rcsb.exdb 1.31__py3-none-any.whl → 1.33__py3-none-any.whl

rcsb/exdb/tests/testReferenceSequenceAssignmentAdapter.py

@@ -1,121 +0,0 @@
-##
-# File:    ReferenceSequenceAssignmentAdapterTests.py
-# Author:  J. Westbrook
-# Date:    25-Apr-2019
-#
-# Updates:
-#  2GKI_1,3ZXR_1,2I6F_1,1NQP_1,1NQP_2,1BL4_1,1F9E_1,1SFI_2,1EBO_1,1R6Z_1,1MH3_1,1MH4_1,1MOW_3,1BWM_1 --2I6F_1
-##
-"""
-Tests of reference seequence 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.seq.ReferenceSequenceAssignmentAdapter import ReferenceSequenceAssignmentAdapter
-from rcsb.exdb.seq.ReferenceSequenceAssignmentProvider import ReferenceSequenceAssignmentProvider
-from rcsb.exdb.utils.ObjectTransformer import ObjectTransformer
-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 ReferenceSequenceAssignmentAdapterTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ReferenceSequenceAssignmentAdapterTests, 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")
-        # self.__testEntityCacheKwargs = {"fmt": "json", "indent": 3}
-        self.__testEntityCacheKwargs = {"fmt": "pickle"}
-        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 testAssignmentAdapter(self):
-        """Test case - create and read cache reference sequences assignments and related data."""
-        try:
-            databaseName = "pdbx_core"
-            collectionName = "pdbx_core_polymer_entity"
-            polymerType = "Protein"
-            referenceDatabaseName = "UniProt"
-            provSource = "PDB"
-            #
-            #  -- create cache ---
-            rsaP = ReferenceSequenceAssignmentProvider(
-                self.__cfgOb,
-                databaseName=databaseName,
-                collectionName=collectionName,
-                polymerType=polymerType,
-                referenceDatabaseName=referenceDatabaseName,
-                provSource=provSource,
-                useCache=True,
-                cachePath=self.__cachePath,
-                cacheKwargs=self.__testEntityCacheKwargs,
-                fetchLimit=self.__fetchLimit,
-                siftsAbbreviated="TEST",
-            )
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef1 = rsaP.getRefDataCount()
-            #
-            # ---  Reload from cache ---
-            rsaP = ReferenceSequenceAssignmentProvider(
-                self.__cfgOb, referenceDatabaseName=referenceDatabaseName, useCache=True, cachePath=self.__cachePath, cacheKwargs=self.__testEntityCacheKwargs
-            )
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef2 = rsaP.getRefDataCount()
-            self.assertEqual(numRef1, numRef2)
-            #
-            rsa = ReferenceSequenceAssignmentAdapter(refSeqAssignProvider=rsaP)
-            obTr = ObjectTransformer(self.__cfgOb, objectAdapter=rsa)
-            ok = obTr.doTransform(
-                databaseName=databaseName, collectionName=collectionName, fetchLimit=self.__fetchLimit, selectionQuery={"entity_poly.rcsb_entity_polymer_type": polymerType}
-            )
-            self.assertTrue(ok)
-
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def referenceSequenceAssignmentAdapterSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ReferenceSequenceAssignmentAdapterTests("testAssignmentAdapter"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = referenceSequenceAssignmentAdapterSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testReferenceSequenceAssignmentAdapterValidate.py

