rcsb.exdb 1.31__py3-none-any.whl → 1.32__py3-none-any.whl

{rcsb_exdb-1.31.dist-info → rcsb_exdb-1.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb.exdb
-Version: 1.31
+Version: 1.32
 Summary: RCSB Python ExDB data extraction and loading workflows
 Project-URL: Homepage, https://github.com/rcsb/py-rcsb_exdb
 Author-email: John Westbrook <john.westbrook@rcsb.org>

{rcsb_exdb-1.31.dist-info → rcsb_exdb-1.32.dist-info}/RECORD

@@ -43,43 +43,6 @@ rcsb/exdb/seq/TaxonomyExtractor.py,sha256=I7jsb5Kanrnh4X-znl9kZPZMJ7o2dp4fsnp2IW
 rcsb/exdb/seq/UniProtCoreEtlWorker.py,sha256=-fEojXF3lAJ1tbMsPIxT9In6ooiPThuKSoIRQ0YlZ1s,7590
 rcsb/exdb/seq/UniProtExtractor.py,sha256=pR_A9e82YvbQ813M8rNPu1bCPOHMjGnCqJmLDMM23Qo,2695
 rcsb/exdb/seq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rcsb/exdb/tests/TEST-EXDB-CLI-EXEC.sh,sha256=DWiM-DeyG_GFRki4WWSIl41ErYVxrp8t0lPypizterc,778
-rcsb/exdb/tests/TEST-EXDB-CLI-REFSEQ-EXEC.sh,sha256=CPQ8rRpfBVIl5r6IFt2t-P4aBBIWUo4NioR7M0LM6Nc,769
-rcsb/exdb/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rcsb/exdb/tests/fixtureDictMethodResourceProvider.py,sha256=h_iRfmZR9UG0nFYnVoPDtAE3VPpyrnwJRXbrdfeh0gY,3999
-rcsb/exdb/tests/fixturePdbxLoader.py,sha256=wfXyJ4k2Z-85J6sCSArf-eAuYQVbsTilwWmnm8cNPa4,10167
-rcsb/exdb/tests/testAnnotationExtractor.py,sha256=rpeB4RtOcYD27S3ZwnePHHSaac2j4bmvqfu-wJ5254U,2657
-rcsb/exdb/tests/testBranchedEntityExtractor.py,sha256=efchTzuQylD7L7Kc0j-rEvBeLjnPzvSWVLA8I7JIBys,2936
-rcsb/exdb/tests/testChemRefLoader.py,sha256=pZqWiSIQZ9bfZMJplw_ym9swCe0N6rjq63mfcqWtNO0,3696
-rcsb/exdb/tests/testChemRefMappingProvider.py,sha256=wxypTg-Y5DsAksT4a2x2yh1_JCf-7HqP9z0jKDmNcNg,3353
-rcsb/exdb/tests/testCitationAdapter.py,sha256=ZlvG6aTHzKVnREj3LXQd1iniwC-KXR45vbyzBgdoiu8,3625
-rcsb/exdb/tests/testCitationExtractor.py,sha256=7Xg75JHtnZkfrFnZVNggLRVFeRNW6V5O0tGse40C9fc,3141
-rcsb/exdb/tests/testCitationUtils.py,sha256=lCn5n_49vAnQIaUd4fSY-sQ6Ld5r5G32WRaprErryo8,3064
-rcsb/exdb/tests/testEntryInfoEtlWorkflow.py,sha256=TutfC949U0nDkFbmMdXo_MgbxMfvll4O-5C7N8Qj3TA,2340
-rcsb/exdb/tests/testEntryInfoProvider.py,sha256=2Ti-o2A8QlB0reJHFqXHjyrvehlLRFtycFhCTBTY_d0,3360
-rcsb/exdb/tests/testGlycanEtlWorkflow.py,sha256=Olml-71jiWAGOU-NQNHiRSPrew7RJtLK3R6u6WTlUSc,2295
-rcsb/exdb/tests/testGlycanProvider.py,sha256=n15qTncV289o-E5J_AsizPW1tgeCHZH8A7_qXG2Afr4,3201
-rcsb/exdb/tests/testGlycanUtils.py,sha256=h59g_iuEEzhcWRW50VdYlRHw3UrpqiRYgJZKDU4C9Wc,1953
-rcsb/exdb/tests/testLigandNeighborMappingProvider.py,sha256=JjY4y5a4ZuZPJ4gdOxIwRLVz5U6F0f0K963OeDZmFAM,3144
-rcsb/exdb/tests/testObjectExtractor.py,sha256=aHP6q9UQqDFd44u8KNQrnfTWy8Rf9dQ8FnHhUHAmqq0,14122
-rcsb/exdb/tests/testObjectTransformer.py,sha256=7fPWTfN4G6wFj6MZkw_L0dtONMsVBlBCzoHvxzrgsUo,2944
-rcsb/exdb/tests/testObjectUpdater.py,sha256=Kq-Mk4ZbD-eMoIsR3zGJvamFq-OEX4tFXyPB9FePWxc,4950
