f0919e569848bc7c172f2ec9d2d47d17e6cb747a
wong
  Thu Oct 27 15:24:55 2011 -0700
fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
diff --git python/lib/ucscgenomics/mkChangeNotes.py python/lib/ucscgenomics/mkChangeNotes.py
index 562990f..8aa66b2 100644
--- python/lib/ucscgenomics/mkChangeNotes.py
+++ python/lib/ucscgenomics/mkChangeNotes.py
@@ -284,30 +284,37 @@
             caps = title.upper()
         elif title == 'gbdbs':
             caps = "GBDBS"
             title = "gbdb files"
         elif title == "download":
             title = title + " files"
             caps = title.upper()
         if all:
             output.append("\n")
             output.append("%s:" % caps)
             output.append("New: %s" % len(new))
             output.append("Untouched: %s" % len(untouched))
             output.append("%s: %s" % (removeline, len(revoked)))
             output.append("New + Untouched: %s" % len(new | untouched))
             output.append("%s: %s" % (totaline, len(all)))
+            intersect = new & revoked
+            if intersect:
+                output.append("")
+                output.append("The following exist in both new and revoked %s:" % title)
+                for i in intersect:
+                    output.append("%s" % i)
+            
         if all and not summary:
             output.append("")
             output.append("New %s (%s):" % (title.title(), len(new)))
             output.extend(self.__printIter(new, path))
             output.append("")
             output.append("Untouched %s (%s):" % (title.title(), len(untouched)))
             output.extend(self.__printIter(untouched, path))
             output.append("")
             output.append("%s %s (%s):" % (removeline, title.title(), len(revoked)))
             output.extend(self.__printIter(revoked, path))
         return output
 
     def __qaHeader(self, output, newTableSet, filesNoRevoke, newGbdbSet, newSupp, additionalList, revokedTables, revokedFiles, revokedGbdbs, pushFiles, pushGbdbs, args, c):
         output = []
         tableSize = self.__getTableSize()
@@ -358,36 +365,36 @@
         newFiles = pushFiles - revokedFiles
         untouchedFiles = (totalFiles & oldReleaseFiles) - revokedFiles
         allGbdbs = newGbdbSet | oldGbdbSet | revokedGbdbs
         untouchedGbdbs = (newGbdbSet & oldGbdbSet) - revokedGbdbs
         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(newFiles, untouchedFiles, revokedFiles, allFiles, "download", self.releasePath, 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']))
 
         self.newTables = set(pushTables)
-        self.newFiles = set(self.__printIter(newFiles, self.releasePath))
+        self.newFiles = set(self.__printIter(pushFiles, self.releasePath))
         self.newGbdbs = set(self.__printIter(pushGbdbs, self.gbdbPath))
         self.newSupplemental = set(self.__printIter(newSupp, self.releasePath))
         self.newOthers = set(self.__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)))
@@ -485,30 +492,33 @@
         if int(self.releaseNew) > 1 and str(self.releaseOld) != 'solo':
 
             self.newReleaseFiles = c.releases[int(self.releaseNew)-1]
             self.oldReleaseFiles = c.releases[int(self.releaseOld)-1]
 
             self.newMdb = c.alphaMetaDb
             self.oldMdb = c.publicMetaDb
 
             #make a list of missing files
             self.missingFiles = self.__checkFilesForDropped()
             
             #check if all files listed in release directories have associated metaDb entries
             (self.newMdb, self.revokedSet, self.revokedFiles, self.atticSet, self.newSupplementalSet, newFileErrors) = self.checkMetaDbForFiles("alpha metaDb", "new")
             (self.oldMdb, spam, eggs, ham, self.oldSupplementalSet, oldFileErrors) = self.checkMetaDbForFiles("public metaDb", "old")
 
+
+
+
             #checks to see that nothing has disappeared between public and alpha
             errors.extend(self.__checkAlphaForDropped("alpha metaDb", "stanza"))
             errors.extend(self.__checkMd5sums())
 
             #checks and gets tables that are present, also returns a revoked set of tables for new
             (self.newTableSet, self.revokedTableSet, newTableError) = self.checkTableStatus("alpha metaDb", "new")
             (self.oldTableSet, spam, oldTableError) = self.checkTableStatus("public metaDb", "old")
 
             #same as above except for gbdbs
             (self.newGbdbSet, self.revokedGbdbs, newGbdbError) = self.getGbdbFiles("new")
             (self.oldGbdbSet, eggs, oldGbdbError) = self.getGbdbFiles("old")
 
             #fill in the errors
             errors.extend(newFileErrors)
             errors.extend(oldFileErrors)