cd52f66464cce415303d7ae24ba28603c927ee4f
hiram
  Thu Mar 6 15:39:33 2025 -0800
better names in ncbiRefSeq track fields and updated related trackDb URLs refs #32704

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 2a600ed423d..8df11135e9b 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -507,83 +507,83 @@
 longLabel RefSeq gene predictions from NCBI
 group genes
 visibility pack
 type bigBed
 dragAndDrop subTracks
 allButtonPair on
 dataVersion $dataVersion
 html html/%s.refSeqComposite
 priority 2
 
         track ncbiRefSeq
         parent refSeqComposite on
         color 12,12,120
         shortLabel RefSeq All
         type bigGenePred
-        urls geneName=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$?report=genbank\" geneName2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\"
+        urls name2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
         labelFields name,geneName,geneName2
         defaultLabelFields geneName2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeq.ix
         bigDataUrl bbi/%s.ncbiRefSeq.bb
         longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 1\n\n" "${asmId}" "${asmId}" "${asmId}"
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx
 
     printf "        track ncbiRefSeqCurated
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Curated
         longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
         type bigGenePred
-        urls geneName=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$?report=genbank\" geneName2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\"
+        urls name2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
         labelFields name,geneName,geneName2
         defaultLabelFields geneName2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeqCurated.ix
         idXref ncbiRefSeqLink mrnaAcc name
         bigDataUrl bbi/%s.ncbiRefSeqCurated.bb
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 2\n\n" "${asmId}" "${asmId}"
   fi
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx
 
     printf "        track ncbiRefSeqPredicted
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Predicted
         longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
         type bigGenePred
-        urls geneName=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$?report=genbank\" geneName2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\"
+        urls name2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
         labelFields name,geneName,geneName2
         defaultLabelFields geneName2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeqPredicted.ix
         idXref ncbiRefSeqLink mrnaAcc name
         bigDataUrl bbi/%s.ncbiRefSeqPredicted.bb
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 3\n\n" "${asmId}" "${asmId}"
   fi
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqOther.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ixx