-rcsb/exdb/tests/testPolymerEntityExtractor.py,sha256=RTsEWZDarrtdVn2Xy7fbPIrZTw7Nd9VJ21aBBr3QFU0,3536
-rcsb/exdb/tests/testPubChemDataCacheProvider.py,sha256=K2Fg4Bibtdg9Z9zLwwJqZDa-XlIKHiSb9A6ewIa2-sM,4679
-rcsb/exdb/tests/testPubChemEtlWorkflow.py,sha256=vENOnc7D-EukdjElvhsZqTL0h5N6alPso4Gn3rDNMXg,5187
-rcsb/exdb/tests/testPubChemEtlWrapper.py,sha256=yGg0HvtYvFTvEEK9OsqvSSRVzCIG90UPEK_Lh7SifAk,6511
-rcsb/exdb/tests/testPubChemIndexCacheProvider.py,sha256=KVPfgnMdp7V57LnuwLLkbcZ-DjGHdEx4q0V1RAyOCXw,4947
-rcsb/exdb/tests/testReferenceSequenceAnnotationAdapter.py,sha256=hABmh743REIhFe3vP_dKr0uUvUH6-Ci71fpHGUIzt6E,4495
-rcsb/exdb/tests/testReferenceSequenceAssignmentAdapter.py,sha256=g9-t6-TMZNqxtjgZy9cYCXA19ZkOfjb0un7o8sasuAA,4897
-rcsb/exdb/tests/testReferenceSequenceAssignmentAdapterValidate.py,sha256=p3wPa-9_Il9eHP3fQGI1ag2FE0mvuOdeGu2uet6APOU,5005
-rcsb/exdb/tests/testReferenceSequenceAssignmentProvider.py,sha256=6qzk-xt0QVrX4IC8Ml6HnDzFcee14vIUs14AKAWFg9w,4631
-rcsb/exdb/tests/testReferenceSequenceCacheProvider.py,sha256=thQnpv1dxnL46PfZS6alhyS2N_rnATRmvh8SU9HJHAM,3469
-rcsb/exdb/tests/testTaxonomyExtractor.py,sha256=NZv0UFBnnRUxQN3gzPIruOqyJEG6F81avI8tQu9ILao,2536
-rcsb/exdb/tests/testTreeNodeListWorker.py,sha256=PiVaSOG0140fonhHsp0yxft3KlYaBzDb2hwmPKZxy5Y,3653
-rcsb/exdb/tests/testUniProtCoreEtlWorker.py,sha256=8LyJjeMiKkGSYZ1641xpO1clKSJSESWrHywrNqMeJ9o,3403
-rcsb/exdb/tests/testUniProtExtractor.py,sha256=jNNAI1GIedEbZhpdG1C9CjuZskUwxFg8jxgZJi1tr2U,2604
-rcsb/exdb/tests/test-data/components-abbrev.cif,sha256=Vodm2R_8ipO2X4e8W3Wa1MiH3YF7RSczdtXC0TA13sM,139314
-rcsb/exdb/tests/test-data/prdcc-abbrev.cif,sha256=pA2yCImadbuh51q59fdIOsGnyXVBPFv-8Z8Zrk2jUqA,415606
 rcsb/exdb/tree/TreeNodeListWorker.py,sha256=VLd7MWCxw9fONoC3xYbjvARp2O2V8Vyy-kUZnwQWi30,10233
 rcsb/exdb/tree/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rcsb/exdb/utils/ObjectAdapterBase.py,sha256=w-MGvs-TFQXzfgOfAX3aNyCfaN9gY8WP-7MU2FcMAYs,466
@@ -92,7 +55,7 @@ rcsb/exdb/wf/EntryInfoEtlWorkflow.py,sha256=YVr75Wz1BPjLr_satd28B9BeD3QL6HwmkR17
 rcsb/exdb/wf/GlycanEtlWorkflow.py,sha256=oJ6wf438K2e-eLmy8Ni3MCPxjAKgVJY38SWO885gnmg,2820
 rcsb/exdb/wf/PubChemEtlWorkflow.py,sha256=fNX3A6kf0S1XiJMz7ywNpFuuua5lT3XaUFjcCJtvQsU,11235
 rcsb/exdb/wf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rcsb_exdb-1.31.dist-info/METADATA,sha256=QWvZc5fDZqWlHPTXgBsRhu8Q7W7yZy4hOSp6sMJGxuk,3845
-rcsb_exdb-1.31.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rcsb_exdb-1.31.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-rcsb_exdb-1.31.dist-info/RECORD,,
+rcsb_exdb-1.32.dist-info/METADATA,sha256=ZKtnT7xFqpDHcUGISba091bqV1ckkjVPBKd-ot1ICJ4,3845
+rcsb_exdb-1.32.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rcsb_exdb-1.32.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+rcsb_exdb-1.32.dist-info/RECORD,,

