bugfixes for BGsync

VariantEffect · Jun 28, 2018 · 15e0f3f · 15e0f3f
1 parent 237ff24
commit 15e0f3f
Show file tree

Hide file tree

Showing 4 changed files with 7 additions and 9 deletions.
diff --git a/docker/cgi/mavevis.js b/docker/cgi/mavevis.js
@@ -259,7 +259,7 @@ $(document).ready(function(){
 
 		resetMost();
 
-		ssid = items.ssid;
+		ssid = items.urn;
 
 		$("#molecule").val(items.value);
 		//if a uniprot ID is available, automatically fill it in
@@ -525,7 +525,6 @@ $(document).ready(function(){
 	function processURLParameters() {
 		//get URL parameters
 		params = getURLParameters();
-		console.log(params);
 		//if there are any, process them
 		if (params && ("ssid" in params)) {
 			//query the backend to find matching datasets
@@ -538,7 +537,7 @@ $(document).ready(function(){
 					//(even though there should be at most one match)
 					$.each(data,function(i,items) {
 						//if this is the matching entry, select it.
-						if (items["ssid"] == params["ssid"]) {
+						if (items["urn"] == params["ssid"]) {
 							selectScoreset(items);
 						}
 					})

diff --git a/docker/cgi/searchScoresets.R b/docker/cgi/searchScoresets.R
@@ -25,7 +25,7 @@ tryCatch({
 
 #if a search term was provided, filter the index by it
 if (("term" %in% names(input))) {
-	is <- which(grepl(tolower(input$term),tolower(idx$label)) | idx$ssid == input$term)
+	is <- which(grepl(tolower(input$term),tolower(idx$label)) | idx$urn == input$term)
 	if (length(is) == 0) {
 		respondJSON(list())
 		quit(save="no",status=0)

diff --git a/docker/searchIndex.csv b/docker/searchIndex.csv
@@ -1,3 +1,2 @@
-value,label,ssid,uniprot,syn,stop,offset,wt
-"SCS000001A.1: YAP65 WW-domain","YAP65 WW-domain",SCS000001A.1,P46937,manual,auto,170,GACGTTCCACTGCCGGCTGGTTGGGAAATGGCTAAAACTAGTTCTGGTCAGCGTTACTTCCTGAACCACATCGACCAGACCACCACGTGGCAGGACCCGCGT
-"SCS000002A.1: UBE2I imputed & refined","UBE2I imputed & refined",SCS000002A.1,P63279,manual,manual,0,
+"value","label","urn","target","uniprot","syn","stop","offset","wt"
+"urn:mavedb:00000001-a-1: UBE2I imputed & refined","UBE2I imputed & refined","urn:mavedb:00000001-a-1","UBE2I","P63279","auto","manual",0,"ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCATGGAGGAAAGACCACCCATTTGGTTTCGTGGCTGTCCCAACAAAAAATCCCGATGGCACGATGAACCTCATGAACTGGGAGTGCGCCATTCCAGGAAAGAAAGGGACTCCGTGGGAAGGAGGCTTGTTTAAACTACGGATGCTTTTCAAAGATGATTATCCATCTTCGCCACCAAAATGTAAATTCGAACCACCATTATTTCACCCGAATGTGTACCCTTCGGGGACAGTGTGCCTGTCCATCTTAGAGGAGGACAAGGACTGGAGGCCAGCCATCACAATCAAACAGATCCTATTAGGAATACAGGAACTTCTAAATGAACCAAATATCCAAGACCCAGCTCAAGCAGAGGCCTACACGATTTACTGCCAAAACAGAGTGGAGTACGAGAAAAGGGTCCGAGCACAAGCCAAGAAGTTTGCGCCCTCATAA"
diff --git a/docker/sync.R b/docker/sync.R
@@ -125,11 +125,11 @@ tryCatch({
 		mutCacheFile <- paste0(cache.dir,urn,"_muts.csv")
 		if (!file.exists(mutCacheFile)) {
 			#if not, do so
-			if (!exists(scoreTable)) {
+			if (!exists("scoreTable")) {
 				scoreTable <- read.csv(scoreCacheFile)
 			}
 			if (!all(is.na(scoreTable$hgvs_pro))) {
-				varInfo <- parseHGVS(scoreTable$hgvs_pro)
+				varInfo <- parseHGVS(scoreTable$hgvs_pro,aacode=1)
 				write.table(varInfo,mutCacheFile,sep=",",row.names=FALSE)
 			} else {
 				logger(paste("WARNING: Scoreset",urn,"has no protein-level variant descriptors."))