@@ -1,122 +0,0 @@
-##
-# File:    ReferenceSequenceAssignmentAdapterValidateTests.py
-# Author:  J. Westbrook
-# Date:    25-Apr-2019
-#
-# Updates:
-#  2GKI_1,3ZXR_1,2I6F_1,1NQP_1,1NQP_2,1BL4_1,1F9E_1,1SFI_2,1EBO_1,1R6Z_1,1MH3_1,1MH4_1,1MOW_3,1BWM_1 --2I6F_1
-##
-"""
-Tests of reference seequence 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.seq.ReferenceSequenceAssignmentAdapter import ReferenceSequenceAssignmentAdapter
-from rcsb.exdb.seq.ReferenceSequenceAssignmentProvider import ReferenceSequenceAssignmentProvider
-from rcsb.exdb.utils.ObjectValidator import ObjectValidator
-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 ReferenceSequenceAssignmentAdapterTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ReferenceSequenceAssignmentAdapterTests, 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")
-        # self.__testEntityCacheKwargs = {"fmt": "json", "indent": 3}
-        self.__testEntityCacheKwargs = {"fmt": "pickle"}
-        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)
-
-    @unittest.skip("Disable test - for troubleshooting only")
-    def testAssignmentAdapter(self):
-        """Test case - create and read cache reference sequences assignments and related data."""
-        try:
-            databaseName = "pdbx_core"
-            collectionName = "pdbx_core_polymer_entity"
-            polymerType = "Protein"
-            referenceDatabaseName = "UniProt"
-            provSource = "PDB"
-            #
-            #  -- create cache ---
-            rsaP = ReferenceSequenceAssignmentProvider(
-                self.__cfgOb,
-                databaseName=databaseName,
-                collectionName=collectionName,
-                polymerType=polymerType,
-                referenceDatabaseName=referenceDatabaseName,
-                provSource=provSource,
-                useCache=True,
-                cachePath=self.__cachePath,
-                cacheKwargs=self.__testEntityCacheKwargs,
-                fetchLimit=self.__fetchLimit,
-                siftsAbbreviated="TEST",
-            )
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef1 = rsaP.getRefDataCount()
-            #
-            # ---  Reload from cache ---
-            rsaP = ReferenceSequenceAssignmentProvider(
-                self.__cfgOb, referenceDatabaseName=referenceDatabaseName, useCache=True, cachePath=self.__cachePath, cacheKwargs=self.__testEntityCacheKwargs
-            )
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef2 = rsaP.getRefDataCount()
-            self.assertEqual(numRef1, numRef2)
-            #
-            rsa = ReferenceSequenceAssignmentAdapter(refSeqAssignProvider=rsaP)
-            obTr = ObjectValidator(self.__cfgOb, objectAdapter=rsa, cachePath=self.__cachePath, useCache=False)
-            ok = obTr.doTransform(
-                databaseName=databaseName, collectionName=collectionName, fetchLimit=self.__fetchLimit, selectionQuery={"entity_poly.rcsb_entity_polymer_type": polymerType}
-            )
-            self.assertTrue(ok)
-
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def referenceSequenceAssignmentAdapterSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ReferenceSequenceAssignmentAdapterTests("testAssignmentAdapter"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = referenceSequenceAssignmentAdapterSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testReferenceSequenceAssignmentProvider.py

@@ -1,117 +0,0 @@
-##
-# File:    ReferenceSequenceAssignmentProviderTests.py
-# Author:  J. Westbrook
-# Date:    17-Oct-2019
-#
-# Updates:
-#
-##
-"""
-Tests for reference sequence assignment update operations
-"""
-
-__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.ReferenceSequenceAssignmentProvider import ReferenceSequenceAssignmentProvider
-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 ReferenceSequenceAssignmentProviderTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ReferenceSequenceAssignmentProviderTests, self).__init__(methodName)
-        self.__verbose = True
-        self.__traceMemory = False
-
-    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")
-        # self.__testEntityCacheKwargs = {"fmt": "json", "indent": 3}
-        self.__testEntityCacheKwargs = {"fmt": "pickle"}
-        self.__fetchLimitTest = None
-        self.__useCache = False
-        #
-        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 testAssignmentProvider(self):
-        """Test case - create and read cache reference sequences assignments and related data.
-
-        Some profiling statistics -
-         Current memory usage is 0.711864MB; Peak was 4646.476926MB (full cache no limit)
-         Current memory usage is 1.080839MB; Peak was 1258.231275MB (163)
-         Current memory usage is 0.874476MB; Peak was 1920.689116MB (918)
-         Current memory usage is 0.937091MB; Peak was 2086.910197MB (2739)
-         Current memory usage is 1.3539 MB; Peak was 2300.5170 MB (10000)
-         Current memory usage is 1.3517 MB; Peak was 2714.5467 MB (20K entries)
-        """
-        try:
-            #  -- create cache ---
-            rsaP = ReferenceSequenceAssignmentProvider(
-                self.__cfgOb,
-                databaseName="pdbx_core",
-                collectionName="pdbx_core_polymer_entity",
-                polymerType="Protein",
-                referenceDatabaseName="UniProt",
-                provSource="PDB",
-                useCache=self.__useCache,
-                cachePath=self.__cachePath,
-                cacheKwargs=self.__testEntityCacheKwargs,
-                fetchLimit=self.__fetchLimitTest,
-                siftsAbbreviated="TEST",
-            )
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef = rsaP.getRefDataCount()
-            self.assertGreaterEqual(numRef, 49)
-            #
-            # ---  Reload from cache ---
-            rsaP = ReferenceSequenceAssignmentProvider(
-                self.__cfgOb, referenceDatabaseName="UniProt", useCache=True, cachePath=self.__cachePath, cacheKwargs=self.__testEntityCacheKwargs
-            )
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef = rsaP.getRefDataCount()
-            self.assertGreaterEqual(numRef, 49)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def referenceSequenceAssignmentProviderSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ReferenceSequenceAssignmentProviderTests("testAssignmentProvider"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = referenceSequenceAssignmentProviderSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testReferenceSequenceCacheProvider.py

