomend",{boxZoomBounds:t})))},_onKeyDown:function(t){27===t.keyCode&&(this._finish(),this._clearDeferredResetState(),this._resetState())}}),Ct=(A.addInitHook("addHandler","boxZoom",_t),A.mergeOptions({doubleClickZoom:!0}),n.extend({addHooks:function(){this._map.on("dblclick",this._onDoubleClick,this)},removeHooks:function(){this._map.off("dblclick",this._onDoubleClick,this)},_onDoubleClick:function(t){var e=this._map,i=e.getZoom(),n=e.options.zoomDelta,i=t.originalEvent.shiftKey?i-n:i+n;"center"===e.options.doubleClickZoom?e.setZoom(i):e.setZoomAround(t.containerPoint,i)}})),Zt=(A.addInitHook("addHandler","doubleClickZoom",Ct),A.mergeOptions({dragging:!0,inertia:!0,inertiaDeceleration:3400,inertiaMaxSpeed:1/0,easeLinearity:.2,worldCopyJump:!1,maxBoundsViscosity:0}),n.extend({addHooks:function(){var t;this._draggable||(t=this._map,this._draggable=new Xe(t._mapPane,t._container),this._draggable.on({dragstart:this._onDragStart,drag:this._onDrag,dragend:this._onDragEnd},this),this._draggable.on("predrag",this._onPreDragLimit,this),t.options.worldCopyJump&&(this._draggable.on("predrag",this._onPreDragWrap,this),t.on("zoomend",this._onZoomEnd,this),t.whenReady(this._onZoomEnd,this))),M(this._map._container,"leaflet-grab leaflet-touch-drag"),this._draggable.enable(),this._positions=[],this._times=[]},removeHooks:function(){z(this._map._container,"leaflet-grab"),z(this._map._container,"leaflet-touch-drag"),this._draggable.disable()},moved:function(){return this._draggable&&this._draggable._moved},moving:function(){return this._draggable&&this._draggable._moving},_onDragStart:function(){var t,e=this._map;e._stop(),this._map.options.maxBounds&&this._map.options.maxBoundsViscosity?(t=g(this._map.options.maxBounds),this._offsetLimit=_(this._map.latLngToContainerPoint(t.getNorthWest()).multiplyBy(-1),this._map.latLngToContainerPoint(t.getSouthEast()).multiplyBy(-1).add(this._map.getSize())),this._viscosity=Math.min(1,Math.max(0,this._map.options.maxBoundsViscosity))):this._offsetLimit=null,e.fire("movestart").fire("dragstart"),e.options.inertia&&(this._positions=[],this._times=[])},_onDrag:function(t){var e,i;this._map.options.inertia&&(e=this._lastTime=+new Date,i=this._lastPos=this._draggable._absPos||this._draggable._newPos,this._positions.push(i),this._times.push(e),this._prunePositions(e)),this._map.fire("move",t).fire("drag",t)},_prunePositions:function(t){for(;1e.max.x&&(t.x=this._viscousLimit(t.x,e.max.x)),t.y>e.max.y&&(t.y=this._viscousLimit(t.y,e.max.y)),this._draggable._newPos=this._draggable._startPos.add(t))},_onPreDragWrap:function(){var t=this._worldWidth,e=Math.round(t/2),i=this._initialWorldOffset,n=this._draggable._newPos.x,o=(n-e+i)%t+e-i,n=(n+e+i)%t-e-i,t=Math.abs(o+i)e.getMaxZoom()&&1 Router { + Router::new() + .route("/biosamples/map", get(map_page)) + .route("/biosamples/geo-data", get(geo_data)) +} + +#[derive(askama::Template)] +#[template(path = "biosamples/map.html")] +struct MapTemplate { + t: T, + next: String, +} + +async fn map_page(locale: Locale) -> Response { + html(&MapTemplate { t: locale.t, next: locale.next }) +} + +/// GeoJSON FeatureCollection of biosample locations for Leaflet. +async fn geo_data(State(st): State) -> Result, AppError> { + let points = du_db::biosample::geo_points(&st.pool).await?; + let features: Vec = points + .into_iter() + .map(|p| { + json!({ + "type": "Feature", + "geometry": { "type": "Point", "coordinates": [p.lon, p.lat] }, + "properties": { "accession": p.accession, "source": p.source.label() }, + }) + }) + .collect(); + Ok(Json(json!({ "type": "FeatureCollection", "features": features }))) +} diff --git a/rust/crates/du-web/src/routes/mod.rs b/rust/crates/du-web/src/routes/mod.rs index 5aeb73d..783f19f 100644 --- a/rust/crates/du-web/src/routes/mod.rs +++ b/rust/crates/du-web/src/routes/mod.rs @@ -12,6 +12,7 @@ use axum::Router; use serde::Deserialize; use tower_http::services::ServeDir; +pub mod maps; pub mod references; pub mod tree; pub mod variants; @@ -33,6 +34,7 @@ pub fn app(state: AppState) -> Router { .merge(variants::router()) .merge(tree::router()) .merge(references::router()) + .merge(maps::router()) .nest_service("/assets", ServeDir::new(assets_dir())) .with_state(state) } diff --git a/rust/crates/du-web/templates/base.html b/rust/crates/du-web/templates/base.html index a2b183f..ed4025e 100644 --- a/rust/crates/du-web/templates/base.html +++ b/rust/crates/du-web/templates/base.html @@ -7,6 +7,7 @@ + {% block head %}{% endblock %} diff --git a/rust/crates/du-web/templates/curator/dashboard.html b/rust/crates/du-web/templates/curator/dashboard.html new file mode 100644 index 0000000..a5550bf --- /dev/null +++ b/rust/crates/du-web/templates/curator/dashboard.html @@ -0,0 +1,11 @@ +{% extends "base.html" %} +{% block title %}{{ t.get("curator.title") }} — {{ t.get("app.name") }}{% endblock %} +{% block content %} +

{{ t.get("curator.title") }}

+

{{ t.get("curator.welcome") }} {{ display_name }} · {{ t.get("curator.roles") }}: {{ roles }}

+
+ + {{ t.get("curator.tool.haplogroups") }} + +
+{% endblock %} diff --git a/rust/crates/du-web/templates/curator/haplogroups/detail.html b/rust/crates/du-web/templates/curator/haplogroups/detail.html new file mode 100644 index 0000000..4139830 --- /dev/null +++ b/rust/crates/du-web/templates/curator/haplogroups/detail.html @@ -0,0 +1,25 @@ +{# Fragment: haplogroup detail + actions. Target of #hg-detail. #} +
+
+ {{ hg.name }} + {{ hg.dna }} +
+
+ {% if let Some(err) = error %}
{{ err }}
{% endif %} +
+
{{ t.get("hg.field.lineage") }}
{{ hg.lineage }}
+
{{ t.get("hg.field.source") }}
{{ hg.source }}
+
{{ t.get("hg.field.formed") }}
{{ hg.formed_ybp }}
+
{{ t.get("hg.field.tmrca") }}
{{ hg.tmrca_ybp }}
+
+
+ + {% if can_delete %} + + {% endif %} +
+
+
diff --git a/rust/crates/du-web/templates/curator/haplogroups/empty.html b/rust/crates/du-web/templates/curator/haplogroups/empty.html new file mode 100644 index 0000000..29ca6a1 --- /dev/null +++ b/rust/crates/du-web/templates/curator/haplogroups/empty.html @@ -0,0 +1,2 @@ +{# Shown in #hg-detail after a deletion. #} +

{{ t.get("hg.select") }}

diff --git a/rust/crates/du-web/templates/curator/haplogroups/form.html b/rust/crates/du-web/templates/curator/haplogroups/form.html new file mode 100644 index 0000000..0965a3a --- /dev/null +++ b/rust/crates/du-web/templates/curator/haplogroups/form.html @@ -0,0 +1,48 @@ +{# Fragment: create/edit form. Posts to {action}, swaps #hg-detail with the saved + panel; the server's HX-Trigger then reloads the list. Target of #hg-detail. #} +
+
{% if is_edit %}{{ t.get("hg.edit") }}{% else %}{{ t.get("hg.new") }}{% endif %}
+
+
+
+ + +
+
+ + +
+
+ + +
+
+ + +
+
+
+ + +
+
+ + +
+
+
+ + {% if is_edit %} + + {% else %} + + {% endif %} +
+
+
+
diff --git a/rust/crates/du-web/templates/curator/haplogroups/list.html b/rust/crates/du-web/templates/curator/haplogroups/list.html new file mode 100644 index 0000000..09b7e94 --- /dev/null +++ b/rust/crates/du-web/templates/curator/haplogroups/list.html @@ -0,0 +1,30 @@ +{# Fragment: haplogroup rows + pager. Target of #hg-table. #} + + + + + + {% for r in list.rows %} + + + + + + {% else %} + + {% endfor %} + +
{{ t.get("hg.col.name") }}{{ t.get("hg.col.type") }}{{ t.get("hg.col.lineage") }}
{{ r.name }}{{ r.dna }}{{ r.lineage }}
{{ t.get("hg.none") }}
+{% if list.total_pages > 1 %} + +{% else %} +{{ list.total }} {{ t.get("pagination.total") }} +{% endif %} diff --git a/rust/crates/du-web/templates/curator/haplogroups/page.html b/rust/crates/du-web/templates/curator/haplogroups/page.html new file mode 100644 index 0000000..a1c83fd --- /dev/null +++ b/rust/crates/du-web/templates/curator/haplogroups/page.html @@ -0,0 +1,39 @@ +{% extends "base.html" %} +{% block title %}{{ t.get("hg.title") }} — {{ t.get("app.name") }}{% endblock %} +{% block content %} +
+

{{ t.get("hg.title") }}

+ +
+
+
+
+ + +
+ {# Reloads on load and whenever a mutation fires hg-changed on the body. #} +
+ {% include "curator/haplogroups/list.html" %} +
+
+
+
+

