def testAABuildDependencies(self):
"""Test case - build all dependencies (convenience method)"""
try:
ccsw = ChemCompSearchWrapper()
ccUrlTarget = os.path.join(
self.__dataPath,
"components-abbrev.cif") if not self.__testFlagFull else None
birdUrlTarget = os.path.join(
self.__dataPath,
"prdcc-abbrev.cif") if not self.__testFlagFull else None
ok = ccsw.buildDependenices(ccUrlTarget=ccUrlTarget,
birdUrlTarget=birdUrlTarget)
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAABuildDependenciesAndStash(self):
"""Test case - build, stash and restore dependencies -"""
try:
ccsw = ChemCompSearchWrapper()
ccUrlTarget = os.path.join(
self.__dataPath,
"components-abbrev.cif") if not self.__testFlagFull else None
birdUrlTarget = os.path.join(
self.__dataPath,
"prdcc-abbrev.cif") if not self.__testFlagFull else None
ok = ccsw.buildDependenices(ccUrlTarget=ccUrlTarget,
birdUrlTarget=birdUrlTarget)
self.assertTrue(ok)
#
if self.__testStash:
url = "sftp://bl-east.rcsb.org"
userName = ""
pw = ""
dirPath = "4-coastal"
ok = ccsw.stashDependencies(url,
dirPath,
userName=userName,
pw=pw)
self.assertTrue(ok)
#
fileU = FileUtil()
fileU.remove(self.__cachePath)
#
url = "http://bl-east.rcsb.org"
ok = ccsw.restoreDependencies(url, dirPath)
#
fileU.remove(self.__cachePath)
#
url = "sftp://bl-east.rcsb.org"
ok = ccsw.restoreDependencies(url,
dirPath,
userName=userName,
pw=pw)
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
class ChemCompSearchIndexWorkflow(object):
def __init__(self, **kwargs):
""" Module entry point for chemical component and BIRD search index generation workflow.
Args:
cachePath(str, optional): cache directory to store indices and temporary files (default: '.')
licenseFilePath (str, optional) = path to OpenEye license text file (default: use enviroment OE_LICENSE setting)
ccFilNamePrefix (str, optional) = index prefix (default: "cc-full")
"""
self.__licensePath = kwargs.get("licenseFilePath", "oe_license.txt")
cachePath = kwargs.get("cachePath", ".")
self.__cachePath = os.path.abspath(cachePath)
self.__ccFileNamePrefix = kwargs.get("ccFilNamePrefix", "cc-full")
self.__ccsw = ChemCompSearchWrapper(
cachePath=self.__cachePath,
ccFileNamePrefix=self.__ccFileNamePrefix)
def __setLicense(self, licensePath):
ok = False
try:
if os.environ.get("OE_LICENSE") and os.access(
os.environ["OE_LICENSE"], os.R_OK):
logger.info("Using license from environment %r",
os.environ["OE_LICENSE"])
ok = True
elif os.access(licensePath, os.R_OK):
os.environ["OE_LICENSE"] = licensePath
logger.info("Setting environmenal variable OE_LICENSE to %r",
os.environ["OE_LICENSE"])
ok = True
except Exception as e:
logger.error("Setting Openeye license file %r failing %s",
licensePath, str(e))
return ok
def testCache(self):
return True
def makeIndices(self, ccUrlTarget, birdUrlTarget, **kwargs):
"""Build chemical component and BIRD search indices.
Args:
ccUrlTarget (str): URL or path for concatenated chemical component dictionary
birdUrlTarget (str): URL or path for concatenated BIRD dictionary
Other arguments may be supplied to change defaults for index generators (testing/troubleshooting)
Returns:
bool: True for success or False otherwise
"""
ok = False
if not self.__setLicense(self.__licensePath):
logger.error("Invalid OpenEye license details - exiting")
return ok
#
try:
ok = self.__ccsw.buildDependenices(ccUrlTarget, birdUrlTarget,
**kwargs)
except Exception as e:
logger.exception("Failing with %s", str(e))
return ok
def stashIndices(self,
url,
dirPath,
bundleLabel="A",
userName=None,
pw=None):
""" Store a copy of the bundled search dependencies remotely -
Args:
url (str): URL string for the destination host (e.g. sftp://myserver.net or None for a local file)
dirPath (str): directory path on the remote resource
bundleLabel (str, optional): optional label preppended to the stashed dependency bundle artifact (default='A')
userName (str, optional): optional access information. Defaults to None.
password (str, optional): optional access information. Defaults to None.
Returns:
bool: True for success or False otherwise
"""
#
ok = False
try:
ok = self.__ccsw.stashDependencies(url,
dirPath,
bundleLabel=bundleLabel,
userName=userName,
pw=pw)
except Exception as e:
logger.exception("Failing with %s", str(e))
return ok