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

rcsb/exdb/tests/testObjectExtractor.py

@@ -1,342 +0,0 @@
-##
-# File:    ObjectExtractorTests.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 pprint
-import time
-import unittest
-from collections import defaultdict
-
-from rcsb.db.mongo.Connection import Connection
-from rcsb.exdb.utils.ObjectExtractor import ObjectExtractor
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-from rcsb.utils.io.TimeUtil import TimeUtil
-
-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 ObjectExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ObjectExtractorTests, self).__init__(methodName)
-        self.__verbose = 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.__workPath = os.path.join(TOPDIR, "CACHE", "exdb")
-        #
-        self.__testEntryCacheKwargs = {"fmt": "json", "indent": 3}
-        self.__objectLimitTest = 5
-        #
-        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 testCreateMultipleConnections(self):
-        """Test case -  multiple connection creation"""
-        try:
-            for _ in range(5):
-                with Connection(cfgOb=self.__cfgOb, resourceName=self.__resourceName) as client:
-                    self.assertNotEqual(client, None)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExtractDrugbankMapping(self):
-        """Test case - extract Drugbank mapping"""
-        try:
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName="dw",
-                collectionName="core_chem_comp",
-                cacheFilePath=os.path.join(self.__workPath, "drugbank-mapping-cache.json"),
-                useCache=False,
-                cacheKwargs=self.__testEntryCacheKwargs,
-                keyAttribute="chem_comp",
-                uniqueAttributes=["rcsb_id"],
-                selectionQuery={"rcsb_chem_comp_container_identifiers.drugbank_id": {"$exists": True}},
-                selectionList=["rcsb_id", "rcsb_chem_comp_container_identifiers", "rcsb_chem_comp_related"],
-            )
-            eCount = obEx.getCount()
-            logger.info("Component count ifs %d", eCount)
-            self.assertGreaterEqual(eCount, 3)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExtractEntriesBefore(self):
-        """Test case - extract entries subject to date restriction"""
-        try:
-            tU = TimeUtil()
-            tS = tU.getTimestamp(useUtc=True, before={"days": 365 * 7})
-            tD = tU.getDateTimeObj(tS)
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName="pdbx_core",
-                collectionName="pdbx_core_entry",
-                useCache=False,
-                keyAttribute="entry",
-                uniqueAttributes=["rcsb_id"],
-                selectionQuery={"rcsb_accession_info.initial_release_date": {"$gt": tD}},
-                selectionList=["rcsb_id", "rcsb_accession_info"],
-            )
-            eD = obEx.getObjects()
-            eCount = obEx.getCount()
-            logger.info("Entry count is %d", eCount)
-            logger.info("Entries are %r", list(eD.keys()))
-            self.assertGreaterEqual(eCount, 5)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExtractEntries(self):
-        """Test case - extract entries"""
-        try:
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName="pdbx_core",
-                collectionName="pdbx_core_entry",
-                cacheFilePath=os.path.join(self.__workPath, "entry-data-test-cache.json"),
-                useCache=False,
-                keyAttribute="entry",
-                uniqueAttributes=["rcsb_id"],
-                cacheKwargs=self.__testEntryCacheKwargs,
-                objectLimit=self.__objectLimitTest,
-            )
-            eCount = obEx.getCount()
-            logger.info("Entry count is %d", eCount)
-            self.assertGreaterEqual(eCount, self.__objectLimitTest)
-
-            objD = obEx.getObjects()
-            for _, obj in objD.items():
-                # obEx.genPathList(obj["software"], path=["software"])
-                obEx.genPathList(obj, path=None)
-
-            #
-            pL = obEx.getPathList(filterList=True)
-            obEx.setPathList(pL)
-            if self.__verbose:
-                for ky, obj in objD.items():
-                    obEx.genValueList(obj, path=None)
-                    tD = obEx.getValues()
-                    logger.debug("Index object %r %s", ky, pprint.pformat(tD, indent=3, width=120))
-
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExtractEntities(self):
-        """Test case - extract entities"""
-        try:
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName="pdbx_core",
-                collectionName="pdbx_core_polymer_entity",