{{ t.get("hg.select") }}

+
+
+
+{% endblock %} diff --git a/rust/locales/en.txt b/rust/locales/en.txt index 56285d6..0d699d7 100644 --- a/rust/locales/en.txt +++ b/rust/locales/en.txt @@ -7,6 +7,9 @@ nav.variants=Variants nav.references=References nav.map=Map nav.coverage=Coverage +nav.curator=Curator +nav.login=Login +nav.logout=Logout lang.label=Language lang.en=English lang.es=Español @@ -78,3 +81,36 @@ coverage.col.meanDepth=Mean depth coverage.col.cov10x=Coverage ≥10× coverage.col.expectedDepth=Expected coverage.none=No coverage data yet. + +auth.login.title=Sign in +auth.login.handle=Handle or email +auth.login.password=Password +auth.login.submit=Sign in +auth.login.error=Invalid handle or password. + +curator.title=Curator Dashboard +curator.welcome=Signed in as +curator.roles=Roles +curator.tool.haplogroups=Haplogroups + +hg.title=Haplogroups +hg.new=New haplogroup +hg.search=Search by name… +hg.filter.all=All lineages +hg.col.name=Name +hg.col.type=Lineage +hg.col.lineage=Path +hg.none=No haplogroups match. +hg.select=Select a haplogroup, or create one. +hg.field.name=Name +hg.field.type=Lineage +hg.field.lineage=Path +hg.field.source=Source +hg.field.formed=Formed (ybp) +hg.field.tmrca=TMRCA (ybp) +hg.save=Save +hg.cancel=Cancel +hg.edit=Edit +hg.delete=Delete +hg.delete.confirm=Delete this haplogroup? +hg.deleteBlocked=Cannot delete: it still has tree relationships. diff --git a/rust/locales/es.txt b/rust/locales/es.txt index cb526ff..d92d9b9 100644 --- a/rust/locales/es.txt +++ b/rust/locales/es.txt @@ -7,6 +7,9 @@ nav.variants=Variantes nav.references=Referencias nav.map=Mapa nav.coverage=Cobertura +nav.curator=Curador +nav.login=Iniciar sesión +nav.logout=Cerrar sesión lang.label=Idioma lang.en=English lang.es=Español @@ -78,3 +81,36 @@ coverage.col.meanDepth=Profundidad media coverage.col.cov10x=Cobertura ≥10× coverage.col.expectedDepth=Esperada coverage.none=Aún no hay datos de cobertura. + +auth.login.title=Iniciar sesión +auth.login.handle=Usuario o correo +auth.login.password=Contraseña +auth.login.submit=Iniciar sesión +auth.login.error=Usuario o contraseña no válidos. + +curator.title=Panel del curador +curator.welcome=Sesión iniciada como +curator.roles=Roles +curator.tool.haplogroups=Haplogrupos + +hg.title=Haplogrupos +hg.new=Nuevo haplogrupo +hg.search=Buscar por nombre… +hg.filter.all=Todos los linajes +hg.col.name=Nombre +hg.col.type=Linaje +hg.col.lineage=Ruta +hg.none=No hay haplogrupos coincidentes. +hg.select=Seleccione un haplogrupo o cree uno. +hg.field.name=Nombre +hg.field.type=Linaje +hg.field.lineage=Ruta +hg.field.source=Fuente +hg.field.formed=Formado (ybp) +hg.field.tmrca=TMRCA (ybp) +hg.save=Guardar +hg.cancel=Cancelar +hg.edit=Editar +hg.delete=Eliminar +hg.delete.confirm=¿Eliminar este haplogrupo? +hg.deleteBlocked=No se puede eliminar: aún tiene relaciones en el árbol. diff --git a/rust/locales/fr.txt b/rust/locales/fr.txt index 69810d8..bce5705 100644 --- a/rust/locales/fr.txt +++ b/rust/locales/fr.txt @@ -7,6 +7,9 @@ nav.variants=Variants nav.references=Références nav.map=Carte nav.coverage=Couverture +nav.curator=Curateur +nav.login=Connexion +nav.logout=Déconnexion lang.label=Langue lang.en=English lang.es=Español @@ -78,3 +81,36 @@ coverage.col.meanDepth=Profondeur moyenne coverage.col.cov10x=Couverture ≥10× coverage.col.expectedDepth=Attendue coverage.none=Aucune donnée de couverture pour le moment. + +auth.login.title=Connexion +auth.login.handle=Identifiant ou e-mail +auth.login.password=Mot de passe +auth.login.submit=Se connecter +auth.login.error=Identifiant ou mot de passe invalide. + +curator.title=Tableau de bord du curateur +curator.welcome=Connecté en tant que +curator.roles=Rôles +curator.tool.haplogroups=Haplogroupes + +hg.title=Haplogroupes +hg.new=Nouvel haplogroupe +hg.search=Rechercher par nom… +hg.filter.all=Toutes les lignées +hg.col.name=Nom +hg.col.type=Lignée +hg.col.lineage=Chemin +hg.none=Aucun haplogroupe correspondant. +hg.select=Sélectionnez un haplogroupe ou créez-en un. +hg.field.name=Nom +hg.field.type=Lignée +hg.field.lineage=Chemin +hg.field.source=Source +hg.field.formed=Formé (ybp) +hg.field.tmrca=TMRCA (ybp) +hg.save=Enregistrer +hg.cancel=Annuler +hg.edit=Modifier +hg.delete=Supprimer +hg.delete.confirm=Supprimer cet haplogroupe ? +hg.deleteBlocked=Suppression impossible : des relations d’arbre existent encore. From 44411842781c8c24698189d80b45448e0796307c Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 09:51:02 -0500 Subject: [PATCH 009/191] feat(rust): extend curator to variants + genome regions Two more curator surfaces on the established two-panel HTMX write-flow. Variants: - du-db variant: create/update/delete + is_referenced (guards delete when the variant defines a current haplogroup association). - Curator variant CRUD editing scalar fields + alias lists (common_names/rs_ids as comma-separated, stored into the aliases JSONB); coordinates preserved. Genome regions: - du-domain GenomeRegion; du-db genome_region list/get/create/update/delete. - Curator region CRUD with JSON textareas for the coordinates/properties JSONB documents, parse-validated: invalid JSON re-renders the form with an error and no HX-Trigger (so the list does not reload on failure). - Mutations fire distinct HX-Trigger events (variant-changed / region-changed); dashboard links to all three tools; i18n var.*/region.* across en/es/fr (the catalog-coverage test enforces es/fr parity). Verified live (as the seeded curator): variant create stores aliases JSONB + trigger + delete; region create stores coordinates JSONB, invalid-JSON error path, list + delete. Workspace 11/11 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/crates/du-db/src/genome_region.rs | 125 +++++++ rust/crates/du-db/src/lib.rs | 1 + rust/crates/du-db/src/variant.rs | 73 +++- rust/crates/du-domain/src/genome_region.rs | 14 + rust/crates/du-domain/src/lib.rs | 1 + .../du-web/src/routes/curator_regions.rs | 301 ++++++++++++++++ .../du-web/src/routes/curator_variants.rs | 322 ++++++++++++++++++ rust/crates/du-web/src/routes/mod.rs | 4 + .../du-web/templates/curator/dashboard.html | 6 + .../templates/curator/regions/detail.html | 18 + .../templates/curator/regions/empty.html | 1 + .../templates/curator/regions/form.html | 35 ++ .../templates/curator/regions/list.html | 26 ++ .../templates/curator/regions/page.html | 27 ++ .../templates/curator/variants/detail.html | 23 ++ .../templates/curator/variants/empty.html | 1 + .../templates/curator/variants/form.html | 49 +++ .../templates/curator/variants/list.html | 26 ++ .../templates/curator/variants/page.html | 27 ++ rust/locales/en.txt | 41 +++ rust/locales/es.txt | 41 +++ rust/locales/fr.txt | 41 +++ 22 files changed, 1202 insertions(+), 1 deletion(-) create mode 100644 rust/crates/du-db/src/genome_region.rs create mode 100644 rust/crates/du-domain/src/genome_region.rs create mode 100644 rust/crates/du-web/src/routes/curator_regions.rs create mode 100644 rust/crates/du-web/src/routes/curator_variants.rs create mode 100644 rust/crates/du-web/templates/curator/regions/detail.html create mode 100644 rust/crates/du-web/templates/curator/regions/empty.html create mode 100644 rust/crates/du-web/templates/curator/regions/form.html create mode 100644 rust/crates/du-web/templates/curator/regions/list.html create mode 100644 rust/crates/du-web/templates/curator/regions/page.html create mode 100644 rust/crates/du-web/templates/curator/variants/detail.html create mode 100644 rust/crates/du-web/templates/curator/variants/empty.html create mode 100644 rust/crates/du-web/templates/curator/variants/form.html create mode 100644 rust/crates/du-web/templates/curator/variants/list.html create mode 100644 rust/crates/du-web/templates/curator/variants/page.html diff --git a/rust/crates/du-db/src/genome_region.rs b/rust/crates/du-db/src/genome_region.rs new file mode 100644 index 0000000..71b7472 --- /dev/null +++ b/rust/crates/du-db/src/genome_region.rs @@ -0,0 +1,125 @@ +//! Queries for `core.genome_region` (curator-managed multi-build regions). + +use crate::{DbError, Page}; +use du_domain::genome_region::GenomeRegion; +use sqlx::PgPool; + +#[derive(sqlx::FromRow)] +struct RegionRow { + id: i64, + region_type: String, + name: String, + coordinates: serde_json::Value, + properties: serde_json::Value, +} + +impl From for GenomeRegion { + fn from(r: RegionRow) -> Self { + GenomeRegion { + id: r.id, + region_type: r.region_type, + name: r.name, + coordinates: r.coordinates, + properties: r.properties, + } + } +} + +const SELECT: &str = "SELECT id, region_type, name, coordinates, properties FROM core.genome_region"; + +pub async fn get_by_id(pool: &PgPool, id: i64) -> Result, DbError> { + let row: Option = sqlx::query_as(&format!("{SELECT} WHERE id = $1")) + .bind(id) + .fetch_optional(pool) + .await?; + Ok(row.map(Into::into)) +} + +/// Paginated list, optionally filtered by name/type substring and region type. +pub async fn list_paginated( + pool: &PgPool, + query: Option<&str>, + region_type: Option<&str>, + page: i64, + page_size: i64, +) -> Result, DbError> { + let offset = Page::<()>::offset(page, page_size); + let limit = page_size.clamp(1, 200); + let like = query.map(str::trim).filter(|q| !q.is_empty()).map(|q| format!("%{q}%")); + let rtype = region_type.map(str::trim).filter(|q| !q.is_empty()).map(str::to_string); + + let where_sql = "WHERE ($1::text IS NULL OR name ILIKE $1 OR region_type ILIKE $1) \ + AND ($2::text IS NULL OR region_type = $2)"; + + let total: i64 = sqlx::query_scalar(&format!("SELECT count(*) FROM core.genome_region {where_sql}")) + .bind(&like) + .bind(&rtype) + .fetch_one(pool) + .await?; + let rows: Vec = + sqlx::query_as(&format!("{SELECT} {where_sql} ORDER BY region_type, name LIMIT $3 OFFSET $4")) + .bind(&like) + .bind(&rtype) + .bind(limit) + .bind(offset) + .fetch_all(pool) + .await?; + + Ok(Page { + items: rows.into_iter().map(Into::into).collect(), + total, + page: page.max(1), + page_size: limit, + }) +} + +pub async fn create( + pool: &PgPool, + region_type: &str, + name: &str, + coordinates: &serde_json::Value, + properties: &serde_json::Value, +) -> Result { + let id: i64 = sqlx::query_scalar( + "INSERT INTO core.genome_region (region_type, name, coordinates, properties) \ + VALUES ($1, $2, $3, $4) RETURNING id", + ) + .bind(region_type) + .bind(name) + .bind(coordinates) + .bind(properties) + .fetch_one(pool) + .await?; + Ok(id) +} + +pub async fn update( + pool: &PgPool, + id: i64, + region_type: &str, + name: &str, + coordinates: &serde_json::Value, + properties: &serde_json::Value, +) -> Result { + let affected = sqlx::query( + "UPDATE core.genome_region SET region_type=$2, name=$3, coordinates=$4, properties=$5, updated_at=now() WHERE id=$1", + ) + .bind(id) + .bind(region_type) + .bind(name) + .bind(coordinates) + .bind(properties) + .execute(pool) + .await? + .rows_affected(); + Ok(affected > 0) +} + +pub async fn delete(pool: &PgPool, id: i64) -> Result { + let affected = sqlx::query("DELETE FROM core.genome_region WHERE id=$1") + .bind(id) + .execute(pool) + .await? + .rows_affected(); + Ok(affected > 0) +} diff --git a/rust/crates/du-db/src/lib.rs b/rust/crates/du-db/src/lib.rs index b50e635..7e6ad3d 100644 --- a/rust/crates/du-db/src/lib.rs +++ b/rust/crates/du-db/src/lib.rs @@ -12,6 +12,7 @@ use thiserror::Error; pub mod auth; pub mod biosample; pub mod coverage; +pub mod genome_region; pub mod haplogroup; pub mod pagination; pub mod publication; diff --git a/rust/crates/du-db/src/variant.rs b/rust/crates/du-db/src/variant.rs index 529ba24..1c42ce4 100644 --- a/rust/crates/du-db/src/variant.rs +++ b/rust/crates/du-db/src/variant.rs @@ -2,7 +2,8 @@ //! enum columns are fetched as `::text` and parsed via serde; JSONB columns are //! read through `sqlx::types::Json` into the du-domain payload structs. -use crate::{parse_pg_enum, DbError, Page}; +use crate::{parse_pg_enum, pg_enum_label, DbError, Page}; +use du_domain::enums::{MutationType, NamingStatus}; use du_domain::ids::VariantId; use du_domain::variant::{Aliases, Annotations, Coordinates, Variant}; use sqlx::types::Json; @@ -44,6 +45,76 @@ pub async fn get_by_id(pool: &PgPool, id: VariantId) -> Result, row.map(VariantRow::into_domain).transpose() } +/// Create a variant (scalar fields + aliases; coordinates/annotations default +/// empty and are managed elsewhere). Returns the new id. +pub async fn create( + pool: &PgPool, + canonical_name: &str, + mutation_type: MutationType, + naming_status: NamingStatus, + aliases: &Aliases, +) -> Result { + let aliases_json = serde_json::to_value(aliases).map_err(|e| DbError::Decode(e.to_string()))?; + let id: i64 = sqlx::query_scalar( + "INSERT INTO core.variant (canonical_name, mutation_type, naming_status, aliases) \ + VALUES ($1, $2::core.mutation_type, $3::core.naming_status, $4) RETURNING id", + ) + .bind(canonical_name) + .bind(pg_enum_label(&mutation_type)?) + .bind(pg_enum_label(&naming_status)?) + .bind(aliases_json) + .fetch_one(pool) + .await?; + Ok(VariantId(id)) +} + +/// Update a variant's scalar fields + aliases. Coordinates and annotations are +/// left untouched. Returns whether a row was affected. +pub async fn update( + pool: &PgPool, + id: VariantId, + canonical_name: &str, + mutation_type: MutationType, + naming_status: NamingStatus, + aliases: &Aliases, +) -> Result { + let aliases_json = serde_json::to_value(aliases).map_err(|e| DbError::Decode(e.to_string()))?; + let affected = sqlx::query( + "UPDATE core.variant SET canonical_name=$2, mutation_type=$3::core.mutation_type, \ + naming_status=$4::core.naming_status, aliases=$5, updated_at=now() WHERE id=$1", + ) + .bind(id.0) + .bind(canonical_name) + .bind(pg_enum_label(&mutation_type)?) + .bind(pg_enum_label(&naming_status)?) + .bind(aliases_json) + .execute(pool) + .await? + .rows_affected(); + Ok(affected > 0) +} + +/// Whether the variant is referenced by a current haplogroup association +/// (a guard before deletion). +pub async fn is_referenced(pool: &PgPool, id: VariantId) -> Result { + let n: i64 = sqlx::query_scalar( + "SELECT count(*) FROM tree.haplogroup_variant WHERE variant_id = $1 AND valid_until IS NULL", + ) + .bind(id.0) + .fetch_one(pool) + .await?; + Ok(n > 0) +} + +pub async fn delete(pool: &PgPool, id: VariantId) -> Result { + let affected = sqlx::query("DELETE FROM core.variant WHERE id=$1") + .bind(id.0) + .execute(pool) + .await? + .rows_affected(); + Ok(affected > 0) +} + /// Paginated search by canonical name OR any alias in the `common_names`/`rs_ids` /// JSONB arrays (the public variant browser). `query = None`/empty lists all. pub async fn search( diff --git a/rust/crates/du-domain/src/genome_region.rs b/rust/crates/du-domain/src/genome_region.rs new file mode 100644 index 0000000..7d43757 --- /dev/null +++ b/rust/crates/du-domain/src/genome_region.rs @@ -0,0 +1,14 @@ +//! Genome region domain type — multi-build structural regions (centromere, +//! telomere, PAR, …). Coordinates and properties are JSONB documents keyed by +//! reference build, e.g. `{ "GRCh38": {contig, start, end}, "hs1": {...} }`. + +use serde::{Deserialize, Serialize}; + +#[derive(Debug, Clone, Serialize, Deserialize)] +pub struct GenomeRegion { + pub id: i64, + pub region_type: String, + pub name: String, + pub coordinates: serde_json::Value, + pub properties: serde_json::Value, +} diff --git a/rust/crates/du-domain/src/lib.rs b/rust/crates/du-domain/src/lib.rs index e3d130f..ab9a428 100644 --- a/rust/crates/du-domain/src/lib.rs +++ b/rust/crates/du-domain/src/lib.rs @@ -9,6 +9,7 @@ pub mod biosample; pub mod coverage; pub mod enums; pub mod error; +pub mod genome_region; pub mod haplogroup; pub mod ids; pub mod publication; diff --git a/rust/crates/du-web/src/routes/curator_regions.rs b/rust/crates/du-web/src/routes/curator_regions.rs new file mode 100644 index 0000000..ed55f38 --- /dev/null +++ b/rust/crates/du-web/src/routes/curator_regions.rs @@ -0,0 +1,301 @@ +//! Curator genome-region CRUD. The multi-build `coordinates` and `properties` +//! are JSONB documents, edited here as JSON textareas (parse-validated on save, +//! re-rendering the form with an error on invalid JSON). + +use crate::auth::Curator; +use crate::error::AppError; +use crate::htmx::HxHeaders; +use crate::i18n::{Locale, T}; +use crate::render::html; +use crate::state::AppState; +use axum::extract::{Path, Query, State}; +use axum::response::{IntoResponse, Response}; +use axum::routing::{get, post}; +use axum::{Form, Router}; +use serde::Deserialize; + +const CHANGED: &str = "region-changed"; + +pub fn router() -> Router { + Router::new() + .route("/curator/regions", get(page)) + .route("/curator/regions/fragment", get(list)) + .route("/curator/regions/new", get(new_form)) + .route("/curator/regions", post(create)) + .route("/curator/regions/:id/panel", get(panel)) + .route("/curator/regions/:id/edit", get(edit_form)) + .route("/curator/regions/:id", post(update)) + .route("/curator/regions/:id", axum::routing::delete(remove)) +} + +#[derive(Deserialize)] +struct ListQuery { + query: Option, + page: Option, +} + +struct Row { + id: i64, + region_type: String, + name: String, + builds: String, +} +struct ListView { + query: String, + rows: Vec, + page: i64, + total: i64, + total_pages: i64, +} + +/// Top-level keys of a JSONB object, comma-joined (the build labels). +fn keys_of(v: &serde_json::Value) -> String { + v.as_object() + .map(|o| o.keys().cloned().collect::>().join(", ")) + .unwrap_or_default() +} + +async fn load_list(st: &AppState, q: &ListQuery) -> Result { + let result = + du_db::genome_region::list_paginated(&st.pool, q.query.as_deref(), None, q.page.unwrap_or(1), 20).await?; + Ok(ListView { + query: q.query.clone().unwrap_or_default(), + rows: result + .items + .iter() + .map(|r| Row { + id: r.id, + region_type: r.region_type.clone(), + name: r.name.clone(), + builds: keys_of(&r.coordinates), + }) + .collect(), + page: result.page, + total: result.total, + total_pages: result.total_pages(), + }) +} + +#[derive(askama::Template)] +#[template(path = "curator/regions/page.html")] +struct PageTemplate { + t: T, + next: String, + user: Option, + list: ListView, +} +#[derive(askama::Template)] +#[template(path = "curator/regions/list.html")] +struct ListTemplate { + t: T, + list: ListView, +} + +async fn page( + Curator(s): Curator, + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&PageTemplate { + t: locale.t, + next: locale.next, + user: Some(crate::auth::NavUser { display_name: s.display_name, is_curator: true }), + list, + })) +} + +async fn list( + _c: Curator, + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&ListTemplate { t: locale.t, list })) +} + +#[derive(askama::Template)] +#[template(path = "curator/regions/detail.html")] +struct DetailTemplate { + t: T, + id: i64, + region_type: String, + name: String, + coordinates: String, + properties: String, +} + +fn pretty(v: &serde_json::Value) -> String { + serde_json::to_string_pretty(v).unwrap_or_else(|_| "{}".into()) +} + +async fn detail(st: &AppState, t: T, id: i64) -> Result { + let r = du_db::genome_region::get_by_id(&st.pool, id) + .await? + .ok_or_else(|| AppError::NotFound(format!("region {id}")))?; + Ok(html(&DetailTemplate { + t, + id: r.id, + region_type: r.region_type, + name: r.name, + coordinates: pretty(&r.coordinates), + properties: pretty(&r.properties), + })) +} + +async fn panel( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { + detail(&st, locale.t, id).await +} + +#[derive(askama::Template)] +#[template(path = "curator/regions/form.html")] +struct FormTemplate { + t: T, + action: String, + is_edit: bool, + id: i64, + region_type: String, + name: String, + coordinates: String, + properties: String, + error: Option, +} + +async fn new_form(_c: Curator, locale: Locale) -> Response { + html(&FormTemplate { + t: locale.t, + action: "/curator/regions".into(), + is_edit: false, + id: 0, + region_type: String::new(), + name: String::new(), + coordinates: "{\n \"GRCh38\": { \"contig\": \"chr1\", \"start\": 0, \"end\": 0 }\n}".into(), + properties: "{}".into(), + error: None, + }) +} + +async fn edit_form( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { + let r = du_db::genome_region::get_by_id(&st.pool, id) + .await? + .ok_or_else(|| AppError::NotFound(format!("region {id}")))?; + Ok(html(&FormTemplate { + t: locale.t, + action: format!("/curator/regions/{id}"), + is_edit: true, + id, + region_type: r.region_type, + name: r.name, + coordinates: pretty(&r.coordinates), + properties: pretty(&r.properties), + error: None, + })) +} + +#[derive(Deserialize)] +struct RegionForm { + region_type: String, + name: String, + coordinates: String, + properties: String, +} + +fn changed(body: Response) -> Response { + (HxHeaders::new().trigger(CHANGED), body).into_response() +} + +/// Parse the two JSON fields; on failure re-render the form with an error. +fn parse_json( + t: T, + action: String, + is_edit: bool, + id: i64, + f: &RegionForm, +) -> Result<(serde_json::Value, serde_json::Value), Response> { + let coords = serde_json::from_str::(&f.coordinates); + let props = serde_json::from_str::(&f.properties); + match (coords, props) { + (Ok(c), Ok(p)) => Ok((c, p)), + (c, p) => { + let mut msg = String::new(); + if let Err(e) = &c { + msg = format!("coordinates: {e}"); + } else if let Err(e) = &p { + msg = format!("properties: {e}"); + } + Err(html(&FormTemplate { + t, + action, + is_edit, + id, + region_type: f.region_type.clone(), + name: f.name.clone(), + coordinates: f.coordinates.clone(), + properties: f.properties.clone(), + error: Some(msg), + })) + } + } +} + +async fn create( + _c: Curator, + State(st): State, + locale: Locale, + Form(f): Form, +) -> Result { + if f.name.trim().is_empty() || f.region_type.trim().is_empty() { + return Err(AppError::BadRequest("region_type and name are required".into())); + } + let (coords, props) = match parse_json(locale.t, "/curator/regions".into(), false, 0, &f) { + Ok(v) => v, + Err(resp) => return Ok(resp), + }; + let id = du_db::genome_region::create(&st.pool, f.region_type.trim(), f.name.trim(), &coords, &props).await?; + Ok(changed(detail(&st, locale.t, id).await?)) +} + +async fn update( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, + Form(f): Form, +) -> Result { + if f.name.trim().is_empty() || f.region_type.trim().is_empty() { + return Err(AppError::BadRequest("region_type and name are required".into())); + } + let (coords, props) = match parse_json(locale.t, format!("/curator/regions/{id}"), true, id, &f) { + Ok(v) => v, + Err(resp) => return Ok(resp), + }; + du_db::genome_region::update(&st.pool, id, f.region_type.trim(), f.name.trim(), &coords, &props).await?; + Ok(changed(detail(&st, locale.t, id).await?)) +} + +async fn remove( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { + du_db::genome_region::delete(&st.pool, id).await?; + #[derive(askama::Template)] + #[template(path = "curator/regions/empty.html")] + struct Empty { + t: T, + } + Ok(changed(html(&Empty { t: locale.t }))) +} diff --git a/rust/crates/du-web/src/routes/curator_variants.rs b/rust/crates/du-web/src/routes/curator_variants.rs new file mode 100644 index 0000000..aadbfb9 --- /dev/null +++ b/rust/crates/du-web/src/routes/curator_variants.rs @@ -0,0 +1,322 @@ +//! Curator variant CRUD. Same HTMX two-panel write-flow as haplogroups; edits +//! the scalar fields + alias lists (common_names / rs_ids). Coordinate editing +//! is out of scope for this panel and is preserved across updates. + +use crate::auth::Curator; +use crate::error::AppError; +use crate::htmx::HxHeaders; +use crate::i18n::{Locale, T}; +use crate::render::html; +use crate::state::AppState; +use axum::extract::{Path, Query, State}; +use axum::response::{IntoResponse, Response}; +use axum::routing::{get, post}; +use axum::{Form, Router}; +use du_domain::enums::{MutationType, NamingStatus}; +use du_domain::ids::VariantId; +use du_domain::variant::Aliases; +use serde::Deserialize; + +const CHANGED: &str = "variant-changed"; + +pub fn router() -> Router { + Router::new() + .route("/curator/variants", get(page)) + .route("/curator/variants/fragment", get(list)) + .route("/curator/variants/new", get(new_form)) + .route("/curator/variants", post(create)) + .route("/curator/variants/:id/panel", get(panel)) + .route("/curator/variants/:id/edit", get(edit_form)) + .route("/curator/variants/:id", post(update)) + .route("/curator/variants/:id", axum::routing::delete(remove)) +} + +fn parse_mutation(s: &str) -> MutationType { + match s { + "INDEL" => MutationType::Indel, + "STR" => MutationType::Str, + "DEL" => MutationType::Del, + "INS" => MutationType::Ins, + "MNP" => MutationType::Mnp, + _ => MutationType::Snp, + } +} +fn parse_naming(s: &str) -> NamingStatus { + match s { + "NAMED" => NamingStatus::Named, + "PENDING_REVIEW" => NamingStatus::PendingReview, + _ => NamingStatus::Unnamed, + } +} +/// "a, b ,c" -> ["a","b","c"] +fn csv(s: Option) -> Vec { + s.unwrap_or_default() + .split(',') + .map(|t| t.trim().to_string()) + .filter(|t| !t.is_empty()) + .collect() +} + +#[derive(Deserialize)] +struct ListQuery { + query: Option, + page: Option, +} + +struct Row { + id: i64, + name: String, + mutation_type: String, + naming_status: String, +} +struct ListView { + query: String, + rows: Vec, + page: i64, + total: i64, + total_pages: i64, +} + +async fn load_list(st: &AppState, q: &ListQuery) -> Result { + let result = du_db::variant::search(&st.pool, q.query.as_deref(), q.page.unwrap_or(1), 20).await?; + Ok(ListView { + query: q.query.clone().unwrap_or_default(), + rows: result + .items + .iter() + .map(|v| Row { + id: v.id.0, + name: v.canonical_name.clone(), + mutation_type: v.mutation_type.label().to_string(), + naming_status: v.naming_status.label().to_string(), + }) + .collect(), + page: result.page, + total: result.total, + total_pages: result.total_pages(), + }) +} + +#[derive(askama::Template)] +#[template(path = "curator/variants/page.html")] +struct PageTemplate { + t: T, + next: String, + user: Option, + list: ListView, +} + +#[derive(askama::Template)] +#[template(path = "curator/variants/list.html")] +struct ListTemplate { + t: T, + list: ListView, +} + +async fn page( + Curator(s): Curator, + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&PageTemplate { + t: locale.t, + next: locale.next, + user: Some(crate::auth::NavUser { display_name: s.display_name, is_curator: true }), + list, + })) +} + +async fn list( + _c: Curator, + State(st): State, + locale: Locale, + Query(q): Query, +) -> Result { + let list = load_list(&st, &q).await?; + Ok(html(&ListTemplate { t: locale.t, list })) +} + +struct DetailView { + id: i64, + name: String, + mutation_type: String, + naming_status: String, + common_names: String, + rs_ids: String, + builds: String, +} + +#[derive(askama::Template)] +#[template(path = "curator/variants/detail.html")] +struct DetailTemplate { + t: T, + v: DetailView, + can_delete: bool, + error: Option, +} + +async fn detail_view(st: &AppState, id: VariantId) -> Result { + let v = du_db::variant::get_by_id(&st.pool, id) + .await? + .ok_or_else(|| AppError::NotFound(format!("variant {}", id.0)))?; + let mut builds: Vec<&str> = v.coordinates.0.keys().map(String::as_str).collect(); + builds.sort_unstable(); + Ok(DetailView { + id: v.id.0, + name: v.canonical_name, + mutation_type: v.mutation_type.label().to_string(), + naming_status: v.naming_status.label().to_string(), + common_names: v.aliases.common_names.join(", "), + rs_ids: v.aliases.rs_ids.join(", "), + builds: builds.join(", "), + }) +} + +async fn render_detail(st: &AppState, t: T, id: VariantId, error: Option) -> Result { + let v = detail_view(st, id).await?; + let can_delete = !du_db::variant::is_referenced(&st.pool, id).await?; + Ok(html(&DetailTemplate { t, v, can_delete, error })) +} + +async fn panel( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { + render_detail(&st, locale.t, VariantId(id), None).await +} + +#[derive(askama::Template)] +#[template(path = "curator/variants/form.html")] +struct FormTemplate { + t: T, + action: String, + is_edit: bool, + id: i64, + name: String, + mutation_type: String, + naming_status: String, + common_names: String, + rs_ids: String, +} + +async fn new_form(_c: Curator, locale: Locale) -> Response { + html(&FormTemplate { + t: locale.t, + action: "/curator/variants".into(), + is_edit: false, + id: 0, + name: String::new(), + mutation_type: "SNP".into(), + naming_status: "UNNAMED".into(), + common_names: String::new(), + rs_ids: String::new(), + }) +} + +async fn edit_form( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { + let d = detail_view(&st, VariantId(id)).await?; + Ok(html(&FormTemplate { + t: locale.t, + action: format!("/curator/variants/{id}"), + is_edit: true, + id, + name: d.name, + mutation_type: d.mutation_type, + naming_status: d.naming_status, + common_names: d.common_names, + rs_ids: d.rs_ids, + })) +} + +#[derive(Deserialize)] +struct VariantForm { + name: String, + mutation_type: Option, + naming_status: Option, + common_names: Option, + rs_ids: Option, +} + +fn aliases_from(form: &VariantForm) -> Aliases { + Aliases { + common_names: csv(form.common_names.clone()), + rs_ids: csv(form.rs_ids.clone()), + ..Default::default() + } +} + +fn changed(body: Response) -> Response { + (HxHeaders::new().trigger(CHANGED), body).into_response() +} + +async fn create( + _c: Curator, + State(st): State, + locale: Locale, + Form(f): Form, +) -> Result { + if f.name.trim().is_empty() { + return Err(AppError::BadRequest("name is required".into())); + } + let id = du_db::variant::create( + &st.pool, + f.name.trim(), + parse_mutation(f.mutation_type.as_deref().unwrap_or("SNP")), + parse_naming(f.naming_status.as_deref().unwrap_or("UNNAMED")), + &aliases_from(&f), + ) + .await?; + Ok(changed(render_detail(&st, locale.t, id, None).await?)) +} + +async fn update( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, + Form(f): Form, +) -> Result { + if f.name.trim().is_empty() { + return Err(AppError::BadRequest("name is required".into())); + } + du_db::variant::update( + &st.pool, + VariantId(id), + f.name.trim(), + parse_mutation(f.mutation_type.as_deref().unwrap_or("SNP")), + parse_naming(f.naming_status.as_deref().unwrap_or("UNNAMED")), + &aliases_from(&f), + ) + .await?; + Ok(changed(render_detail(&st, locale.t, VariantId(id), None).await?)) +} + +async fn remove( + _c: Curator, + State(st): State, + locale: Locale, + Path(id): Path, +) -> Result { + let vid = VariantId(id); + if du_db::variant::is_referenced(&st.pool, vid).await? { + let msg = locale.t.get("var.deleteBlocked").to_string(); + return render_detail(&st, locale.t, vid, Some(msg)).await; + } + du_db::variant::delete(&st.pool, vid).await?; + + #[derive(askama::Template)] + #[template(path = "curator/variants/empty.html")] + struct Empty { + t: T, + } + Ok(changed(html(&Empty { t: locale.t }))) +} diff --git a/rust/crates/du-web/src/routes/mod.rs b/rust/crates/du-web/src/routes/mod.rs index 77fa017..8294f3b 100644 --- a/rust/crates/du-web/src/routes/mod.rs +++ b/rust/crates/du-web/src/routes/mod.rs @@ -17,6 +17,8 @@ use tower_http::services::ServeDir; pub mod auth_routes; pub mod coverage; pub mod curator; +pub mod curator_regions; +pub mod curator_variants; pub mod maps; pub mod references; pub mod tree; @@ -43,6 +45,8 @@ pub fn app(state: AppState) -> Router { .merge(coverage::router()) .merge(auth_routes::router()) .merge(curator::router()) + .merge(curator_variants::router()) + .merge(curator_regions::router()) .nest_service("/assets", ServeDir::new(assets_dir())) .layer(CookieManagerLayer::new()) .with_state(state) diff --git a/rust/crates/du-web/templates/curator/dashboard.html b/rust/crates/du-web/templates/curator/dashboard.html index a5550bf..fa3864c 100644 --- a/rust/crates/du-web/templates/curator/dashboard.html +++ b/rust/crates/du-web/templates/curator/dashboard.html @@ -7,5 +7,11 @@

