cb4fbb9fa0dd10f12642472971a197b2b17a94a3
lrnassar
  Mon Oct 11 08:36:03 2021 -0700
Adding full path to hgsql util for cron environment.

diff --git src/utils/qa/hubPublicAutoUpdate src/utils/qa/hubPublicAutoUpdate
index 0061574..91a26c8 100755
--- src/utils/qa/hubPublicAutoUpdate
+++ src/utils/qa/hubPublicAutoUpdate
@@ -50,31 +50,31 @@
 def evaluateServer(serverToQuery):
     """Evaluate the input server, ensure it is valid and return corresponding hgsqlInputs"""
     if serverToQuery == 'dev':
         hgsqlInput = ['','hgcentraltest']
     elif serverToQuery == 'hgwbeta':
         hgsqlInput = ['-h hgwbeta ','hgcentralbeta']
     elif serverToQuery == 'rr':
         hgsqlInput = ['-h genome-centdb ','hgcentral']
     else:
         sys.exit("Server called must be either 'dev', 'hgwbeta', or 'rr'")
     return(hgsqlInput)
 
 def buildPubHubDic(hgsqlInput):
     """Build a dictionary out of the requested server's hubPublic table"""
     hubPublicDic = {}    
-    hubPublic = subprocess.run("hgsql "+hgsqlInput[0]+"-e 'select * from hubPublic' "+hgsqlInput[1],\
+    hubPublic = subprocess.run("/cluster/bin/x86_64/hgsql "+hgsqlInput[0]+"-e 'select * from hubPublic' "+hgsqlInput[1],\
                          check=True, shell=True, stdout=subprocess.PIPE, universal_newlines=True)
     hubPublicOutput = hubPublic.stdout.split('\n')[1:-1]
 
     for hub in hubPublicOutput:
         hub = hub.split('\t')
         hubPublicDic[hub[0]] = {}
         hubPublicDic[hub[0]] = {'hubUrl':hub[0],'shortLabel':hub[1],'longLabel':hub[2],\
                             'registrationTime':hub[3],'dbCount':hub[4],\
                             'dbList':hub[5],'descriptionUrl':hub[5]}
     return(hubPublicDic)
 
 def escapeDoubleQuotesOnLabels(label):
     """Look for single and double quotes in labels"""
     if '"' in label:
         label = label.replace('"','\\"')
@@ -119,31 +119,31 @@
             if line[0].rstrip().lstrip() == 'genome':
                 while "" in line:
                     line.remove("")
                 currentHub['dbList'].append(line[1].rstrip().lstrip())
         else:
             line = line.split(" ")
             if line[0].rstrip().lstrip() == 'genome':
                 while "" in line:
                     line.remove("")
                 currentHub['dbList'].append(line[1].rstrip().lstrip())
     currentHub['dbCount'] = len(currentHub['dbList'])
     return(currentHub)
 
 def printHgsql(hub,varToEdit,newVarValue,hgsqlInput,testMode):
     """hgsql command to fix the difference"""
-    cmd = "hgsql "+hgsqlInput[0]+"-e \"update hubPublic set "+varToEdit+" = '"+str(newVarValue)+ \
+    cmd = "/cluster/bin/x86_64/hgsql "+hgsqlInput[0]+"-e \"update hubPublic set "+varToEdit+" = '"+str(newVarValue)+ \
     "' where hubUrl = '"+hub+"'\" "+hgsqlInput[1]
     if not testMode:
         subprocess.run(cmd, check=True, shell=True, stdout=subprocess.PIPE, universal_newlines=True)
     print(cmd)
 
 def compareResults(hubPublicDic,currentHub,hub,hgsqlInput,testMode):
     """Compare the hubPublic values to the queried currentHub values and report"""
 
     if hubPublicDic[hub]['shortLabel'] != currentHub['shortLabel'].rstrip().lstrip():
         printHgsql(hub,'shortLabel',escapeDoubleQuotesOnLabels(currentHub['shortLabel'].rstrip().lstrip()),hgsqlInput,testMode)
         
     if hubPublicDic[hub]['longLabel'] != currentHub['longLabel'].rstrip().lstrip():     
         printHgsql(hub,'longLabel',escapeDoubleQuotesOnLabels(currentHub['longLabel'].rstrip().lstrip()),hgsqlInput,testMode)
 
     if int(hubPublicDic[hub]['dbCount']) != int(currentHub['dbCount']):