rcsb/exdb/tests/TEST-EXDB-CLI-EXEC.sh

@@ -1,19 +0,0 @@
-#!/bin/bash
-# File: TEST-EXDB-CL-EXEC.sh
-# Date: 3-Sep-2019 jdw
-#
-# Examples
-#
-# tree node list load
-#
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache --cache_path ../../../CACHE  --config_path ../../mock-data/config/dbload-setup-example.yml --config_name site_info_configuration >& ./test-output/LOGTREENODELIST
-#
-# Chemref load
-#
-exdb_exec_cli --mock --full --etl_chemref --cache_path ../../../CACHE  --config_path ../../mock-data/config/dbload-setup-example.yml --config_name site_info_configuration >& ./test-output/LOGCHEMREF
-#
-# Reference sequence update
-#
-exdb_exec_cli --mock --upd_ref_seq --cache_path ../../../CACHE  --config_path ../../mock-data/config/dbload-setup-example.yml --config_name site_info_configuration >& ./test-output/LOGUPDREFSEQ
-#
-#

rcsb/exdb/tests/TEST-EXDB-CLI-REFSEQ-EXEC.sh

@@ -1,12 +0,0 @@
-#!/bin/bash
-# File: TEST-EXDB-CLI-REFSEQ-EXEC.sh
-# Date: 17-Oct-2019 jdw
-#
-# Reference sequence update --mock is required for example SIFTS files -
-#
-exdb_exec_cli --mock  --upd_ref_seq --cache_path ../../../CACHE  --config_path ../../mock-data/config/dbload-setup-example.yml --config_name site_info_configuration >& ./test-output/LOGUPDREFSEQ
-#
-exdb_exec_cli --test_req_seq_cache --mock  --upd_ref_seq --cache_path ../../../CACHE  --config_path ../../mock-data/config/dbload-setup-example.yml --config_name site_info_configuration >& ./test-output/LOGUPDREFSEQTEST
-#
-exdb_exec_cli --mock --full --etl_uniprot --cache_path ../../../CACHE  --config_path ../../mock-data/config/dbload-setup-example.yml --config_name site_info_configuration >& ./test-output/LOGUNIPROT
-#

rcsb/exdb/tests/fixtureDictMethodResourceProvider.py

@@ -1,104 +0,0 @@
-# File:    DictMethodResourceProviderFixture.py
-# Author:  J. Westbrook
-# Date:    12-Aug-2019
-# Version: 0.001
-#
-# Update:
-
-##
-"""
-Fixture for setting up cached resources for dictionary method helpers
-
-"""
-
-__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.utils.config.ConfigUtil import ConfigUtil
-from rcsb.utils.dictionary.DictMethodResourceProvider import DictMethodResourceProvider
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-logger.setLevel(logging.INFO)
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class DictMethodResourceProviderFixture(unittest.TestCase):
-    def setUp(self):
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        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.__configName = configName
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=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 testBuildResourceCache(self):
-        """Fixture - generate and check selected resource caches"""
-        try:
-            resourceNameL = [
-                "AtcProvider instance",
-                "DrugBankProvider instance",
-                "PubChemProvider instance",
-                "CitationReferenceProvider instance",
-                "JournalTitleAbbreviationProvider instance",
-                "EnzymeDatabaseProvider instance",
-                "PfamProvider instance",
-                "SiftsSummaryProvider instance",
-                "CathProvider instance",
-                "ScopProvider instance",
-                "EcodProvider instance",
-                "Scop2Provider instance",
-                "TaxonomyProvider instance",
-            ]
-            rP = DictMethodResourceProvider(self.__cfgOb, configName=self.__configName, cachePath=self.__cachePath, restoreUseStash=False, restoreUseGit=True)
-            for resourceName in resourceNameL:
-                rP.getResource(resourceName, useCache=True, default=None, doRestore=True, doBackup=False)
-            #
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-    @unittest.skip("Troubleshooting test")
-    def testRecoverResourceCache(self):
-        """Fixture - generate and check resource caches"""
-        try:
-            rp = DictMethodResourceProvider(self.__cfgOb, configName=self.__configName, cachePath=self.__cachePath)
-            ret = rp.cacheResources(useCache=True)
-            self.assertTrue(ret)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-
-
-def dictMethodResourceProviderSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(DictMethodResourceProviderFixture("testBuildResourceCache"))
-    # suiteSelect.addTest(DictMethodResourceProviderFixture("testRecoverResourceCache"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-
-    mySuite = dictMethodResourceProviderSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)

