cleanup microservices, build out loom chart

README.md

@@ -32,6 +32,18 @@ In a production deployment:
 
 ## Configuration
 
+### Loom FHIR dataframe service
+
+The optional `helm/loom` chart deploys the Loom FHIR dataframe GraphQL server
+alongside a single chart-owned ClickHouse instance. See
+[`helm/loom/README.md`](./helm/loom/README.md) for the local-cluster smoke test,
+managed-backend configuration, and persistence settings.
+
+The local ClickHouse service is `clickhouse:9000`. ArangoDB is not
+silently deployed by the Gen3 parent chart: production installs must provide a
+managed/operator-owned ArangoDB service, while local smoke tests may enable
+the disposable backend in `helm/loom/values-local.yaml`.
+
 For a full set of configuration options see the [CONFIGURATION.md](./docs/CONFIGURATION.md) for a more in depth instructions on how to configure each service. 
 
 There's also an auto-generated table of basic configuration options here: 

docs/CONFIGURATION.md

@@ -232,7 +232,7 @@ guppy:
 
 You will also need a mapping file to map the fields you want to pull from postgres into the elasticsearch indices. There are too many fields to describe here, but an example mapping file can be found [here](https://github.com/uc-cdis/cdis-manifest/blob/master/gen3.biodatacatalyst.nhlbi.nih.gov/etlMapping.yaml).
 
-Last, guppy works closely with portal to render the explorer page. You will need to ensure a proper [dataExplorer block](https://github.com/uc-cdis/cdis-manifest/blob/master/gen3.biodatacatalyst.nhlbi.nih.gov/portal/gitops.json#L212) is setup within the gitops.json file, referencing fields that have been pulled from postgres into the elasticsearch indices.
+Last, guppy works closely with frontend-framework to render the explorer page. Ensure the frontend explorer configuration references fields that have been pulled from Postgres into the Elasticsearch indices.
 
 ## Extra Information
 
@@ -423,44 +423,6 @@ To configure peregrine we require an entry in the versions block. It also requir
 
 ---
 
-# Portal
-
-## What Does it Do
-
-Portal is a core service that renders the complete commons webpage, it is the front end service.
-
-## How to Configure it
-
-To configure portal we require an entry in the versions block. The portal_app also needs to be defined in the global block. Gitops sets to use the files in the ~/cdis-manifest/(commons url)/ portal directory, dev is the common setup for development environments and [there are default gitops.json](https://github.com/uc-cdis/data-portal/tree/master/data/config) files for most commons that the portal app can be set to.
-
-```yaml
-portal:
-  enabled: true
-
-  gitops:
-    # -- (string) multiline string - gitops.json
-    json: |
-      {}
-    # -- (string) - favicon in base64
-    favicon: ""
-    # -- (string) - multiline string - gitops.css
-    css: |
-      /* gitops default css */
-    # -- (string) - logo in base64
-    logo: ""
-    # -- (string) - createdby.png - base64
-    createdby: ""
-    sponsors:
-```
-
-
-To do this you can follow the example [here](https://github.com/uc-cdis/data-portal/blob/master/docs/portal_config.md).
-
-Portal can also be configured with different images and icons by updating the values, similar to [this](https://github.com/uc-cdis/cdis-manifest/tree/master/gen3.biodatacatalyst.nhlbi.nih.gov/portal).
-
-## Extra Information
-
----
 # Revproxy
 
 ## What Does it Do
@@ -605,4 +567,4 @@ sower:
       restart_policy: Never
 ```
 
-## Extra Information -->
+## Extra Information -->

docs/aced.md

@@ -28,18 +28,6 @@ helm repo update
 
 ## Aced specific files:
 
-* gitops.json - Controls windmill UI configuration - see values.yaml
-  Gitops values are encoded as a json string under portal.gitops.json
-  ```
-  portal:
-  ...  
-  # -- (map) GitOps configuration for portal
-    gitops:
-      # -- (string) multiline string - gitops.json
-      json: |
-
-  ```
-
 * fence-config.yaml - Authentication config. Same as legacy compose services file except addition of header
     ```
     fence:

docs/gen3_developer_environments.md

@@ -129,7 +129,7 @@ This is by design, it’s waiting for your dbcreate job(s) to finish which signa
 
 ## Local Dev Linux (Ubuntu) / Rancher Desktop Problems:
 
-If you've followed the instructions, see services running, but can't go to `https://localhost` to see portal... keep reading.
+If you've followed the instructions, see services running, but can't go to `https://localhost` to see the frontend... keep reading.
 
 If you see an Apache webpage at `localhost` (installed by default in Ubuntu), you have to kill the Apache service.
 
@@ -196,4 +196,3 @@ Other similar tools for developers include:
 These command-line tools can be a great option for developers who prefer to work in the terminal and want a more streamlined and efficient way to interact with their cluster. They are lightweight, easy to install and have a small footprint. They provide a simple and efficient way to manage and monitor your cluster.
 
 
-

docs/kubernetes-in-docker.md

@@ -95,21 +95,11 @@ fence:
         client_id: "<from previous step>"
         client_secret: "<from previous step>"
 
-# Use a prebuilt portal image if you're deploying to a laptop, less resources consumed by gen3
-portal:
-  resources:
-    requests:
-      cpu: "0.2"
-      memory: 100Mi
-  image:
-    repository: quay.io/cdis/data-portal-prebuilt
-    tag: dev
-
 ```
 
 ## deploy gen3
 
 ```bash
 helm repo add gen3 http://helm.gen3.org
 helm upgrade --install gen3 gen3/gen3 -f ./values.yaml 
-```
+```