More fixes for GBrowse / GMOD communication, tool now includes command line, display in GBrowse links now functional.

lib/galaxy/datatypes/interval.py

@@ -430,6 +430,7 @@ class Bed( Interval ):
 class Gff( Tabular ):
     """Tab delimited data in Gff format"""
     file_ext = "gff"
+    column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
 
     """Add metadata elements"""
     MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False )
@@ -455,8 +456,21 @@ class Gff( Tabular ):
                         pass
         Tabular.set_meta( self, dataset, skip=i )
 
-    def make_html_table( self, dataset ):
-        return Tabular.make_html_table( self, dataset, skipchars=['#'] )
+    def make_html_table( self, dataset, skipchars=[] ):
+        """Create HTML table, used for displaying peek"""
+        out = ['<table cellspacing="0" cellpadding="3">']
+        comments = []
+        try:
+            # Generate column header
+            out.append( '<tr>' )
+            for i, name in enumerate( self.column_names ):
+                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
+            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
+            out.append( '</table>' )
+            out = "".join( out )
+        except Exception, exc:
+            out = "Can't create peek %s" % exc
+        return out
     
     def as_gbrowse_display_file( self, dataset, **kwd ):
         """Returns file contents that can be displayed in GBrowse apps."""
@@ -465,26 +479,40 @@ class Gff( Tabular ):
 
     def get_estimated_display_viewport( self, dataset ):
         """
-        Return a chrom, start, stop tuple for viewing a file.  There are slight differences between gff and gff version 3
+        Return a chrom, start, stop tuple for viewing a file.  There are slight differences between gff 2 and gff 3
         formats.  This function should correctly handle both...
         """
         if dataset.has_data() and dataset.state == dataset.states.OK:
             try:
-                seqid_col = 0
-                start_col = 3
-                stop_col = 4
-                peek = []
+                seqid = None
+                start = None
+                stop = None
                 for idx, line in enumerate( file( dataset.file_name ) ):
-                    if line[0] != '#':
-                        peek.append( line.split() )
-                        if idx > 10:
-                            break
-                seqid, start, stop = peek[0][seqid_col], int( peek[0][start_col] ), int( peek[0][stop_col] )
-                for p in peek[1:]:
-                    if p[0] == seqid:
-                        start = min( start, int( p[start_col] ) )
-                        stop = max( stop, int( p[stop_col] ) )
-            except Exception, exc:
+                    line = line.rstrip( '\r\n' )
+                    if line and line.startswith( '##sequence-region' ): # ##sequence-region IV 6000000 6030000
+                        elems = line.split()
+                        seqid = elems[1] # IV
+                        start = elems[2] # 6000000
+                        stop = elems[3] # 6030000
+                    if idx > 10:
+                        break
+                if not seqid or not start or not stop:
+                    # Perhaps the data is missing the gff3 comments fields.  This is not good
+                    # because we need to parse the entire dataset to find the stop / start
+                    for idx, line in enumerate( file( dataset.file_name ) ):
+                        line = line.rstrip( '\r\n' )
+                        if line and not line.startswith( '#' ):
+                            elems = line.split( '\t' )
+                            if len( elems ) != 9:
+                                continue # Invalid line
+                            if not seqid:
+                                seqid = elems[0]
+                            # Assume all Sequence IDs are the same.Is this true for GFF3?
+                            if not start or start < int( elems[3] ):
+                                start = int( elems[3] )
+                            if not end or end > int( elems[4] ):
+                                end = int( elems[4] )
+            except:
                 seqid, start, stop = ( '', '', '' ) 
             return ( seqid, str( start ), str( stop ) )
         else:
@@ -494,12 +522,13 @@ class Gff( Tabular ):
         ret_val = []
         if dataset.has_data:
             viewport_tuple = self.get_estimated_display_viewport( dataset )
-            if viewport_tuple:
-                start = viewport_tuple[1]
-                stop = viewport_tuple[2]
+            seqid = viewport_tuple[0]
+            start = viewport_tuple[1]
+            stop = viewport_tuple[2]
+            if seqid and start and stop:
                 for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ):
                     if site_name in app.config.gbrowse_display_sites:
-                        link = "%s?start=%s&stop=%s&ref=%s" % ( site_url, start, stop, dataset.dbkey )
+                        link = "%s?start=%s&stop=%s&ref=%s&dbkey=%s" % ( site_url, start, stop, seqid, dataset.dbkey )
                         ret_val.append( ( site_name, link ) )
         return ret_val
 
@@ -551,6 +580,7 @@ class Gff3( Gff ):
     file_ext = "gff3"
     valid_gff3_strand = ['+', '-', '.', '?']
     valid_gff3_phase = ['.', '0', '1', '2']
+    column_names = [ 'Seqid', 'Source', 'Type', 'Start', 'End', 'Score', 'Strand', 'Phase', 'Attributes' ]
         
