def generate(self, gpml=None, node_colors=None):
# Add our urls to the defaults
xref_urls = {
'MetaCyc compound': 'pathomx://db/compound/%s/view',
'MetaCyc gene': 'pathomx://db/gene/%s/view',
'MetaCyc protein': 'pathomx://db/protein/%s/view',
'WikiPathways': 'pathomx://wikipathway/%s/import',
}
if gpml:
svg, metadata = gpml2svg.gpml2svg(gpml, xref_urls=xref_urls, xref_synonyms_fn=self.w.get_extended_xref_via_unification_list, node_colors=node_colors) # Add Pathomx required customisations here
self.setHtml(svg, QUrl("~"))
def generate(self, gpml=None, node_colors=None):
# Add our urls to the defaults
xref_urls = {
'MetaCyc compound': 'pathomx://db/compound/%s/view',
'MetaCyc gene': 'pathomx://db/gene/%s/view',
'MetaCyc protein': 'pathomx://db/protein/%s/view',
'WikiPathways': 'pathomx://wikipathway/%s/import',
}
if gpml:
svg, metadata = gpml2svg.gpml2svg(
gpml,
xref_urls=xref_urls,
xref_synonyms_fn=self.w.get_extended_xref_via_unification_list,
node_colors=node_colors
) # Add Pathomx required customisations here
self.setHtml(svg, QUrl("~"))
elif config['gpml_wikipathways_id']:
r = requests.get('http://www.wikipathways.org//wpi/wpi.php',
params={
'action': 'downloadFile',
'type': 'gpml',
'pwTitle':
'Pathway:%s' % config['gpml_wikipathways_id'],
'revision': 0,
})
if r.status_code == 200:
print("Loaded GPML from WikiPathways")
gpml = r.text
else:
raise Exception("Error loading GPML from WikiPathways (%d)" %
r.status_code)
else:
raise Exception("Select a source for GPML")
if gpml:
# xref_synonyms_fn=get_extended_xref_via_unification_list,
svg, metadata = gpml2svg.gpml2svg(gpml,
xref_urls=xref_urls,
xref_synonyms=xref_syns,
node_colors=node_colors)
View = SVG(svg)
View
}
gpml = None
if config['gpml_file']:
print("Loaded GPML from WikiPathways")
with open(config['gpml_file'], 'rU') as f:
gpml = f.read()
elif config['gpml_wikipathways_id']:
r = requests.get('http://www.wikipathways.org//wpi/wpi.php', params={
'action': 'downloadFile',
'type': 'gpml',
'pwTitle': 'Pathway:%s' % config['gpml_wikipathways_id'],
'revision': 0,
})
if r.status_code == 200:
print("Loaded GPML from WikiPathways")
gpml = r.text
else:
raise Exception("Error loading GPML from WikiPathways (%d)" % r.status_code)
else:
raise Exception("Select a source for GPML")
if gpml:
# xref_synonyms_fn=get_extended_xref_via_unification_list,
svg, metadata = gpml2svg.gpml2svg(gpml, xref_urls=xref_urls, xref_synonyms=xref_syns, node_colors=node_colors)
View = SVG(svg)
View