def search(args):
data = {}
# Converting the given taxon id into the KEGG organism code
tid = ''
if 'taxon_id' in args.keys():
tid = args['taxon_id']
orgcode = tools.taxon_to_kegg(tid)
if orgcode is None:
raise Exception("Not a valid taxon id")
# If a pathway id is specified
if 'identifier' in args.keys():
# Sets the default organism code to map
org = 'map'
if 'taxon_id' in args.keys():
org = orgcode
# If the pathway given is not in the form of a KEGG pathway id, raises
# exception.
if not tools.valid_pathway_id(args['identifier']):
raise Exception('Not a valid identifier')
id = org + args['identifier']
# If a field of the specific pathway is requested. Can still be used,
# but is not displayed in any documentation.
if 'field' in args.keys():
url = vars.url + 'get/' + id
text = tools.openurl(url)
data = tools.find_cat(text, args['field'])
# No field is specified
else:
url = vars.url + 'list/' + id
text = tools.openurl(url)
data = tools.two_col_path(text, tid)
# If the user has provided a search term to search pathways for
elif 'term' in args.keys():
term = args['term']
# If no species is provided, just gets from the KEGG find function
if 'taxon_id' not in args.keys():
url = vars.url + 'find/pathway/' + term
text = tools.openurl(url)
data = tools.two_col_path(text, '')
# If a species is specified, has to confirm that the pathway exists in
# the given species
else:
org = orgcode
return_data = []
thread = Thread(target = pathway_set, args = (org, return_data))
thread.start()
# First searches all pathways
url = vars.url + 'find/pathway/' + term
text = tools.openurl(url)
tempdata = tools.two_col_path(text, tid)
# Then lists all pathway in given organism
thread.join()
data2 = return_data[0]
data = []
# Takes the intersection of both lists
for element in tempdata:
if element['KEGG_pathway_id'] in data2:
data.append(element)
# No pathway is specified. Lists all pathways in Arabidopsis
else:
org = ''
if 'taxon_id' in args.keys():
org = orgcode
url = vars.url + 'list/pathway/' + org
text = tools.openurl(url)
data = tools.two_col_path(text, tid)
# Prints the data as a dict for Adama to return
print json.dumps(data)
def search(args):
# Converting the given taxon id into the KEGG organism code
orgcode = ''
taxon_id = None
taxon_name = None
if 'taxon_id' in args.keys():
taxon_id = args['taxon_id']
orgcode, taxon_name = tools.taxon_to_kegg(taxon_id)
if orgcode is None:
raise Exception("Not a valid taxon id")
# If a pathway id is specified, it will get fields of the specific pathway
if 'pathway_id' in args.keys():
# Sets the default organism code to map if no organism is specified
org = 'map'
if 'taxon_id' in args.keys():
org = orgcode
# If the pathway given is not in the form of a KEGG pathway id, raises
# exception.
if not tools.valid_pathway_id(args['pathway_id']):
raise Exception('Not a valid identifier')
# Creates the full KEGG pathway ID with organism code and pathway ID
id = org + args['pathway_id']
# Accesses the KEGG API
url = vars.url + 'get/' + id
text = tools.openurl(url)
# Parses the text received from the KEGG API
data = parser.parse(text)
# Adds the pathway ID to the returned information
data['pathway_id'] = args['pathway_id']
data['taxon_id'] = taxon_id
data['taxon_name'] = taxon_name
# Removes the organism name from the pathway
if org != '' and 'name' in data:
data['name'] = data['name'].rsplit(' - ', 1)[0]
# Prints the data for ADAMA to return to the user
print json.dumps(data)
else: #No pathway specified
# If an organism is given, set it to search through that organism
org = ''
if 'taxon_id' in args.keys():
org = orgcode
# Accesses the KEGG API
url = vars.url + 'list/pathway/' + org
text = tools.openurl(url)
# Parses the text received into a list of pathways
data = tools.two_col_path(text, taxon_id, taxon_name)
# Prints the data in JSON form with elements in the list separated by
# three dashes
for element in data:
print json.dumps(element)
print '---'