rcsb.exdb 1.27__tar.gz → 1.28__tar.gz

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/HISTORY.txt

@@ -108,4 +108,5 @@
                   Update CI/CD to python 3.10
 10-Dec-2024 V1.26 Update PolymerEntityExtractor to sort extracted sequence data;
                   Update Azure pipelines to run on latest macOS and ubuntu version
-23-Jan-2025 V1.27 Update TreeNodeListWorker to index 'id' field
+23-Jan-2025 V1.27 Update TreeNodeListWorker to index 'id' field
+11-Feb-2025 V1.28 Move ExDB CLI code (workflow, exec, and tests) and Dockerfile to rcsb.workflow to avoid circular imports

{rcsb_exdb-1.27/rcsb.exdb.egg-info → rcsb_exdb-1.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rcsb.exdb
-Version: 1.27
+Version: 1.28
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook
@@ -16,25 +16,20 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: OpenEye-toolkits>=2024.1.1
 Requires-Dist: numpy
 Requires-Dist: jsonschema>=2.6.0
 Requires-Dist: rcsb.utils.io>=1.48
-Requires-Dist: rcsb.db>=1.725
-Requires-Dist: rcsb.utils.chem>=0.79
+Requires-Dist: rcsb.db>=1.800
+Requires-Dist: rcsb.utils.chem>=0.81
 Requires-Dist: rcsb.utils.chemref>=0.91
-Requires-Dist: rcsb.utils.citation>=0.22
 Requires-Dist: rcsb.utils.config>=0.40
 Requires-Dist: rcsb.utils.ec>=0.25
 Requires-Dist: rcsb.utils.go>=0.18
 Requires-Dist: rcsb.utils.seq>=0.82
-Requires-Dist: rcsb.utils.seqalign>=0.31
 Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.struct>=0.47
 Requires-Dist: rcsb.utils.taxonomy>=0.43
 Requires-Dist: rcsb.utils.dictionary>=1.27
-Requires-Dist: rcsb.workflow>=0.46
-Requires-Dist: statistics; python_version < "3.0"
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test
@@ -115,57 +110,3 @@ install this system.   Once HomeBrew is installed, you can further install the
 [MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
 are required to support the ExDB tools.  HomeBrew also provides a variety of options for
 managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).
-
-### Command Line Interfaces
-
-A convenience CLI `exdb_exec_cli` is provided for performing update and loading operations.
-
-```bash
-exdb_exec_cli --help
-
-usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
-                     [--etl_tree_node_lists] [--config_path CONFIG_PATH]
-                     [--config_name CONFIG_NAME] [--db_type DB_TYPE]
-                     [--read_back_check] [--num_proc NUM_PROC]
-                     [--chunk_size CHUNK_SIZE]
-                     [--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
-                     [--cache_path CACHE_PATH] [--rebuild_cache]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --data_set_id DATA_SET_ID
-                        Data set identifier (default= 2019_14 for current
-                        week)
-  --full                Fresh full load in a new tables/collections (Default)
-  --etl_chemref         ETL integrated chemical reference data
-  --etl_tree_node_lists
-                        ETL tree node lists
-  --config_path CONFIG_PATH
-                        Path to configuration options file
-  --config_name CONFIG_NAME
-                        Configuration section name
-  --db_type DB_TYPE     Database server type (default=mongo)
-  --read_back_check     Perform read back check on all documents
-  --num_proc NUM_PROC   Number of processes to execute (default=2)
-  --chunk_size CHUNK_SIZE
-                        Number of files loaded per process
-  --document_limit DOCUMENT_LIMIT
-                        Load document limit for testing
-  --debug               Turn on verbose logging
-  --mock                Use MOCK repository configuration for testing
-  --cache_path CACHE_PATH
-                        Top cache path for external and local resource files
-  --rebuild_cache       Rebuild cached files from remote resources
-________________________________________________________________________________
-
-```
-
-For example, to construct and load tree nodes list data collections, the following
-command may be used:
-
-```bash
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
-              --cache_path ./CACHE  \
-              --config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
-              --config_name site_info_configuration >& LOGTREE \
-```

