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
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
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
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
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