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

rcsb/exdb/tests/testEntryInfoEtlWorkflow.py

@@ -1,70 +0,0 @@
-##
-# File:    EntryInfoEtlWorkflowTests.py
-# Author:  J. Westbrook
-# Date:    22-Sep-2021
-#
-# Updates:
-#
-##
-"""
-Tests for entry information extraction ETL workflow methods
-"""
-
-__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.wf.EntryInfoEtlWorkflow import EntryInfoEtlWorkflow
-
-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 EntryInfoEtlWorkflowTests(unittest.TestCase):
-    def setUp(self):
-        #
-        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
-        self.__configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        self.__configName = "site_info_configuration"
-        #
-        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 testUpdateEntryInfo(self):
-        """Test case - update extracted entry-level annotations."""
-        try:
-            eiP = EntryInfoEtlWorkflow(configPath=self.__configPath, configName=self.__configName, cachePath=self.__cachePath)
-            ok = eiP.update(backup=False)
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def entryInfoEtlWorkflowSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(EntryInfoEtlWorkflowTests("testUpdateEntryInfo"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = entryInfoEtlWorkflowSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testEntryInfoProvider.py

@@ -1,97 +0,0 @@
-##
-# File:    EntryInfoProviderTests.py
-# Author:  J. Westbrook
-# Date:    22-Sep-2021
-#
-# Update:
-#
-#
-##
-"""
-Tests for accessors entry-level annotations.
-
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import logging
-import os
-import unittest
-
-from rcsb.exdb.entry.EntryInfoProvider import EntryInfoProvider
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-
-class EntryInfoProviderTests(unittest.TestCase):
-    doInternal = False
-
-    def setUp(self):
-        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=self.__configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-
-    def tearDown(self):
-        pass
-
-    def testGetEntryInfo(self):
-        minCount = 12
-        eiP = EntryInfoProvider(cachePath=self.__cachePath, useCache=False)
-        ok = eiP.testCache(minCount=0)
-        self.assertTrue(ok)
-        ok = eiP.update(self.__cfgOb, fmt="json", indent=3)
-        self.assertTrue(ok)
-        riD = eiP.getEntryInfo("4en8")
-        logger.info("riD (%d) %r", len(riD), riD)
-        rL = eiP.getEntriesByPolymerEntityCount(count=2)
-        self.assertGreaterEqual(len(rL), 5)
-        ok = eiP.testCache(minCount=minCount)
-        self.assertTrue(ok)
-        eiP = EntryInfoProvider(cachePath=self.__cachePath, useCache=True)
-        ok = eiP.testCache(minCount=minCount)
-        self.assertTrue(ok)
-
-    @unittest.skipUnless(doInternal, "Internal full test")
-    def testEntryInfoRemote(self):
-        minCount = 182000
-        configName = "site_info_remote_configuration"
-        cfgOb = ConfigUtil(configPath=self.__configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        eiP = EntryInfoProvider(cachePath=self.__cachePath, useCache=True)
-        ok = eiP.testCache(minCount=minCount)
-        ok = eiP.update(cfgOb, fmt="json", indent=3)
-        self.assertTrue(ok)
-        riD = eiP.getEntryInfo("1kip")
-        logger.info("riD (%d)", len(riD))
-        self.assertGreaterEqual(len(riD), 1)
-        configName = "site_info_configuration"
-        cfgOb = ConfigUtil(configPath=self.__configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        ok = eiP.backup(cfgOb, configName, useStash=False, useGit=True)
-        self.assertTrue(ok)
-        ok = eiP.restore(cfgOb, configName, useStash=False, useGit=True)
-        self.assertTrue(ok)
-        eiP = EntryInfoProvider(cachePath=self.__cachePath, useCache=True)
-        ok = eiP.testCache(minCount=minCount)
-
-
-def entryInfoSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(EntryInfoProviderTests("testGetEntryInfo"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-
-    mySuite = entryInfoSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testGlycanEtlWorkflow.py

@@ -1,70 +0,0 @@
-##
-# File:    GlycanEtlWorkflowTests.py
-# Author:  J. Westbrook
-# Date:    30-Jun-2021
-#
-# Updates:
-#
-##
-"""
-Tests for Glycan ETL workflow methods
-"""
-
-__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.wf.GlycanEtlWorkflow import GlycanEtlWorkflow
-
-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 GlycanEtlWorkflowTests(unittest.TestCase):
-    def setUp(self):
-        #
-        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
-        self.__configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        self.__configName = "site_info_configuration"
-        #
-        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 testUpdateIndex(self):
-        """Test case - update the glycan corrrespondence index."""
-        try:
-            gP = GlycanEtlWorkflow(configPath=self.__configPath, configName=self.__configName, cachePath=self.__cachePath)
-            ok = gP.updateMatchedIndex(backup=False)
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def glycanEtlWorkflowSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(GlycanEtlWorkflowTests("testUpdateIndex"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = glycanEtlWorkflowSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testGlycanProvider.py