@@ -1,94 +0,0 @@
-##
-# File:    ReferenceSequenceCacheProviderTests.py
-# Author:  J. Westbrook
-# Date:    10-Feb-2020
-#
-# Updates:
-#
-##
-"""
-Tests for reference sequence cache maintenance operations
-"""
-
-__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.ReferenceSequenceCacheProvider import ReferenceSequenceCacheProvider
-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 ReferenceSequenceCacheProviderTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ReferenceSequenceCacheProviderTests, self).__init__(methodName)
-        self.__verbose = True
-        self.__traceMemory = False
-
-    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.__fetchLimitTest = 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 testReferenceCacheProvider(self):
-        """Test case - create and read cached reference sequences."""
-        try:
-            #  -- Update/create cache ---
-            databaseName = "pdbx_core"
-            collectionName = "pdbx_core_polymer_entity"
-            polymerType = "Protein"
-            #
-            rsaP = ReferenceSequenceCacheProvider(self.__cfgOb, databaseName, collectionName, polymerType, maxChunkSize=50, numProc=2, expireDays=0)
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef = rsaP.getRefDataCount()
-            self.assertGreaterEqual(numRef, 44)
-            #
-            # ---  Reload from cache ---
-            rsaP = ReferenceSequenceCacheProvider(self.__cfgOb, databaseName, collectionName, polymerType, maxChunkSize=50, numProc=2, expireDays=14)
-            ok = rsaP.testCache()
-            self.assertTrue(ok)
-            numRef = rsaP.getRefDataCount()
-            self.assertGreaterEqual(numRef, 44)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def referenceSequenceCacheProviderSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ReferenceSequenceCacheProviderTests("testCacheProvider"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = referenceSequenceCacheProviderSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testTaxonomyExtractor.py

@@ -1,75 +0,0 @@
-##
-# File:    TaxonomyExtractorTests.py
-# Author:  J. Westbrook
-# Date:    15-Oct-2019
-#
-# Updates:
-#
-##
-"""
-Tests for extraction of taxonomy 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.seq.TaxonomyExtractor import TaxonomyExtractor
-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 TaxonomyExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(TaxonomyExtractorTests, 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 testGetTaxons(self):
-        """Test case - get reference sequences and update candidates"""
-        try:
-            urs = TaxonomyExtractor(self.__cfgOb)
-            taxIdL = urs.getUniqueTaxons()
-            logger.info("Unique taxon count %d", len(taxIdL))
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def extractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(TaxonomyExtractorTests("testGetTaxons"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = extractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testTreeNodeListWorker.py

@@ -1,111 +0,0 @@
-##
-# File:    testTreeNodeListWorker.py
-# Author:  J. Westbrook
-# Date:    23-Apr-2019
-#
-# Updates:
-#
-##
-"""
-Tests for for tree node list worker ---
-
-"""
-
-__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.db.utils.TimeUtil import TimeUtil
-from rcsb.exdb.tree.TreeNodeListWorker import TreeNodeListWorker
-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 TreeNodeListWorkerTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(TreeNodeListWorkerTests, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        self.__isMac = platform.system() == "Darwin"
-        self.__doLoad = True if self.__isMac else False
-        #
-        #
-        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.__mU = MarshalUtil()
-        #
-        self.__readBackCheck = True
-        self.__numProc = 2
-        self.__chunkSize = 10
-        self.__documentLimit = None
-        self.__debugFlag = False
-        self.__loadType = "full"
-        self.__useCache = True
-        self.__useFilteredLists = True
-        #
-        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 testTreeLoader(self):
-        """Test case - extract entity polymer info"""
-        try:
-            tU = TimeUtil()
-            updateId = tU.getCurrentWeekSignature()
-            rhw = TreeNodeListWorker(
-                self.__cfgOb,
-                self.__cachePath,
-                numProc=self.__numProc,
-                chunkSize=self.__chunkSize,
-                documentLimit=self.__documentLimit,
-                verbose=self.__debugFlag,
-                readBackCheck=self.__readBackCheck,
-                useCache=self.__useCache,
-                useFilteredLists=self.__useFilteredLists,
-            )
-            #
-            ok = rhw.load(updateId, loadType=self.__loadType, doLoad=self.__doLoad)
-            self.assertTrue(ok)
-            #
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def treeNodeListSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(TreeNodeListWorkerTests("testTreeLoader"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = treeNodeListSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)