b2c798d893c2ba4d477a91de5c02dc49455d1796
hiram
  Wed Jul 10 12:52:41 2024 -0700
correctly start priority after know browsers refs #33720

diff --git src/hg/hubApi/genomePriority.py src/hg/hubApi/genomePriority.py
index 3760c80..6279bd4 100755
--- src/hg/hubApi/genomePriority.py
+++ src/hg/hubApi/genomePriority.py
@@ -609,43 +609,30 @@
             priorityCounter += 1
             itemCount += 1
     totalItemCount += itemCount
     print(f"{totalItemCount:4} - total\tgenArk GCA count: {itemCount:4}")
     
     itemCount = 0
     for entry in dbDb:
         dbName = entry['name']
         if dbName not in allPriorities:
             allPriorities[dbName] = priorityCounter
             priorityCounter += 1
             itemCount += 1
     totalItemCount += itemCount
     print(f"{totalItemCount:4} - total\tthe rest of dbDb count: {itemCount:4}")
 
-def notUsed():
-    itemCount = 0
-    # finally the rest of the database genomes names
-    for dbName in sorted(allDbDbNames):
-        if dbName not in allPriorities:
-            allPriorities[dbName] = priorityCounter
-            priorityCounter += 1
-            itemCount += 1
-    totalItemCount += itemCount
-    print(f"{totalItemCount:4} - total\tthe rest of dbDb count: {itemCount:4}")
-
-
-
 ####################################################################
 
 """
 table load procedure:
 
   hgsql -e 'DROP TABLE IF EXISTS genomePriority;' hgcentraltest
   hgsql hgcentraltest < ../lib/genomePriority.sql
   hgsql -e 'LOAD DATA LOCAL INFILE "genomePriority.tsv" INTO
 TABLE genomePriority;' hgcentraltest
   hgsql -e 'ALTER TABLE genomePriority
 ADD FULLTEXT INDEX gdIx
 (name, commonName, scientificName, clade, description);' \
   hgcentraltest
 
 """
@@ -736,31 +723,31 @@
         else:
             print("no priority for ", gcAccession)
             sys.exit(255)
 
         cleanName = removeNonAlphanumeric(entry['commonName'])
         clade = entry['clade']
         descr = f"{entry['asmName']}"
         description = re.sub(r'\s+', ' ', descr).strip()
         outLine = f"{entry['gcAccession']}\t{priority}\t{entry['commonName'].encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description}\t1\n"
         fileOut.write(outLine)
         itemCount += 1
 
     totalItemCount += itemCount
     print(f"{totalItemCount:4} - total\tgenArk count: {itemCount:4}")
 
-    incrementPriority = len(allPriorities)
+    incrementPriority = len(allPriorities) + 1
     print("# incrementing priorities from: ", incrementPriority)
 
     itemCount = 0
     # Print the refSeq/genBank data
     for entry in refSeqGenBankSorted:
         gcAccession = entry['gcAccession']
         commonName = entry['commonName']
         scientificName = entry['scientificName']
         clade = entry['clade']
         descr = f"{entry['other']}"
         description = re.sub(r'\s+', ' ', descr).strip()
         outLine = f"{entry['gcAccession']}\t{incrementPriority}\t{entry['commonName'].encode('ascii', 'ignore').decode('ascii')}\t{entry['scientificName']}\t{entry['taxId']}\t{clade}\t{description.encode('ascii', 'ignore').decode('ascii')}\t0\n"
         fileOut.write(outLine)
         incrementPriority += 1
         itemCount += 1