-                cacheFilePath=os.path.join(self.__workPath, "entity-data-test-cache.json"),
-                useCache=False,
-                keyAttribute="entity",
-                uniqueAttributes=["rcsb_id"],
-                cacheKwargs=self.__testEntryCacheKwargs,
-                objectLimit=self.__objectLimitTest,
-            )
-            eCount = obEx.getCount()
-            logger.info("Entity count is %d", eCount)
-            self.assertGreaterEqual(eCount, self.__objectLimitTest)
-
-            objD = obEx.getObjects()
-            for _, obj in objD.items():
-                obEx.genPathList(obj, path=None)
-            #
-            pL = obEx.getPathList(filterList=False)
-            logger.debug("Path list (unfiltered) %r", pL)
-            #
-            pL = obEx.getPathList()
-            logger.debug("Path list %r", pL)
-            obEx.setPathList(pL)
-            if self.__verbose:
-                for ky, obj in objD.items():
-                    obEx.genValueList(obj, path=None)
-                    tD = obEx.getValues()
-                    logger.info("Index object %r %s", ky, pprint.pformat(tD, indent=3, width=120))
-
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExtractSelectedEntityContent(self):
-        """Test case - extract selected entity content
-
-        "reference_sequence_identifiers": [
-                    {
-                        "database_name": "UniProt",
-                        "database_accession": "Q5SHN1",
-                        "provenance_source": "SIFTS"
-                    },
-                    {
-                        "database_name": "UniProt",
-                        "database_accession": "Q5SHN1",
-                        "provenance_source": "PDB"
-                    }
-                    ]
-        """
-        try:
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName="pdbx_core",
-                collectionName="pdbx_core_polymer_entity",
-                cacheFilePath=os.path.join(self.__workPath, "entity-selected-content-test-cache.json"),
-                useCache=False,
-                keyAttribute="entity",
-                uniqueAttributes=["rcsb_id"],
-                cacheKwargs=self.__testEntryCacheKwargs,
-                # objectLimit=self.__objectLimitTest,
-                objectLimit=None,
-                selectionQuery={"entity_poly.rcsb_entity_polymer_type": "Protein"},
-                selectionList=["rcsb_id", "rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers"],
-            )
-            eCount = obEx.getCount()
-            logger.info("Entity count is %d", eCount)
-            #
-            #
-            if self.__objectLimitTest is not None:
-                self.assertGreaterEqual(eCount, self.__objectLimitTest)
-                objD = obEx.getObjects()
-                for _, obj in objD.items():
-                    obEx.genPathList(obj, path=None)
-                #
-                pL = obEx.getPathList(filterList=False)
-                logger.debug("Path list (unfiltered) %r", pL)
-                #
-                pL = obEx.getPathList()
-                logger.debug("Path list %r", pL)
-                obEx.setPathList(pL)
-                if self.__verbose:
-                    for ky, obj in objD.items():
-                        obEx.genValueList(obj, path=None)
-                        tD = obEx.getValues()
-                        logger.info("Index object %r %s", ky, pprint.pformat(tD, indent=3, width=120))
-
-            objD = obEx.getObjects()
-            # logger.info("objD.keys() %r", list(objD.keys()))
-            totCount = 0
-            difCount = 0
-            pdbUnpIdD = defaultdict(int)
-            siftsUnpIdD = defaultdict(int)
-            pdbDifUnpIdD = defaultdict(int)
-            for entityKey, eD in objD.items():
-                try:
-                    siftsS = set()
-                    pdbS = set()
-                    for tD in eD["rcsb_polymer_entity_container_identifiers"]["reference_sequence_identifiers"]:
-                        if tD["database_name"] == "UniProt":
-                            if tD["provenance_source"] == "SIFTS":
-                                siftsS.add(tD["database_accession"])
-                                siftsUnpIdD[tD["database_accession"]] += 1
-                            elif tD["provenance_source"] == "PDB":
-                                pdbS.add(tD["database_accession"])
-                                pdbUnpIdD[tD["database_accession"]] += 1
-                        else:
-                            logger.debug("No UniProt for %r", eD["rcsb_polymer_entity_container_identifiers"])
