aee8ef5ddbb8cabd33efa4767fcf761aff0be5a5
chmalee
  Wed Feb 6 12:06:12 2019 -0800
Fixing quoting error in copyHgcentral so chuck wills widow genome can be updated

diff --git src/utils/qa/copyHgcentral src/utils/qa/copyHgcentral
index ed4cf31..3b5369c 100755
--- src/utils/qa/copyHgcentral
+++ src/utils/qa/copyHgcentral
@@ -96,32 +96,32 @@
             diffList.append(i)
     print dbDbOrig + ":"
     for i in range(0,len(diffList)):
         print dbDbList[diffList[i]], "=", dbDb1[diffList[i]]
     print "\n" + dbDbDest + ":"
     for i in range(0,len(diffList)):
         print dbDbList[diffList[i]], "=", dbDb2[diffList[i]]
     print
 
 
 def runTest(testOptions, testTable, testField1, testField2, testOrder):
     """This function handles the running of test mode.  In test mode, all three
        servers are queried and tested for special cases.  The state of all three
        servers and any relevant error messages are output."""
     fileDev, fileBeta, fileRr = getFilename(testTable, testOptions.assembly)
-    testQuery = "select * from " + testTable + " where " + testField1 + "='" + \
-                 testField2 + "' order by " + testOrder
+    testQuery = "select * from " + testTable + " where " + testField1 + "=\"" + \
+                 testField2 + "\" order by " + testOrder
     queryDev = createFile(fileDev, "hgcentraltest", testQuery, "hgwdev")
     queryBeta = createFile(fileBeta, "hgcentralbeta", testQuery, "mysqlbeta")
     queryRr = createFile(fileRr, "hgcentral", testQuery, "genome-centdb")
     if queryDev == "" and queryBeta == "" and queryRr == "":
         printHeader(testTable)
         print "*** There is no", testTable, "data for", testOptions.assembly + ".  Check to make " \
               "sure you typed the\nassembly name properly. ***\n\n"
         return
     printOutput(testTable, queryDev, queryBeta, queryRr)
     if queryDev != queryBeta:
         print "*** There are", testTable, "differences between dev and beta ***"
         if testTable == "dbDb" and queryDev != "" and queryBeta != "":
             parseDbDb("dev", "beta", testOptions.assembly)
         else:
             print
@@ -136,38 +136,38 @@
     else:
         print "*** The", testTable, "data on beta and rr is identical ***\n"
     print
 
 
 def runExecute(execOptions, execTable, execField1, execField2, execOrder):
     """This function handles the running of execute mode.  If test mode has not
        been run first, the user is forced to run test mode.  If the data has
        changed on any server since test mode was run, the user is forced to run
        test mode again.  If the data is identical between the origin and destination,
        no data is copied.  If there are data differences between the origin and destination,
        the user is informed and forced to respond before anything is copied.  If the
        destination server is blank, the data is copied from the origin to the
        destination."""
     fileTestDev, fileTestBeta, fileTestRr = getFilename(execTable, execOptions.assembly)
-    execQuery = "select * from " + execTable + " where " + execField1 + "='" + \
-                 execField2 + "' order by " + execOrder
-    cladeQuery =  "select clade from genomeClade where genome='" + execField2 + "' limit 1"
+    execQuery = "select * from " + execTable + " where " + execField1 + "=\"" + \
+                 execField2 + "\" order by " + execOrder
+    cladeQuery =  "select clade from genomeClade where genome=\"" + execField2 + "\" limit 1"
     cladeBetaQuery = "select distinct(clade) from genomeClade order by clade"
-    deleteQuery = "delete from " + execTable + " where " + execField1 + "='" + execField2 + "'"
+    deleteQuery = "delete from " + execTable + " where " + execField1 + "=\"" + execField2 + "\""
     loadQueryBeta = "load data local infile '" + fileTestDev + "' into table " + execTable
     loadQueryRr = "load data local infile '" + fileTestBeta + "' into table " + execTable
-    activeZeroQuery = "update dbDb set active=0 where name='" + execField2 + "'"
+    activeZeroQuery = "update dbDb set active=0 where name=\"" + execField2 + "\""
     if not os.path.isfile(fileTestDev) or not os.path.isfile(fileTestBeta) or not \
             os.path.isfile(fileTestRr):
         printHeader(execTable)
         print "*** Test mode must be run before execute mode.  If test mode was already " \
               "run, it is\npossible that one of the output files was deleted.  Please " \
               "re-run test mode. ***\n\n"
         return
     queryTestDev = openFile(fileTestDev)
     queryExecuteDev = chopper(callHgsql("hgcentraltest", execQuery, "hgwdev"), "strip", "")
     queryTestBeta = openFile(fileTestBeta)
     queryExecuteBeta = chopper(callHgsql("hgcentralbeta", execQuery, "mysqlbeta"), "strip", "")
     queryTestRr = openFile(fileTestRr)
     queryExecuteRr = chopper(callHgsql("hgcentral", execQuery, "genome-centdb"), "strip", "")
     if queryTestDev != queryExecuteDev or queryTestBeta != queryExecuteBeta or \
             queryTestRr != queryExecuteRr: