9569314078469a67c56e832c06406f5d4984200e
gperez2
  Wed Aug 4 13:40:27 2021 -0700
Updating the cron to expect 3 table discrepancy due to the relatedTrack table in hg38, no RM

diff --git src/utils/qa/checkSyncAndMetaDataAll.py src/utils/qa/checkSyncAndMetaDataAll.py
index dbcedd5..6919894 100755
--- src/utils/qa/checkSyncAndMetaDataAll.py
+++ src/utils/qa/checkSyncAndMetaDataAll.py
@@ -1,95 +1,98 @@
 #Lou - 14/08/19
 
 #Make a list of all assemblies in hgCentral with active=1
 allDbs = get_ipython().getoutput(u'hgsql -h genome-centdb -e "SELECT name FROM dbDb WHERE active = 1 ORDER BY RAND()" hgcentral | grep -v "name"')
 
 #Initialize list to hold assemblies with errors
 troubleDbs = []
 
 #Iterate through allDbs and run checkSync.csh comparing to hgw1
 for db in allDbs:
     checkSyncResults = get_ipython().getoutput(u"checkSync.csh '$db' hgw1 hgwbeta")
     if db == 'mm9':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     elif db == 'hg18':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     elif db == 'hg19':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  5 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
+    elif db == 'hg38':
+        if '  0 hgw1.only' not in str(checkSyncResults) and '  3 hgwbeta.only' not in str(checkSyncResults):
+            troubleDbs.append(db)
     else:
         if '  0 hgw1.only' not in str(checkSyncResults) and '  2 hgwbeta.only' not in str(checkSyncResults):
             troubleDbs.append(db)
     
 #Iterate through allDbs and run checkSync.csh comparing to hgw2, informing of discrepancies
 for db in allDbs:
     checkSyncResults = get_ipython().getoutput(u"checkSync.csh '$db' hgw2 hgwbeta")
     
     if db == 'mm9':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
     elif db == 'hg18':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  4 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
     elif db == 'hg19':
         if '  0 hgw1.only' not in str(checkSyncResults) and '  5 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
     else:
         if '  0 hgw1.only' not in str(checkSyncResults) and '  2 hgwbeta.only' not in str(checkSyncResults)             and db not in troubleDbs:
             get_ipython().system(u" echo There looks to be a discrepancy between hgw1 and hgw2 checkSync for: '$db'")
             get_ipython().system(u" echo Follow up with checkSync.csh '$db' hgw1 hgw2")
             get_ipython().system(u' echo')
             troubleDbs.append(db)
     
 #Only if an error is found, rerun checkSyncs and display those results
 if troubleDbs == []:
     get_ipython().system(u' echo "There were no errors found between hgw1/hgw2 and beta tables (checkSync.csh)"')
     get_ipython().system(u' echo')
 else:
     get_ipython().system(u' echo Discrepancies between hgw1/hgw2 and beta tables:')
     get_ipython().system(u' echo')
     for db in troubleDbs:
         get_ipython().system(u" echo checkSync.csh for '$db'")
         get_ipython().system(u" checkSync.csh '$db' hgw1 hgwbeta")
 
 troubleDbs = []
 
 #Run checkMetaData on allDbs filtering out for only unexpected results
 for db in allDbs:
     checkMetaDataResults = get_ipython().getoutput(u"checkMetaData.csh '$db' rr hgwbeta")
     if str('0 dbDb.'+db+'.hgcentralOnly') and str('0 dbDb.'+db+'.hgcentralbetaOnly')     and str('0 blatServers.'+db+'.hgcentralOnly') and str('0 blatServers.'+db+'.hgcentralbetaOnly')     and str('0 defaultDb.'+db+'.hgcentralOnly') and str('0 defaultDb.'+db+'.hgcentralbetaOnly')     and str('0 genomeClade.'+db+'.hgcentralOnly') and str('0 genomeClade.'+db+'.hgcentralbetaOnly')     and str('0 liftOverChain.'+db+'.hgcentralOnly') and str('0 liftOverChain.'+db+'.hgcentralbetaOnly')     not in str(checkMetaDataResults):
         troubleDbs.append(db)
         
 #Only if an error is found, rerun checkMetaData and display those results
 if troubleDbs == []:
     get_ipython().system(u' echo "There were no errors found between rr and hgwbeta MetaData (checkMetaData.csh)"')
     get_ipython().system(u' echo')
 else:
     get_ipython().system(u' echo Discrepancies between rr and hgwbeta MetaData:')
     get_ipython().system(u' echo')
     for db in troubleDbs:
         get_ipython().system(u" checkMetaData.csh '$db' rr hgwbeta")
         
 get_ipython().system(u' echo')
 get_ipython().system(u' echo Additional Resources:')
 get_ipython().system(u' echo checkMetaData example 1: http://genomewiki.ucsc.edu/genecats/index.php/Monitoring_Tasks_Notes#Cronjob:_Results_from_checkMetaAday.csh')
 get_ipython().system(u' echo checkMetaData example 2: http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_4_RR_Steps#RR:_checkMetaData')
 get_ipython().system(u' echo RM ticket: http://redmine.soe.ucsc.edu/issues/23998')
         
 #Remove all temp files
 get_ipython().system(u' rm blatServers.*')
 get_ipython().system(u' rm dbDb.*')
 get_ipython().system(u' rm defaultDb.*')
 get_ipython().system(u' rm genomeClade.*')
 get_ipython().system(u' rm liftOverChain.*')