-                    logger.debug("PDB assigned sequence length %d", len(pdbS))
-                    logger.debug("SIFTS assigned sequence length %d", len(siftsS))
-
-                    if pdbS and siftsS:
-                        totCount += 1
-                        if pdbS != siftsS:
-                            difCount += 1
-                            for idV in pdbS:
-                                pdbDifUnpIdD[idV] += 1
-
-                except Exception as e:
-                    logger.warning("No identifiers for %s with %s", entityKey, str(e))
-            logger.info("Total %d differences %d", totCount, difCount)
-            logger.info("Unique UniProt ids  PDB %d  SIFTS %d", len(pdbUnpIdD), len(siftsUnpIdD))
-            logger.info("Unique UniProt differences %d ", len(pdbDifUnpIdD))
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExtractEntityTaxonomyContent(self):
-        """Test case - extract unique entity source and host taxonomies"""
-        try:
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName="pdbx_core",
-                collectionName="pdbx_core_polymer_entity",
-                cacheFilePath=os.path.join(self.__workPath, "entity-taxonomy-test-cache.json"),
-                useCache=False,
-                keyAttribute="entity",
-                uniqueAttributes=["rcsb_id"],
-                cacheKwargs=self.__testEntryCacheKwargs,
-                # objectLimit=self.__objectLimitTest,
-                objectLimit=None,
-                selectionQuery=None,
-                selectionList=["rcsb_id", "rcsb_entity_source_organism.ncbi_taxonomy_id", "rcsb_entity_host_organism.ncbi_taxonomy_id"],
-            )
-            eCount = obEx.getCount()
-            logger.info("Polymer entity count is %d", eCount)
-            taxIdS = set()
-            objD = obEx.getObjects()
-            for _, eD in objD.items():
-                try:
-                    for tD in eD["rcsb_entity_source_organism"]:
-                        taxIdS.add(tD["ncbi_taxonomy_id"])
-                except Exception:
-                    pass
-                try:
-                    for tD in eD["rcsb_entity_host_organism"]:
-                        taxIdS.add(tD["ncbi_taxonomy_id"])
-                except Exception:
-                    pass
-
-            logger.info("Unique taxons %d", len(taxIdS))
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def objectExtractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ObjectExtractorTests("testExtractEntries"))
-    suiteSelect.addTest(ObjectExtractorTests("testExtractEntities"))
-    suiteSelect.addTest(ObjectExtractorTests("testExtractSelectedEntityContent"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = objectExtractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testObjectTransformer.py

@@ -1,83 +0,0 @@
-##
-# File:    ObjectTransformerTests.py
-# Author:  J. Westbrook
-# Date:    25-Apr-2019
-#
-# Updates:
-#
-##
-"""
-Tests for extractor and updater or 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.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 ObjectTransformerTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ObjectTransformerTests, 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.__fetchLimit = 5
-        #
-        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 testTranformEntityProteinContent(self):
-        """Test case - transform selected entity protein documents"""
-        try:
-            databaseName = "pdbx_core"
-            collectionName = "pdbx_core_polymer_entity"
-            obTr = ObjectTransformer(self.__cfgOb)
-            ok = obTr.doTransform(
-                databaseName=databaseName, collectionName=collectionName, fetchLimit=self.__fetchLimit, selectionQuery={"entity_poly.rcsb_entity_polymer_type": "Protein"}
-            )
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def objectTransformerSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ObjectTransformerTests("testTransformEntityProteinContent"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = objectTransformerSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testObjectUpdater.py

@@ -1,120 +0,0 @@
-##
-# File:    ObjectUpdaterTests.py
-# Author:  J. Westbrook
-# Date:    25-Apr-2019
-#
-# Updates:
-#
-##
-"""
-Tests for extractor and updater or 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.utils.ObjectExtractor import ObjectExtractor
-from rcsb.exdb.utils.ObjectUpdater import ObjectUpdater
-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 ObjectUpdaterTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(ObjectUpdaterTests, 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.__workPath = os.path.join(TOPDIR, "CACHE", "exdb")
