Fixes for GBrowse communication.

lib/galaxy/config.py

@@ -56,6 +56,7 @@ class Configuration( object ):
         self.pbs_stage_path = kwargs.get('pbs_stage_path', "" )
         self.use_heartbeat = kwargs.get( 'use_heartbeat', False )
         self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea" ).lower().split(",")
+        self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,flybase,elegans" ).lower().split(",")
         self.brand = kwargs.get( 'brand', None )
         self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' )
         self.bugs_email = kwargs.get( 'bugs_email', None )

lib/galaxy/datatypes/interval.py

@@ -499,7 +499,7 @@ class Gff( Tabular ):
                 stop = viewport_tuple[2]
                 for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ):
                     if site_name in app.config.gbrowse_display_sites:
-                        link = "%sstart=%s;stop=%s;ref=%s" % ( site_url, start, stop, dataset.dbkey )
+                        link = "%s?start=%s&stop=%s&ref=%s" % ( site_url, start, stop, dataset.dbkey )
                         ret_val.append( ( site_name, link ) )
         return ret_val
 
@@ -620,8 +620,11 @@ class Gff3( Gff ):
             if len(headers) < 2:
                 return False
             for hdr in headers:
-                if hdr and hdr[0].startswith( '##gff-version' ) and hdr[0].find( '3' ) < 0:
+                if hdr and hdr[0].startswith( '##gff-version' ) and hdr[0].find( '3' ) >= 0:
+                    return True
+                elif hdr and hdr[0].startswith( '##gff-version' ) and hdr[0].find( '3' ) < 0:
                     return False
+                # Header comments may have been stripped, so inspect the data
                 if hdr and hdr[0] and not hdr[0].startswith( '#' ):
                     if len(hdr) != 9: 
                         return False

static/gbrowse/gbrowse_build_sites.txt

@@ -1,8 +1,5 @@
 #Harvested from http://www.wormbase.org/db/seq/gbrowse/wormbase/
-# TODO: Uncomment the 1st lines and eliminate the 2nd test lines when the prototype is completed.
 #wormbase	http://gvk.bx.psu.edu/cgi-bin/gbrowse/volvox?	briggsae,briggsae_cb25,brugia,elegans,elegans_gmap,elegans_pmap,fly,fly31,nGASP,nGASP_submissions,remanei,wormbase,ws77,yeast_chr1
-# 2nd test line: wormbase	http://gvk.bx.psu.edu/cgi-bin/gbrowse/volvox?	ctgA,tmpfiller1,tmpfiller2
 #Harvested from http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/
 #flybase	http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/	dana,dere,dgri,dmel,dmoj,dper,dpse,dsec,dsim,dvir,dwil,dyak,dmelstocks
-# 2nd test line: flybase	http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/	tmpfiller1,tmpfiller2
-elegans	http://brie3.cshl.edu:9000/cgi-bin/gbrowse/elegans/	brugia,briggsae_cb25,briggsae,elegans,wormbase,elegans_gmap,elegans_pmap,nGASP,ws77,remanei,mouse,nGASP_submissions,Gbrowse_karyotype,yeast_chr1,yeast_chr1
+elegans	http://brie3.cshl.edu:9000/cgi-bin/gbrowse/elegans/	cb1,cb2,cb3,ce1,ce2,ce3,ce4

tools/data_source/gbrowse_filter.py

@@ -9,13 +9,14 @@ log = logging.getLogger( __name__ )
 
 def exec_before_job( app, inp_data, out_data, param_dict, tool=None ):
     """Sets the name of the data"""
-    data_name = param_dict.get( 'name', 'GBrowse query' )
+    data_name = urllib.unquote( param_dict.get( 't', 'GBrowse query' ) ).replace( '+', ' ' )
+    data_region = param_dict.get( 'q', '' )
     data_type = param_dict.get( 'type', 'txt' )
     name, data = out_data.items()[0]
     if data_type == 'txt': 
         data_type = sniff.guess_ext( data.file_name )
     data = app.datatypes_registry.change_datatype( data, data_type )
-    data.name = data_name
+    data.name = '%s %s' % ( data_name, data_region )
     out_data[name] = data
 
 def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None ):