464aa35bb5735dfb8f565621dbde8b3b2ead1581
mmaddren
  Thu May 10 14:53:09 2012 -0700
fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
diff --git python/programs/viewTrack/viewTrack python/programs/viewTrack/viewTrack
index ba460ea..111768b 100755
--- python/programs/viewTrack/viewTrack
+++ python/programs/viewTrack/viewTrack
@@ -1,19 +1,22 @@
 #!/usr/bin/env python2.7
 
 import sys, os, shutil, argparse, urllib2, re
-from ucscgenomics import ra, soft, track, styles, geo
+from ucscGb.gbData.ra import raFile
+from ucscGb.encode import track
+from ucscGb.encode import styles
+from ucscGb.externalData.geo import submission
 
 def filesize(val):
     if val > 1099511627776:
         return str(round(float(val) / 1099511627776, 2)) + 'TB'
     if val > 1073741824:
         return str(round(float(val) / 1073741824, 2)) + 'GB'
     if val > 1048576:
         return str(round(float(val) / 1048576, 2)) + 'MB'
     if val > 1024:
         return str(round(float(val) / 1024, 2)) + 'KB'
     else:
         return str(val) + 'B'
 
 
 def printTrackRefLine():
@@ -66,32 +69,32 @@
             datatype = t.alphaMetaDb.dataType.name
             if t.alphaMetaDb.dataType.type == 'MicroArray':
                     datatype = styles.style(datatype.ljust(16), 'yellow')
             elif t.alphaMetaDb.dataType.valid:
                 datatype = styles.style(datatype.ljust(16), 'green')
             else:
                 if t.alphaMetaDb.dataType.shouldSubmit:
                     datatype = styles.style(datatype.ljust(16), 'red')
                 else:
                     datatype = styles.style(datatype.ljust(16), 'blue')
                     #subtext = ''
                     wantSubmit = 0
         if datatype == '' and len(t.alphaMetaDb.experiments) == 0:
             datatype = styles.style('no expIds'.ljust(16), 'red')
                 
-        if wantSubmit:
-            nametext = styles.style(nametext, 'green')
+        #if wantSubmit:
+        #    nametext = styles.style(nametext, 'green')
             
         geouptodate = ''    
         if args.geo and t.geo != None:
             exps = dict()
             local = 0
             offsite = 0
             mismatch = 0
             matched = 0
             for expId in t.alphaMetaDb.experiments.iterkeys():
                 k = t.alphaMetaDb.experiments[expId].title
                 exps[k] = t.alphaMetaDb.experiments[expId]
                 if k in t.geo.accessions.iterkeys():
                     happened = 0
                     for stanza in exps[k]:
                         if 'geoSampleAccession' in stanza and stanza['geoSampleAccession'] != t.geo.accessions[k]:
@@ -184,42 +187,42 @@
     
     if len(sys.argv) == 1:
         parser.print_usage()
         return
     
     args = parser.parse_args(sys.argv[1:])
     
     tracks = track.TrackCollection(args.database)
     
     if args.composite == None:
         if args.geo:
             for t in tracks.itervalues():
                 t.geo = None
                 try:
                     if 'geoSeriesAccession' in t.alphaMetaDb.compositeStanza:
-                        t.geo = geo.Submission(t.alphaMetaDb.compositeStanza['geoSeriesAccession'])
+                        t.geo = submission.Submission(t.alphaMetaDb.compositeStanza['geoSeriesAccession'])
                 except KeyError:
                     pass
         displayAll(args, tracks)
     else:
         if args.expIds == None or len(args.expIds) == 0:
             displayTrack(args, tracks[args.composite])
         else:
             ids = list()
             for id in args.expIds:
                 if '-' in id:
                     start, end = id.split('-', 1)
                     ids.extend(range(int(start), int(end) + 1))
                 else:
                     ids.append(int(id))
             if args.geo:
                 tracks[args.composite].geo = None
                 if 'geoSeriesAccession' in tracks[args.composite].alphaMetaDb.compositeTrack:
-                    tracks[args.composite].geo = geo.Submission(tracks[args.composite].alphaMetaDb.compositeTrack['geoSeriesAccession'])
+                    tracks[args.composite].geo = submission.Submission(tracks[args.composite].alphaMetaDb.compositeTrack['geoSeriesAccession'])
             displayTrack(args, tracks[args.composite], ids)        
                     
                     
                     
                     
 if __name__ == '__main__':
     main()                   
                     
\ No newline at end of file