updated scripts for new pfocr folders

gladstone-institutes · Sep 23, 2024 · cf7f6c1 · cf7f6c1
1 parent c971114
commit cf7f6c1
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/shiny_run/scripts/build_db.R b/shiny_run/scripts/build_db.R
@@ -12,7 +12,7 @@ build_db <- function(gmt.list, db.name){
   if(http_error(r.info)){
     stop("Failed to fetch PFOCR getFigureInfo.")
   }
-  json_content <- content(r.info, as = "text", encoding = "UTF-8")
+  json_content <- httr::content(r.info, as = "text", encoding = "UTF-8")
   json_list <- fromJSON(json_content, flatten = TRUE)
   df.pfocr <- as.data.frame(json_list) %>%
     dplyr::mutate(term = paste(figureInfo.pmcid,figureInfo.number,sep = "__")) %>%

diff --git a/shiny_run/scripts/build_db_ghaction.R b/shiny_run/scripts/build_db_ghaction.R
@@ -19,7 +19,7 @@ for(o in orgs){
   if(http_error(r.info)){
     stop("Failed to fetch PFOCR getFigureInfo.")
   }
-  json_content <- content(r.info, as = "text", encoding = "UTF-8")
+  json_content <- httr::content(r.info, as = "text", encoding = "UTF-8")
   json_list <- fromJSON(json_content, flatten = TRUE)
   df.pfocr <- as.data.frame(json_list) %>%
     dplyr::mutate(term = paste(figureInfo.pmcid,figureInfo.number,sep = "__")) %>%

diff --git a/shiny_run/scripts/fetch_gmts.sh b/shiny_run/scripts/fetch_gmts.sh
@@ -9,7 +9,7 @@ wget -O "shiny_run/databases/gmts/wp_hs_"${DATE}".gmt" "https://data.wikipathway
 wget -O "shiny_run/databases/gmts/wp_mm_"${DATE}".gmt" "https://data.wikipathways.org/current/gmt/wikipathways-"${WP_REL}"-gmt-Mus_musculus.gmt"
 
 ##PFOCR
-PFOCR_DATE=$(curl --silent https://data.wikipathways.org/pfocr/ | grep -oP '<a class=file-link href="\K\d+' | tail -n 1)
+PFOCR_DATE=$(curl --silent https://data.wikipathways.org/pfocr/current/ | grep 'pfocr-[0-9]\{8\}-gmt-Homo_sapiens\.gmt' | sed -E 's/.*pfocr-([0-9]{8})-gmt-Homo_sapiens\.gmt.*/\1/' | tail -n 1)
 wget -O "shiny_run/databases/gmts/pfocr_hs_"${DATE}".gmt" "https://data.wikipathways.org/pfocr/"${PFOCR_DATE}"/pfocr-"${PFOCR_DATE}"-gmt-Homo_sapiens.gmt"
 wget -O "shiny_run/databases/gmts/pfocr_mm_"${DATE}".gmt" "https://data.wikipathways.org/pfocr/"${PFOCR_DATE}"/pfocr-"${PFOCR_DATE}"-gmt-Mus_musculus.gmt"