def testGetChemSearchRequests(self):
"""ChemSearch repetition GET protocol test (using requests module)"""
# dev instances east
# baseUrl = ["http://128.6.159.86"]
#
# Production west instances
# baseUrlList = ["http://132.249.213.210", "http://132.249.213.110", "https://chemsearch-west.rcsb.org"]
# baseUrlList = ["http://128.6.158.85", "http://128.6.158.158", "https://chemsearch-east.rcsb.org"]
baseUrlList = [
"https://chemsearch-west.rcsb.org",
"https://chemsearch-east.rcsb.org"
]
#
endPoint = "chem-match-v1/InChI"
resultLen = 13
descr = "InChI=1S/C9H15N5O3/c1-3(15)6(16)4-2-11-7-5(12-4)8(17)14-9(10)13-7/h3-4,6,12,15-16H,2H2,1H3,(H4,10,11,13,14,17)/t3-,4-,6-/m1/s1"
try:
for baseUrl in baseUrlList:
pD = {"query": descr, "matchType": "fingerprint-similarity"}
for ii in range(100):
ureq = UrlRequestUtil()
ret, retCode = ureq.getUnWrapped(baseUrl,
endPoint,
pD,
headers={},
sslCert="enable",
returnContentType="JSON")
if len(ret["matchedIdList"]) != resultLen:
logger.info(">>> %3d (%r) (%r) result length %r",
ii, baseUrl, retCode,
len(ret["matchedIdList"]))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testUnpBatchFetchGetRequests(self):
"""UniProt batch fetch (uploadlists) get test (requests)"""
baseUrl = "https://www.uniprot.org"
# baseUrl = "https://pir3.uniprot.org"
endPoint = "uploadlists"
idList = self.__unpIdList1[:10]
try:
hD = {"Accept": "application/xml"}
# hL = [("Accept", "application/xml")]
pD = {
"from": "ACC+ID",
"to": "ACC",
"format": "xml",
"query": " ".join(idList)
}
ureq = UrlRequestUtil()
# using unwrapped (requests) version
ret, retCode = ureq.getUnWrapped(baseUrl,
endPoint,
pD,
headers=hD,
sslCert="enable")
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 __doSequenceRequestSecondary(self, unpIdList):
""" """
sD = {}
baseUrl = self.__urlSecondary
hD = {"Accept": "text/x-fasta"}
pD = {}
ok = True
for unpId in unpIdList:
endPoint = "proteins/api/proteins/" + unpId
ureq = UrlRequestUtil()
ret, retCode = ureq.getUnWrapped(baseUrl, endPoint, pD, headers=hD)
if retCode in [200] and ret and len(ret) > 0:
rOk, seqId, rD = self.__parseFastaResponse(ret)
if rOk:
sD[seqId] = rD
else:
logger.error("Parsing error in sequence data for %r",
unpId)
else:
ok = False
return ok, sD
def __doSequenceRequestPrimary(self, unpIdList):
""" """
sD = {}
fmt = "fasta"
baseUrl = self.__urlPrimary
hD = {"Accept": "text/x-fasta"}
pD = {}
ureq = UrlRequestUtil()
ok = True
for unpId in unpIdList:
endPoint = "uniprot/" + unpId + "." + fmt
ret, retCode = ureq.getUnWrapped(baseUrl, endPoint, pD, headers=hD)
logger.debug("unpId %r url %s endpoint %r ret %r retCode %r",
unpId, baseUrl, endPoint, ret, retCode)
if retCode in [200] and ret and len(ret) > 0:
rOk, seqId, rD = self.__parseFastaResponse(ret)
if rOk:
sD[seqId] = rD
else:
logger.error("Parsing error in sequence data for %r",
unpId)
else:
ok = False
return ok, sD
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()
def testPubChemFetch(self):
"""PubChem fetch test"""
idTupList = [("JTOKYIBTLUQVQV-FGHQGBLESA-N", 404, None),
("CXHHBNMLPJOKQD-UHFFFAOYSA-N", 200, 78579)]
nameSpace = "inchikey"
domain = "compound"
searchType = "lookup"
returnType = "record"
requestType = "GET"
outputType = "JSON"
baseUrl = "https://pubchem.ncbi.nlm.nih.gov"
httpCodesCatch = [404]
try:
for (identifier, testRetCode, testPcId) in idTupList:
for requestType in ["GET", "POST"]:
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.getUnWrapped(
baseUrl,
endPoint,
pD,
headers=hL,
httpCodesCatch=httpCodesCatch,
returnContentType="JSON",
sslCert="enable")
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.postUnWrapped(
baseUrl,
endPoint,
pD,
headers=hL,
httpCodesCatch=httpCodesCatch,
returnContentType="JSON",
sslCert="enable")
#
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 = {nameSpace: identifier}
ret, retCode = ureq.getUnWrapped(
baseUrl,
endPoint,
pD,
headers=hL,
httpCodesCatch=httpCodesCatch,
returnContentType="JSON",
sslCert="enable")
#
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=hL,
httpCodesCatch=httpCodesCatch,
returnContentType="JSON",
sslCert="enable")
#
#
logger.debug("Result status code %r", retCode)
self.assertEqual(retCode, testRetCode)
if retCode == 200:
pcId = ret["PC_Compounds"][0]["id"]["id"]["cid"]
self.assertEqual(pcId, testPcId)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()