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

rcsb/exdb/tests/testUniProtCoreEtlWorker.py

@@ -1,99 +0,0 @@
-##
-# File:    UniProtCoreEtlWorkerTests.py
-# Author:  J. Westbrook
-# Date:    9-Dec-2018
-#
-# Updates:
-#
-##
-"""
-Tests for loading UniProt core collection
-
-"""
-
-__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.UniProtCoreEtlWorker import UniProtCoreEtlWorker
-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 UniProtCoreEtlWorkerTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(UniProtCoreEtlWorkerTests, 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 = "2018_23"
-        #
-        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 - deprecated")
-    def testLoadUniProtCore(self):
-        """Test case - load UniProt core collection reference data -"""
-        try:
-            uw = UniProtCoreEtlWorker(self.__cfgOb, self.__cachePath)
-            ok = uw.load(self.__updateId, extResource="UniProt", loadType="full")
-            #
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    @unittest.skip("Disable test - deprecated")
-    def testValidateUniProtCore(self):
-        """Test case - validate UniProt core collection reference data -"""
-        try:
-            uw = UniProtCoreEtlWorker(self.__cfgOb, self.__cachePath, doValidate=True)
-            ok = uw.load(self.__updateId, extResource="UniProt", loadType="full")
-            #
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def uniProtCoreEtlWorkerSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(UniProtCoreEtlWorkerTests("testLoadUniProtCore"))
-    suiteSelect.addTest(UniProtCoreEtlWorkerTests("testValidateUniProtCore"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    #
-    mySuite = uniProtCoreEtlWorkerSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/testUniProtExtractor.py

@@ -1,77 +0,0 @@
-##
-# File:    UniProtExtractorTests.py
-# Author:  J. Westbrook
-# Date:    5-Dec-2020
-#
-# Updates:
-#
-##
-"""
-Tests for extraction of UniProt reference sequence details from the ExDB UniProt collection.
-"""
-__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.UniProtExtractor import UniProtExtractor
-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 UniProtExtractorTests(unittest.TestCase):
-    def __init__(self, methodName="runTest"):
-        super(UniProtExtractorTests, 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 testGetUniProtDetails(self):
-        """Test case - get UniProt reference sequences and essential details"""
-        try:
-            uEx = UniProtExtractor(self.__cfgOb)
-            unpD = uEx.getReferenceSequenceDetails()
-            logger.info("UniProt count %d", len(unpD))
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def extractorSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(UniProtExtractorTests("testGetGoIds"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = extractorSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)