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/README.md

@@ -63,57 +63,3 @@ install this system.   Once HomeBrew is installed, you can further install the
 [MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
 are required to support the ExDB tools.  HomeBrew also provides a variety of options for
 managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).
-
-### Command Line Interfaces
-
-A convenience CLI `exdb_exec_cli` is provided for performing update and loading operations.
-
-```bash
-exdb_exec_cli --help
-
-usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
-                     [--etl_tree_node_lists] [--config_path CONFIG_PATH]
-                     [--config_name CONFIG_NAME] [--db_type DB_TYPE]
-                     [--read_back_check] [--num_proc NUM_PROC]
-                     [--chunk_size CHUNK_SIZE]
-                     [--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
-                     [--cache_path CACHE_PATH] [--rebuild_cache]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --data_set_id DATA_SET_ID
-                        Data set identifier (default= 2019_14 for current
-                        week)
-  --full                Fresh full load in a new tables/collections (Default)
-  --etl_chemref         ETL integrated chemical reference data
-  --etl_tree_node_lists
-                        ETL tree node lists
-  --config_path CONFIG_PATH
-                        Path to configuration options file
-  --config_name CONFIG_NAME
-                        Configuration section name
-  --db_type DB_TYPE     Database server type (default=mongo)
-  --read_back_check     Perform read back check on all documents
-  --num_proc NUM_PROC   Number of processes to execute (default=2)
-  --chunk_size CHUNK_SIZE
-                        Number of files loaded per process
-  --document_limit DOCUMENT_LIMIT
-                        Load document limit for testing
-  --debug               Turn on verbose logging
-  --mock                Use MOCK repository configuration for testing
-  --cache_path CACHE_PATH
-                        Top cache path for external and local resource files
-  --rebuild_cache       Rebuild cached files from remote resources
-________________________________________________________________________________
-
-```
-
-For example, to construct and load tree nodes list data collections, the following
-command may be used:
-
-```bash
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
-              --cache_path ./CACHE  \
-              --config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
-              --config_name site_info_configuration >& LOGTREE \
-```

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/rcsb/exdb/cli/__init__.py

@@ -2,4 +2,4 @@ __docformat__ = "google en"
 __author__ = "John Westbrook"
 __email__ = "john.westbrook@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "1.27"
+__version__ = "1.28"

{rcsb_exdb-1.27 → rcsb_exdb-1.28/rcsb.exdb.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rcsb.exdb
-Version: 1.27
+Version: 1.28
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook
@@ -16,25 +16,20 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: OpenEye-toolkits>=2024.1.1
 Requires-Dist: numpy
 Requires-Dist: jsonschema>=2.6.0
 Requires-Dist: rcsb.utils.io>=1.48
-Requires-Dist: rcsb.db>=1.725
-Requires-Dist: rcsb.utils.chem>=0.79
+Requires-Dist: rcsb.db>=1.800
+Requires-Dist: rcsb.utils.chem>=0.81
 Requires-Dist: rcsb.utils.chemref>=0.91
-Requires-Dist: rcsb.utils.citation>=0.22
 Requires-Dist: rcsb.utils.config>=0.40
 Requires-Dist: rcsb.utils.ec>=0.25
 Requires-Dist: rcsb.utils.go>=0.18
 Requires-Dist: rcsb.utils.seq>=0.82
-Requires-Dist: rcsb.utils.seqalign>=0.31
 Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.struct>=0.47
 Requires-Dist: rcsb.utils.taxonomy>=0.43
 Requires-Dist: rcsb.utils.dictionary>=1.27
-Requires-Dist: rcsb.workflow>=0.46
-Requires-Dist: statistics; python_version < "3.0"
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test
@@ -115,57 +110,3 @@ install this system.   Once HomeBrew is installed, you can further install the
 [MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
 are required to support the ExDB tools.  HomeBrew also provides a variety of options for
 managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).
-
-### Command Line Interfaces
-
-A convenience CLI `exdb_exec_cli` is provided for performing update and loading operations.
-
-```bash
-exdb_exec_cli --help
-
-usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
-                     [--etl_tree_node_lists] [--config_path CONFIG_PATH]
-                     [--config_name CONFIG_NAME] [--db_type DB_TYPE]
-                     [--read_back_check] [--num_proc NUM_PROC]
-                     [--chunk_size CHUNK_SIZE]
-                     [--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
-                     [--cache_path CACHE_PATH] [--rebuild_cache]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --data_set_id DATA_SET_ID
-                        Data set identifier (default= 2019_14 for current
-                        week)
-  --full                Fresh full load in a new tables/collections (Default)
-  --etl_chemref         ETL integrated chemical reference data
-  --etl_tree_node_lists
-                        ETL tree node lists
-  --config_path CONFIG_PATH
-                        Path to configuration options file
-  --config_name CONFIG_NAME
-                        Configuration section name
-  --db_type DB_TYPE     Database server type (default=mongo)
-  --read_back_check     Perform read back check on all documents
-  --num_proc NUM_PROC   Number of processes to execute (default=2)
-  --chunk_size CHUNK_SIZE
-                        Number of files loaded per process
-  --document_limit DOCUMENT_LIMIT
-                        Load document limit for testing
-  --debug               Turn on verbose logging
-  --mock                Use MOCK repository configuration for testing
-  --cache_path CACHE_PATH
-                        Top cache path for external and local resource files
-  --rebuild_cache       Rebuild cached files from remote resources
-________________________________________________________________________________
-
-```
-
-For example, to construct and load tree nodes list data collections, the following
-command may be used:
-
-```bash
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
-              --cache_path ./CACHE  \
-              --config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
-              --config_name site_info_configuration >& LOGTREE \
-```

