예제 #1
0
 def gbrowse_links( self, dataset, type, app, base_url ):
     ret_val = []
     chrom, start, stop = self._get_viewer_range( dataset )
     if chrom is not None:
         for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ):
             if site_name in app.config.gbrowse_display_sites:
                 redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
                 link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                 ret_val.append( ( site_name, link ) )
     return ret_val
예제 #2
0
 def gbrowse_links( self, dataset, type, app, base_url ):
     ret_val = []
     if dataset.has_data:
         viewport_tuple = self.get_estimated_display_viewport( dataset )
         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&dbkey=%s" % ( site_url, start, stop, seqid, dataset.dbkey )
                     ret_val.append( ( site_name, link ) )
     return ret_val
예제 #3
0
 def gbrowse_links( self, dataset, type, app, base_url ):
     ret_val = []
     if dataset.has_data:
         viewport_tuple = self.get_estimated_display_viewport(dataset)
         if viewport_tuple:
             chrom = viewport_tuple[0]
             start = viewport_tuple[1]
             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:
                     display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) )
                     link = "%sname=%s&ref=%s:%s..%s&eurl=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url )                        
                     ret_val.append( (site_name, link) )
     return ret_val
예제 #4
0
 def gbrowse_links(self, dataset, type, app, base_url):
     ret_val = []
     if dataset.has_data:
         viewport_tuple = self.get_estimated_display_viewport(dataset)
         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&dbkey=%s" % (
                         site_url, start, stop, seqid, dataset.dbkey)
                     ret_val.append((site_name, link))
     return ret_val
예제 #5
0
 def gbrowse_links( self, dataset, type, app, base_url ):
     ret_val = []
     if dataset.has_data:
         viewport_tuple = self.get_estimated_display_viewport( dataset )
         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:
                     redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % 
                             ( site_url, dataset.dbkey, seqid, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
     return ret_val