dcbac768dccd258dcad4034ab114f3185dc262e1
steve
  Fri Dec 20 12:52:25 2013 -0800
Made commenting changes
diff --git src/utils/qa/copyHgcentral src/utils/qa/copyHgcentral
index 61f947f..75f7839 100755
--- src/utils/qa/copyHgcentral
+++ src/utils/qa/copyHgcentral
@@ -92,41 +92,33 @@
         dbDb1 = chopper(openFile("dbDb." + dbDbAssembly + ".hgcentralbeta"), "split", "\t")
         dbDb2 = chopper(openFile("dbDb." + dbDbAssembly + ".hgcentral"), "split", "\t")
     for i in range(0,len(dbDbList)):
         if dbDb1[i] != dbDb2[i]:
             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 is the main function.  In test mode, it queries all three servers
-       and tests for special cases.  It outputs the state of all three servers
-       and any relevant error messages.  In execute mode, it checks to make
-       sure test mode has been run first.  If test mode has not been run, it
-       forces the user to run test mode.  If the data has changed on any server
-       since test mode was run, it forces the user to run test mode again.  If
-       the data is identical between the origin and destination, it doesn't copy
-       anything.  If the data is different between the origin and destination,
-       it informs the user and makes the user respond before copying.  If the
-       destination server is blank, it copies the data from the origin to the
-       destination."""
+    """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
     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 != "":
@@ -135,30 +127,38 @@
             print
     else:
         print "*** The", testTable, "data on dev and beta is identical ***\n"
     if queryBeta != queryRr:
         print "*** There are", testTable, "differences between beta and rr ***"
         if testTable == "dbDb" and queryBeta != "" and queryRr != "":
             parseDbDb("beta", "rr", testOptions.assembly)
         else:
             print
     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"
     cladeBetaQuery = "select distinct(clade) from genomeClade order by clade"
     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 + "'"
     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"