def find_cat(text, cat):
cat = cat.upper()
if cat not in vars.fields:
raise Exception("Not a valid field")
lines = text.split('\n')
flag = False;
data = []
for line in lines:
parts = line.split(None, 1)
if len(parts) == 0:
return {}
if parts[0] == cat and not flag:
data.append(parts[1])
flag = True
elif flag and line[0] != ' ':
break
elif flag:
data.append(line.strip())
return parser.parse(data, cat)
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 '---'