rcsb/exdb/tests/fixturePdbxLoader.py

@@ -1,298 +0,0 @@
-##
-# File:    PdbxLoaderFixture.py
-# Author:  J. Westbrook
-# Date:    4-Sep-2019
-# Version: 0.001
-#
-# Updates:
-#
-##
-"""
-Fixture for loading the chemical reference and pdbx_core collections in a loca mongo instance.
-
-"""
-
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-# import glob
-import logging
-import os
-import platform
-import resource
-import time
-import unittest
-
-from rcsb.db.mongo.DocumentLoader import DocumentLoader
-from rcsb.db.mongo.PdbxLoader import PdbxLoader
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-# from rcsb.utils.io.FileUtil import FileUtil
-
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-logger = logging.getLogger()
-logger.setLevel(logging.INFO)
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-TOPDIR = os.path.dirname(os.path.dirname(os.path.dirname(HERE)))
-
-
-class PdbxLoaderFixture(unittest.TestCase):
-
-    def __init__(self, methodName="runTest"):
-        super(PdbxLoaderFixture, self).__init__(methodName)
-        self.__verbose = True
-
-    def setUp(self):
-        #
-        #
-        self.__isMac = platform.system() == "Darwin"
-        self.__excludeTypeL = None if self.__isMac else ["optional"]
-        self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example.yml")
-        # configPath = os.path.join(TOPDIR, "rcsb", "mock-data", "config", "dbload-setup-example-local.yml")
-        # To Do: Investigate why GitUtil sometimes gives divergence error when using 'DISCOVERY_MODE: remote', but not with 'local':
-        #            stderr: 'fatal: Need to specify how to reconcile divergent branches.'
-        #        Behavior isn't entirely predictable, since it happens sometimes but not all the time.
-        #        To fully debug, will need to add more logging statements to GitUtil, StashableBase, & StashUtil (in rcsb.utils.io)
-        #        Or, can try to resolve error directly by specifying how to reconcile diverent branches in git.Repo class.
-        configName = "site_info_configuration"
-        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath)
-        #
-        self.__resourceName = "MONGO_DB"
-        self.__failedFilePath = os.path.join(HERE, "test-output", "failed-list.txt")
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        self.__readBackCheck = True
-        self.__numProc = 1
-        self.__chunkSize = 2
-        self.__fileLimit = 38
-        self.__documentStyle = "rowwise_by_name_with_cardinality"
-        #
-        self.__birdChemCompCoreIdList = [
-            "PRD_000010",
-            "PRD_000060",
-            "PRD_000220",
-            "PRD_000882",
-            "PRD_000154",
-            "PRD_000877",
-            "PRD_000198",
-            "PRD_000009",
-            "PRD_000979",
-            "PRDCC_000010",
-            "PRDCC_000220",
-            "PRDCC_000882",
-            "PRDCC_000154",
-            "PRDCC_000198",
-            "PRDCC_000009",
-            "FAM_000010",
-            "FAM_000210",
-            "FAM_000220",
-            "FAM_000001",
-            "FAM_000391",
-            "FAM_000093",
-            "FAM_000084",
-            "FAM_000016",
-            "FAM_000336",
-            "1G1",
-            "2RT",
-            "2XL",
-            "2XN",
-            "ATP",
-            "BJA",
-            "BM3",
-            "CNC",
-            "DAL",
-            "DDZ",
-            "DHA",
-            "DSN",
-            "GTP",
-            "HKL",
-            "NAC",
-            "NAG",
-            "NND",
-            "PTR",
-            "SEP",
-            "SMJ",
-            "STL",
-            "UNK",
-            "UNX",
-            "UVL",
-        ]
-        #
-        self.__pdbIdList = [
-            "1AH1",
-            "1B5F",
-            "1BMV",
-            "1C58",
-            "1DSR",
-            "1DUL",
-            "1KQE",
-            "1O3Q",
-            "1SFO",
-            "2HW3",
-            "2HYV",
-            "2OSL",
-            "2VOO",
-            "2WMG",
-            "3AD7",
-            "3HYA",
-            "3IYD",
-            "3MBG",
-            "3RER",
-            "3VD8",
-            "3VFJ",
-            "3X11",
-            "3ZTJ",
-            "4E2O",
-            "4EN8",
-            "4MEY",
-            "5EU8",
-            "5KDS",
-            # "5TM0",
-            "5VH4",
-            # "5VP2",
-            # "6FSZ",
-            "6LU7",
-            "6NN7",
-            # "6Q20",
-            "6RFK",
-            "6RKU",
-            "6YRQ",
-        ]
-        self.__ldList = [
-            {
-                # "databaseName": "dw",
-                "collectionGroupName": "core_chem_comp",
-                "contentType": "bird_chem_comp_core",
-                "collectionNameList": None,
