async def startupEvent():
logger.info("Startup - loading search dependencies")
#
ccsw = ChemCompSearchWrapper()
#
clDataUrl = os.environ.get("CHEM_SEARCH_DATA_HOSTNAME", None)
clDataPath = os.environ.get("CHEM_SEARCH_DATA_PATH", None)
clChannel = os.environ.get("CHEM_SEARCH_UPDATE_CHANNEL", None)
#
logger.info("Dependency data host %r path %r update channel %r", clDataUrl,
clDataPath, clChannel)
if clDataUrl and clDataPath and clChannel in ["A", "B", "a", "b"]:
ccsw.restoreDependencies("http://" + clDataUrl,
clDataPath,
bundleLabel=clChannel.upper())
#
ok1 = ccsw.readConfig()
ok2 = ccsw.updateChemCompIndex(useCache=True)
ok3 = ccsw.reloadSearchDatabase()
ok4 = ccsw.updateSearchIndex(useCache=True)
#
logger.info("Completed - loading search dependencies status %r", ok1
and ok2 and ok3 and ok4)
ccdw = ChemCompDepictWrapper()
ok1 = ccdw.readConfig()
logger.info("Completed - loading depict dependencies status %r", ok1)
#
ccsw.status()
def __reload(self):
ccsw = ChemCompSearchWrapper(cachePath=self.__cachePath)
ok1 = ccsw.setConfig(
self.__ccUrlTarget, self.__birdUrlTarget, ccFileNamePrefix=self.__ccFileNamePrefix, useCache=self.__useCache, numProc=self.__numProc, maxChunkSize=self.__chunkSize
)
ok2 = ccsw.readConfig()
ok3 = ccsw.reloadSearchDatabase()
return ccsw if ok1 and ok2 and ok3 else None
def testAReadConfig(self):
"""Test read/access configuration"""
try:
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testEReloadSearchDatabase(self):
"""Test reload search databases."""
try:
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.reloadSearchDatabase()
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDUpdateSearchMoleculeProvider(self):
"""Test update of the search molecule provider."""
try:
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.updateSearchMoleculeProvider()
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testCUpdateSearchIndex(self):
"""Test update search index."""
try:
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.updateSearchIndex()
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testBUpdateChemCompIndex(self):
"""Test update chemical component/Bird basic index."""
try:
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.updateChemCompIndex()
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testZoomSubStructSearch(self):
"""Test substructure search"""
try:
numMolsTest = self.__numMolsTest
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.updateChemCompIndex(useCache=True)
self.assertTrue(ok)
ccIdx = ccsw.getChemCompIndex()
ok = ccsw.updateSearchIndex(useCache=True)
self.assertTrue(ok)
ok = ccsw.reloadSearchDatabase()
self.assertTrue(ok)
#
logger.debug("ccIdx (%d) keys %r entry %r", len(ccIdx),
list(ccIdx.keys())[:10], ccIdx["000"])
#
logger.info(
"Dependencies loaded - Starting search test scan of (limit=%r)",
numMolsTest)
for ii, (ccId, ccD) in enumerate(ccIdx.items(), 1):
if numMolsTest and ii > numMolsTest:
break
for buildType in self.__buildTypeList:
if buildType in ccD:
startTime = time.time()
retStatus, ssL, _ = ccsw.searchByDescriptor(
ccD[buildType],
buildType,
matchOpts="sub-struct-graph-relaxed")
if retStatus == -100:
logger.warning("Descriptor error continuing...")
continue
mOk = self.__resultContains(ccId, ssL)
self.assertTrue(mOk)
#
ssCcIdList = list(
set([t.ccId.split("|")[0] for t in ssL]))
logger.info(
"%s (%d) for buildType %s (%d) (%r) %r (%.4f secs)",
ccId,
ii,
buildType,
len(ssCcIdList),
mOk and retStatus == 0,
ssCcIdList,
time.time() - startTime,
)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def updateDependencies(self):
"""Rebuild search indices using configuration files."""
try:
logger.info("Starting update %r in %r", self.__ccFileNamePrefix,
self.__cachePath)
ccsw = ChemCompSearchWrapper(
cachePath=self.__cachePath,
ccFileNamePrefix=self.__ccFileNamePrefix)
ok1 = ccsw.readConfig()
ok2 = ccsw.updateChemCompIndex()
ok3 = ccsw.updateSearchIndex()
ok4 = ccsw.updateSearchMoleculeProvider()
# verify access -
ok5 = ccsw.reloadSearchDatabase()
return ok1 and ok2 and ok3 and ok4 and ok5
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
def testZoomMatchFormula(self):
"""Test formula matching"""
try:
numMolsTest = self.__numMolsTest
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.updateChemCompIndex(useCache=True)
self.assertTrue(ok)
ccIdx = ccsw.getChemCompIndex()
#
logger.debug("ccIdx (%d) keys %r entry %r", len(ccIdx),
list(ccIdx.keys())[:10], ccIdx["000"])
#
logger.info(
"Dependencies loaded - Starting formula test scan of (limit=%r)",
numMolsTest)
for ii, (ccId, idxD) in enumerate(ccIdx.items(), 1):
if numMolsTest and ii > numMolsTest:
break
#
startTime = time.time()
elementRangeD = {
el: {
"min": eCount,
"max": eCount
}
for el, eCount in idxD["type-counts"].items()
}
retStatus, rL = ccsw.matchByFormulaRange(elementRangeD, ccId)
mOk = self.__resultContains(ccId, rL)
self.assertTrue(mOk)
logger.info(
"%s (%d) (%d) (%r) (%.4f secs)",
ccId,
ii,
len(rL),
mOk and retStatus == 0,
time.time() - startTime,
)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testZoomFingerprintRepeat(self):
"""Test substructure search"""
try:
ccsw = ChemCompSearchWrapper()
ok = ccsw.readConfig()
self.assertTrue(ok)
ok = ccsw.updateChemCompIndex(useCache=True)
self.assertTrue(ok)
ccIdx = ccsw.getChemCompIndex()
ok = ccsw.updateSearchIndex(useCache=True)
self.assertTrue(ok)
ok = ccsw.reloadSearchDatabase()
self.assertTrue(ok)
#
logger.debug("ccIdx (%d)", len(ccIdx))
#
fpL = []
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"
for ii in range(100):
startTime = time.time()
retStatus, _, fpL = ccsw.searchByDescriptor(
descr, "InChI", matchOpts="fingerprint-similarity")
if retStatus == -100:
logger.warning("Descriptor error continuing...")
continue
rD = {}
for mr in fpL:
ccId = mr.ccId.split("|")[0]
rD[ccId] = max(rD[ccId],
mr.fpScore) if ccId in rD else mr.fpScore
rTupL = sorted(rD.items(), key=lambda kv: kv[1], reverse=True)
rL = [rTup[0] for rTup in rTupL]
scoreL = [rTup[1] for rTup in rTupL]
logger.info("%4d (%3d) %r (%.4f secs)", ii, len(rL),
retStatus == 0,
time.time() - startTime)
logger.info("rL %r", rL)
logger.info("scoreL %r", scoreL)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()