def getAccessionMapping(self, wurcsTupL):
"""Fetch GlyTouCan accessions for the input WURCS desriptor list"""
accessionMapD = {}
logger.info("Fetching (%d) WURCS descriptors", len(wurcsTupL))
baseUrl = "https://api.glycosmos.org"
endPoint = "glytoucan/sparql/wurcs2gtcids"
numDescriptors = len(wurcsTupL)
for ii, (entityId, wurcs) in enumerate(wurcsTupL, 1):
try:
pD = {}
pD["wurcs"] = wurcs
uR = UrlRequestUtil()
rDL, retCode = uR.post(baseUrl, endPoint, pD, returnContentType="JSON")
logger.debug(" %r wurcs fetch result (%r) %r", entityId, retCode, rDL)
if rDL:
for rD in rDL:
if "id" in rD:
accessionMapD.setdefault(wurcs, []).append(rD["id"])
else:
logger.info("%r fetch fails (%r) (%r) %r", entityId, retCode, wurcs, rDL)
if ii % 5 == 0:
logger.info("Fetched %d/%d", ii, numDescriptors)
except Exception as e:
logger.exception("Failing for (%r) wurcs (%r) with %s", entityId, wurcs, str(e))
return accessionMapD
def testUnpBatchFetchPost(self):
"""UniProt batch fetch (ebi dbfetch) post test"""
baseUrl = "https://www.ebi.ac.uk"
endPoint = "Tools/dbfetch/dbfetch"
idList = self.__unpIdList1[:10]
try:
pD = {}
pD["db"] = "uniprotkb"
pD["id"] = ",".join(idList)
pD["format"] = "uniprotxml"
pD["style"] = "raw"
#
ureq = UrlRequestUtil()
ret, retCode = ureq.post(baseUrl, endPoint, pD)
logger.debug("XML result %r", ret)
nm = ret.count("<entry ")
logger.info("Result count %d status code %r", nm, retCode)
self.assertGreaterEqual(nm, len(idList))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testPubChemFetchClassification(self):
"""PubChem fetch classification test - can timeout"""
idTupList = [("2244", 200, "2244", "record"),
("123631", 200, "123631", "record"),
("2244", 200, "2244", "classification"),
("123631", 200, "123631", "classification")]
nameSpace = "cid"
domain = "compound"
searchType = "lookup"
# returnType = "record"
requestType = "GET"
outputType = "JSON"
baseUrl = "https://pubchem.ncbi.nlm.nih.gov"
httpCodesCatch = [404]
try:
for (identifier, testRetCode, testPcId, returnType) in idTupList:
for requestType in ["GET", "POST"]:
logger.info(
"namespace %r identifier %r returnType %r requestType %r",
nameSpace, identifier, returnType, requestType)
ret, retCode = None, None
pD = {}
hL = []
ureq = UrlRequestUtil()
if nameSpace in [
"cid", "name", "inchikey"
] and returnType in ["record"] and searchType in [
"lookup"
] and requestType == "GET":
uId = quote(identifier.encode("utf8"))
endPoint = "/".join([
"rest", "pug", domain, nameSpace, uId, outputType
])
ret, retCode = ureq.get(baseUrl,
endPoint,
pD,
headers=hL,
httpCodesCatch=httpCodesCatch,
returnContentType="JSON")
elif nameSpace in [
"cid", "name", "inchikey"
] and returnType in ["record"] and searchType in [
"lookup"
] and requestType == "POST":
endPoint = "/".join(
["rest", "pug", domain, nameSpace, outputType])
pD = {nameSpace: identifier}
ret, retCode = ureq.post(baseUrl,
endPoint,
pD,
headers=hL,
httpCodesCatch=httpCodesCatch,
returnContentType="JSON")
#
elif nameSpace in ["cid"] and returnType in [
"classification"
] and searchType in ["lookup"] and requestType == "GET":
# Needs to be specifically targeted on a particular compound ...
uId = quote(identifier.encode("utf8"))
endPoint = "/".join([
"rest", "pug", domain, nameSpace, uId, returnType,
outputType
])
# pD = {"classification_type": "simple"}
pD = {}
# pD = {nameSpace: identifier}
ret, retCode = ureq.getUnWrapped(
baseUrl,
endPoint,
pD,
headers={},
httpCodesCatch=httpCodesCatch,
returnContentType="JSON")
#
elif nameSpace in ["cid"] and returnType in [
"classification"
] and searchType in ["lookup"] and requestType == "POST":
# Needs to be specifically targeted on a particular compound ...
endPoint = "/".join([
"rest", "pug", domain, nameSpace, returnType,
outputType
])
# This is a long request return server codes may be observed 500
# pD = {nameSpace: identifier, "classification_type": "simple"}
pD = {nameSpace: identifier}
ret, retCode = ureq.postUnWrapped(
baseUrl,
endPoint,
pD,
headers={},
httpCodesCatch=httpCodesCatch,
returnContentType="JSON")
#
#
logger.debug("Result status code %r", retCode)
self.assertEqual(retCode, testRetCode)
if retCode == 200 and returnType == "record":
pcId = str(ret["PC_Compounds"][0]["id"]["id"]["cid"])
self.assertEqual(pcId, testPcId)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()