-        self.__testEntryCacheKwargs = {"fmt": "json", "indent": 3}
-        self.__objectLimitTest = 5
-        #
-        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 testUpdateSelectedEntityContent(self):
-        """Test case - update of selected entity reference sequence content"""
-        try:
-            databaseName = "pdbx_core"
-            collectionName = "pdbx_core_polymer_entity"
-            obEx = ObjectExtractor(
-                self.__cfgOb,
-                databaseName=databaseName,
-                collectionName=collectionName,
-                cacheFilePath=os.path.join(self.__workPath, "entity-selected-content-test-cache.json"),
-                useCache=False,
-                keyAttribute="entity",
-                uniqueAttributes=["rcsb_id"],
-                cacheKwargs=self.__testEntryCacheKwargs,
-                objectLimit=self.__objectLimitTest,
-                # objectLimit=None,
-                selectionQuery={"entity_poly.rcsb_entity_polymer_type": "Protein"},
-                selectionList=["rcsb_id", "rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers"],
-            )
-            eCount = obEx.getCount()
-            logger.info("Entity count is %d", eCount)
-            objD = obEx.getObjects()
-            updateDL = []
-            for entityKey, eD in objD.items():
-                try:
-                    selectD = {"rcsb_id": entityKey}
-                    tL = (
-                        eD["rcsb_polymer_entity_container_identifiers"]["reference_sequence_identifiers"]
-                        if "reference_sequence_identifiers" in eD["rcsb_polymer_entity_container_identifiers"]
-                        else []
-                    )
-                    tL.append({"database_accession": "1111111", "database_name": "PDB", "provenance_source": "RCSB"})
-                    #
-                    updateD = {"rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers": tL}
-                    updateDL.append({"selectD": selectD, "updateD": updateD})
-                except Exception as e:
-                    logger.exception("Failing with %s", str(e))
-            for ii, uD in enumerate(updateDL):
-                logger.debug(" >>>> (%d) selectD %r updateD %r", ii, uD["selectD"], uD["updateD"])
-            #
-            obUpd = ObjectUpdater(self.__cfgOb)
-            numUpd = obUpd.update(databaseName, collectionName, updateDL)
-            self.assertGreaterEqual(numUpd, len(updateDL))
-            logger.info("Update count is %d", numUpd)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def objectUpdaterSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(ObjectUpdaterTests("testUpdateSelectedEntityContent"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = objectUpdaterSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testPolymerEntityExtractor.py

@@ -1,93 +0,0 @@
-##
-# File:    PolymerEntityExtractorTests.py
-# Author:  J. Westbrook
-# Date:    5-Dec-2020
-#
-# 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.seq.PolymerEntityExtractor import PolymerEntityExtractor
-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 PolymerEntityExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(PolymerEntityExtractorTests, 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.__fastaPath = os.path.join(HERE, "test-output", "CACHE", "pdb-protein-entity.fa")
-        self.__taxonPath = os.path.join(HERE, "test-output", "CACHE", "pdb-protein-entity-taxon.tdd")
-        self.__detailsPath = os.path.join(HERE, "test-output", "CACHE", "pdb-protein-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 testGetProteinEntityDetails(self):
-        """Test case - get protein entity sequences and essential details"""
-        try:
-            pEx = PolymerEntityExtractor(self.__cfgOb)
-            pD, _ = pEx.getProteinSequenceDetails()
-            #
-            self.assertGreaterEqual(len(pD), 70)
-            logger.info("Polymer entity count %d", len(pD))
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    def testExportProteinEntityFasta(self):
-        """Test case - export protein entity sequence Fasta"""
-        try:
-            pEx = PolymerEntityExtractor(self.__cfgOb)
-            ok = pEx.exportProteinEntityFasta(self.__fastaPath, self.__taxonPath, self.__detailsPath)
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def extractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(PolymerEntityExtractorTests("testGetProteinEntityDetails"))
-    suiteSelect.addTest(PolymerEntityExtractorTests("testExportProteinEntityFasta"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = extractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)