ba6b31f2a96fc3720971e888928de9d28d40b60d
wong
  Fri Oct 28 14:45:43 2011 -0700
declared some attributes earlier to bypass a qa check.
diff --git python/lib/ucscgenomics/mkChangeNotes.py python/lib/ucscgenomics/mkChangeNotes.py
index 8a9a3ba..5109596 100644
--- python/lib/ucscgenomics/mkChangeNotes.py
+++ python/lib/ucscgenomics/mkChangeNotes.py
@@ -333,71 +333,63 @@
             output.extend(ucscUtils.printIter(missing, path))
             output.append("\n")
         return output
 
     def __checkAtticNotInTrackDb(self):
         errors = []
         atticTables = self.newMdb.filter(lambda s: s['objType'] == 'table' and 'attic' in s, lambda s: s['tableName'])
         for i in atticTables:
             foo = self.trackDb.filter(lambda s: i in s['track'], lambda s: s['track'])
             if foo:
                 errors.append("trackDb: %s is attic in metaDb, has an active trackDb entry" % i)
 
         return errors
 
     def printReport(self, args, c):
-        (totalFiles, newGbdbSet, newTableSet, additionalList, oldAdditionalList, oldTableSet, oldReleaseFiles, oldGbdbSet, atticSet, revokedFiles, revokedTableSet, revokedGbdbs, missingFiles, newSupplementalSet, oldSupplementalSet) = (self.totalFiles, self.newGbdbSet, self.newTableSet, self.additionalList, self.oldAdditionalList, self.oldTableSet, self.oldTotalFiles, self.oldGbdbSet, self.atticSet, self.revokedFiles, self.revokedTableSet, self.revokedGbdbs, self.missingFiles, self.newSupplementalSet, self.oldSupplementalSet)
+        (totalFiles, newGbdbSet, newTableSet, additionalList, oldAdditionalList, oldTableSet, oldReleaseFiles, oldGbdbSet, atticSet, revokedFiles, revokedTableSet, revokedGbdbs, missingFiles, newSupplementalSet, oldSupplementalSet, pushTables, pushFiles, pushGbdbs, newSupp) = (self.totalFiles, self.newGbdbSet, self.newTableSet, self.additionalList, self.oldAdditionalList, self.oldTableSet, self.oldTotalFiles, self.oldGbdbSet, self.atticSet, self.revokedFiles, self.revokedTableSet, self.revokedGbdbs, self.missingFiles, self.newSupplementalSet, self.oldSupplementalSet, self.pushTables, self.pushFiles, self.pushGbdbs, self.newSupp)
         #the groups here need to be predefined, I just copied and pasted after working out what they were
         sep = "\n"
         output = []
 
         #maths
         allTables = newTableSet | oldTableSet | revokedTableSet
-        pushTables = set(sorted((self.newTableSet - self.oldTableSet)))
         untouchedTables = oldTableSet & newTableSet
 
         allFiles = totalFiles | oldReleaseFiles | revokedFiles
-        pushFiles = set(sorted((self.totalFiles - self.oldTotalFiles)))
         newFiles = pushFiles - revokedFiles
         untouchedFiles = (totalFiles & oldReleaseFiles) - revokedFiles
         filesNoRevoke = totalFiles - revokedFiles
 
         allGbdbs = newGbdbSet | oldGbdbSet | revokedGbdbs
         untouchedGbdbs = (newGbdbSet & oldGbdbSet) - revokedGbdbs
-        pushGbdbs = set(sorted((self.newGbdbSet - self.oldGbdbSet)))
 
         allSupp = newSupplementalSet | oldSupplementalSet
-        newSupp = newSupplementalSet - oldSupplementalSet
         removedSupp = oldSupplementalSet - newSupplementalSet
         untouchedSupp = oldSupplementalSet & newSupplementalSet
 
         allOther = additionalList | oldAdditionalList
         removedOther = oldAdditionalList - additionalList
 
         output.extend(self.__qaHeader(output, newTableSet, filesNoRevoke, newGbdbSet, newSupp, additionalList, revokedTableSet, revokedFiles, revokedGbdbs, pushFiles, pushGbdbs, args, c))
 
