rcsb.exdb 1.31__py3-none-any.whl → 1.32__py3-none-any.whl

rcsb/exdb/tests/testAnnotationExtractor.py

@@ -1,79 +0,0 @@
-##
-# File:    AnnotationExtractorTests.py
-# Author:  J. Westbrook
-# Date:    26-Jan-2020
-#
-# Updates:
-#
-##
-"""
-Tests for extraction of annotation identifiers from the polymer entity collection.
-Currently
-"""
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-from rcsb.exdb.seq.AnnotationExtractor import AnnotationExtractor
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class AnnotationExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(AnnotationExtractorTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-        #
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testGetGoIds(self):
-        """Test case - get reference sequences and update candidates"""
-        try:
-            urs = AnnotationExtractor(self.__cfgOb)
-            goIdL = urs.getUniqueIdentifiers("GO")
-            logger.debug("goIdL %r", goIdL)
-            logger.info("Unique GO ID count %d", len(goIdL))
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def extractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(AnnotationExtractorTests("testGetGoIds"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = extractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testBranchedEntityExtractor.py

@@ -1,81 +0,0 @@
-##
-# File:    BranchedEntityExtractorTests.py
-# Author:  J. Westbrook
-# Date:    24-May-2021
-#
-# Updates:
-#
-##
-"""
-Tests for extraction of polymer entity sequence details from the ExDB core collections.
-"""
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-from rcsb.exdb.branch.BranchedEntityExtractor import BranchedEntityExtractor
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class BranchedEntityExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(BranchedEntityExtractorTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-        self.__detailsPath = os.path.join(HERE, "test-output", "CACHE", "branched-entity-details.json")
-        #
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testGetBranchedEntityDetails(self):
-        """Test case - get branched entity BIRD and WURCS details"""
-        try:
-            bEx = BranchedEntityExtractor(self.__cfgOb)
-            rD = bEx.getBranchedDetails()
-            self.assertGreaterEqual(len(rD), 12)
-            logger.info("Branched entity descriptor count %d", len(rD))
-            ok = bEx.exportBranchedEntityDetails(self.__detailsPath, fmt="json")
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def extractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(BranchedEntityExtractorTests("testGetBranchedEntityDetails"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = extractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testChemRefLoader.py

@@ -1,106 +0,0 @@
-##
-# File:    ChemRefLoaderTests.py
-# Author:  J. Westbrook
-# Date:    18-Jun-2021
-#
-# Updates:
-#
-##
-"""
-Tests for loading chemical reference data and identifer mapping information.
-
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-from rcsb.exdb.chemref.ChemRefExtractor import ChemRefExtractor
-from rcsb.exdb.chemref.ChemRefEtlWorker import ChemRefEtlWorker
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-from rcsb.utils.io.MarshalUtil import MarshalUtil
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class ChemRefLoaderTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ChemRefLoaderTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        #
-        # sample data set
-        self.__updateId = "2021_10"
-        #
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testLoadIntegratedDrugBankData(self):
-        """Test case - load integrated DrugBank chemical reference data -"""
-        try:
-            crw = ChemRefEtlWorker(self.__cfgOb, self.__cachePath)
-            crExt = ChemRefExtractor(self.__cfgOb)
-
-            idD = crExt.getChemCompAccessionMapping(referenceResourceName="DrugBank")
-            logger.info("Mapping dictionary %r", len(idD))
-            #
-            ok = crw.load(self.__updateId, extResource="DrugBank", loadType="full")
-            #
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testDrugBankDataMapping(self):
-        """Test case - get DrugBank mapping -"""
-        try:
-            crExt = ChemRefExtractor(self.__cfgOb)
-            idD = crExt.getChemCompAccessionMapping(referenceResourceName="DrugBank")
-            logger.info("Mapping dictionary %r", len(idD))
-            #
-            mU = MarshalUtil()
-            fp = os.path.join(HERE, "test-output", "drugbank-mapping.json")
-            mU.doExport(fp, idD, fmt="json", indent=3)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def chemRefLoadSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ChemRefLoaderTests("testLoadIntegratedDrugBankData"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    #
-    mySuite = chemRefLoadSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testChemRefMappingProvider.py

@@ -1,95 +0,0 @@
-##
-# File:    ChemRefMappingProviderTests.py
-# Author:  J. Westbrook
-# Date:    18-Jun-2021
-#
-# Updates:
-#
-##
-"""
-Tests for
-
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-from rcsb.exdb.chemref.ChemRefMappingProvider import ChemRefMappingProvider
-
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class ChemRefMappingProviderTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ChemRefMappingProviderTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testChemRefMapping(self):
-        """Test case - load and access mapping cache"""
-        try:
-            crmP = ChemRefMappingProvider(self.__cachePath, useCache=True)
-            ok = crmP.testCache()
-            self.assertTrue(ok)
-            #
-            ok = crmP.fetchChemRefMapping(self.__cfgOb, referenceResourceNameList=None)
-            self.assertTrue(ok)
-            crmP = ChemRefMappingProvider(self.__cachePath, useCache=True)
-            ok = crmP.testCache(minCount=2)
-            self.assertTrue(ok)
-            # tD = {"CHEMBL": ("CHEMBL14249", "ATP"), "DRUGBANK": ("DB00171", "ATP")}
-            tD = {"DRUGBANK": ("DB00171", "ATP")}
-            for refName, refTup in tD.items():
-                tL = crmP.getReferenceIds(refName, refTup[1])
-                logger.info("tL %r", tL)
-                self.assertTrue(refTup[0] in tL)
-                tL = crmP.getLocalIds(refName, refTup[0])
-                logger.info("tL %r", tL)
-                self.assertTrue(refTup[1] in tL)
-            #
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def chemRefMappingSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ChemRefMappingProviderTests("testChemRefMapping"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    #
-    mySuite = chemRefMappingSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testCitationAdapter.py

