From 1158e94040f0bd2686f6a6860108ed814be22ae1 Mon Sep 17 00:00:00 2001
From: Vince Carey <stvjc@channing.harvard.edu>
Date: Sun, 29 Sep 2024 06:17:19 -0400
Subject: [PATCH 1/4] Update DESCRIPTION

remove import of ontoProc
---
 DESCRIPTION | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 42a8ca1..6a0728a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: xCell2
 Type: Package
 Title: A Tool for Generic Cell Type Enrichment Analysis
-Version: 0.99.5
+Version: 0.99.5001
 Authors@R: 
     c(person(given = "Almog", 
              family = "Angel", 
@@ -23,7 +23,6 @@ Imports:
     SummarizedExperiment,
     Rfast,
     singscore,
-    ontoProc,
     ontologyIndex,
     tibble,
     dplyr,

From dd46f220395303baa427b3709d391d405183254c Mon Sep 17 00:00:00 2001
From: Vince Carey <stvjc@channing.harvard.edu>
Date: Sun, 29 Sep 2024 06:20:29 -0400
Subject: [PATCH 2/4] Update xCell2GetLineage.R, remove ontoProc refs

adds getOntoLocal
---
 R/xCell2GetLineage.R | 32 ++++++++++++++++++++++++++++++--
 1 file changed, 30 insertions(+), 2 deletions(-)

diff --git a/R/xCell2GetLineage.R b/R/xCell2GetLineage.R
index bef5d4c..e854706 100644
--- a/R/xCell2GetLineage.R
+++ b/R/xCell2GetLineage.R
@@ -4,7 +4,6 @@
 #' If no output file is specified, the function returns a list of cell type dependencies.
 #' If an output file is specified, the function writes the cell type dependencies to a TSV file.
 #'
-#' @importFrom ontoProc getOnto
 #' @importFrom ontologyIndex get_descendants get_ancestors
 #' @importFrom dplyr select mutate rowwise
 #' @importFrom tibble as_tibble
@@ -57,7 +56,7 @@ xCell2GetLineage <- function(labels, outFile = NULL) {
     lineageOut <- labelsUniq %>%
       dplyr::mutate(descendants = "", ancestors = "")
   } else {
-    cl <- ontoProc::getOnto(ontoname = "cellOnto", year_added = "2023")
+    cl <- getOntoLocal(ontoname = "cellOnto", year_added = "2023")
     labelsUniq$descendants <- NA
     labelsUniq$ancestors <- NA
     for (i in seq_len(nrow(labelsUniq))) {
@@ -99,3 +98,32 @@ xCell2GetLineage <- function(labels, outFile = NULL) {
     warning("It is recommended that you manually check the cell type lineage file: ", outFile)
   }
 }
+
+getOntoLocal = function( ontoname="cellOnto", year_added = "2023" ) {
+ stopifnot(ontoname %in% c("caro", "cellLineOnto", "cellOnto", "cellosaurusOnto", "chebi_full",
+"chebi_lite", "diseaseOnto", "efoOnto", "goOnto", "hcaoOnto", "mondo",
+"patoOnto", "PROnto", "uberon", "Pronto")   # only Pronto will get a 2021 PRO
+}
+ ah = AnnotationHub::AnnotationHub()
+ opd = AnnotationHub::query(ah, "ontoProcData")
+ meta = mcols(opd)
+ tmp = meta |> as.data.frame() |> dplyr::filter(grepl(year_added, rdatadateadded)) |> dplyr::select(title, description)
+
+
+ if (year_added == "2023") {
+     if( ontoname %in% c("caro", "cellLineOnto")) stop("this ontology not updated in 2023, use a different year_added value")
+    ontoname = paste0(ontoname, "_")
+    stopifnot(length(grep(ontoname, tmp$title))==1)
+ }
+ else if (year_added == "2022") {
+    ontoname = paste0(ontoname, "_")
+    stopifnot(length(grep(ontoname, tmp$title))==1)
+    }
+ else if (year_added == "2021") {
+    stopifnot(length(grep(paste0("^", ontoname, "$"), tmp$title))==1)
+    }
+ tmp = tmp |> filter(grepl(ontoname, title))
+ tag = rownames(tmp)
+ stopifnot(length(tag)==1)
+ ah[[tag]]
+}

From a05d1872b88570fd1f3d708fb6cf67cccea1ea20 Mon Sep 17 00:00:00 2001
From: Vince Carey <stvjc@channing.harvard.edu>
Date: Sun, 29 Sep 2024 06:23:33 -0400
Subject: [PATCH 3/4] fix typo

---
 R/xCell2GetLineage.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/xCell2GetLineage.R b/R/xCell2GetLineage.R
index e854706..a3e0e63 100644
--- a/R/xCell2GetLineage.R
+++ b/R/xCell2GetLineage.R
@@ -103,7 +103,7 @@ getOntoLocal = function( ontoname="cellOnto", year_added = "2023" ) {
  stopifnot(ontoname %in% c("caro", "cellLineOnto", "cellOnto", "cellosaurusOnto", "chebi_full",
 "chebi_lite", "diseaseOnto", "efoOnto", "goOnto", "hcaoOnto", "mondo",
 "patoOnto", "PROnto", "uberon", "Pronto")   # only Pronto will get a 2021 PRO
-}
+
  ah = AnnotationHub::AnnotationHub()
  opd = AnnotationHub::query(ah, "ontoProcData")
  meta = mcols(opd)

From e60655c8766ff70ed94b40802d62e0c1bca52085 Mon Sep 17 00:00:00 2001
From: Vince Carey <stvjc@channing.harvard.edu>
Date: Sun, 29 Sep 2024 06:24:22 -0400
Subject: [PATCH 4/4] fix typo

---
 R/xCell2GetLineage.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/xCell2GetLineage.R b/R/xCell2GetLineage.R
index a3e0e63..20197e7 100644
--- a/R/xCell2GetLineage.R
+++ b/R/xCell2GetLineage.R
@@ -102,7 +102,7 @@ xCell2GetLineage <- function(labels, outFile = NULL) {
 getOntoLocal = function( ontoname="cellOnto", year_added = "2023" ) {
  stopifnot(ontoname %in% c("caro", "cellLineOnto", "cellOnto", "cellosaurusOnto", "chebi_full",
 "chebi_lite", "diseaseOnto", "efoOnto", "goOnto", "hcaoOnto", "mondo",
-"patoOnto", "PROnto", "uberon", "Pronto")   # only Pronto will get a 2021 PRO
+"patoOnto", "PROnto", "uberon", "Pronto"))   # only Pronto will get a 2021 PRO
 
  ah = AnnotationHub::AnnotationHub()
  opd = AnnotationHub::query(ah, "ontoProcData")