rcsb.exdb 1.31__py3-none-any.whl

rcsb/exdb/tests/testAnnotationExtractor.py

@@ -0,0 +1,79 @@
+##
+# 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

@@ -0,0 +1,81 @@
+##
+# 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

@@ -0,0 +1,106 @@
+##
+# 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

@@ -0,0 +1,95 @@
+##
+# 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

@@ -0,0 +1,97 @@
+##
+# 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

@@ -0,0 +1,93 @@
+##
+# 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

@@ -0,0 +1,92 @@
+##
+# 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)