@@ -1,97 +0,0 @@
-##
-# File:    CitationAdapterTests.py
-# Author:  J. Westbrook
-# Date:    22-Nov-2019
-#
-# Updates:
-#
-##
-"""
-Tests of reference sequence assignment adapter.
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-from rcsb.exdb.citation.CitationAdapter import CitationAdapter
-from rcsb.exdb.utils.ObjectTransformer import ObjectTransformer
-from rcsb.utils.citation.CitationReferenceProvider import CitationReferenceProvider
-from rcsb.utils.citation.JournalTitleAbbreviationProvider import JournalTitleAbbreviationProvider
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class CitationAdapterTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(CitationAdapterTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-        self.__resourceName = "MONGO_DB"
-        self.__cachePath = os.path.join(TOPDIR, "CACHE", "cit_ref")
-        self.__testEntityCacheKwargs = {"fmt": "json", "indent": 3}
-        self.__fetchLimit = None
-        #
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testCitationAdapter(self):
-        """Test case - create and read cache reference sequences assignments and related data."""
-        try:
-            databaseName = "pdbx_core"
-            collectionName = "pdbx_core_entry"
-            useCache = False
-            #
-            crP = CitationReferenceProvider(cachePath=self.__cachePath, useCache=useCache)
-            ok = crP.testCache()
-            self.assertTrue(ok)
-            jtaP = JournalTitleAbbreviationProvider(cachePath=self.__cachePath, useCache=useCache)
-            ok = jtaP.testCache()
-            self.assertTrue(ok)
-            #
-            ca = CitationAdapter(crP, jtaP)
-            obTr = ObjectTransformer(self.__cfgOb, objectAdapter=ca)
-            ok = obTr.doTransform(databaseName=databaseName, collectionName=collectionName, fetchLimit=self.__fetchLimit)
-            self.assertTrue(ok)
-
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def citationAdapterSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(CitationAdapterTests("testCitationAdapter"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = citationAdapterSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testCitationExtractor.py

@@ -1,93 +0,0 @@
-##
-# File:    CitationExtractorTests.py
-# Author:  J. Westbrook
-# Date:    25-Apr-2019
-#
-# Updates:
-#
-##
-"""
-Tests for extractor selected values from collections (limited tests from mock-data repos)
-
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-
-from rcsb.exdb.citation.CitationExtractor import CitationExtractor
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-from rcsb.utils.io.MarshalUtil import MarshalUtil
-
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class CitationExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(CitationExtractorTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        #
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        #
-        self.__cacheKwargs = {"fmt": "json", "indent": 3}
-        self.__exdbDirPath = os.path.join(self.__cachePath, self.__cfgOb.get("EXDB_CACHE_DIR", sectionName=configName))
-        #
-        self.__mU = MarshalUtil()
-        self.__entryLimitTest = 20
-        #
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testExtractEntryCitations(self):
-        """Test case - extract entry citations"""
-        try:
-            ce = CitationExtractor(self.__cfgOb, exdbDirPath=self.__exdbDirPath, useCache=True, cacheKwargs=self.__cacheKwargs, entryLimit=self.__entryLimitTest)
-            eCount = ce.getEntryCount()
-            self.assertGreaterEqual(eCount, self.__entryLimitTest)
-            #
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def citationExtractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(CitationExtractorTests("testExtractEntryCitations"))
-
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = citationExtractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testCitationUtils.py

@@ -1,92 +0,0 @@
-##
-# File:    CitationUtilsTests.py
-# Author:  J. Westbrook
-# Date:    25-Apr-2019
-#
-# Updates:
-#
-##
-"""
-Tests for citation process and normalization.
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-
-from rcsb.exdb.citation.CitationUtils import CitationUtils
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-from rcsb.utils.io.MarshalUtil import MarshalUtil
-
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class CitationUtilsTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(CitationUtilsTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        #
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-
-        #
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        #
-        self.__cacheKwargs = {"fmt": "json", "indent": 3}
-        self.__exdbDirPath = os.path.join(self.__cachePath, self.__cfgOb.get("EXDB_CACHE_DIR", sectionName=configName))
-        #
-        self.__mU = MarshalUtil()
-        self.__entryLimitTest = 20
-        #
-        self.__startTime = time.time()
-        logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
-
-    def tearDown(self):
-        unitS = "MB" if platform.system() == "Darwin" else "GB"
-        rusageMax = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-        logger.info("Maximum resident memory size %.4f %s", rusageMax / 10 ** 6, unitS)
-        endTime = time.time()
-        logger.info("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime)
-
-    def testEntryCitationAccess(self):
-        """Test case - extract entry citations"""
-        try:
-            ce = CitationUtils(self.__cfgOb, exdbDirPath=self.__exdbDirPath, useCache=True, cacheKwargs=self.__cacheKwargs, entryLimit=self.__entryLimitTest)
-            eCount = ce.getCitationEntryCount()
-            self.assertGreaterEqual(eCount, self.__entryLimitTest)
-            #
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def citationUtilsSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(CitationUtilsTests("testEntryCitationAccess"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = citationUtilsSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)