{{ t.get("curator.title") }}

{{ t.get("curator.tool.haplogroups") }} + + {{ t.get("curator.tool.variants") }} + + + {{ t.get("curator.tool.regions") }} + {% endblock %} diff --git a/rust/crates/du-web/templates/curator/regions/detail.html b/rust/crates/du-web/templates/curator/regions/detail.html new file mode 100644 index 0000000..fa752a1 --- /dev/null +++ b/rust/crates/du-web/templates/curator/regions/detail.html @@ -0,0 +1,18 @@ +{# Fragment: region detail + actions. Target of #region-detail. #} +
+
+ {{ name }} + {{ region_type }} +
+
+
{{ t.get("region.field.coordinates") }}
+ 
{{ coordinates }}
+
{{ t.get("region.field.properties") }}
+ 
{{ properties }}
+
+ + +
+
+
diff --git a/rust/crates/du-web/templates/curator/regions/empty.html b/rust/crates/du-web/templates/curator/regions/empty.html new file mode 100644 index 0000000..6401f8c --- /dev/null +++ b/rust/crates/du-web/templates/curator/regions/empty.html @@ -0,0 +1 @@ +

{{ t.get("region.select") }}

diff --git a/rust/crates/du-web/templates/curator/regions/form.html b/rust/crates/du-web/templates/curator/regions/form.html new file mode 100644 index 0000000..51da44b --- /dev/null +++ b/rust/crates/du-web/templates/curator/regions/form.html @@ -0,0 +1,35 @@ +{# Fragment: region create/edit form with JSON textareas. Target of #region-detail. #} +
+
{% if is_edit %}{{ t.get("region.edit") }}{% else %}{{ t.get("region.new") }}{% endif %}
+
+ {% if let Some(err) = error %}
{{ err }}
{% endif %} +
+
+
+ + +
+
+ + +
+
+
+ + +
+
+ + +
+
+ + {% if is_edit %} + + {% else %} + + {% endif %} +
+
+
+
diff --git a/rust/crates/du-web/templates/curator/regions/list.html b/rust/crates/du-web/templates/curator/regions/list.html new file mode 100644 index 0000000..e6a30d6 --- /dev/null +++ b/rust/crates/du-web/templates/curator/regions/list.html @@ -0,0 +1,26 @@ +{# Fragment: region rows + pager. Target of #region-table. #} + + + + {% for r in list.rows %} + + + + + + {% else %} + + {% endfor %} + +
{{ t.get("region.col.type") }}{{ t.get("region.col.name") }}{{ t.get("region.col.builds") }}
{{ r.region_type }}{{ r.name }}{{ r.builds }}
{{ t.get("region.none") }}
+{% if list.total_pages > 1 %} + +{% else %} +{{ list.total }} {{ t.get("pagination.total") }} +{% endif %} diff --git a/rust/crates/du-web/templates/curator/regions/page.html b/rust/crates/du-web/templates/curator/regions/page.html new file mode 100644 index 0000000..903e19f --- /dev/null +++ b/rust/crates/du-web/templates/curator/regions/page.html @@ -0,0 +1,27 @@ +{% extends "base.html" %} +{% block title %}{{ t.get("region.title") }} — {{ t.get("app.name") }}{% endblock %} +{% block content %} +
+

{{ t.get("region.title") }}

+ +
+
+
+ +
+ {% include "curator/regions/list.html" %} +
+
+
+

{{ t.get("region.select") }}

+
+
+{% endblock %} diff --git a/rust/crates/du-web/templates/curator/variants/detail.html b/rust/crates/du-web/templates/curator/variants/detail.html new file mode 100644 index 0000000..1e27615 --- /dev/null +++ b/rust/crates/du-web/templates/curator/variants/detail.html @@ -0,0 +1,23 @@ +{# Fragment: variant detail + actions. Target of #variant-detail. #} +
+
+ {{ v.name }} + {{ v.mutation_type }} +
+
+ {% if let Some(err) = error %}
{{ err }}
{% endif %} +
+
{{ t.get("var.field.status") }}
{{ v.naming_status }}
+
{{ t.get("var.field.commonNames") }}
{{ v.common_names }}
+
{{ t.get("var.field.rsIds") }}
{{ v.rs_ids }}
+
{{ t.get("var.field.builds") }}
{{ v.builds }}
+
+
+ + {% if can_delete %} + + {% endif %} +
+
+
diff --git a/rust/crates/du-web/templates/curator/variants/empty.html b/rust/crates/du-web/templates/curator/variants/empty.html new file mode 100644 index 0000000..7e3fd92 --- /dev/null +++ b/rust/crates/du-web/templates/curator/variants/empty.html @@ -0,0 +1 @@ +

{{ t.get("var.select") }}

diff --git a/rust/crates/du-web/templates/curator/variants/form.html b/rust/crates/du-web/templates/curator/variants/form.html new file mode 100644 index 0000000..641325c --- /dev/null +++ b/rust/crates/du-web/templates/curator/variants/form.html @@ -0,0 +1,49 @@ +{# Fragment: variant create/edit form. Target of #variant-detail. #} +
+
{% if is_edit %}{{ t.get("var.edit") }}{% else %}{{ t.get("var.new") }}{% endif %}
+
+
+
+ + +
+
+
+ + +
+
+ + +
+
+
+ + +
+
+ + +
+
+ + {% if is_edit %} + + {% else %} + + {% endif %} +
+
+
+
diff --git a/rust/crates/du-web/templates/curator/variants/list.html b/rust/crates/du-web/templates/curator/variants/list.html new file mode 100644 index 0000000..333cc2a --- /dev/null +++ b/rust/crates/du-web/templates/curator/variants/list.html @@ -0,0 +1,26 @@ +{# Fragment: variant rows + pager. Target of #variant-table. #} + + + + {% for r in list.rows %} + + + + + + {% else %} + + {% endfor %} + +
{{ t.get("var.col.name") }}{{ t.get("var.col.type") }}{{ t.get("var.col.status") }}
{{ r.name }}{{ r.mutation_type }}{{ r.naming_status }}
{{ t.get("var.none") }}
+{% if list.total_pages > 1 %} + +{% else %} +{{ list.total }} {{ t.get("pagination.total") }} +{% endif %} diff --git a/rust/crates/du-web/templates/curator/variants/page.html b/rust/crates/du-web/templates/curator/variants/page.html new file mode 100644 index 0000000..99a9e8c --- /dev/null +++ b/rust/crates/du-web/templates/curator/variants/page.html @@ -0,0 +1,27 @@ +{% extends "base.html" %} +{% block title %}{{ t.get("var.title") }} — {{ t.get("app.name") }}{% endblock %} +{% block content %} +
+

