402c2d84232e0d2b00eeef77e56a1372ac31c710
wong
  Wed Feb 22 13:12:55 2012 -0800
changed some error handling stuff in mkChangeNotes, and made revoked gbdbs removed from the changed gbdbs list
diff --git python/lib/ucscgenomics/mkChangeNotes.py python/lib/ucscgenomics/mkChangeNotes.py
index 4783754..425abc8 100644
--- python/lib/ucscgenomics/mkChangeNotes.py
+++ python/lib/ucscgenomics/mkChangeNotes.py
@@ -480,48 +480,54 @@
             output.extend(self.__printSectionOne(output, ucscUtils.printIter(revokedFiles, self.releasePath), "Revoked Files"))
             output.extend(self.__printSectionOne(output, ucscUtils.printIter(revokedGbdbs, self.gbdbPath), "Revoked Gbdbs"))
         if self.atticSet:
             output.append("Attic Objects")
             output.extend(ucscUtils.printIter((self.atticSet), self.releasePath))
 
         if not args['ignore']:
             output.append("No Errors")
         else:
             output.append("The counts here were generated by ignoring errors, they may not be correct")
         return output
 
     def printErrors(self, errors, missingFiles):
         errorsDict = {}
         output = []
+        lastpart = []
         for i in errors:
+            if not re.match(".+:.+", i):
+                lastpart.append(i)
+                continue
             line = i.split(":", 1)
             try:
                 errorsDict[line[0]].append(line[1])
             except:
                 errorsDict[line[0]] = []
                 errorsDict[line[0]].append(line[1])
         output.append("Errors (%s):" % len(errors))
         for i in sorted(errorsDict.keys()):
             output.append("%s:" % i)
             for j in sorted(errorsDict[i]):
                 output.append("%s" % j)
         output.append("\n")
         if missingFiles:
             output.extend(self.__addMissingToReport(missingFiles, "Files", self.releasePathOld))
             output.append("\n")
         if self.droppedTables:
             output.extend(self.__addMissingToReport(self.droppedTables, "Tables"))
+        if lastpart:
+            output.extend(lastpart)
         return output
 
     def __init__(self, args):
         self.releaseNew = args['releaseNew']
         self.releaseOld = args['releaseOld']
         self.database = args['database']
         self.composite = args['composite']
         self.loose = args['loose']
         self.ignore = args['ignore']
         self.summary = args['summary']
         self.specialMdb = args['specialMdb']
         self.args = args
         if 'verbose' in args:
             self.verbose = args['verbose']
         else:
@@ -603,31 +609,31 @@
             self.stillInAttic = self.oldAtticSet & self.atticSet
             self.oldTableSet = self.oldTableSet - self.atticSet
             self.noMoreAttic = self.oldAtticSet - self.atticSet
 
             self.changedTables = self.oldTableSet - self.newTableSet - self.revokedTableSet
 
 
             #same as above except for gbdbs
             if self.verbose >= 1:
                 sys.stderr.write("Checking GBDB status\n")
             (self.newGbdbSet, self.revokedGbdbs, newGbdbError) = self.getGbdbFiles("new")
             (self.oldGbdbSet, eggs, oldGbdbError) = self.getGbdbFiles("old")
             #remove missing files from gbdbs
             self.oldGbdbSet = self.oldGbdbSet - self.missingFiles
             self.oldGbdbSet = self.oldGbdbSet - self.atticSet
-            self.changedGbdbs = self.oldGbdbSet - self.newGbdbSet
+            self.changedGbdbs = self.oldGbdbSet - self.newGbdbSet - self.revokedGbdbs
             for i in self.missingFiles:
                 if i in self.oldReleaseFiles:
                     del self.oldReleaseFiles[i]
 
             #fill in the errors
             errors.extend(newFileErrors)
             errors.extend(oldFileErrors)
             errors.extend(newTableError)
             errors.extend(oldTableError)
             errors.extend(newGbdbError)
             errors.extend(oldGbdbError)
 
             if self.changedTables:
                 errors.append("These tables were tables in the old release, but are no longer tables in the new release:")
                 errors.extend(list(self.changedTables))