00364a3fb61c20b7431109d4482a73a6f739e4e7
wong
  Wed Oct 19 11:00:19 2011 -0700
removed checking of table dropping, as the table list was generated off mdb, so it's redundant to the mdb errors, and there's no way to tell the state of the tables at time fo release
diff --git python/programs/mkChangeNotes/mkChangeNotes python/programs/mkChangeNotes/mkChangeNotes
index 56dd1e6..8d92565 100755
--- python/programs/mkChangeNotes/mkChangeNotes
+++ python/programs/mkChangeNotes/mkChangeNotes
@@ -127,31 +127,31 @@
     output = p.stdout.read()
     
     revokedtableset = set(output.split("\n")[1:])
     
     file1stanzalist = mdb.filter(lambda s: s['tableName'] in gbdbtableset, lambda s: s)
     revokedstanzalist = mdb.filter(lambda s: s['tableName'] in revokedtableset, lambda s: s)
     gbdbfileset = set()
     revokedfileset = set()
     
     for i in file1stanzalist:
         filelist = i['fileName'].split(',')
         for j in filelist:
             if os.path.isfile("/gbdb/%s/bbi/%s" % (database, j)):
                 gbdbfileset.add(j)
             else:
-                errors.append("gbdb: %s does not exist in /gbdb/%s/bbi" % (j, databsase))
+                errors.append("gbdb: %s does not exist in /gbdb/%s/bbi" % (j, database))
     
     for i in revokedstanzalist:
         filelist = i['fileName'].split(',')
         for j in filelist:
             if os.path.isfile("/gbdb/%s/bbi/%s" % (database, j)):
                 revokedfileset.add(j)
             else:
                 errors.append("gbdb: revoked gbdb %s does not exist in /gbdb/%s/bbi" % (j, databsase))
     
     return (gbdbfileset, revokedfileset, errors)
 
 def getTableSize(mdbtableset, database):
     tablesize = float(0)
     tablelist = list()
     for i in mdbtableset:
@@ -483,31 +483,31 @@
 """Examples:
 
 mkChangeNotes hg19 wgEncodeUwDnase 3 2 --loose
 mkChangeNotes hg19 wgEncodeSydhTfbs 1 - --full
 mkChangeNotes hg19 wgEncodeCshlLongRnaSeq 1 -
 
 """
         )
     parser.add_argument('-t', '--trackPath', help='Overrides the default track path ~/kent/src/hg/makeDb/trackDb/')
     parser.add_argument('-l', '--loose', action="store_true", default=0, help='Loose checking for legacy elements. Will be retired once all tracks go through a release cycle')
     parser.add_argument('-i', '--ignore', action="store_true", default=0, help='Ignore errors, print out report.')
     parser.add_argument('-f', '--full', action="store_true", default=0, help='Print full stats.')
     parser.add_argument('database', help='The database, typically hg19 or mm9')
     parser.add_argument('composite', help='The composite name, wgEncodeCshlLongRnaSeq for instance')
     parser.add_argument('releaseNew', help='The new release to be released')
-    parser.add_argument('releaseOld', nargs='?', default='-', help='The old release that is already released, if on release 1, put anything here')
+    parser.add_argument('releaseOld', nargs='?', default='-', help='The old release that is already released, if on release 1, or solo release mode, put anything here')
 
     if len(sys.argv) == 1:
         parser.print_help()
         return
     args = parser.parse_args(sys.argv[1:])
     if not args.releaseNew.isdigit():
         parser.print_help()
         return
 
     c = track.CompositeTrack(args.database,args.composite)
 
     loose = args.loose
 
     errors = []
     
@@ -539,36 +539,30 @@
         missingFiles = checkFilesForDropped(newReleaseFiles, oldReleaseFiles)
         errors.extend(checkMd5sums(newReleaseFiles, oldReleaseFiles, loose))
 
         #checks and gets tables that are present, also returns a revoked set of tables for new
         (newTableSet, revokedTableSet, newTableError) = checkTableStatus(newMdb, newReleaseFiles, args.database, args.composite, "alpha metaDb", loose, revokedSet)
         (oldTableSet, spam, oldTableError) = checkTableStatus(oldMdb, oldReleaseFiles, args.database, args.composite, "public metaDb", loose, revokedSet)
         errors.extend(newTableError)
         errors.extend(oldTableError)
 
         #same as above except for gbdbs
         (newGbdbSet, revokedGbdbs, newGbdbError) = getGbdbFiles(args.database, newTableSet, revokedTableSet, newMdb)
         (oldGbdbSet, eggs, oldGbdbError) = getGbdbFiles(args.database, oldTableSet, set(), oldMdb)
         errors.extend(newGbdbError)
         errors.extend(oldGbdbError)
     
-        #check to see if tables were dropped between releases
-        droppedTables = oldTableSet - newTableSet
-        if droppedTables:
-            for i in droppedTables:
-                errors.append("table: %s was dropped between releases" % i)
-        
         #for ease of typing
         totalFiles = set(newReleaseFiles)
 
         #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.
         totalFiles = cleanSpecialFiles(totalFiles)
         oldReleaseFiles = cleanSpecialFiles(set(oldReleaseFiles))
         (oldReleaseFiles, additionalList, oldAdditionalList, totalFiles) = separateOutAdditional(oldReleaseFiles, totalFiles, newSupplementalSet, oldSupplementalSet)
 
         #get the stuff you need to push, also table sizes        
         pushTables = set(sorted((newTableSet - oldTableSet)))
         tableSize = getTableSize(pushTables, args.database)
         pushFiles = set(sorted((totalFiles - oldReleaseFiles)))
         pushGbdbs = set(sorted((newGbdbSet - oldGbdbSet)))