{{ t.get("var.title") }}

+ +
+
+
+ +
+ {% include "curator/variants/list.html" %} +
+
+
+

{{ t.get("var.select") }}

+
+
+{% endblock %} diff --git a/rust/locales/en.txt b/rust/locales/en.txt index 0d699d7..a06c687 100644 --- a/rust/locales/en.txt +++ b/rust/locales/en.txt @@ -92,6 +92,8 @@ curator.title=Curator Dashboard curator.welcome=Signed in as curator.roles=Roles curator.tool.haplogroups=Haplogroups +curator.tool.variants=Variants +curator.tool.regions=Genome regions hg.title=Haplogroups hg.new=New haplogroup @@ -114,3 +116,42 @@ hg.edit=Edit hg.delete=Delete hg.delete.confirm=Delete this haplogroup? hg.deleteBlocked=Cannot delete: it still has tree relationships. + +var.title=Variants +var.new=New variant +var.search=Search by name or alias… +var.col.name=Name +var.col.type=Type +var.col.status=Status +var.none=No variants match. +var.select=Select a variant, or create one. +var.field.name=Canonical name +var.field.type=Mutation type +var.field.status=Naming status +var.field.commonNames=Common names (comma-separated) +var.field.rsIds=rs IDs (comma-separated) +var.field.builds=Coordinate builds +var.save=Save +var.cancel=Cancel +var.edit=Edit +var.delete=Delete +var.delete.confirm=Delete this variant? +var.deleteBlocked=Cannot delete: it defines a haplogroup. + +region.title=Genome Regions +region.new=New region +region.search=Search by name or type… +region.col.type=Type +region.col.name=Name +region.col.builds=Builds +region.none=No regions match. +region.select=Select a region, or create one. +region.field.type=Region type +region.field.name=Name +region.field.coordinates=Coordinates (JSON) +region.field.properties=Properties (JSON) +region.save=Save +region.cancel=Cancel +region.edit=Edit +region.delete=Delete +region.delete.confirm=Delete this region? diff --git a/rust/locales/es.txt b/rust/locales/es.txt index d92d9b9..0e8a56f 100644 --- a/rust/locales/es.txt +++ b/rust/locales/es.txt @@ -92,6 +92,8 @@ curator.title=Panel del curador curator.welcome=Sesión iniciada como curator.roles=Roles curator.tool.haplogroups=Haplogrupos +curator.tool.variants=Variantes +curator.tool.regions=Regiones genómicas hg.title=Haplogrupos hg.new=Nuevo haplogrupo @@ -114,3 +116,42 @@ hg.edit=Editar hg.delete=Eliminar hg.delete.confirm=¿Eliminar este haplogrupo? hg.deleteBlocked=No se puede eliminar: aún tiene relaciones en el árbol. + +var.title=Variantes +var.new=Nueva variante +var.search=Buscar por nombre o alias… +var.col.name=Nombre +var.col.type=Tipo +var.col.status=Estado +var.none=No hay variantes coincidentes. +var.select=Seleccione una variante o cree una. +var.field.name=Nombre canónico +var.field.type=Tipo de mutación +var.field.status=Estado de nomenclatura +var.field.commonNames=Nombres comunes (separados por comas) +var.field.rsIds=Identificadores rs (separados por comas) +var.field.builds=Ensamblajes de coordenadas +var.save=Guardar +var.cancel=Cancelar +var.edit=Editar +var.delete=Eliminar +var.delete.confirm=¿Eliminar esta variante? +var.deleteBlocked=No se puede eliminar: define un haplogrupo. + +region.title=Regiones genómicas +region.new=Nueva región +region.search=Buscar por nombre o tipo… +region.col.type=Tipo +region.col.name=Nombre +region.col.builds=Ensamblajes +region.none=No hay regiones coincidentes. +region.select=Seleccione una región o cree una. +region.field.type=Tipo de región +region.field.name=Nombre +region.field.coordinates=Coordenadas (JSON) +region.field.properties=Propiedades (JSON) +region.save=Guardar +region.cancel=Cancelar +region.edit=Editar +region.delete=Eliminar +region.delete.confirm=¿Eliminar esta región? diff --git a/rust/locales/fr.txt b/rust/locales/fr.txt index bce5705..f18b9fc 100644 --- a/rust/locales/fr.txt +++ b/rust/locales/fr.txt @@ -92,6 +92,8 @@ curator.title=Tableau de bord du curateur curator.welcome=Connecté en tant que curator.roles=Rôles curator.tool.haplogroups=Haplogroupes +curator.tool.variants=Variants +curator.tool.regions=Régions génomiques hg.title=Haplogroupes hg.new=Nouvel haplogroupe @@ -114,3 +116,42 @@ hg.edit=Modifier hg.delete=Supprimer hg.delete.confirm=Supprimer cet haplogroupe ? hg.deleteBlocked=Suppression impossible : des relations d’arbre existent encore. + +var.title=Variants +var.new=Nouveau variant +var.search=Rechercher par nom ou alias… +var.col.name=Nom +var.col.type=Type +var.col.status=Statut +var.none=Aucun variant correspondant. +var.select=Sélectionnez un variant ou créez-en un. +var.field.name=Nom canonique +var.field.type=Type de mutation +var.field.status=Statut de nomenclature +var.field.commonNames=Noms communs (séparés par des virgules) +var.field.rsIds=Identifiants rs (séparés par des virgules) +var.field.builds=Assemblages de coordonnées +var.save=Enregistrer +var.cancel=Annuler +var.edit=Modifier +var.delete=Supprimer +var.delete.confirm=Supprimer ce variant ? +var.deleteBlocked=Suppression impossible : il définit un haplogroupe. + +region.title=Régions génomiques +region.new=Nouvelle région +region.search=Rechercher par nom ou type… +region.col.type=Type +region.col.name=Nom +region.col.builds=Assemblages +region.none=Aucune région correspondante. +region.select=Sélectionnez une région ou créez-en une. +region.field.type=Type de région +region.field.name=Nom +region.field.coordinates=Coordonnées (JSON) +region.field.properties=Propriétés (JSON) +region.save=Enregistrer +region.cancel=Annuler +region.edit=Modifier +region.delete=Supprimer +region.delete.confirm=Supprimer cette région ? From ef2d33711aef6f84ef3d30f306c2f7d361f451e6 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 10:16:35 -0500 Subject: [PATCH 010/191] feat(rust): du-migrate ETL (legacy -> new schema) + mock-legacy verification MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit One-time ETL binary. Production source is a self-managed Postgres on EC2 — --legacy takes that DSN (typically sslmode=require via opened SG / SSH tunnel), --target the new DB. rustls TLS supports remote/SSL connections. Design: preserve legacy primary keys (OVERRIDING SYSTEM VALUE) and sample_guid UUIDs so all foreign keys carry over 1:1 with no id-remapping. Transformers run in FK order, upsert idempotently (re-runnable/resumable), then identity sequences are advanced and a reconciliation pass compares legacy vs new counts. Transformers: specimen_donor; unified biosample (legacy biosample + citizen_biosample + pgp_biosample -> core.biosample, deriving source, folding at_uri/at_cid into the atproto JSONB and PGP fields into source_attrs); variant (enum normalization, JSONB passthrough); haplogroup (+relationship +variant, Y/MT -> Y_DNA/MT_DNA); genomic_study; publication (+links, resolving legacy integer biosample ids to sample_guid across both link tables). CLI: --legacy/--target/--verify. Reconcile prints a per-aggregate count table. Verified without prod access: scripts/mock-legacy.sql seeds a legacy-shaped subset; the ETL into a fresh target reconciles all 9 aggregates, spot-checks confirm unification/JSONB/enum/geocoord/FK preservation, and a re-run is idempotent. NOTE: transformer SELECTs encode the reconstructed legacy layout — validate against the live EC2 schema before the production run. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/Cargo.lock | 122 ++++++ rust/Cargo.toml | 3 + rust/crates/du-migrate/Cargo.toml | 2 + rust/crates/du-migrate/src/main.rs | 65 +++- rust/crates/du-migrate/src/reconcile.rs | 53 +++ rust/crates/du-migrate/src/transform.rs | 481 ++++++++++++++++++++++++ rust/scripts/mock-legacy.sql | 164 ++++++++ 7 files changed, 884 insertions(+), 6 deletions(-) create mode 100644 rust/crates/du-migrate/src/reconcile.rs create mode 100644 rust/crates/du-migrate/src/transform.rs create mode 100644 rust/scripts/mock-legacy.sql diff --git a/rust/Cargo.lock b/rust/Cargo.lock index 5fd3134..9db42b6 100644 --- a/rust/Cargo.lock +++ b/rust/Cargo.lock @@ -43,6 +43,56 @@ dependencies = [ "libc", ] +[[package]] +name = "anstream" +version = "1.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "824a212faf96e9acacdbd09febd34438f8f711fb84e09a8916013cd7815ca28d" +dependencies = [ + "anstyle", + "anstyle-parse", + "anstyle-query", + "anstyle-wincon", + "colorchoice", + "is_terminal_polyfill", + "utf8parse", +] + +[[package]] +name = "anstyle" +version = "1.0.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "940b3a0ca603d1eade50a4846a2afffd5ef57a9feac2c0e2ec2e14f9ead76000" + +[[package]] +name = "anstyle-parse" +version = "1.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "52ce7f38b242319f7cabaa6813055467063ecdc9d355bbb4ce0c68908cd8130e" +dependencies = [ + "utf8parse", +] + +[[package]] +name = "anstyle-query" +version = "1.1.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "40c48f72fd53cd289104fc64099abca73db4166ad86ea0b4341abe65af83dadc" +dependencies = [ + "windows-sys 0.61.2", +] + +[[package]] +name = "anstyle-wincon" +version = "3.0.11" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "291e6a250ff86cd4a820112fb8898808a366d8f9f58ce16d1f538353ad55747d" +dependencies = [ + "anstyle", + "once_cell_polyfill", + "windows-sys 0.61.2", +] + [[package]] name = "anyhow" version = "1.0.102" @@ -415,6 +465,52 @@ dependencies = [ "inout", ] +[[package]] +name = "clap" +version = "4.6.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1ddb117e43bbf7dacf0a4190fef4d345b9bad68dfc649cb349e7d17d28428e51" +dependencies = [ + "clap_builder", + "clap_derive", +] + +[[package]] +name = "clap_builder" +version = "4.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "714a53001bf66416adb0e2ef5ac857140e7dc3a0c48fb28b2f10762fc4b5069f" +dependencies = [ + "anstream", + "anstyle", + "clap_lex", + "strsim", +] + +[[package]] +name = "clap_derive" +version = "4.6.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f2ce8604710f6733aa641a2b3731eaa1e8b3d9973d5e3565da11800813f997a9" +dependencies = [ + "heck", + "proc-macro2", + "quote", + "syn 2.0.117", +] + +[[package]] +name = "clap_lex" +version = "1.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c8d4a3bb8b1e0c1050499d1815f5ab16d04f0959b233085fb31653fbfc9d98f9" + +[[package]] +name = "colorchoice" +version = "1.0.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1d07550c9036bf2ae0c684c4297d503f838287c83c53686d05370d0e139ae570" + [[package]] name = "compression-codecs" version = "0.4.38" @@ -647,6 +743,7 @@ name = "du-migrate" version = "0.1.0" dependencies = [ "anyhow", + "clap", "du-db", "du-domain", "serde", @@ -655,6 +752,7 @@ dependencies = [ "tokio", "tracing", "tracing-subscriber", + "uuid", ] [[package]] @@ -1215,6 +1313,12 @@ dependencies = [ "generic-array", ] +[[package]] +name = "is_terminal_polyfill" +version = "1.70.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a6cb138bb79a146c1bd460005623e142ef0181e3d0219cb493e02f7d08a35695" + [[package]] name = "itoa" version = "1.0.18" @@ -1454,6 +1558,12 @@ version = "1.21.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9f7c3e4beb33f85d45ae3e3a1792185706c8e16d043238c593331cc7cd313b50" +[[package]] +name = "once_cell_polyfill" +version = "1.70.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "384b8ab6d37215f3c5301a95a4accb5d64aa607f1fcb26a11b5303878451b4fe" + [[package]] name = "parking" version = "2.2.1" @@ -2253,6 +2363,12 @@ dependencies = [ "unicode-properties", ] +[[package]] +name = "strsim" +version = "0.11.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f" + [[package]] name = "subtle" version = "2.6.1" @@ -2674,6 +2790,12 @@ version = "1.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be" +[[package]] +name = "utf8parse" +version = "0.2.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821" + [[package]] name = "uuid" version = "1.23.2" diff --git a/rust/Cargo.toml b/rust/Cargo.toml index 3d25f35..0d88dc9 100644 --- a/rust/Cargo.toml +++ b/rust/Cargo.toml @@ -59,6 +59,9 @@ reqwest = { version = "0.12", default-features = false, features = ["json", "rus # URL/query encoding (language-switcher `next` param) percent-encoding = "2" +# CLI +clap = { version = "4", features = ["derive"] } + # Errors / logging / config thiserror = "2" anyhow = "1" diff --git a/rust/crates/du-migrate/Cargo.toml b/rust/crates/du-migrate/Cargo.toml index 394f318..dbec8a1 100644 --- a/rust/crates/du-migrate/Cargo.toml +++ b/rust/crates/du-migrate/Cargo.toml @@ -21,3 +21,5 @@ serde_json = { workspace = true } tracing = { workspace = true } tracing-subscriber = { workspace = true } anyhow = { workspace = true } +clap = { workspace = true } +uuid = { workspace = true } diff --git a/rust/crates/du-migrate/src/main.rs b/rust/crates/du-migrate/src/main.rs index c37a475..8ae58bb 100644 --- a/rust/crates/du-migrate/src/main.rs +++ b/rust/crates/du-migrate/src/main.rs @@ -1,17 +1,70 @@ -//! Legacy -> new schema ETL binary (plan §8). Scaffold only. +//! One-time ETL: legacy DecodingUs Postgres -> redesigned schema (plan §8). //! -//! Usage (planned): -//! decodingus-migrate --legacy --target run the ETL -//! decodingus-migrate --legacy --target --verify reconcile counts +//! The production source is a self-managed Postgres on EC2; point `--legacy` at +//! it (typically `...?sslmode=require`, via an opened security group or an SSH +//! tunnel). `--target` is the new schema's database. +//! +//! Strategy: preserve legacy primary keys (via `OVERRIDING SYSTEM VALUE`) and +//! existing `sample_guid` UUIDs, so foreign keys carry over 1:1 with no id +//! remapping. Transformers run in dependency order, upsert idempotently +//! (re-runnable / resumable), then identity sequences are advanced and a +//! reconciliation pass compares counts. +//! +//! decodingus-migrate --legacy --target run + reconcile +//! decodingus-migrate --legacy --target --verify reconcile only + +use clap::Parser; + +mod reconcile; +mod transform; + +#[derive(Parser, Debug)] +#[command(name = "decodingus-migrate", about = "Legacy -> redesigned schema ETL")] +struct Args { + /// Legacy (source) DSN, e.g. postgres://user:pass@ec2-host:5432/decodingus?sslmode=require + #[arg(long)] + legacy: String, + /// Target (new schema) DSN. + #[arg(long)] + target: String, + /// Reconcile counts only; perform no writes. + #[arg(long)] + verify: bool, +} #[tokio::main] async fn main() -> anyhow::Result<()> { tracing_subscriber::fmt() .with_env_filter( tracing_subscriber::EnvFilter::try_from_default_env() - .unwrap_or_else(|_| "info".into()), + .unwrap_or_else(|_| "info,du_migrate=debug".into()), ) .init(); - tracing::info!("decodingus-migrate scaffold — ETL transformers not yet implemented"); + + let args = Args::parse(); + let legacy = du_db::connect(&args.legacy, 4).await?; + let target = du_db::connect(&args.target, 4).await?; + + if args.verify { + reconcile::run(&legacy, &target).await?; + return Ok(()); + } + + tracing::info!("ETL starting"); + // Dependency order: donors before biosamples; variants/haplogroups before + // their join tables; publications/studies before their links. + transform::specimen_donor(&legacy, &target).await?; + transform::biosample(&legacy, &target).await?; + transform::variant(&legacy, &target).await?; + transform::haplogroup(&legacy, &target).await?; + transform::haplogroup_relationship(&legacy, &target).await?; + transform::haplogroup_variant(&legacy, &target).await?; + transform::genomic_study(&legacy, &target).await?; + transform::publication(&legacy, &target).await?; + transform::publication_biosample(&legacy, &target).await?; + + transform::fix_sequences(&target).await?; + tracing::info!("ETL complete; reconciling"); + reconcile::run(&legacy, &target).await?; Ok(()) } diff --git a/rust/crates/du-migrate/src/reconcile.rs b/rust/crates/du-migrate/src/reconcile.rs new file mode 100644 index 0000000..77db1a1 --- /dev/null +++ b/rust/crates/du-migrate/src/reconcile.rs @@ -0,0 +1,53 @@ +//! Reconciliation: compare legacy vs new row counts per aggregate. Unified +//! aggregates sum the contributing legacy tables. Mismatches are flagged (a +//! lower target count for links can be legitimate de-duplication). + +use sqlx::PgPool; + +struct Check { + label: &'static str, + legacy_sql: &'static str, + target_sql: &'static str, +} + +const CHECKS: &[Check] = &[ + Check { label: "specimen_donor", legacy_sql: "SELECT count(*) FROM specimen_donor", target_sql: "SELECT count(*) FROM core.specimen_donor" }, + Check { + label: "biosample", + legacy_sql: "SELECT (SELECT count(*) FROM biosample) + (SELECT count(*) FROM citizen_biosample) + (SELECT count(*) FROM pgp_biosample)", + target_sql: "SELECT count(*) FROM core.biosample", + }, + Check { label: "variant", legacy_sql: "SELECT count(*) FROM variant_v2", target_sql: "SELECT count(*) FROM core.variant" }, + Check { label: "haplogroup", legacy_sql: "SELECT count(*) FROM tree.haplogroup", target_sql: "SELECT count(*) FROM tree.haplogroup" }, + Check { label: "haplogroup_relationship", legacy_sql: "SELECT count(*) FROM tree.haplogroup_relationship", target_sql: "SELECT count(*) FROM tree.haplogroup_relationship" }, + Check { label: "haplogroup_variant", legacy_sql: "SELECT count(*) FROM tree.haplogroup_variant", target_sql: "SELECT count(*) FROM tree.haplogroup_variant" }, + Check { label: "genomic_study", legacy_sql: "SELECT count(*) FROM genomic_studies", target_sql: "SELECT count(*) FROM pubs.genomic_study" }, + Check { label: "publication", legacy_sql: "SELECT count(*) FROM publication", target_sql: "SELECT count(*) FROM pubs.publication" }, + Check { + label: "publication_biosample", + legacy_sql: "SELECT (SELECT count(*) FROM publication_biosample) + (SELECT count(*) FROM publication_citizen_biosample)", + target_sql: "SELECT count(*) FROM pubs.publication_biosample", + }, +]; + +pub async fn run(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let mut mismatches = 0; + println!("{:<26} {:>10} {:>10} status", "aggregate", "legacy", "target"); + for c in CHECKS { + let l: i64 = sqlx::query_scalar(c.legacy_sql).fetch_one(legacy).await?; + let t: i64 = sqlx::query_scalar(c.target_sql).fetch_one(target).await?; + let status = if l == t { + "ok" + } else { + mismatches += 1; + "MISMATCH" + }; + println!("{:<26} {:>10} {:>10} {}", c.label, l, t, status); + } + if mismatches > 0 { + tracing::warn!(mismatches, "reconciliation found count mismatches (review before cutover)"); + } else { + tracing::info!("reconciliation: all aggregate counts match"); + } + Ok(()) +} diff --git a/rust/crates/du-migrate/src/transform.rs b/rust/crates/du-migrate/src/transform.rs new file mode 100644 index 0000000..b39fa8a --- /dev/null +++ b/rust/crates/du-migrate/src/transform.rs @@ -0,0 +1,481 @@ +//! Legacy -> new schema transformers. Each reads from the legacy DB and upserts +//! into the new DB, preserving primary keys (`OVERRIDING SYSTEM VALUE`) and +//! `sample_guid` UUIDs so foreign keys carry over unchanged. All upserts are +//! idempotent (`ON CONFLICT ... DO UPDATE`/`DO NOTHING`) so a re-run is safe. +//! +//! NOTE: the SELECT statements encode the *legacy* column layout (reconstructed +//! from the Play app's evolutions). Validate them against the live EC2 schema +//! before the production run; adjust column names here if they differ. + +use serde_json::{json, Value}; +use sqlx::types::chrono::{DateTime, NaiveDate, Utc}; +use sqlx::PgPool; +use uuid::Uuid; + +type Ts = Option>; + +fn dna(s: &str) -> &'static str { + match s.trim() { + "MT" | "MT_DNA" | "mtDNA" => "MT_DNA", + _ => "Y_DNA", + } +} + +/// Legacy `biosample_type` / donor_type -> new `biosample_source`. +fn source_from_donor(s: &str) -> &'static str { + match s.trim() { + "External" | "EXTERNAL" => "EXTERNAL", + "Ancient" | "ANCIENT" => "ANCIENT", + "PGP" => "PGP", + "Citizen" | "CITIZEN" => "CITIZEN", + _ => "STANDARD", + } +} + +fn upper_opt(s: Option) -> Option { + s.map(|v| v.trim().to_uppercase()) +} + +// ── specimen donors ────────────────────────────────────────────────────────── +pub async fn specimen_donor(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows = sqlx::query_as::<_, (i64, Option, Option, Option, Option, Option)>( + "SELECT id::bigint, donor_identifier, origin_biobank, sex::text, donor_type::text, ST_AsEWKT(geocoord) \ + FROM specimen_donor", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for (id, ident, biobank, sex, donor_type, ewkt) in rows { + sqlx::query( + "INSERT INTO core.specimen_donor (id, donor_identifier, origin_biobank, sex, donor_type, geocoord) \ + OVERRIDING SYSTEM VALUE \ + VALUES ($1,$2,$3,$4::core.biological_sex,$5::core.biosample_source, ST_GeomFromEWKT($6)) \ + ON CONFLICT (id) DO UPDATE SET donor_identifier=EXCLUDED.donor_identifier, \ + origin_biobank=EXCLUDED.origin_biobank, sex=EXCLUDED.sex, donor_type=EXCLUDED.donor_type, \ + geocoord=EXCLUDED.geocoord", + ) + .bind(id) + .bind(ident) + .bind(biobank) + .bind(upper_opt(sex)) + .bind(source_from_donor(donor_type.as_deref().unwrap_or("Standard"))) + .bind(ewkt) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "specimen_donor", rows = n, "migrated"); + Ok(()) +} + +// ── unified biosample (3 legacy tables -> 1) ───────────────────────────────── +pub async fn biosample(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + const UPSERT: &str = "INSERT INTO core.biosample \ + (sample_guid, donor_id, source, accession, alias, description, center_name, locked, deleted, \ + source_attrs, original_haplogroups, atproto) \ + VALUES ($1,$2,$3::core.biosample_source,$4,$5,$6,$7,$8,$9,$10,$11,$12) \ + ON CONFLICT (sample_guid) DO UPDATE SET donor_id=EXCLUDED.donor_id, source=EXCLUDED.source, \ + accession=EXCLUDED.accession, alias=EXCLUDED.alias, description=EXCLUDED.description, \ + center_name=EXCLUDED.center_name, locked=EXCLUDED.locked, deleted=EXCLUDED.deleted, \ + source_attrs=EXCLUDED.source_attrs, original_haplogroups=EXCLUDED.original_haplogroups, \ + atproto=EXCLUDED.atproto"; + + let mut tx = target.begin().await?; + let mut total = 0usize; + + // Standard/external/ancient samples — source derived from the donor type. + let std_rows = sqlx::query_as::<_, (Uuid, Option, Option, Option, Option, Option, bool, Option, Value)>( + "SELECT b.sample_guid, b.specimen_donor_id::bigint, b.sample_accession, b.alias, b.description, \ + b.center_name, COALESCE(b.locked,false), d.donor_type::text, \ + COALESCE(b.original_haplogroups,'[]'::jsonb) \ + FROM biosample b LEFT JOIN specimen_donor d ON d.id = b.specimen_donor_id", + ) + .fetch_all(legacy) + .await?; + for (guid, donor, acc, alias, desc, center, locked, donor_type, orig) in std_rows { + sqlx::query(UPSERT) + .bind(guid) + .bind(donor) + .bind(source_from_donor(donor_type.as_deref().unwrap_or("Standard"))) + .bind(acc) + .bind(alias) + .bind(desc) + .bind(center) + .bind(locked) + .bind(false) + .bind(json!({})) + .bind(orig) + .bind(None::) + .execute(&mut *tx) + .await?; + total += 1; + } + + // Citizen samples — federated; at_uri/at_cid fold into the `atproto` doc. + let cit_rows = sqlx::query_as::<_, (Uuid, Option, bool, Value, Option, Option)>( + "SELECT sample_guid, accession, COALESCE(deleted,false), \ + COALESCE(original_haplogroups,'[]'::jsonb), at_uri, at_cid \ + FROM citizen_biosample", + ) + .fetch_all(legacy) + .await?; + for (guid, acc, deleted, orig, at_uri, at_cid) in cit_rows { + let atproto = at_uri.as_ref().map(|uri| json!({ "uri": uri, "cid": at_cid })); + sqlx::query(UPSERT) + .bind(guid) + .bind(None::) + .bind("CITIZEN") + .bind(acc) + .bind(None::) + .bind(None::) + .bind(None::) + .bind(false) + .bind(deleted) + .bind(json!({})) + .bind(orig) + .bind(atproto) + .execute(&mut *tx) + .await?; + total += 1; + } + + // PGP samples — PGP-specific fields fold into source_attrs. + let pgp_rows = sqlx::query_as::<_, (Uuid, Option, Option)>( + "SELECT sample_guid, ena_biosample_accession, pgp_participant_id FROM pgp_biosample", + ) + .fetch_all(legacy) + .await?; + for (guid, ena, pgp_id) in pgp_rows { + let attrs = json!({ "pgp_participant_id": pgp_id, "ena_biosample_accession": ena }); + sqlx::query(UPSERT) + .bind(guid) + .bind(None::) + .bind("PGP") + .bind(ena) + .bind(None::) + .bind(None::) + .bind(None::) + .bind(false) + .bind(false) + .bind(attrs) + .bind(json!([])) + .bind(None::) + .execute(&mut *tx) + .await?; + total += 1; + } + + tx.commit().await?; + tracing::info!(table = "biosample", rows = total, "migrated (standard+citizen+pgp -> core.biosample)"); + Ok(()) +} + +// ── variants ───────────────────────────────────────────────────────────────── +pub async fn variant(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows = sqlx::query_as::<_, (i64, String, String, String, Value, Value, Value)>( + "SELECT variant_id::bigint, canonical_name, mutation_type::text, naming_status::text, \ + COALESCE(aliases,'{}'::jsonb), COALESCE(coordinates,'{}'::jsonb), COALESCE(annotations,'{}'::jsonb) \ + FROM variant_v2", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for (id, name, mtype, nstatus, aliases, coords, annots) in rows { + sqlx::query( + "INSERT INTO core.variant (id, canonical_name, mutation_type, naming_status, aliases, coordinates, annotations) \ + OVERRIDING SYSTEM VALUE \ + VALUES ($1,$2,$3::core.mutation_type,$4::core.naming_status,$5,$6,$7) \ + ON CONFLICT (id) DO UPDATE SET canonical_name=EXCLUDED.canonical_name, mutation_type=EXCLUDED.mutation_type, \ + naming_status=EXCLUDED.naming_status, aliases=EXCLUDED.aliases, coordinates=EXCLUDED.coordinates, \ + annotations=EXCLUDED.annotations", + ) + .bind(id) + .bind(name) + .bind(mtype.trim().to_uppercase()) + .bind(nstatus.trim().to_uppercase()) + .bind(aliases) + .bind(coords) + .bind(annots) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "variant", rows = n, "migrated"); + Ok(()) +} + +// ── haplogroups + edges + variant associations ────────────────────────────── +pub async fn haplogroup(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows = sqlx::query_as::<_, (i64, String, String, Option, Option, Option, Option, Option, Value, Ts, Ts)>( + "SELECT haplogroup_id::bigint, name, haplogroup_type::text, lineage, source, confidence_level, \ + formed_ybp, tmrca_ybp, COALESCE(provenance,'{}'::jsonb), valid_from, valid_until \ + FROM tree.haplogroup", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for (id, name, htype, lineage, source, conf, formed, tmrca, prov, vfrom, vuntil) in rows { + sqlx::query( + "INSERT INTO tree.haplogroup (id, name, haplogroup_type, lineage, source, confidence_level, \ + formed_ybp, tmrca_ybp, provenance, valid_from, valid_until) OVERRIDING SYSTEM VALUE \ + VALUES ($1,$2,$3::core.dna_type,$4,$5,$6,$7,$8,$9,COALESCE($10, now()),$11) \ + ON CONFLICT (id) DO UPDATE SET name=EXCLUDED.name, haplogroup_type=EXCLUDED.haplogroup_type, \ + lineage=EXCLUDED.lineage, source=EXCLUDED.source, confidence_level=EXCLUDED.confidence_level, \ + formed_ybp=EXCLUDED.formed_ybp, tmrca_ybp=EXCLUDED.tmrca_ybp, provenance=EXCLUDED.provenance, \ + valid_from=EXCLUDED.valid_from, valid_until=EXCLUDED.valid_until", + ) + .bind(id) + .bind(name) + .bind(dna(&htype)) + .bind(lineage) + .bind(source) + .bind(conf) + .bind(formed) + .bind(tmrca) + .bind(prov) + .bind(vfrom) + .bind(vuntil) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "haplogroup", rows = n, "migrated"); + Ok(()) +} + +pub async fn haplogroup_relationship(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows = sqlx::query_as::<_, (i64, i64, Option, Option, Option, Ts, Ts)>( + "SELECT id::bigint, child_haplogroup_id::bigint, parent_haplogroup_id::bigint, \ + revision_id, source, valid_from, valid_until FROM tree.haplogroup_relationship", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for (id, child, parent, rev, source, vfrom, vuntil) in rows { + sqlx::query( + "INSERT INTO tree.haplogroup_relationship (id, child_haplogroup_id, parent_haplogroup_id, \ + revision_id, source, revision, valid_from, valid_until) OVERRIDING SYSTEM VALUE \ + VALUES ($1,$2,$3,COALESCE($4,1),$5,'{}'::jsonb,COALESCE($6, now()),$7) \ + ON CONFLICT (id) DO UPDATE SET child_haplogroup_id=EXCLUDED.child_haplogroup_id, \ + parent_haplogroup_id=EXCLUDED.parent_haplogroup_id, revision_id=EXCLUDED.revision_id, \ + source=EXCLUDED.source, valid_from=EXCLUDED.valid_from, valid_until=EXCLUDED.valid_until", + ) + .bind(id) + .bind(child) + .bind(parent) + .bind(rev) + .bind(source) + .bind(vfrom) + .bind(vuntil) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "haplogroup_relationship", rows = n, "migrated"); + Ok(()) +} + +pub async fn haplogroup_variant(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows = sqlx::query_as::<_, (i64, i64, i64, Ts, Ts)>( + "SELECT haplogroup_variant_id::bigint, haplogroup_id::bigint, variant_id::bigint, valid_from, valid_until \ + FROM tree.haplogroup_variant", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for (id, hg, var, vfrom, vuntil) in rows { + sqlx::query( + "INSERT INTO tree.haplogroup_variant (id, haplogroup_id, variant_id, revision, valid_from, valid_until) \ + OVERRIDING SYSTEM VALUE VALUES ($1,$2,$3,'{}'::jsonb,COALESCE($4, now()),$5) \ + ON CONFLICT (id) DO UPDATE SET haplogroup_id=EXCLUDED.haplogroup_id, variant_id=EXCLUDED.variant_id, \ + valid_from=EXCLUDED.valid_from, valid_until=EXCLUDED.valid_until", + ) + .bind(id) + .bind(hg) + .bind(var) + .bind(vfrom) + .bind(vuntil) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "haplogroup_variant", rows = n, "migrated"); + Ok(()) +} + +// ── publications + studies + links ─────────────────────────────────────────── +#[derive(sqlx::FromRow)] +struct StudyRow { + id: i64, + accession: String, + title: Option, + center_name: Option, + study_name: Option, + source: Option, + bio_project_id: Option, + molecule: Option, + topology: Option, + taxonomy_id: Option, + version: Option, + submission_date: Option, + details: Value, +} + +pub async fn genomic_study(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows: Vec = sqlx::query_as( + "SELECT id::bigint, accession, title, center_name, study_name, source::text AS source, \ + bio_project_id, molecule, topology, taxonomy_id, version, submission_date, \ + COALESCE(details,'{}'::jsonb) AS details FROM genomic_studies", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for r in rows { + sqlx::query( + "INSERT INTO pubs.genomic_study (id, accession, title, center_name, study_name, source, \ + bio_project_id, molecule, topology, taxonomy_id, version, submission_date, details) \ + OVERRIDING SYSTEM VALUE \ + VALUES ($1,$2,$3,$4,$5,COALESCE($6,'ENA')::pubs.study_source,$7,$8,$9,$10,$11,$12,$13) \ + ON CONFLICT (id) DO UPDATE SET accession=EXCLUDED.accession, title=EXCLUDED.title, \ + center_name=EXCLUDED.center_name, study_name=EXCLUDED.study_name, source=EXCLUDED.source, \ + bio_project_id=EXCLUDED.bio_project_id, molecule=EXCLUDED.molecule, topology=EXCLUDED.topology, \ + taxonomy_id=EXCLUDED.taxonomy_id, version=EXCLUDED.version, submission_date=EXCLUDED.submission_date, \ + details=EXCLUDED.details", + ) + .bind(r.id) + .bind(r.accession) + .bind(r.title) + .bind(r.center_name) + .bind(r.study_name) + .bind(r.source.map(|s| s.to_uppercase())) + .bind(r.bio_project_id) + .bind(r.molecule) + .bind(r.topology) + .bind(r.taxonomy_id) + .bind(r.version) + .bind(r.submission_date) + .bind(r.details) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "genomic_study", rows = n, "migrated"); + Ok(()) +} + +#[derive(sqlx::FromRow)] +struct PubRow { + id: i64, + pubmed_id: Option, + doi: Option, + open_alex_id: Option, + title: String, + journal: Option, + publication_date: Option, + url: Option, + authors: Option, + abstract_summary: Option, + cited_by_count: Option, + open_access_status: Option, +} + +pub async fn publication(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let rows: Vec = sqlx::query_as( + "SELECT id::bigint, pubmed_id, doi, open_alex_id, title, journal, publication_date, url, authors, \ + abstract_summary, cited_by_count, open_access_status FROM publication", + ) + .fetch_all(legacy) + .await?; + let n = rows.len(); + let mut tx = target.begin().await?; + for r in rows { + sqlx::query( + "INSERT INTO pubs.publication (id, pubmed_id, doi, open_alex_id, title, journal, publication_date, \ + url, authors, abstract_summary, cited_by_count, open_access_status) OVERRIDING SYSTEM VALUE \ + VALUES ($1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12) \ + ON CONFLICT (id) DO UPDATE SET pubmed_id=EXCLUDED.pubmed_id, doi=EXCLUDED.doi, \ + open_alex_id=EXCLUDED.open_alex_id, title=EXCLUDED.title, journal=EXCLUDED.journal, \ + publication_date=EXCLUDED.publication_date, url=EXCLUDED.url, authors=EXCLUDED.authors, \ + abstract_summary=EXCLUDED.abstract_summary, cited_by_count=EXCLUDED.cited_by_count, \ + open_access_status=EXCLUDED.open_access_status", + ) + .bind(r.id) + .bind(r.pubmed_id) + .bind(r.doi) + .bind(r.open_alex_id) + .bind(r.title) + .bind(r.journal) + .bind(r.publication_date) + .bind(r.url) + .bind(r.authors) + .bind(r.abstract_summary) + .bind(r.cited_by_count) + .bind(r.open_access_status) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "publication", rows = n, "migrated"); + Ok(()) +} + +/// Both legacy link tables (standard + citizen) -> the unified link, resolving +/// the legacy integer biosample id to the preserved `sample_guid`. +pub async fn publication_biosample(legacy: &PgPool, target: &PgPool) -> anyhow::Result<()> { + let std = sqlx::query_as::<_, (i64, Uuid)>( + "SELECT pb.publication_id::bigint, b.sample_guid \ + FROM publication_biosample pb JOIN biosample b ON b.id = pb.biosample_id", + ) + .fetch_all(legacy) + .await?; + let cit = sqlx::query_as::<_, (i64, Uuid)>( + "SELECT pcb.publication_id::bigint, c.sample_guid \ + FROM publication_citizen_biosample pcb JOIN citizen_biosample c ON c.id = pcb.citizen_biosample_id", + ) + .fetch_all(legacy) + .await?; + let n = std.len() + cit.len(); + let mut tx = target.begin().await?; + for (pub_id, guid) in std.into_iter().chain(cit) { + sqlx::query( + "INSERT INTO pubs.publication_biosample (publication_id, sample_guid) VALUES ($1,$2) \ + ON CONFLICT DO NOTHING", + ) + .bind(pub_id) + .bind(guid) + .execute(&mut *tx) + .await?; + } + tx.commit().await?; + tracing::info!(table = "publication_biosample", rows = n, "migrated"); + Ok(()) +} + +// ── post-load: advance identity sequences past the copied max id ───────────── +pub async fn fix_sequences(target: &PgPool) -> anyhow::Result<()> { + for (schema, table) in [ + ("core", "specimen_donor"), + ("core", "variant"), + ("tree", "haplogroup"), + ("tree", "haplogroup_relationship"), + ("tree", "haplogroup_variant"), + ("pubs", "genomic_study"), + ("pubs", "publication"), + ] { + let qualified = format!("{schema}.{table}"); + // Set the identity sequence so the next nextval is max(id)+1. + let sql = format!( + "SELECT setval(pg_get_serial_sequence('{qualified}','id'), \ + COALESCE((SELECT max(id) FROM {qualified}), 0) + 1, false)" + ); + sqlx::query(&sql).execute(target).await?; + } + tracing::info!("identity sequences advanced"); + Ok(()) +} diff --git a/rust/scripts/mock-legacy.sql b/rust/scripts/mock-legacy.sql new file mode 100644 index 0000000..634cc3a --- /dev/null +++ b/rust/scripts/mock-legacy.sql @@ -0,0 +1,164 @@ +-- Mock of the legacy DecodingUs schema (subset the ETL reads), for verifying +-- du-migrate without production access. Shapes follow the reconstructed legacy +-- layout; the real EC2 schema is the contract for the production run. +CREATE EXTENSION IF NOT EXISTS postgis; +CREATE SCHEMA IF NOT EXISTS tree; + +CREATE TABLE specimen_donor ( + id SERIAL PRIMARY KEY, + donor_identifier TEXT, + origin_biobank TEXT, + sex TEXT, -- legacy biological_sex (lowercase) + donor_type TEXT, -- legacy biosample_type: Standard/External/Ancient/... + geocoord geometry(Point, 4326) +); + +CREATE TABLE biosample ( + id SERIAL PRIMARY KEY, + sample_guid UUID NOT NULL, + sample_accession TEXT, + alias TEXT, + description TEXT, + center_name TEXT, + locked BOOLEAN DEFAULT false, + specimen_donor_id INTEGER REFERENCES specimen_donor(id), + original_haplogroups JSONB DEFAULT '[]'::jsonb +); + +CREATE TABLE citizen_biosample ( + id SERIAL PRIMARY KEY, + sample_guid UUID NOT NULL, + accession TEXT, + deleted BOOLEAN DEFAULT false, + original_haplogroups JSONB DEFAULT '[]'::jsonb, + at_uri TEXT, + at_cid TEXT +); + +CREATE TABLE pgp_biosample ( + pgp_biosample_id SERIAL PRIMARY KEY, + sample_guid UUID NOT NULL, + ena_biosample_accession TEXT, + pgp_participant_id TEXT +); + +CREATE TABLE variant_v2 ( + variant_id SERIAL PRIMARY KEY, + canonical_name TEXT NOT NULL, + mutation_type TEXT, + naming_status TEXT, + aliases JSONB DEFAULT '{}'::jsonb, + coordinates JSONB DEFAULT '{}'::jsonb, + annotations JSONB DEFAULT '{}'::jsonb +); + +CREATE TABLE tree.haplogroup ( + haplogroup_id SERIAL PRIMARY KEY, + name TEXT NOT NULL, + haplogroup_type TEXT, -- Y / MT + lineage TEXT, + source TEXT, + confidence_level TEXT, + formed_ybp INTEGER, + tmrca_ybp INTEGER, + provenance JSONB DEFAULT '{}'::jsonb, + valid_from TIMESTAMPTZ DEFAULT now(), + valid_until TIMESTAMPTZ +); + +CREATE TABLE tree.haplogroup_relationship ( + id SERIAL PRIMARY KEY, + child_haplogroup_id INTEGER, + parent_haplogroup_id INTEGER, + revision_id INTEGER DEFAULT 1, + source TEXT, + valid_from TIMESTAMPTZ DEFAULT now(), + valid_until TIMESTAMPTZ +); + +CREATE TABLE tree.haplogroup_variant ( + haplogroup_variant_id SERIAL PRIMARY KEY, + haplogroup_id INTEGER, + variant_id INTEGER, + valid_from TIMESTAMPTZ DEFAULT now(), + valid_until TIMESTAMPTZ +); + +CREATE TABLE genomic_studies ( + id SERIAL PRIMARY KEY, + accession TEXT NOT NULL, + title TEXT, + center_name TEXT, + study_name TEXT, + source TEXT, + bio_project_id TEXT, + molecule TEXT, + topology TEXT, + taxonomy_id INTEGER, + version INTEGER, + submission_date DATE, + details JSONB DEFAULT '{}'::jsonb +); + +CREATE TABLE publication ( + id SERIAL PRIMARY KEY, + pubmed_id TEXT, + doi TEXT, + open_alex_id TEXT, + title TEXT NOT NULL, + journal TEXT, + publication_date DATE, + url TEXT, + authors TEXT, + abstract_summary TEXT, + cited_by_count INTEGER, + open_access_status TEXT +); + +CREATE TABLE publication_biosample ( + publication_id INTEGER, + biosample_id INTEGER +); +CREATE TABLE publication_citizen_biosample ( + publication_id INTEGER, + citizen_biosample_id INTEGER +); + +-- ── seed ───────────────────────────────────────────────────────────────────── +INSERT INTO specimen_donor (donor_identifier, origin_biobank, sex, donor_type, geocoord) VALUES + ('D1','Biobank A','male','Standard', ST_SetSRID(ST_MakePoint(-0.12,51.50),4326)), + ('D2','Biobank B','female','Ancient', ST_SetSRID(ST_MakePoint(35.0,47.0),4326)); + +INSERT INTO biosample (sample_guid, sample_accession, alias, description, center_name, locked, specimen_donor_id, original_haplogroups) VALUES + ('11111111-1111-1111-1111-111111111111','SAMN001','std-1','Standard sample','Center X', false, 1, '[{"publication_id":1,"y":"R-M269"}]'::jsonb), + ('22222222-2222-2222-2222-222222222222','SAMN002','anc-1','Ancient sample','Center Y', false, 2, '[]'::jsonb); + +INSERT INTO citizen_biosample (sample_guid, accession, deleted, original_haplogroups, at_uri, at_cid) VALUES + ('33333333-3333-3333-3333-333333333333','CIT001', false, '[]'::jsonb, 'at://did:plc:abc123/app.decodingus.biosample/xyz', 'bafyreigh2akiscaildc'); + +INSERT INTO pgp_biosample (sample_guid, ena_biosample_accession, pgp_participant_id) VALUES + ('44444444-4444-4444-4444-444444444444','ERS999','hu1A2B3C'); + +INSERT INTO variant_v2 (canonical_name, mutation_type, naming_status, aliases, coordinates) VALUES + ('M269','SNP','NAMED','{"common_names":["PF6517"],"rs_ids":["rs9786153"]}'::jsonb,'{"GRCh38":{"contig":"chrY","position":22739367}}'::jsonb), + ('L21','snp','named','{"common_names":["S145"]}'::jsonb,'{"GRCh38":{"contig":"chrY","position":13668077}}'::jsonb); + +INSERT INTO tree.haplogroup (name, haplogroup_type, lineage, formed_ybp) VALUES + ('R','Y','R',28200), + ('R1b','Y','R>R1b',22800); + +INSERT INTO tree.haplogroup_relationship (child_haplogroup_id, parent_haplogroup_id) VALUES + (2, 1); -- R1b child of R + +INSERT INTO tree.haplogroup_variant (haplogroup_id, variant_id) VALUES + (2, 1); -- R1b defined by M269 + +INSERT INTO genomic_studies (accession, title, source, taxonomy_id) VALUES + ('PRJEB12345','Steppe ancient genomes','ENA',9606); + +INSERT INTO publication (pubmed_id, doi, title, journal, publication_date, cited_by_count) VALUES + ('30001','10.1000/euro1','Peopling of Europe','Nature','2021-03-15',142), + ('30002','10.1000/steppe2','Steppe Y diversity','Cell','2019-07-01',88); + +INSERT INTO publication_biosample (publication_id, biosample_id) VALUES (1, 1); -- pub1 -> standard biosample 1 +INSERT INTO publication_citizen_biosample (publication_id, citizen_biosample_id) VALUES (2, 1); -- pub2 -> citizen 1 From 25444e3f432e1232c9b91d6fc95fce06453783f1 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 10:32:40 -0500 Subject: [PATCH 011/191] docs(rust): add port status README Status-oriented README for the Rust port: rationale, stack, workspace layout, schema redesign summary, what's implemented (public surface + auth/curator + ETL), getting started with Apple `container`, testing, ETL usage (EC2 source), deploy, and a roadmap checklist. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/README.md | 189 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 189 insertions(+) create mode 100644 rust/README.md diff --git a/rust/README.md b/rust/README.md new file mode 100644 index 0000000..4343c8f --- /dev/null +++ b/rust/README.md @@ -0,0 +1,189 @@ +# DecodingUs — Rust port + +A work-in-progress rewrite of the DecodingUs platform (originally Play Framework +/ Scala 3) in Rust. It coexists with the Scala app under `rust/` during the +transition and will replace it at a single cutover. + +**Status:** foundation + public read surface + auth/curator + ETL are working and +verified against a live PostGIS database. Workspace builds clean; **11/11 tests +pass**. Not yet production-complete — see [Roadmap](#roadmap). + +--- + +## Why the rewrite + +- Drop the JVM's memory/startup overhead for a single static binary. +- Replace a sprawling, accreted schema (~84 tables across 6 schemas + a second + "metadata" DB) with a de-sprawled design that leans on Postgres **JSONB** for + document-shaped data. +- Run fully **Docker-less for local dev/test** on Apple Silicon via Apple's + `container` CLI, while remaining Docker-deployable for production. + +## Stack + +| Concern | Choice | +|---|---| +| Web | **Axum** 0.7 (+ tower / tower-http / tower-cookies) | +| Templates | **Askama** (compile-time typed, Twirl analog) | +| Frontend | **HTMX** 2 + Bootstrap 5 (vendored), HATEOAS-first | +| Database | **SQLx** 0.8 (Postgres, runtime-checked queries) | +| Genomics I/O | **noodles** (pure Rust; replaces JVM htsjdk) — *planned* | +| Async | **tokio** | +| Auth | Argon2 (bcrypt-verify fallback), signed-cookie sessions | +| i18n | embedded `key=value` catalogs (en/es/fr) | +| Local Postgres | Apple `container` running `imresamu/postgis` (arm64) | + +## Workspace layout + +``` +rust/ + crates/ + du-domain/ pure types + (planned) algorithms, no IO; JSONB payload structs + du-db/ SQLx pool + per-aggregate query modules + du-bio/ genomics file I/O (noodles) — scaffold + du-atproto/ AT Protocol / PDS federation — scaffold + du-external/ OpenAlex / ENA / AWS SES / Secrets — scaffold + du-web/ Axum app: routes, Askama templates, i18n, HTMX, auth + du-jobs/ scheduled workers — scaffold + du-migrate/ one-time legacy -> new-schema ETL + migrations/ redesigned schema (0001–0009) + locales/ en / es / fr message catalogs + scripts/ test-db.sh (Apple container), mock-legacy.sql + Dockerfile, compose.yaml, .env.example +``` + +## Schema redesign (`migrations/0001`–`0009`) + +Ten Postgres schemas: `core`, `tree`, `genomics`, `pubs`, `ident`, `ibd`, `fed`, +`social`, `support`, `billing`. Key de-sprawl moves: + +- **3 biosample tables → 1** `core.biosample` (a `source` enum discriminator + + `source_attrs` JSONB). +- **Deprecated child tables folded into JSONB** on their parents (variant aliases + & coordinates, sequence-file checksums/locations, alignment coverage, original + haplogroups). +- The legacy second **"metadata" database collapses into the `fed` schema**. +- Scattered `at_uri`/`at_cid` columns → one consistent **`atproto` JSONB** column. +- PostGIS (`geometry(Point,4326)`), `citext`, native enums, GIN/GiST/expression + indexes on queried JSONB paths. + +## What's implemented + +**Public surface** (server-rendered, HTMX, i18n en/es/fr): + +| Area | Routes | +|---|---| +| Home | `/` | +| Variant browser | `/variants` (+ list/detail fragments; JSONB alias search) | +| Y/MT tree | `/ytree` `/mtree` (unified page/fragment via `HX-Request`) | +| References + biosample report | `/references` (+ list / per-publication report) | +| Biosample map | `/biosamples/map` (PostGIS `ST_X/ST_Y` → Leaflet GeoJSON) | +| Coverage benchmarks | `/coverage-benchmarks` (coverage-JSONB aggregation) | +| Health | `/health` | + +**Auth & curator** (Argon2 + signed-cookie sessions, RBAC): + +- `/login` `/logout`; `Curator` route guard (`TreeCurator`/`Admin`). +- Two-panel HTMX CRUD for **haplogroups**, **variants**, and **genome regions** + (the region editor edits the coordinates/properties JSONB as validated JSON). + Mutations are server-driven via `HX-Trigger` (the panel returns + the list + reloads), with delete guards for referenced rows. + +**ETL** (`du-migrate`): legacy → new schema, preserving PKs and `sample_guid` so +FKs carry over 1:1; idempotent; reconciliation pass. Verified against a mock +legacy DB (see below). + +## Getting started + +### Prerequisites + +- Rust (stable/nightly) — `cargo`. +- **Apple `container`** for the local database. First run once: + ```sh + container system start # installs the default Linux kernel on first run + ``` + (No Docker required. Any `DATABASE_URL` also works as a fallback.) +- *Optional:* `sqlx-cli` (`cargo install sqlx-cli --no-default-features --features postgres,rustls`) + to auto-apply migrations and, later, enable compile-time `query!` checking. + +### Run the app + +```sh +# Start Postgres (PostGIS) and print the DATABASE_URL to export: +eval "$(./scripts/test-db.sh up)" # Apple container gives it its own IP + +# Run the web server (connects + applies migrations on startup): +cargo run -p du-web --bin decodingus # serves on http://localhost:9000 +``` + +Apple `container` assigns each container its own IP (no `localhost` port +forwarding), so `test-db.sh` discovers it and emits the right `DATABASE_URL` +(e.g. `postgres://postgres:dev@192.168.64.2:5432/decodingus`). Stop it with +`./scripts/test-db.sh down`. + +### Seed a curator (to use the curator tools) + +```sh +HASH=$(cargo run -q -p du-web --bin decodingus -- hash-password 'yourpassword') +# then insert ident.users + ident.user_login_info(provider_id='credentials', +# provider_key='', password_hash=$HASH) + ident.user_roles('TreeCurator'). +``` + +## Testing + +```sh +eval "$(./scripts/test-db.sh up)" +cargo test --workspace +``` + +Integration tests are gated on `DATABASE_URL`: with it set they run against the +live PostGIS (migrations, JSONB round-trips, query modules); without it they skip +and the suite stays green. The i18n test enforces that es/fr cover every English +key. + +## Running the ETL + +The production source is a self-managed Postgres on EC2. + +```sh +decodingus-migrate \ + --legacy "postgres://user:pass@ec2-host:5432/decodingus?sslmode=require" \ + --target "$DATABASE_URL" # runs transformers + reconciliation + +decodingus-migrate --legacy ... --target ... --verify # counts only +``` + +Verify the transformers locally first with the mock legacy DB: + +```sh +# create decodingus_legacy + decodingus_etl, load scripts/mock-legacy.sql into the +# former and the migrations into the latter, then run the ETL between them. +``` + +> ⚠️ The transformer `SELECT`s encode the *reconstructed* legacy column layout. +> Validate them against the live EC2 schema before the production run. + +## Deploy + +Multi-stage `Dockerfile` builds a single binary on a slim runtime (no JRE, no C +deps); `compose.yaml` runs it with `postgis/postgis`. `SQLX_OFFLINE=true` is set +for DB-less builds. + +## Roadmap + +- [x] Workspace + redesigned schema (verified on live PostGIS) +- [x] `du-db` query modules + read-side domain types +- [x] Public read surface (trees, variants, references, map, coverage) +- [x] Asset vendoring, i18n (en/es/fr), `HX-Request` negotiation +- [x] Session auth + RBAC; curator CRUD (haplogroups, variants, regions) +- [x] `du-migrate` ETL core aggregates (verified vs mock legacy DB) +- [ ] ETL: remaining aggregates (genomics, ibd, ident, fed, social, billing) — + validate read SQL against the live EC2 schema +- [ ] Genomics ingestion (`du-bio` / noodles) + scheduled jobs (`du-jobs`) +- [ ] AT Protocol federation (`du-atproto`): DID login, firehose, PDS fleet +- [ ] External clients (`du-external`): OpenAlex, ENA, AWS SES/Secrets +- [ ] Tree-versioning change-sets; haplogroup↔variant association editing +- [ ] Vendor remaining assets; full OpenAPI parity; cutover rehearsal + +> The tree-merge algorithm is a known-buggy area in the legacy app and will be +> re-implemented (not faithfully ported) when that subsystem lands. From 126b6cf9ecbe2c32659a1d707aeadbb0eaf58e42 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 10:49:36 -0500 Subject: [PATCH 012/191] feat(rust): du-atproto identity/crypto core; federation pivots to permissions/OAuth MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Federation direction updated after reviewing current atproto specs: the custom "private firehose" is dropped in favor of the protocol's permissions/OAuth + notify-then-fetch model (private data deliberately bypasses the firehose; consumers fetch records from the PDS over scoped OAuth). Group-private data spec is still maturing upstream. This lands the foundation needed under any model: - did: DID + AT-URI parsing; did:key <-> Ed25519 pubkey (multibase + multicodec). - signature: verify_did_key — Ed25519 verification against a self-certifying did:key (no network needed); tested with sign/verify/tamper/wrong-key. - resolve: DID-document parsing (PDS endpoint, handle, signing did:key) + a Resolver for handle->DID (well-known) and DID->doc (PLC directory / did:web); parsing unit-tested via fixture, HTTP fetch isolated. README roadmap updated for the pivot. Workspace 17/17 tests green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/Cargo.lock | 413 +++++++++++++++++++++++- rust/Cargo.toml | 4 + rust/README.md | 9 +- rust/crates/du-atproto/Cargo.toml | 8 +- rust/crates/du-atproto/src/did.rs | 113 +++++++ rust/crates/du-atproto/src/error.rs | 17 + rust/crates/du-atproto/src/lib.rs | 20 +- rust/crates/du-atproto/src/resolve.rs | 177 ++++++++++ rust/crates/du-atproto/src/signature.rs | 61 ++++ 9 files changed, 802 insertions(+), 20 deletions(-) create mode 100644 rust/crates/du-atproto/src/did.rs create mode 100644 rust/crates/du-atproto/src/error.rs create mode 100644 rust/crates/du-atproto/src/resolve.rs create mode 100644 rust/crates/du-atproto/src/signature.rs diff --git a/rust/Cargo.lock b/rust/Cargo.lock index 9db42b6..9d78dc7 100644 --- a/rust/Cargo.lock +++ b/rust/Cargo.lock @@ -272,6 +272,22 @@ dependencies = [ "syn 2.0.117", ] +[[package]] +name = "base-x" +version = "0.2.11" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4cbbc9d0964165b47557570cce6c952866c2678457aca742aafc9fb771d30270" + +[[package]] +name = "base256emoji" +version = "1.0.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b5e9430d9a245a77c92176e649af6e275f20839a48389859d1661e9a128d077c" +dependencies = [ + "const-str", + "match-lookup", +] + [[package]] name = "base64" version = "0.22.1" @@ -543,6 +559,12 @@ version = "0.9.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c2459377285ad874054d797f3ccebf984978aa39129f6eafde5cdc8315b612f8" +[[package]] +name = "const-str" +version = "0.4.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2f421161cb492475f1661ddc9815a745a1c894592070661180fdec3d4872e9c3" + [[package]] name = "cookie" version = "0.18.1" @@ -552,7 +574,7 @@ dependencies = [ "base64", "hmac", "percent-encoding", - "rand", + "rand 0.8.6", "sha2", "subtle", "time", @@ -623,6 +645,59 @@ dependencies = [ "typenum", ] +[[package]] +name = "curve25519-dalek" +version = "4.1.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "97fb8b7c4503de7d6ae7b42ab72a5a59857b4c937ec27a3d4539dba95b5ab2be" +dependencies = [ + "cfg-if", + "cpufeatures", + "curve25519-dalek-derive", + "digest", + "fiat-crypto", + "rustc_version", + "subtle", + "zeroize", +] + +[[package]] +name = "curve25519-dalek-derive" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f46882e17999c6cc590af592290432be3bce0428cb0d5f8b6715e4dc7b383eb3" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.117", +] + +[[package]] +name = "data-encoding" +version = "2.11.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a4ae5f15dda3c708c0ade84bfee31ccab44a3da4f88015ed22f63732abe300c8" + +[[package]] +name = "data-encoding-macro" +version = "0.1.20" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3259c913752a86488b501ed8680446a5ed2d5aeac6e596cb23ba3800768ea32c" +dependencies = [ + "data-encoding", + "data-encoding-macro-internal", +] + +[[package]] +name = "data-encoding-macro-internal" +version = "0.1.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ccc2776f0c61eca1ca32528f85548abd1a4be8fb53d1b21c013e4f18da1e7090" +dependencies = [ + "data-encoding", + "syn 2.0.117", +] + [[package]] name = "der" version = "0.7.10" @@ -676,7 +751,11 @@ checksum = "1aaf95b3e5c8f23aa320147307562d361db0ae0d51242340f558153b4eb2439b" name = "du-atproto" version = "0.1.0" dependencies = [ + "base64", "du-domain", + "ed25519-dalek", + "multibase", + "reqwest", "serde", "serde_json", "thiserror", @@ -778,6 +857,30 @@ dependencies = [ "uuid", ] +[[package]] +name = "ed25519" +version = "2.2.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "115531babc129696a58c64a4fef0a8bf9e9698629fb97e9e40767d235cfbcd53" +dependencies = [ + "pkcs8", + "signature", +] + +[[package]] +name = "ed25519-dalek" +version = "2.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "70e796c081cee67dc755e1a36a0a172b897fab85fc3f6bc48307991f64e4eca9" +dependencies = [ + "curve25519-dalek", + "ed25519", + "serde", + "sha2", + "subtle", + "zeroize", +] + [[package]] name = "either" version = "1.16.0" @@ -825,6 +928,12 @@ dependencies = [ "pin-project-lite", ] +[[package]] +name = "fiat-crypto" +version = "0.2.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "28dea519a9695b9977216879a3ebfddf92f1c08c05d984f8996aecd6ecdc811d" + [[package]] name = "find-msvc-tools" version = "0.1.9" @@ -973,8 +1082,24 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ff2abc00be7fca6ebc474524697ae276ad847ad0a6b3faa4bcb027e9a4614ad0" dependencies = [ "cfg-if", + "js-sys", "libc", "wasi", + "wasm-bindgen", +] + +[[package]] +name = "getrandom" +version = "0.3.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "899def5c37c4fd7b2664648c28120ecec138e4d395b459e5ca34f9cce2dd77fd" +dependencies = [ + "cfg-if", + "js-sys", + "libc", + "r-efi 5.3.0", + "wasip2", + "wasm-bindgen", ] [[package]] @@ -985,7 +1110,7 @@ checksum = "0de51e6874e94e7bf76d726fc5d13ba782deca734ff60d5bb2fb2607c7406555" dependencies = [ "cfg-if", "libc", - "r-efi", + "r-efi 6.0.0", "wasip2", "wasip3", ] @@ -1142,6 +1267,23 @@ dependencies = [ "pin-project-lite", "smallvec", "tokio", + "want", +] + +[[package]] +name = "hyper-rustls" +version = "0.27.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "33ca68d021ef39cf6463ab54c1d0f5daf03377b70561305bb89a8f83aab66e0f" +dependencies = [ + "http", + "hyper", + "hyper-util", + "rustls", + "tokio", + "tokio-rustls", + "tower-service", + "webpki-roots 1.0.7", ] [[package]] @@ -1150,13 +1292,21 @@ version = "0.1.20" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "96547c2556ec9d12fb1578c4eaf448b04993e7fb79cbaad930a656880a6bdfa0" dependencies = [ + "base64", "bytes", + "futures-channel", + "futures-util", "http", "http-body", "hyper", + "ipnet", + "libc", + "percent-encoding", "pin-project-lite", + "socket2", "tokio", "tower-service", + "tracing", ] [[package]] @@ -1313,6 +1463,12 @@ dependencies = [ "generic-array", ] +[[package]] +name = "ipnet" +version = "2.12.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d98f6fed1fde3f8c21bc40a1abb88dd75e67924f9cffc3ef95607bad8017f8e2" + [[package]] name = "is_terminal_polyfill" version = "1.70.2" @@ -1407,6 +1563,23 @@ version = "0.4.30" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "616ec5685824bcc94416c6d4a7a446eea774a31efd7062c8480ba6fd06d7a6e5" +[[package]] +name = "lru-slab" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "112b39cec0b298b6c1999fee3e31427f74f676e4cb9879ed1a121b43661a4154" + +[[package]] +name = "match-lookup" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "757aee279b8bdbb9f9e676796fd459e4207a1f986e87886700abf589f5abf771" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.117", +] + [[package]] name = "matchers" version = "0.2.0" @@ -1481,6 +1654,18 @@ dependencies = [ "windows-sys 0.61.2", ] +[[package]] +name = "multibase" +version = "0.9.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8694bb4835f452b0e3bb06dbebb1d6fc5385b6ca1caf2e55fd165c042390ec77" +dependencies = [ + "base-x", + "base256emoji", + "data-encoding", + "data-encoding-macro", +] + [[package]] name = "nom" version = "7.1.3" @@ -1511,7 +1696,7 @@ dependencies = [ "num-integer", "num-iter", "num-traits", - "rand", + "rand 0.8.6", "smallvec", "zeroize", ] @@ -1600,7 +1785,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "346f04948ba92c43e8469c1ee6736c7563d71012b17d40745260fe106aac2166" dependencies = [ "base64ct", - "rand_core", + "rand_core 0.6.4", "subtle", ] @@ -1730,6 +1915,61 @@ dependencies = [ "syn 1.0.109", ] +[[package]] +name = "quinn" +version = "0.11.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b9e20a958963c291dc322d98411f541009df2ced7b5a4f2bd52337638cfccf20" +dependencies = [ + "bytes", + "cfg_aliases", + "pin-project-lite", + "quinn-proto", + "quinn-udp", + "rustc-hash", + "rustls", + "socket2", + "thiserror", + "tokio", + "tracing", + "web-time", +] + +[[package]] +name = "quinn-proto" +version = "0.11.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "434b42fec591c96ef50e21e886936e66d3cc3f737104fdb9b737c40ffb94c098" +dependencies = [ + "bytes", + "getrandom 0.3.4", + "lru-slab", + "rand 0.9.4", + "ring", + "rustc-hash", + "rustls", + "rustls-pki-types", + "slab", + "thiserror", + "tinyvec", + "tracing", + "web-time", +] + +[[package]] +name = "quinn-udp" +version = "0.5.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "addec6a0dcad8a8d96a771f815f0eaf55f9d1805756410b39f5fa81332574cbd" +dependencies = [ + "cfg_aliases", + "libc", + "once_cell", + "socket2", + "tracing", + "windows-sys 0.52.0", +] + [[package]] name = "quote" version = "1.0.45" @@ -1739,6 +1979,12 @@ dependencies = [ "proc-macro2", ] +[[package]] +name = "r-efi" +version = "5.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "69cdb34c158ceb288df11e18b4bd39de994f6657d83847bdffdbd7f346754b0f" + [[package]] name = "r-efi" version = "6.0.0" @@ -1758,8 +2004,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5ca0ecfa931c29007047d1bc58e623ab12e5590e8c7cc53200d5202b69266d8a" dependencies = [ "libc", - "rand_chacha", - "rand_core", + "rand_chacha 0.3.1", + "rand_core 0.6.4", +] + +[[package]] +name = "rand" +version = "0.9.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "44c5af06bb1b7d3216d91932aed5265164bf384dc89cd6ba05cf59a35f5f76ea" +dependencies = [ + "rand_chacha 0.9.0", + "rand_core 0.9.5", ] [[package]] @@ -1769,7 +2025,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88" dependencies = [ "ppv-lite86", - "rand_core", + "rand_core 0.6.4", +] + +[[package]] +name = "rand_chacha" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb" +dependencies = [ + "ppv-lite86", + "rand_core 0.9.5", ] [[package]] @@ -1781,6 +2047,15 @@ dependencies = [ "getrandom 0.2.17", ] +[[package]] +name = "rand_core" +version = "0.9.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "76afc826de14238e6e8c374ddcc1fa19e374fd8dd986b0d2af0d02377261d83c" +dependencies = [ + "getrandom 0.3.4", +] + [[package]] name = "redox_syscall" version = "0.5.18" @@ -1825,6 +2100,44 @@ dependencies = [ "bytecheck", ] +[[package]] +name = "reqwest" +version = "0.12.28" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "eddd3ca559203180a307f12d114c268abf583f59b03cb906fd0b3ff8646c1147" +dependencies = [ + "base64", + "bytes", + "futures-core", + "http", + "http-body", + "http-body-util", + "hyper", + "hyper-rustls", + "hyper-util", + "js-sys", + "log", + "percent-encoding", + "pin-project-lite", + "quinn", + "rustls", + "rustls-pki-types", + "serde", + "serde_json", + "serde_urlencoded", + "sync_wrapper", + "tokio", + "tokio-rustls", + "tower", + "tower-http", + "tower-service", + "url", + "wasm-bindgen", + "wasm-bindgen-futures", + "web-sys", + "webpki-roots 1.0.7", +] + [[package]] name = "ring" version = "0.17.14" @@ -1881,7 +2194,7 @@ dependencies = [ "num-traits", "pkcs1", "pkcs8", - "rand_core", + "rand_core 0.6.4", "signature", "spki", "subtle", @@ -1898,13 +2211,28 @@ dependencies = [ "borsh", "bytes", "num-traits", - "rand", + "rand 0.8.6", "rkyv", "serde", "serde_json", "wasm-bindgen", ] +[[package]] +name = "rustc-hash" +version = "2.