-                "loadType": "full",
-                "mergeContentTypes": None,
-                "validationLevel": "min",
-                "inputIdCodeList": self.__birdChemCompCoreIdList
-            },
-            {
-                # "databaseName": "pdbx_core",
-                "collectionGroupName": "pdbx_core",
-                "contentType": "pdbx_core",
-                "collectionNameList": None,
-                "loadType": "replace",
-                "mergeContentTypes": ["vrpt"],
-                "validationLevel": "min",
-                "inputIdCodeList": self.__pdbIdList
-            },
-            # {
-            #     "databaseName": "pdbx_comp_model_core",
-            #     "collectionGroupName": "pdbx_comp_model_core",
-            #     "contentType": "pdbx_comp_model_core",
-            #     "collectionNameList": None,
-            #     "loadType": "full",
-            #     "mergeContentTypes": None,
-            #     "validationLevel": "min",
-            #     "inputIdCodeList": None
-            # },
-        ]
-        #
-        # self.__modelFixture()
-        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 __modelFixture(self):
-    #     fU = FileUtil()
-    #     modelSourcePath = os.path.join(self.__mockTopPath, "AF")
-    #     for iPath in glob.iglob(os.path.join(modelSourcePath, "*.cif.gz")):
-    #         fn = os.path.basename(iPath)
-    #         uId = fn.split("-")[1]
-    #         h3 = uId[-2:]
-    #         h2 = uId[-4:-2]
-    #         h1 = uId[-6:-4]
-    #         oPath = os.path.join(self.__cachePath, "computed-models", h1, h2, h3, fn)
-    #         fU.put(iPath, oPath)
-
-    def testPdbxLoader(self):
-        #
-        for ld in self.__ldList:
-            ok = self.__pdbxLoaderWrapper(**ld)
-            self.assertTrue(ok)
-
-    def __pdbxLoaderWrapper(self, **kwargs):
-        """Wrapper for the PDBx loader module"""
-        ok = False
-        try:
-            logger.info("Loading %s", kwargs["collectionGroupName"])
-            mw = PdbxLoader(
-                self.__cfgOb,
-                cachePath=self.__cachePath,
-                resourceName=self.__resourceName,
-                numProc=self.__numProc,
-                chunkSize=self.__chunkSize,
-                fileLimit=kwargs.get("fileLimit", self.__fileLimit),
-                verbose=self.__verbose,
-                readBackCheck=self.__readBackCheck,
-                maxStepLength=1000,
-                useSchemaCache=True,
-                rebuildSchemaFlag=False,
-            )
-            ok = mw.load(
-                collectionGroupName=kwargs["collectionGroupName"],
-                collectionLoadList=kwargs["collectionNameList"],
-                contentType=kwargs["contentType"],
-                loadType=kwargs["loadType"],
-                inputPathList=None,
-                inputIdCodeList=kwargs["inputIdCodeList"],
-                styleType=self.__documentStyle,
-                dataSelectors=["PUBLIC_RELEASE"],
-                failedFilePath=self.__failedFilePath,
-                saveInputFileListPath=None,
-                pruneDocumentSize=None,
-                logSize=False,
-                validationLevel=kwargs["validationLevel"],
-                mergeContentTypes=kwargs["mergeContentTypes"],
-                useNameFlag=False,
-                providerTypeExcludeL=self.__excludeTypeL,
-                restoreUseGit=True,
-                restoreUseStash=False,
-            )
-            self.assertTrue(ok)
-            ok = self.__loadStatus(mw.getLoadStatus())
-            self.assertTrue(ok)
-        except Exception as e:
-            logger.exception("Failing with %s", str(e))
-            self.fail()
-        return ok
-
-    def __loadStatus(self, statusList):
-        sectionName = "data_exchange_configuration"
-        dl = DocumentLoader(
-            self.__cfgOb,
-            self.__cachePath,
-            resourceName=self.__resourceName,
-            numProc=self.__numProc,
-            chunkSize=self.__chunkSize,
-            documentLimit=None,
-            verbose=self.__verbose,
-            readBackCheck=self.__readBackCheck,
-        )
-        #
-        databaseName = self.__cfgOb.get("DATABASE_NAME", sectionName=sectionName)
-        collectionName = self.__cfgOb.get("COLLECTION_UPDATE_STATUS", sectionName=sectionName)
-        ok = dl.load(databaseName, collectionName, loadType="append", documentList=statusList, indexAttributeList=["update_id", "database_name", "object_name"], keyNames=None)
-        return ok
-
-
-def mongoLoadPdbxSuite():
-    suiteSelect = unittest.TestSuite()
-    suiteSelect.addTest(PdbxLoaderFixture("testPdbxLoader"))
-    return suiteSelect
-
-
-if __name__ == "__main__":
-    mySuite = mongoLoadPdbxSuite()
-    unittest.TextTestRunner(verbosity=2).run(mySuite)