def find_snomedct_server(term):
apikey = "ca310f05-53e6-4984-82fd-8691dc30174e"
AuthClient = Authentication(apikey)
version = "2017AB"
tgt = AuthClient.gettgt()
query = {'ticket': AuthClient.getst(tgt), 'targetSource': 'SNOMEDCT_US'}
base_uri = "https://uts-ws.nlm.nih.gov/rest"
search_uri = "/search/current?string="
content_uri = "/content/current/CUI/"
source = "&sabs=SNOMEDCT_US"
search_type = '&searchType=words'
path = base_uri + search_uri + term + search_type + source
r = requests.get(path, params=query)
code, name, semantic = "", "", ""
try:
items = json.loads(r.text)
pprint(items['result']['results'])
code, name = select_code(items['result']['results'], term)
if code != "":
path2 = base_uri + content_uri + code
tgt2 = AuthClient.gettgt()
query2 = {
'ticket': AuthClient.getst(tgt2),
'targetSource': 'SNOMEDCT_US'
}
r2 = requests.get(path2, params=query2)
try:
items2 = json.loads(r2.text)
semantic = items2['result']['semanticTypes'][0]['name']
except json.decoder.JSONDecodeError:
semantic = "UNKNOWN"
except json.decoder.JSONDecodeError:
code, name = "", ""
return code, name, semantic
class DirectQuery:
"""
For piping queries to MSH and building pools of stems from related concepts.
"""
def __init__(self, identifier):
"""
:param identifier: (str) search term
Other attributes are all defaults by design.
"""
#authorize
self.AuthClient = Authentication()
self.AuthClient.gettgt()
#set attributes
self.identifier = identifier
self.version = "current"
self.source = "MSH"
self.returntype = "concept"
#send the query and return dataframe
self.get_query_result()
self.df = self.parse_query_result()
def get_query_result(self):
"""
Search by human-readable string.
:return: concepts
"""
uri = "https://uts-ws.nlm.nih.gov"
content_endpoint = "/rest/search/{0}?string={1}&sabs={2}&returnIdType={3}".format(
self.version, self.identifier, self.source, self.returntype)
self.query = {'ticket':self.AuthClient.getst()}
r = requests.get(uri+content_endpoint, params=self.query)
items = json.loads(r.text)
self.jsonData = items["result"]
def parse_query_result(self):
"""
Extract name and unique id from results.
:return: pandas dataframe
"""
results = self.jsonData['results']
df = pd.DataFrame(results)
df.drop(['rootSource', 'uri'], axis=1, inplace=True)
return df
def get_umls_ticket2(tgt=tgt, AuthClient=AuthClient, apikey=umls_api):
"""
Get a single use ticket for the UMLS REST services.
It is supposed that an Author Client and a Ticket
Granting Service have already been set-up in case
the apikey = None. If an api-key is given, create the
above needed instances and generate a new ticket.
Input:
- apikey: str,
UMLS REST services api-key. Default is None and
the already establised service is used
Output:
- string of the generated ticket
"""
# Get ticket from the already establised service
if not (tgt) and not (AuthClient):
AuthClient = Authentication(umls_api)
tgt = AuthClient.gettgt()
return AuthClient.getst(tgt)
class CLI:
"""
Command-line interface for querying single terms.
More flexible, keeping around for potential future use/historical reasons.
"""
def __init__(self, argv=None):
"""
:param argv: for testing purposes only
"""
self.parser = argparse.ArgumentParser(description='process user given parameters')
#parser.add_argument("-u", "--username", required = True, dest="username", help = "enter username")
#parser.add_argument("-p", "--password", required = True, dest="password", help = "enter passowrd")
self.parser.add_argument("-k", "--apikey", required = False, dest = "apikey",
default = os.environ.get("APIKEY"),
help = "enter api key from your UTS Profile")
self.parser.add_argument("-v", "--version", required = False, dest="version",
default = "current", help = "enter version example-2015AA")
self.parser.add_argument("-i", "--identifier", required = True, dest="identifier",
help = "enter identifier example-C0018787")
self.parser.add_argument("-s", "--source", required = False, dest="source",
default = 'MSH', help = "enter source name if known")
self.parser.add_argument("-r", "--returntype", required = False, dest='returntype',
default = "concept",
help = "choose return type (‘aui’,‘concept’,‘code’,\
‘sourceConcept’,‘sourceDescriptor’, ‘sourceUi’)")
if argv is not None:
self.args = self.parser.parse_args(argv)
else:
self.args = self.parser.parse_args()
def cli_authenticate(self):
#username = args.username
#password = args.password
self.AuthClient = Authentication()
def construct_query(self):
self.version = self.args.version
self.identifier = self.args.identifier
self.source = self.args.source
self.returntype = self.args.returntype
self.AuthClient.gettgt()
def get_query_result(self):
"""
Search by human-readable string.
:return: concepts
"""
self.construct_query()
uri = "https://uts-ws.nlm.nih.gov"
content_endpoint = "/rest/search/{0}?string={1}&sabs={2}&returnIdType={3}".format(
self.version, self.identifier, self.source, self.returntype)
self.query = {'ticket':self.AuthClient.getst()}
r = requests.get(uri+content_endpoint, params=self.query)
items = json.loads(r.text)
self.jsonData = items["result"]
#print(self.jsonData)
##uncomment the print statment if you want the raw json output, or you can just look at the documentation :=)
#https://documentation.uts.nlm.nih.gov/rest/concept/index.html#sample-output
#https://documentation.uts.nlm.nih.gov/rest/source-asserted-identifiers/index.html#sample-output
#print (json.dumps(items, indent = 4))
def parse_query_result(self):
"""
Extract name and unique id from results.
:return: pandas dataframe
"""
results = self.jsonData['results']
df = pd.DataFrame(results)
df.drop(['rootSource', 'uri'], axis=1, inplace=True)
return df