     """Add metadata elements"""
     MetadataElement( name="column_types", default=['str','str','str','int','int','float','str','int','list'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False )

tools/data_source/gbrowse_datasource.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+#Retreives data from GMOD and stores in a file. GBrowse parameters are provided in the input/output file.
+import urllib, sys, os, gzip, tempfile, shutil
+from galaxy import eggs
+from galaxy.datatypes import data
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    filename = sys.argv[1]
+    params = {}
+    
+    for line in open( filename, 'r' ):
+        try:
+            line = line.strip()
+            fields = line.split( '\t' )
+            params[ fields[0] ] = fields[1]
+        except:
+            continue
+    
+    URL = params.get( 'URL', None )
+    if not URL:
+        open( filename, 'w' ).write( "" )
+        stop_err( 'Datasource has not sent back a URL parameter.' )
+
+    for i, param in enumerate( params.keys() ):
+        if i == 0:
+            sep = '?'
+        else:
+            sep = '&'
+        if param != '__collected_datasets__':
+            URL += "%s%s=%s" % ( sep, param, params.get( param ) )
+
+    CHUNK_SIZE = 2**20 # 1Mb 
+    try:
+        page = urllib.urlopen( URL )
+    except Exception, exc:
+        raise Exception( 'Problems connecting to %s (%s)' % ( URL, exc ) )
+        sys.exit( 1 )
+    
+    fp = open( filename, 'wb' )
+    while 1:
+        chunk = page.read( CHUNK_SIZE )
+        if not chunk:
+            break
+        fp.write( chunk )
+    fp.close()      
+    
+if __name__ == "__main__": __main__()

tools/data_source/gbrowse_elegans.xml

@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <tool name="C. Elegans" id="gbrowse_elegans">
 	<description>server</description>
-	<command/>
+	<command interpreter="python">gbrowse_datasource.py $output</command>
 	<inputs action="http://brie3.cshl.edu:9000/cgi-bin/gbrowse/elegans/" check_values="false" method="get" target="_top">
 		<display>go to C. Elegans server $GALAXY_URL</display>
 		<param name="GALAXY_URL" type="baseurl" value="/tool_runner/gbrowse_elegans" />
 	</inputs>
 	<uihints minwidth="800"/>
-	<code file="gbrowse_filter.py"/>
+	<code file="gbrowse_filter_code.py"/>
 	<outputs>
 		<data name="output" format="txt" />
 	</outputs>

tools/data_source/gbrowse_filter.py

@@ -1,56 +0,0 @@
-import urllib
-
-from galaxy import datatypes, config
-from galaxy.datatypes import sniff
-import tempfile, shutil
-
-import logging
-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 = 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 = '%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 ):
-    """Verifies the data after the run"""
-    URL = param_dict.pop( 'URL', None )
-    if not URL:
-        raise Exception( 'Datasource has not sent back a URL parameter' )
-    for i, param in enumerate( param_dict.keys() ):
-        if i == 0:
-            sep = '?'
-        else:
-            sep = '&'
-        if param != '__collected_datasets__':
-            URL += "%s%s=%s" %( sep, param, param_dict.get( param ) )
-
-    CHUNK_SIZE = 2**20 # 1Mb 
-    try:
-        page = urllib.urlopen( URL )
-    except Exception, exc:
-        raise Exception( 'Problems connecting to %s (%s)' % ( URL, exc ) )
-        sys.exit( 1 )
-
-    name, data = out_data.items()[0]
-
-    fp = open( data.file_name, 'wb' )
-    while 1:
-        chunk = page.read( CHUNK_SIZE )
-        if not chunk:
-            break
-        fp.write( chunk )
-    fp.close()
-
-    data.info = data.name
-    data_type = sniff.guess_ext( data.file_name )
-    data = app.datatypes_registry.change_datatype( data, data_type )
-    data.set_peek()
-    data.flush()

tools/data_source/gbrowse_filter_code.py

@@ -0,0 +1,34 @@
+# Code for direct connection to GMOD
+from galaxy.datatypes import sniff
+import urllib
+
+import logging
+log = logging.getLogger( __name__ )
+
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None ):
+    """Sets the attributes of the data"""
+    gb_settings = urllib.unquote( param_dict.get( 't', None ) ) # t=CG+TS+ESTB+SAGE+EXPR+EXPR_PATTERN+SNPs+PolyA+BLASTX+LINK+ETILE
+    gb_landmark_region = urllib.unquote( param_dict.get( 'q' ) ) # q=IV:6070000..6100000&
+    gb_land_mark, gb_region = gb_landmark_region.split( ':' )
+    items = out_data.items()
+    for name, data in items:
+        data.name = "%s on %s" % ( data.name, gb_landmark_region )
+        data.dbkey = param_dict.get( 'dbkey', '?' )    
+        # Store GMOD / GBrowse parameters temporarily in output file
+        out = open( data.file_name, 'w' )
+        for key, value in param_dict.items():
+            out.write( "%s\t%s\n" % ( key, value ) )
+        out.close()
+        out_data[ name ] = data
+
+def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None ):
+    """Verifies the data after the run"""
+    name, data = out_data.items()[0]
+    if data.state == data.states.OK:
+        data.info = data.name
+    if data.extension == 'txt':
+        data_type = sniff.guess_ext( data.file_name )
+        data = app.datatypes_registry.change_datatype( data, data_type ) 
+    data.set_peek()
+    data.set_size()
+    data.flush()