         output.extend(self.__printSection(pushTables, untouchedTables, revokedTableSet, allTables, "tables", 0, args['summary']))
         output.extend(self.__printSection(pushFiles, untouchedFiles, revokedFiles, allFiles, "download", self.releasePath, args['summary']))
         output.extend(self.__printSection(pushGbdbs, untouchedGbdbs, revokedGbdbs, allGbdbs, "gbdbs", self.gbdbPath, args['summary']))
         output.extend(self.__printSection(newSupp, untouchedSupp, removedSupp, allSupp, "supplemental", self.releasePath, args['summary']))
 
         #These attributes are the critical ones that are used by qaInit, others could potentially use these also.
-        self.newTables = set(pushTables)
-        self.newFiles = set(ucscUtils.printIter(pushFiles, self.releasePath))
-        self.newGbdbs = set(ucscUtils.printIter(pushGbdbs, self.gbdbPath))
-        self.newSupplemental = set(ucscUtils.printIter(newSupp, self.releasePath))
-        self.newOthers = set(ucscUtils.printIter(additionalList, self.releasePath))
+
 
         otherprint = len(allOther)
         if otherprint:
             output.append("\n")
             output.append("OTHER FILES:")
             output.append("New: %s" % len(additionalList))
             output.append("Revoked/Replace: %s" % len(removedOther))
             output.append("Total: %s" % len(allOther))
         if otherprint and not args['summary']:
             output.append("")
             output.append("New Other Files (%s):" % len(additionalList))
             output.extend(sorted(list(self.newOthers)))
             output.append("")
             output.append("Revoked Other Files (%s):" % len(removedOther))
             output.extend(ucscUtils.printIter((removedOther), self.releasePath))
@@ -549,34 +541,45 @@
             errors.extend(oldTableError)
             errors.extend(newGbdbError)
             errors.extend(oldGbdbError)
 
             #for ease of typing
             totalFiles = set(self.newReleaseFiles)
             oldTotalFiles = set(self.oldReleaseFiles)
 
             #these could honestly be moved earlier, get a file list processing section or something
             #they clean out special fiels out and separated the master fiels list into the 3 required
             #ones: wgEncode, supplemental and additional.
             self.totalFiles = self.__cleanSpecialFiles(totalFiles)
             self.oldTotalFiles = self.__cleanSpecialFiles(oldTotalFiles)
             (self.oldTotalFiles, self.additionalList, self.oldAdditionalList, self.totalFiles) = self.__separateOutAdditional()
 
-            #get the stuff you need to push, also table sizes
+            #get the stuff you need to push
+            self.pushTables = set(sorted((self.newTableSet - self.oldTableSet)))
+            self.pushFiles = set(sorted((self.totalFiles - self.oldTotalFiles)))
+            self.pushGbdbs = set(sorted((self.newGbdbSet - self.oldGbdbSet)))
+            self.newSupp = self.newSupplementalSet - self.oldSupplementalSet
+
+            self.newTables = set(self.pushTables)
+            self.newFiles = set(ucscUtils.printIter(self.pushFiles, self.releasePath))
+            self.newGbdbs = set(ucscUtils.printIter(self.pushGbdbs, self.gbdbPath))
+            self.newSupplemental = set(ucscUtils.printIter(self.newSupp, self.releasePath))
+            self.newOthers = set(ucscUtils.printIter(self.additionalList, self.releasePath))
 
             self.errors = errors
             #don't output.append(report unless ignore option is on or no errors
+            #module mode doesn't generate output by default
             if (not errors) or self.ignore:
                 self.output = self.printReport(args, c)
             else:
                 self.output = self.printErrors(errors, self.missingFiles)
 
 
         elif self.releaseOld == 'solo':
 
             self.newReleaseFiles = c.releases[int(self.releaseNew)-1]
 
             self.newMdb = c.alphaMetaDb
 
             #check that attic fiels aren't in trackDb
             errors.extend(self.__checkAtticNotInTrackDb())
 