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "94300abf3f1ae2e2b8ffb7b58043de3d399c73fa6f4b73826402a5c457614dbe" + +[[package]] +name = "rustc_version" +version = "0.4.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cfcb3a22ef46e85b45de6ee7e79d063319ebb6594faafcf1c225ea92ab6e9b92" +dependencies = [ + "semver", +] + [[package]] name = "rustls" version = "0.23.40" @@ -1925,6 +2253,7 @@ version = "1.14.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "30a7197ae7eb376e574fe940d068c30fe0462554a3ddbe4eca7838e049c937a9" dependencies = [ + "web-time", "zeroize", ] @@ -2089,7 +2418,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "77549399552de45a898a580c1b41d445bf730df867cc44e6c0233bbc4b8329de" dependencies = [ "digest", - "rand_core", + "rand_core 0.6.4", ] [[package]] @@ -2267,7 +2596,7 @@ dependencies = [ "memchr", "once_cell", "percent-encoding", - "rand", + "rand 0.8.6", "rsa", "serde", "sha1", @@ -2307,7 +2636,7 @@ dependencies = [ "md-5", "memchr", "once_cell", - "rand", + "rand 0.8.6", "serde", "serde_json", "sha2", @@ -2402,6 +2731,9 @@ name = "sync_wrapper" version = "1.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0bf256ce5efdfa370213c1dabab5935a12e49f2c58d15e9eac2870d3b4f27263" +dependencies = [ + "futures-core", +] [[package]] name = "synstructure" @@ -2533,6 +2865,16 @@ dependencies = [ "syn 2.0.117", ] +[[package]] +name = "tokio-rustls" +version = "0.26.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1729aa945f29d91ba541258c8df89027d5792d85a8841fb65e8bf0f4ede4ef61" +dependencies = [ + "rustls", + "tokio", +] + [[package]] name = "tokio-stream" version = "0.1.18" @@ -2642,9 +2984,11 @@ dependencies = [ "pin-project-lite", "tokio", "tokio-util", + "tower", "tower-layer", "tower-service", "tracing", + "url", ] [[package]] @@ -2721,6 +3065,12 @@ dependencies = [ "tracing-log", ] +[[package]] +name = "try-lock" +version = "0.2.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e421abadd41a4225275504ea4d6566923418b7f05506fbc9c0fe86ba7396114b" + [[package]] name = "typenum" version = "1.20.1" @@ -2826,6 +3176,15 @@ version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a" +[[package]] +name = "want" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bfa7760aed19e106de2c7c0b581b509f2f25d3dacaf737cb82ac61bc6d760b0e" +dependencies = [ + "try-lock", +] + [[package]] name = "wasi" version = "0.11.1+wasi-snapshot-preview1" @@ -2870,6 +3229,16 @@ dependencies = [ "wasm-bindgen-shared", ] +[[package]] +name = "wasm-bindgen-futures" +version = "0.4.72" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9473dbd2991ae90b6291c3c32c30c6187ac49aa32f9905d1cce280ec1e110b0f" +dependencies = [ + "js-sys", + "wasm-bindgen", +] + [[package]] name = "wasm-bindgen-macro" version = "0.2.122" @@ -2936,6 +3305,26 @@ dependencies = [ "semver", ] +[[package]] +name = "web-sys" +version = "0.3.99" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6d621441cfc37b84979402712047321980c178f299193a3589d05b99e8763436" +dependencies = [ + "js-sys", + "wasm-bindgen", +] + +[[package]] +name = "web-time" +version = "1.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5a6580f308b1fad9207618087a65c04e7a10bc77e02c8e84e9b00dd4b12fa0bb" +dependencies = [ + "js-sys", + "wasm-bindgen", +] + [[package]] name = "webpki-roots" version = "0.26.11" diff --git a/rust/Cargo.toml b/rust/Cargo.toml index 0d88dc9..6e7daf6 100644 --- a/rust/Cargo.toml +++ b/rust/Cargo.toml @@ -59,6 +59,10 @@ reqwest = { version = "0.12", default-features = false, features = ["json", "rus # URL/query encoding (language-switcher `next` param) percent-encoding = "2" +# AT Protocol identity/crypto +multibase = "0.9" +base64 = "0.22" + # CLI clap = { version = "4", features = ["derive"] } diff --git a/rust/README.md b/rust/README.md index 4343c8f..3296f32 100644 --- a/rust/README.md +++ b/rust/README.md @@ -41,7 +41,7 @@ rust/ du-domain/ pure types + (planned) algorithms, no IO; JSONB payload structs du-db/ SQLx pool + per-aggregate query modules du-bio/ genomics file I/O (noodles) — scaffold - du-atproto/ AT Protocol / PDS federation — scaffold + du-atproto/ AT Protocol identity/crypto (did:key verify, DID/PDS resolution); OAuth client next du-external/ OpenAlex / ENA / AWS SES / Secrets — scaffold du-web/ Axum app: routes, Askama templates, i18n, HTMX, auth du-jobs/ scheduled workers — scaffold @@ -180,7 +180,12 @@ for DB-less builds. - [ ] ETL: remaining aggregates (genomics, ibd, ident, fed, social, billing) — validate read SQL against the live EC2 schema - [ ] Genomics ingestion (`du-bio` / noodles) + scheduled jobs (`du-jobs`) -- [ ] AT Protocol federation (`du-atproto`): DID login, firehose, PDS fleet +- [x] AT Protocol identity/crypto core (`du-atproto`): DID/AT-URI parse, did:key + Ed25519 verification, DID-doc/PDS resolution +- [ ] AT Protocol OAuth client + permission sets (PAR/DPoP/scopes) → PDS login. + Federation pivoted away from a custom private firehose toward protocol + permissions/OAuth + notify-then-fetch (private data bypasses the firehose); + group-private data spec is still maturing upstream - [ ] External clients (`du-external`): OpenAlex, ENA, AWS SES/Secrets - [ ] Tree-versioning change-sets; haplogroup↔variant association editing - [ ] Vendor remaining assets; full OpenAPI parity; cutover rehearsal diff --git a/rust/crates/du-atproto/Cargo.toml b/rust/crates/du-atproto/Cargo.toml index 16757f3..1d31be7 100644 --- a/rust/crates/du-atproto/Cargo.toml +++ b/rust/crates/du-atproto/Cargo.toml @@ -5,10 +5,14 @@ edition.workspace = true rust-version.workspace = true license.workspace = true -# AT Protocol: DID/handle resolution, Ed25519 signature verification, firehose -# decode, PDS client/fleet. Crypto + HTTP deps added during implementation. +# AT Protocol: DID/handle identity, did:key Ed25519 signature verification, and +# DID-document/PDS resolution. Foundation for the OAuth client + notify/fetch. [dependencies] du-domain = { workspace = true } serde = { workspace = true } serde_json = { workspace = true } thiserror = { workspace = true } +ed25519-dalek = { workspace = true } +multibase = { workspace = true } +base64 = { workspace = true } +reqwest = { workspace = true } diff --git a/rust/crates/du-atproto/src/did.rs b/rust/crates/du-atproto/src/did.rs new file mode 100644 index 0000000..bf09b25 --- /dev/null +++ b/rust/crates/du-atproto/src/did.rs @@ -0,0 +1,113 @@ +//! DID and AT-URI parsing, plus `did:key` <-> Ed25519 public key conversion. + +use crate::error::AtprotoError; +use ed25519_dalek::VerifyingKey; + +/// Multicodec prefix for an Ed25519 public key (`0xed`, varint-encoded as 0xed 0x01). +const ED25519_PUB_MULTICODEC: [u8; 2] = [0xed, 0x01]; + +/// A decentralized identifier. Supports the `did:plc:` and `did:web:` methods +/// used in AT Protocol, plus `did:key:` for self-certifying signing identities. +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct Did(pub String); + +impl Did { + pub fn parse(s: &str) -> Result { + let s = s.trim(); + if !s.starts_with("did:") || s.splitn(3, ':').count() < 3 { + return Err(AtprotoError::Parse(format!("not a DID: {s:?}"))); + } + Ok(Did(s.to_string())) + } + + pub fn method(&self) -> &str { + // did:: + self.0.split(':').nth(1).unwrap_or("") + } + + pub fn as_str(&self) -> &str { + &self.0 + } +} + +impl std::fmt::Display for Did { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + f.write_str(&self.0) + } +} + +/// A parsed AT-URI: `at:////` (collection and rkey +/// optional). The authority is a DID or handle. +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct AtUri { + pub authority: String, + pub collection: Option, + pub rkey: Option, +} + +impl AtUri { + pub fn parse(s: &str) -> Result { + let rest = s + .strip_prefix("at://") + .ok_or_else(|| AtprotoError::Parse(format!("not an at:// URI: {s:?}")))?; + let mut parts = rest.splitn(3, '/'); + let authority = parts + .next() + .filter(|a| !a.is_empty()) + .ok_or_else(|| AtprotoError::Parse("at-uri missing authority".into()))? + .to_string(); + Ok(AtUri { + authority, + collection: parts.next().map(str::to_string).filter(|s| !s.is_empty()), + rkey: parts.next().map(str::to_string).filter(|s| !s.is_empty()), + }) + } +} + +/// Decode a `did:key:z...` Ed25519 identity into a verifying key. +pub fn ed25519_from_did_key(did_key: &str) -> Result { + let mb = did_key + .strip_prefix("did:key:") + .ok_or_else(|| AtprotoError::Parse("not a did:key".into()))?; + let (_base, data) = multibase::decode(mb).map_err(|e| AtprotoError::Parse(e.to_string()))?; + let key = data + .strip_prefix(&ED25519_PUB_MULTICODEC[..]) + .ok_or_else(|| AtprotoError::Unsupported("did:key is not Ed25519".into()))?; + let arr: [u8; 32] = key + .try_into() + .map_err(|_| AtprotoError::Parse("Ed25519 key not 32 bytes".into()))?; + VerifyingKey::from_bytes(&arr).map_err(|e| AtprotoError::Crypto(e.to_string())) +} + +/// Encode an Ed25519 public key as a `did:key:z...` string (multibase base58btc). +pub fn did_key_from_ed25519(vk: &VerifyingKey) -> String { + let mut bytes = ED25519_PUB_MULTICODEC.to_vec(); + bytes.extend_from_slice(vk.as_bytes()); + format!("did:key:{}", multibase::encode(multibase::Base::Base58Btc, bytes)) +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn parses_dids_and_methods() { + assert_eq!(Did::parse("did:plc:abc123").unwrap().method(), "plc"); + assert_eq!(Did::parse("did:web:example.com").unwrap().method(), "web"); + assert!(Did::parse("nope").is_err()); + } + + #[test] + fn parses_at_uris() { + let u = AtUri::parse("at://did:plc:abc/app.decodingus.biosample/3k2l").unwrap(); + assert_eq!(u.authority, "did:plc:abc"); + assert_eq!(u.collection.as_deref(), Some("app.decodingus.biosample")); + assert_eq!(u.rkey.as_deref(), Some("3k2l")); + + let bare = AtUri::parse("at://did:plc:abc").unwrap(); + assert_eq!(bare.authority, "did:plc:abc"); + assert!(bare.collection.is_none()); + + assert!(AtUri::parse("https://x").is_err()); + } +} diff --git a/rust/crates/du-atproto/src/error.rs b/rust/crates/du-atproto/src/error.rs new file mode 100644 index 0000000..e29e3b8 --- /dev/null +++ b/rust/crates/du-atproto/src/error.rs @@ -0,0 +1,17 @@ +use thiserror::Error; + +#[derive(Debug, Error)] +pub enum AtprotoError { + #[error("parse error: {0}")] + Parse(String), + #[error("unsupported: {0}")] + Unsupported(String), + #[error("signature verification failed")] + BadSignature, + #[error("crypto error: {0}")] + Crypto(String), + #[error("resolution failed: {0}")] + Resolve(String), + #[error("http error: {0}")] + Http(#[from] reqwest::Error), +} diff --git a/rust/crates/du-atproto/src/lib.rs b/rust/crates/du-atproto/src/lib.rs index 0c3939b..37ac818 100644 --- a/rust/crates/du-atproto/src/lib.rs +++ b/rust/crates/du-atproto/src/lib.rs @@ -1,5 +1,17 @@ -//! AT Protocol / PDS federation (plan §7). Scaffold only. +//! AT Protocol identity, crypto, and resolution for DecodingUs (plan §7). //! -//! Planned: `did` (PLC directory + handle resolution), `signature` (Ed25519 -//! multibase verification against AT Protocol spec test vectors), `firehose` -//! (Atmosphere lexicon event decode), `pds` (client + fleet heartbeat/submission). +//! Federation direction (June 2026): the custom "private firehose" is replaced +//! by the protocol's permissions/OAuth + notify-then-fetch model. This crate is +//! the foundation needed under either model — DID/handle identity, `did:key` +//! Ed25519 signature verification, and DID-document/PDS resolution. The OAuth +//! client (permission sets, PAR, DPoP) builds on top of this next. + +pub mod did; +pub mod error; +pub mod resolve; +pub mod signature; + +pub use did::{AtUri, Did}; +pub use error::AtprotoError; +pub use resolve::{DidDocument, Resolver}; +pub use signature::verify_did_key; diff --git a/rust/crates/du-atproto/src/resolve.rs b/rust/crates/du-atproto/src/resolve.rs new file mode 100644 index 0000000..3ed0cf5 --- /dev/null +++ b/rust/crates/du-atproto/src/resolve.rs @@ -0,0 +1,177 @@ +//! Handle/DID resolution and DID-document parsing. +//! +//! - handle -> DID via the HTTPS well-known method (`/.well-known/atproto-did`). +//! (The DNS `_atproto` TXT method is a future addition; it needs a DNS dep.) +//! - DID -> DID document via the PLC directory (`did:plc`) or `did:web`. +//! - From the document: the PDS service endpoint and the signing `did:key`. +//! +//! Document parsing is pure and unit-tested; the HTTP fetch is isolated in +//! `Resolver`. + +use crate::did::Did; +use crate::error::AtprotoError; +use serde::Deserialize; + +#[derive(Debug, Clone, Deserialize)] +pub struct DidDocument { + pub id: String, + #[serde(default, rename = "alsoKnownAs")] + pub also_known_as: Vec, + #[serde(default, rename = "verificationMethod")] + pub verification_method: Vec, + #[serde(default)] + pub service: Vec, +} + +#[derive(Debug, Clone, Deserialize)] +pub struct VerificationMethod { + pub id: String, + #[serde(rename = "type")] + pub typ: String, + #[serde(rename = "publicKeyMultibase")] + pub public_key_multibase: Option, +} + +#[derive(Debug, Clone, Deserialize)] +pub struct Service { + pub id: String, + #[serde(rename = "type")] + pub typ: String, + #[serde(rename = "serviceEndpoint")] + pub service_endpoint: String, +} + +impl DidDocument { + /// The PDS service endpoint (`#atproto_pds` / `AtprotoPersonalDataServer`). + pub fn pds_endpoint(&self) -> Option<&str> { + self.service + .iter() + .find(|s| s.id.ends_with("#atproto_pds") || s.typ == "AtprotoPersonalDataServer") + .map(|s| s.service_endpoint.as_str()) + } + + /// The primary handle (`alsoKnownAs` `at://`), if any. + pub fn handle(&self) -> Option { + self.also_known_as + .iter() + .find_map(|a| a.strip_prefix("at://").map(str::to_string)) + } + + /// The signing key as a `did:key` (the Multikey `publicKeyMultibase` is the + /// did:key suffix). + pub fn signing_did_key(&self) -> Option { + self.verification_method + .iter() + .find_map(|vm| vm.public_key_multibase.as_ref().map(|m| format!("did:key:{m}"))) + } +} + +/// Resolves handles and DIDs over HTTPS. +pub struct Resolver { + client: reqwest::Client, + plc_directory: String, +} + +impl Default for Resolver { + fn default() -> Self { + Self::new() + } +} + +impl Resolver { + pub fn new() -> Self { + Resolver { + client: reqwest::Client::new(), + plc_directory: "https://plc.directory".to_string(), + } + } + + /// handle -> DID via `https:///.well-known/atproto-did`. + pub async fn resolve_handle(&self, handle: &str) -> Result { + let url = format!("https://{handle}/.well-known/atproto-did"); + let body = self.client.get(url).send().await?.error_for_status()?.text().await?; + Did::parse(body.trim()) + } + + /// DID -> DID document (`did:plc` via PLC directory, `did:web` via well-known). + pub async fn resolve_did(&self, did: &Did) -> Result { + let url = match did.method() { + "plc" => format!("{}/{}", self.plc_directory, did.as_str()), + "web" => did_web_doc_url(did.as_str())?, + m => return Err(AtprotoError::Unsupported(format!("did method: {m}"))), + }; + let doc = self + .client + .get(url) + .send() + .await? + .error_for_status()? + .json::() + .await?; + Ok(doc) + } + + /// Convenience: resolve a DID straight to its PDS endpoint. + pub async fn resolve_pds(&self, did: &Did) -> Result { + self.resolve_did(did) + .await? + .pds_endpoint() + .map(str::to_string) + .ok_or_else(|| AtprotoError::Resolve("no PDS endpoint in DID document".into())) + } +} + +/// `did:web:example.com` -> `https://example.com/.well-known/did.json`; +/// `did:web:example.com:u:alice` -> `https://example.com/u/alice/did.json`. +fn did_web_doc_url(did: &str) -> Result { + let rest = did + .strip_prefix("did:web:") + .ok_or_else(|| AtprotoError::Parse("not did:web".into()))?; + let mut parts = rest.split(':'); + let host = parts.next().unwrap_or("").replace("%3A", ":"); + let path: Vec<&str> = parts.collect(); + if path.is_empty() { + Ok(format!("https://{host}/.well-known/did.json")) + } else { + Ok(format!("https://{host}/{}/did.json", path.join("/"))) + } +} + +#[cfg(test)] +mod tests { + use super::*; + + // r##"…"## because the JSON contains the sequence `"#` (in "#atproto_pds"). + const FIXTURE: &str = r##"{ + "id": "did:plc:abc123", + "alsoKnownAs": ["at://alice.example.com"], + "verificationMethod": [{ + "id": "did:plc:abc123#atproto", + "type": "Multikey", + "controller": "did:plc:abc123", + "publicKeyMultibase": "zQ3shXjHeiBuRCKmM36cuYnm7YEMzhGnCmCyW92sRJ9pribSF" + }], + "service": [{ + "id": "#atproto_pds", + "type": "AtprotoPersonalDataServer", + "serviceEndpoint": "https://pds.example.com" + }] + }"##; + + #[test] + fn parses_did_document_pds_handle_and_key() { + let doc: DidDocument = serde_json::from_str(FIXTURE).unwrap(); + assert_eq!(doc.pds_endpoint(), Some("https://pds.example.com")); + assert_eq!(doc.handle().as_deref(), Some("alice.example.com")); + assert_eq!( + doc.signing_did_key().as_deref(), + Some("did:key:zQ3shXjHeiBuRCKmM36cuYnm7YEMzhGnCmCyW92sRJ9pribSF") + ); + } + + #[test] + fn did_web_url_host_and_path() { + assert_eq!(did_web_doc_url("did:web:example.com").unwrap(), "https://example.com/.well-known/did.json"); + assert_eq!(did_web_doc_url("did:web:example.com:u:alice").unwrap(), "https://example.com/u/alice/did.json"); + } +} diff --git a/rust/crates/du-atproto/src/signature.rs b/rust/crates/du-atproto/src/signature.rs new file mode 100644 index 0000000..f2ade13 --- /dev/null +++ b/rust/crates/du-atproto/src/signature.rs @@ -0,0 +1,61 @@ +//! Ed25519 signature verification against a `did:key` identity. Self-certifying: +//! the public key is encoded in the DID, so no network resolution is needed to +//! verify a payload signed by that key (used for signed PDS/edge-node requests +//! and IBD attestations). + +use crate::did::ed25519_from_did_key; +use crate::error::AtprotoError; +use base64::engine::general_purpose::STANDARD; +use base64::Engine; +use ed25519_dalek::Signature; + +/// Verify that `signature_b64` (standard base64 of a 64-byte Ed25519 signature) +/// over `message` was produced by the key in `did_key` (`did:key:z...`). +pub fn verify_did_key(did_key: &str, message: &[u8], signature_b64: &str) -> Result<(), AtprotoError> { + let vk = ed25519_from_did_key(did_key)?; + let sig_bytes = STANDARD + .decode(signature_b64.trim()) + .map_err(|e| AtprotoError::Parse(format!("signature base64: {e}")))?; + let sig = Signature::from_slice(&sig_bytes) + .map_err(|e| AtprotoError::Parse(format!("signature bytes: {e}")))?; + vk.verify_strict(message, &sig).map_err(|_| AtprotoError::BadSignature) +} + +#[cfg(test)] +mod tests { + use super::*; + use crate::did::did_key_from_ed25519; + use base64::engine::general_purpose::STANDARD; + use base64::Engine; + use ed25519_dalek::{Signer, SigningKey}; + + fn keypair() -> SigningKey { + // Deterministic seed (tests must not use RNG that breaks reproducibility). + SigningKey::from_bytes(&[7u8; 32]) + } + + #[test] + fn verifies_a_valid_signature() { + let sk = keypair(); + let did = did_key_from_ed25519(&sk.verifying_key()); + assert!(did.starts_with("did:key:z")); + let msg = b"de-identified call signature payload"; + let sig = STANDARD.encode(sk.sign(msg).to_bytes()); + assert!(verify_did_key(&did, msg, &sig).is_ok()); + } + + #[test] + fn rejects_tampered_message_and_wrong_key() { + let sk = keypair(); + let did = did_key_from_ed25519(&sk.verifying_key()); + let sig = STANDARD.encode(sk.sign(b"original").to_bytes()); + assert!(matches!( + verify_did_key(&did, b"tampered", &sig), + Err(AtprotoError::BadSignature) + )); + + let other = SigningKey::from_bytes(&[9u8; 32]); + let other_did = did_key_from_ed25519(&other.verifying_key()); + assert!(verify_did_key(&other_did, b"original", &sig).is_err()); + } +} From 43c0524df28e38a78eadeb33adf35ada653b2805 Mon Sep 17 00:00:00 2001 From: James Kane Date: Mon, 1 Jun 2026 11:10:40 -0500 Subject: [PATCH 013/191] feat(rust): AT Protocol OAuth client wiring + Edge findings The federation wiring pieces (consumer side of permissions/OAuth). Live handshake needs the Edge team's PDS; everything up to the network exchange is implemented and unit-tested. du-atproto oauth module (unit-tested, offline): - PKCE S256 (verified vs RFC 7636 vector), ES256 JOSE sign + JWK + RFC 7638 thumbprint, DPoP proof JWTs, private_key_jwt client assertion. - ClientMetadata (confidential web: private_key_jwt + ES256 + DPoP) and AuthServerMetadata + protected-resource discovery; PAR/authorize/token builders. du-web wiring: - OauthClient from env (OAUTH_BASE_URL/SCOPE/EC_KEY; disabled when unset). - Serves /oauth/client-metadata.json and /oauth/jwks.json (public key only). - /login/atproto: resolve handle->DID->PDS->authserver, PAR (DPoP, nonce retry), redirect; /oauth/callback: token exchange -> upsert user by DID -> session. - du-db: upsert_user_by_did (find-or-create + atproto login_info). - AppError::Upstream (502) for federation failures. Verified live: metadata + JWKS serve correctly (no private material leaks); /login with a bogus handle fails gracefully (502). Full flow pending Edge PDS. docs/atproto-oauth-findings.md enumerates the integration points to settle with the Edge team (client registration, hosting, scopes/permission sets, key lifecycle, DPoP nonce, identity resolution, notify-fetch). Workspace 22/22 green. Co-Authored-By: Claude Opus 4.8 (1M context) --- rust/Cargo.lock | 124 +++++++++ rust/Cargo.toml | 3 + rust/crates/du-atproto/Cargo.toml | 3 + rust/crates/du-atproto/src/lib.rs | 1 + rust/crates/du-atproto/src/oauth.rs | 381 +++++++++++++++++++++++++++ rust/crates/du-db/src/auth.rs | 32 +++ rust/crates/du-web/Cargo.toml | 2 + rust/crates/du-web/src/error.rs | 12 + rust/crates/du-web/src/main.rs | 6 +- rust/crates/du-web/src/oauth.rs | 289 ++++++++++++++++++++ rust/crates/du-web/src/routes/mod.rs | 1 + rust/crates/du-web/src/state.rs | 4 + rust/docs/atproto-oauth-findings.md | 76 ++++++ 13 files changed, 932 insertions(+), 2 deletions(-) create mode 100644 rust/crates/du-atproto/src/oauth.rs create mode 100644 rust/crates/du-web/src/oauth.rs create mode 100644 rust/docs/atproto-oauth-findings.md diff --git a/rust/Cargo.lock b/rust/Cargo.lock index 9d78dc7..a5f4135 100644 --- a/rust/Cargo.lock +++ b/rust/Cargo.lock @@ -278,6 +278,12 @@ version = "0.2.11" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4cbbc9d0964165b47557570cce6c952866c2678457aca742aafc9fb771d30270" +[[package]] +name = "base16ct" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4c7f02d4ea65f2c1853089ffd8d2787bdbc63de2f0d29dedbcf8ccdfa0ccd4cf" + [[package]] name = "base256emoji" version = "1.0.2" @@ -635,6 +641,18 @@ version = "0.8.21" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d0a5c400df2834b80a4c3327b3aad3a4c4cd4de0629063962b03235697506a28" +[[package]] +name = "crypto-bigint" +version = "0.5.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0dc92fb57ca44df6db8059111ab3af99a63d5d0f8375d9972e319a379c6bab76" +dependencies = [ + "generic-array", + "rand_core 0.6.4", + "subtle", + "zeroize", +] + [[package]] name = "crypto-common" version = "0.1.7" @@ -755,9 +773,12 @@ dependencies = [ "du-domain", "ed25519-dalek", "multibase", + "p256", + "rand_core 0.6.4", "reqwest", "serde", "serde_json", + "sha2", "thiserror", ] @@ -843,9 +864,11 @@ dependencies = [ "askama", "axum", "bcrypt", + "du-atproto", "du-db", "du-domain", "percent-encoding", + "reqwest", "serde", "serde_json", "tokio", @@ -857,6 +880,20 @@ dependencies = [ "uuid", ] +[[package]] +name = "ecdsa" +version = "0.16.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ee27f32b5c5292967d2d4a9d7f1e0b0aed2c15daded5a60300e4abb9d8020bca" +dependencies = [ + "der", + "digest", + "elliptic-curve", + "rfc6979", + "signature", + "spki", +] + [[package]] name = "ed25519" version = "2.2.3" @@ -890,6 +927,26 @@ dependencies = [ "serde", ] +[[package]] +name = "elliptic-curve" +version = "0.13.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b5e6043086bf7973472e0c7dff2142ea0b680d30e18d9cc40f267efbf222bd47" +dependencies = [ + "base16ct", + "crypto-bigint", + "digest", + "ff", + "generic-array", + "group", + "pem-rfc7468", + "pkcs8", + "rand_core 0.6.4", + "sec1", + "subtle", + "zeroize", +] + [[package]] name = "equivalent" version = "1.0.2" @@ -928,6 +985,16 @@ dependencies = [ "pin-project-lite", ] +[[package]] +name = "ff" +version = "0.13.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c0b50bfb653653f9ca9095b427bed08ab8d75a137839d9ad64eb11810d5b6393" +dependencies = [ + "rand_core 0.6.4", + "subtle", +] + [[package]] name = "fiat-crypto" version = "0.2.9" @@ -1073,6 +1140,7 @@ checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a" dependencies = [ "typenum", "version_check", + "zeroize", ] [[package]] @@ -1115,6 +1183,17 @@ dependencies = [ "wasip3", ] +[[package]] +name = "group" +version = "0.13.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f0f9ef7462f7c099f518d754361858f86d8a07af53ba9af0fe635bbccb151a63" +dependencies = [ + "ff", + "rand_core 0.6.4", + "subtle", +] + [[package]] name = "hashbrown" version = "0.12.3" @@ -1749,6 +1828,18 @@ version = "1.70.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "384b8ab6d37215f3c5301a95a4accb5d64aa607f1fcb26a11b5303878451b4fe" +[[package]] +name = "p256" +version = "0.13.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c9863ad85fa8f4460f9c48cb909d38a0d689dba1f6f6988a5e3e0d31071bcd4b" +dependencies = [ + "ecdsa", + "elliptic-curve", + "primeorder", + "sha2", +] + [[package]] name = "parking" version = "2.2.1" @@ -1877,6 +1968,15 @@ dependencies = [ "syn 2.0.117", ] +[[package]] +name = "primeorder" +version = "0.13.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "353e1ca18966c16d9deb1c69278edbc5f194139612772bd9537af60ac231e1e6" +dependencies = [ + "elliptic-curve", +] + [[package]] name = "proc-macro-crate" version = "3.5.0" @@ -2138,6 +2238,16 @@ dependencies = [ "webpki-roots 1.0.7", ] +[[package]] +name = "rfc6979" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f8dd2a808d456c4a54e300a23e9f5a67e122c3024119acbfd73e3bf664491cb2" +dependencies = [ + "hmac", + "subtle", +] + [[package]] name = "ring" version = "0.17.14" @@ -2292,6 +2402,20 @@ version = "4.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1c107b6f4780854c8b126e228ea8869f4d7b71260f962fefb57b996b8959ba6b" +[[package]] +name = "sec1" +version = "0.7.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d3e97a565f76233a6003f9f5c54be1d9c5bdfa3eccfb189469f11ec4901c47dc" +dependencies = [ + "base16ct", + "der", + "generic-array", + "pkcs8", + "subtle", + "zeroize", +] + [[package]] name = "semver" version = "1.0.28" diff --git a/rust/Cargo.toml b/rust/Cargo.toml index 6e7daf6..85a7131 100644 --- a/rust/Cargo.toml +++ b/rust/Cargo.toml @@ -62,6 +62,9 @@ percent-encoding = "2" # AT Protocol identity/crypto multibase = "0.9" base64 = "0.22" +sha2 = "0.10" +p256 = { version = "0.13", features = ["ecdsa"] } +rand_core = { version = "0.6", features = ["getrandom"] } # CLI clap = { version = "4", features = ["derive"] } diff --git a/rust/crates/du-atproto/Cargo.toml b/rust/crates/du-atproto/Cargo.toml index 1d31be7..15d9859 100644 --- a/rust/crates/du-atproto/Cargo.toml +++ b/rust/crates/du-atproto/Cargo.toml @@ -16,3 +16,6 @@ ed25519-dalek = { workspace = true } multibase = { workspace = true } base64 = { workspace = true } reqwest = { workspace = true } +sha2 = { workspace = true } +p256 = { workspace = true } +rand_core = { workspace = true } diff --git a/rust/crates/du-atproto/src/lib.rs b/rust/crates/du-atproto/src/lib.rs index 37ac818..651d543 100644 --- a/rust/crates/du-atproto/src/lib.rs +++ b/rust/crates/du-atproto/src/lib.rs @@ -8,6 +8,7 @@ pub mod did; pub mod error; +pub mod oauth; pub mod resolve; pub mod signature; diff --git a/rust/crates/du-atproto/src/oauth.rs b/rust/crates/du-atproto/src/oauth.rs new file mode 100644 index 0000000..55f94e3 --- /dev/null +++ b/rust/crates/du-atproto/src/oauth.rs @@ -0,0 +1,381 @@ +//! AT Protocol OAuth client wiring (plan §7; federation pivot to permissions/ +//! OAuth). The spec-defined, testable pieces: PKCE, ES256 JOSE (client assertion +//! + DPoP proofs), client + authorization-server metadata, and request builders. +//! +//! The interactive handshake (PAR -> redirect -> token) is orchestrated by +//! du-web on top of these; it requires a live PDS / authorization server, so the +//! end-to-end flow is exercised with the Edge team (see docs/atproto-oauth-findings.md). + +use crate::error::AtprotoError; +use base64::engine::general_purpose::URL_SAFE_NO_PAD; +use base64::Engine; +use p256::ecdsa::{signature::Signer, Signature, SigningKey, VerifyingKey}; +use serde::{Deserialize, Serialize}; +use sha2::{Digest, Sha256}; + +fn b64u(bytes: &[u8]) -> String { + URL_SAFE_NO_PAD.encode(bytes) +} + +// ── EC (P-256 / ES256) client key ──────────────────────────────────────────── + +/// The client's P-256 signing key (used for `private_key_jwt` client assertions +/// and DPoP proofs). Persisted as the base64url-encoded 32-byte scalar. +pub struct EcKey { + signing: SigningKey, +} + +impl EcKey { + pub fn generate() -> Self { + EcKey { signing: SigningKey::random(&mut rand_core::OsRng) } + } + + pub fn from_base64(s: &str) -> Result { + let bytes = URL_SAFE_NO_PAD + .decode(s.trim()) + .map_err(|e| AtprotoError::Parse(format!("ec key base64: {e}")))?; + let signing = SigningKey::from_slice(&bytes).map_err(|e| AtprotoError::Crypto(e.to_string()))?; + Ok(EcKey { signing }) + } + + pub fn to_base64(&self) -> String { + b64u(&self.signing.to_bytes()) + } + + pub fn verifying_key(&self) -> VerifyingKey { + *self.signing.verifying_key() + } + + /// Public key as a JWK (`{kty,crv,x,y}`), plus `kid` set to the thumbprint. + pub fn public_jwk(&self) -> serde_json::Value { + let (x, y) = self.xy(); + serde_json::json!({ + "kty": "EC", "crv": "P-256", "x": x, "y": y, + "use": "sig", "alg": "ES256", "kid": self.thumbprint(), + }) + } + + /// Bare public JWK used inside a DPoP header (no kid/use/alg). + pub fn dpop_jwk(&self) -> serde_json::Value { + let (x, y) = self.xy(); + serde_json::json!({ "kty": "EC", "crv": "P-256", "x": x, "y": y }) + } + + /// RFC 7638 JWK thumbprint (base64url SHA-256 of the canonical JWK). + pub fn thumbprint(&self) -> String { + let (x, y) = self.xy(); + // Canonical member ordering: crv, kty, x, y. + let canonical = format!(r#"{{"crv":"P-256","kty":"EC","x":"{x}","y":"{y}"}}"#); + b64u(&Sha256::digest(canonical.as_bytes())) + } + + fn xy(&self) -> (String, String) { + let ep = self.verifying_key().to_encoded_point(false); + (b64u(ep.x().unwrap()), b64u(ep.y().unwrap())) + } + + /// Sign a compact JWS (`b64u(header).b64u(payload).b64u(sig)`) with ES256. + pub fn sign_jws(&self, header: &serde_json::Value, payload: &serde_json::Value) -> String { + let signing_input = format!( + "{}.{}", + b64u(header.to_string().as_bytes()), + b64u(payload.to_string().as_bytes()) + ); + let sig: Signature = self.signing.sign(signing_input.as_bytes()); + format!("{}.{}", signing_input, b64u(&sig.to_bytes())) + } +} + +// ── PKCE ───────────────────────────────────────────────────────────────────── + +pub struct Pkce { + pub verifier: String, + pub challenge: String, +} + +impl Pkce { + pub fn generate() -> Self { + let mut bytes = [0u8; 32]; + rand_core::RngCore::fill_bytes(&mut rand_core::OsRng, &mut bytes); + Self::from_verifier(b64u(&bytes)) + } + + pub fn from_verifier(verifier: String) -> Self { + let challenge = b64u(&Sha256::digest(verifier.as_bytes())); + Pkce { verifier, challenge } + } +} + +/// A random URL-safe token (PKCE-style), for `state` / `jti`. +pub fn random_token() -> String { + let mut bytes = [0u8; 24]; + rand_core::RngCore::fill_bytes(&mut rand_core::OsRng, &mut bytes); + b64u(&bytes) +} + +// ── JWTs: client assertion + DPoP proof ────────────────────────────────────── + +/// `private_key_jwt` client assertion for authenticating at PAR/token endpoints. +pub fn client_assertion(key: &EcKey, client_id: &str, audience: &str, iat: i64) -> String { + let header = serde_json::json!({ "alg": "ES256", "typ": "JWT", "kid": key.thumbprint() }); + let payload = serde_json::json!({ + "iss": client_id, "sub": client_id, "aud": audience, + "jti": random_token(), "iat": iat, "exp": iat + 300, + }); + key.sign_jws(&header, &payload) +} + +/// A DPoP proof JWT binding a request (`htm` method, `htu` URL) to the key. +/// `nonce` is set when the server has supplied one; `ath` is the base64url +/// SHA-256 of the access token (required on token-bound requests). +pub fn dpop_proof( + key: &EcKey, + htm: &str, + htu: &str, + iat: i64, + nonce: Option<&str>, + access_token: Option<&str>, +) -> String { + let header = serde_json::json!({ "typ": "dpop+jwt", "alg": "ES256", "jwk": key.dpop_jwk() }); + let mut payload = serde_json::json!({ + "jti": random_token(), "htm": htm, "htu": htu, "iat": iat, + }); + if let Some(n) = nonce { + payload["nonce"] = serde_json::Value::String(n.to_string()); + } + if let Some(tok) = access_token { + payload["ath"] = serde_json::Value::String(b64u(&Sha256::digest(tok.as_bytes()))); + } + key.sign_jws(&header, &payload) +} + +// ── Metadata documents ─────────────────────────────────────────────────────── + +/// The client metadata document served at `client_id` (a stable HTTPS URL). +#[derive(Debug, Clone, Serialize)] +pub struct ClientMetadata { + pub client_id: String, + pub client_name: String, + pub client_uri: String, + pub redirect_uris: Vec, + pub grant_types: Vec, + pub response_types: Vec, + pub scope: String, + pub token_endpoint_auth_method: String, + pub token_endpoint_auth_signing_alg: String, + pub application_type: String, + pub dpop_bound_access_tokens: bool, + pub jwks_uri: String, +} + +impl ClientMetadata { + /// Confidential web client using `private_key_jwt` + DPoP (the atproto + /// recommendation for server-side apps). + pub fn confidential_web(base_url: &str, scope: &str) -> Self { + ClientMetadata { + client_id: format!("{base_url}/oauth/client-metadata.json"), + client_name: "Decoding Us".to_string(), + client_uri: base_url.to_string(), + redirect_uris: vec![format!("{base_url}/oauth/callback")], + grant_types: vec!["authorization_code".into(), "refresh_token".into()], + response_types: vec!["code".into()], + scope: scope.to_string(), + token_endpoint_auth_method: "private_key_jwt".into(), + token_endpoint_auth_signing_alg: "ES256".into(), + application_type: "web".into(), + dpop_bound_access_tokens: true, + jwks_uri: format!("{base_url}/oauth/jwks.json"), + } + } +} + +/// Authorization-server metadata (`/.well-known/oauth-authorization-server`). +#[derive(Debug, Clone, Deserialize)] +pub struct AuthServerMetadata { + pub issuer: String, + pub authorization_endpoint: String, + pub token_endpoint: String, + pub pushed_authorization_request_endpoint: Option, +} + +/// Protected-resource metadata (`/.well-known/oauth-protected-resource`) — names +/// the authorization server(s) for a PDS. +#[derive(Debug, Clone, Deserialize)] +pub struct ProtectedResourceMetadata { + #[serde(default)] + pub authorization_servers: Vec, +} + +/// Discover the authorization server for a PDS, then its metadata. +pub async fn discover_auth_server( + client: &reqwest::Client, + pds_url: &str, +) -> Result { + let prm: ProtectedResourceMetadata = client + .get(format!("{pds_url}/.well-known/oauth-protected-resource")) + .send() + .await? + .error_for_status()? + .json() + .await?; + let issuer = prm + .authorization_servers + .into_iter() + .next() + .ok_or_else(|| AtprotoError::Resolve("no authorization_servers for PDS".into()))?; + let meta: AuthServerMetadata = client + .get(format!("{issuer}/.well-known/oauth-authorization-server")) + .send() + .await? + .error_for_status()? + .json() + .await?; + Ok(meta) +} + +// ── Request builders (pure) ────────────────────────────────────────────────── + +/// PAR (pushed authorization request) form body. +#[allow(clippy::too_many_arguments)] +pub fn par_form( + client_id: &str, + redirect_uri: &str, + scope: &str, + state: &str, + code_challenge: &str, + login_hint: Option<&str>, + client_assertion_jwt: &str, +) -> Vec<(String, String)> { + let mut form = vec![ + ("response_type".into(), "code".into()), + ("client_id".into(), client_id.into()), + ("redirect_uri".into(), redirect_uri.into()), + ("scope".into(), scope.into()), + ("state".into(), state.into()), + ("code_challenge".into(), code_challenge.into()), + ("code_challenge_method".into(), "S256".into()), + ( + "client_assertion_type".into(), + "urn:ietf:params:oauth:client-assertion-type:jwt-bearer".into(), + ), + ("client_assertion".into(), client_assertion_jwt.into()), + ]; + if let Some(hint) = login_hint { + form.push(("login_hint".into(), hint.into())); + } + form +} + +/// Authorization-code token-exchange form body. +pub fn token_form( + client_id: &str, + redirect_uri: &str, + code: &str, + code_verifier: &str, + client_assertion_jwt: &str, +) -> Vec<(String, String)> { + vec![ + ("grant_type".into(), "authorization_code".into()), + ("code".into(), code.into()), + ("redirect_uri".into(), redirect_uri.into()), + ("client_id".into(), client_id.into()), + ("code_verifier".into(), code_verifier.into()), + ( + "client_assertion_type".into(), + "urn:ietf:params:oauth:client-assertion-type:jwt-bearer".into(), + ), + ("client_assertion".into(), client_assertion_jwt.into()), + ] +} + +/// Build the authorization redirect URL from a PAR `request_uri`. +pub fn authorize_url(authorization_endpoint: &str, client_id: &str, request_uri: &str) -> String { + let q = format!( + "client_id={}&request_uri={}", + urlencode(client_id), + urlencode(request_uri) + ); + let sep = if authorization_endpoint.contains('?') { '&' } else { '?' }; + format!("{authorization_endpoint}{sep}{q}") +} + +fn urlencode(s: &str) -> String { + // Minimal application/x-www-form-urlencoded for query values. + let mut out = String::with_capacity(s.len()); + for b in s.bytes() { + match b { + b'A'..=b'Z' | b'a'..=b'z' | b'0'..=b'9' | b'-' | b'_' | b'.' | b'~' => out.push(b as char), + _ => out.push_str(&format!("%{b:02X}")), + } + } + out +} + +#[cfg(test)] +mod tests { + use super::*; + use p256::ecdsa::signature::Verifier; + + fn decode_part(part: &str) -> serde_json::Value { + serde_json::from_slice(&URL_SAFE_NO_PAD.decode(part).unwrap()).unwrap() + } + + #[test] + fn pkce_matches_rfc7636_vector() { + // RFC 7636 Appendix B. + let p = Pkce::from_verifier("dBjftJeZ4CVP-mB92K27uhbUJU1p1r_wW1gFWFOEjXk".into()); + assert_eq!(p.challenge, "E9Melhoa2OwvFrEMTJguCHaoeK1t8URWbuGJSstw-cM"); + } + + #[test] + fn es256_jws_roundtrips_and_verifies() { + let key = EcKey::generate(); + let jwt = client_assertion(&key, "https://app.example/oauth/client-metadata.json", "https://pds.example", 1_700_000_000); + let parts: Vec<&str> = jwt.split('.').collect(); + assert_eq!(parts.len(), 3); + + let header = decode_part(parts[0]); + assert_eq!(header["alg"], "ES256"); + assert_eq!(header["kid"], key.thumbprint()); + let payload = decode_part(parts[1]); + assert_eq!(payload["iss"], "https://app.example/oauth/client-metadata.json"); + assert_eq!(payload["aud"], "https://pds.example"); + + // signature verifies against the public key over the signing input. + let signing_input = format!("{}.{}", parts[0], parts[1]); + let sig = Signature::from_slice(&URL_SAFE_NO_PAD.decode(parts[2]).unwrap()).unwrap(); + assert!(key.verifying_key().verify(signing_input.as_bytes(), &sig).is_ok()); + } + + #[test] + fn dpop_proof_has_jwk_htm_htu_ath() { + let key = EcKey::generate(); + let jwt = dpop_proof(&key, "POST", "https://pds.example/xrpc/com.atproto.server.getSession", 1_700_000_000, Some("srvnonce"), Some("access-tok")); + let parts: Vec<&str> = jwt.split('.').collect(); + let header = decode_part(parts[0]); + assert_eq!(header["typ"], "dpop+jwt"); + assert_eq!(header["jwk"]["crv"], "P-256"); + let payload = decode_part(parts[1]); + assert_eq!(payload["htm"], "POST"); + assert_eq!(payload["nonce"], "srvnonce"); + assert!(payload["ath"].is_string()); + } + + #[test] + fn ec_key_base64_roundtrips() { + let key = EcKey::generate(); + let b64 = key.to_base64(); + let restored = EcKey::from_base64(&b64).unwrap(); + assert_eq!(key.thumbprint(), restored.thumbprint()); + } + + #[test] + fn client_metadata_shape() { + let m = ClientMetadata::confidential_web("https://decoding-us.com", "atproto transition:generic"); + let v = serde_json::to_value(&m).unwrap(); + assert_eq!(v["client_id"], "https://decoding-us.com/oauth/client-metadata.json"); + assert_eq!(v["token_endpoint_auth_method"], "private_key_jwt"); + assert_eq!(v["dpop_bound_access_tokens"], true); + assert_eq!(v["redirect_uris"][0], "https://decoding-us.com/oauth/callback"); + } +} diff --git a/rust/crates/du-db/src/auth.rs b/rust/crates/du-db/src/auth.rs index f7f2340..0520880 100644 --- a/rust/crates/du-db/src/auth.rs +++ b/rust/crates/du-db/src/auth.rs @@ -35,6 +35,38 @@ pub async fn find_credential(pool: &PgPool, provider_key: &str) -> Result