@@ -1,98 +0,0 @@
-##
-# File:    GlycanProviderTests.py
-# Author:  J. Westbrook
-# Date:    24-May-2021
-#
-# Update:
-#
-#
-##
-"""
-Tests for accessors for managing Glycan extracted annotations.
-
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import logging
-import os
-import unittest
-
-from rcsb.exdb.branch.GlycanProvider import GlycanProvider
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-from rcsb.utils.io.MarshalUtil import MarshalUtil
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-
-class GlycanProviderTests(unittest.TestCase):
-    def setUp(self):
-        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
-        self.__dataPath = os.path.join(HERE, "test-data")
-        self.__mU = MarshalUtil(workPath=self.__cachePath)
-        #
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=self.__configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-        self.__stashUrl = None
-        self.__stashRemotePath = os.path.join(self.__cachePath, "stash-remote")
-
-    def tearDown(self):
-        pass
-
-    def testGlycanMapping(self):
-        minCount = 12
-        gP = GlycanProvider(cachePath=self.__cachePath, useCache=False)
-        ok = gP.testCache(minCount=0)
-        self.assertTrue(ok)
-        ok = gP.update(self.__cfgOb, fmt="json", indent=3)
-        self.assertTrue(ok)
-        riD = gP.getIdentifiers()
-        logger.info("riD (%d)", len(riD))
-        ok = gP.testCache(minCount=minCount)
-        self.assertTrue(ok)
-        gP = GlycanProvider(cachePath=self.__cachePath, useCache=True)
-        ok = gP.testCache(minCount=minCount)
-        self.assertTrue(ok)
-
-    @unittest.skip("Internal test")
-    def testGlycanStashRemote(self):
-        minCount = 12
-        configName = "site_info_remote_configuration"
-        cfgOb = ConfigUtil(configPath=self.__configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        gP = GlycanProvider(cachePath=self.__cachePath, useCache=True)
-        ok = gP.testCache(minCount=minCount)
-        ok = gP.update(cfgOb, fmt="json", indent=3)
-        self.assertTrue(ok)
-        riD = gP.getIdentifiers()
-        logger.info("riD (%d)", len(riD))
-        self.assertTrue(ok)
-        ok = gP.backup(cfgOb, configName)
-        self.assertTrue(ok)
-        ok = gP.restore(cfgOb, configName)
-        self.assertTrue(ok)
-        #
-        ok = gP.update(cfgOb, fmt="json", indent=3)
-        self.assertTrue(ok)
-        #
-
-
-def glycanMappingSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(GlycanProviderTests("testGlycanMapping"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-
-    mySuite = glycanMappingSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testGlycanUtils.py

@@ -1,64 +0,0 @@
-##
-# File:    GlycanUtilsTests.py
-# Author:  J. Westbrook
-# Date:    25-May-2021
-#
-# Update:
-#   9-Feb-2023 aae  Fix TOPDIR path
-##
-"""
-Tests for creating glycan accession mapping details.
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import logging
-import os
-import unittest
-
-from rcsb.exdb.branch.GlycanUtils import GlycanUtils
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-
-
-class GlycanUtilsTests(unittest.TestCase):
-    def setUp(self):
-        self.__dirPath = os.path.join(HERE, "test-output", "CACHE", "glycan")
-        #
-        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)
-        #
-
-    def tearDown(self):
-        pass
-
-    def testGlycanMapping(self):
-        gU = GlycanUtils(self.__cfgOb, self.__dirPath)
-        beD = gU.getBranchedEntityDetails()
-        self.assertGreaterEqual(len(beD), 1)
-        logger.info("branched entity descriptor details (%d)", len(beD))
-        eaD = gU.updateEntityAccessionMap()
-        logger.info("updated entity accession map length (%d)", len(eaD))
-        self.assertGreaterEqual(len(eaD), 12)
-
-
-def glycanMappingSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(GlycanUtilsTests("testGlycanMapping"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-
-    mySuite = glycanMappingSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testLigandNeighborMappingProvider.py

@@ -1,90 +0,0 @@
-##
-# File:    LigandNeighborMappingProviderTests.py
-# Author:  J. Westbrook
-# Date:    28-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.seq.LigandNeighborMappingProvider import LigandNeighborMappingProvider
-
-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 LigandNeighborMappingProviderTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(LigandNeighborMappingProviderTests, 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 testLigandNeighborMapping(self):
-        """Test case - load and access ligand neighbor mapping cache"""
-        try:
-            crmP = LigandNeighborMappingProvider(self.__cachePath, useCache=True)
-            ok = crmP.testCache()
-            self.assertTrue(ok)
-            #
-            ok = crmP.fetchLigandNeighborMapping(self.__cfgOb)
-            self.assertTrue(ok)
-            crmP = LigandNeighborMappingProvider(self.__cachePath, useCache=True)
-            ok = crmP.testCache(minCount=2)
-            self.assertTrue(ok)
-            nL = crmP.getLigandNeighbors("3VFJ_2")
-            logger.info("ligand neighbor list nL %r", nL)
-            self.assertGreaterEqual(len(nL), 4)
-            self.assertGreater(len(nL[0]), 1)
-            #
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def ligandNeighborMappingSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(LigandNeighborMappingProviderTests("testLigandNeighborMapping"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    #
-    mySuite = ligandNeighborMappingSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)