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/rcsb.exdb.egg-info/SOURCES.txt

@@ -9,7 +9,6 @@ rcsb/__init__.py
 rcsb.exdb.egg-info/PKG-INFO
 rcsb.exdb.egg-info/SOURCES.txt
 rcsb.exdb.egg-info/dependency_links.txt
-rcsb.exdb.egg-info/entry_points.txt
 rcsb.exdb.egg-info/not-zip-safe
 rcsb.exdb.egg-info/requires.txt
 rcsb.exdb.egg-info/top_level.txt
@@ -29,7 +28,6 @@ rcsb/exdb/citation/CitationAdapter.py
 rcsb/exdb/citation/CitationExtractor.py
 rcsb/exdb/citation/CitationUtils.py
 rcsb/exdb/citation/__init__.py
-rcsb/exdb/cli/ExDbExec.py
 rcsb/exdb/cli/__init__.py
 rcsb/exdb/entry/EntryInfoProvider.py
 rcsb/exdb/entry/__init__.py
@@ -58,7 +56,6 @@ rcsb/exdb/tests/testCitationExtractor.py
 rcsb/exdb/tests/testCitationUtils.py
 rcsb/exdb/tests/testEntryInfoEtlWorkflow.py
 rcsb/exdb/tests/testEntryInfoProvider.py
-rcsb/exdb/tests/testExDbWorkflow.py
 rcsb/exdb/tests/testGlycanEtlWorkflow.py
 rcsb/exdb/tests/testGlycanProvider.py
 rcsb/exdb/tests/testGlycanUtils.py
@@ -89,7 +86,6 @@ rcsb/exdb/utils/ObjectUpdater.py
 rcsb/exdb/utils/ObjectValidator.py
 rcsb/exdb/utils/__init__.py
 rcsb/exdb/wf/EntryInfoEtlWorkflow.py
-rcsb/exdb/wf/ExDbWorkflow.py
 rcsb/exdb/wf/GlycanEtlWorkflow.py
 rcsb/exdb/wf/PubChemEtlWorkflow.py
 rcsb/exdb/wf/__init__.py

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/rcsb.exdb.egg-info/requires.txt

@@ -1,24 +1,17 @@
-OpenEye-toolkits>=2024.1.1
 numpy
 jsonschema>=2.6.0
 rcsb.utils.io>=1.48
-rcsb.db>=1.725
-rcsb.utils.chem>=0.79
+rcsb.db>=1.800
+rcsb.utils.chem>=0.81
 rcsb.utils.chemref>=0.91
-rcsb.utils.citation>=0.22
 rcsb.utils.config>=0.40
 rcsb.utils.ec>=0.25
 rcsb.utils.go>=0.18
 rcsb.utils.seq>=0.82
-rcsb.utils.seqalign>=0.31
 rcsb.utils.targets>=0.82
 rcsb.utils.struct>=0.47
 rcsb.utils.taxonomy>=0.43
 rcsb.utils.dictionary>=1.27
-rcsb.workflow>=0.46
-
-[:python_version < "3.0"]
-statistics
 
 [dev]
 check-manifest

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/requirements.txt

@@ -1,20 +1,17 @@
 --extra-index-url https://pypi.anaconda.org/OpenEye/simple
-OpenEye-toolkits >= 2024.1.1
+# Above line may be needed despite the OpenEye package not being a direct requirement of this package (it's used by rcsb.utils.chem)
+# OpenEye-toolkits >= 2024.1.1
 numpy
 jsonschema >= 2.6.0
 rcsb.utils.io >= 1.48
-rcsb.db >= 1.725
-rcsb.utils.chem >= 0.79
+rcsb.db >= 1.800
+rcsb.utils.chem >= 0.81
 rcsb.utils.chemref >= 0.91
-rcsb.utils.citation >= 0.22
 rcsb.utils.config >= 0.40
 rcsb.utils.ec >= 0.25
 rcsb.utils.go >= 0.18
 rcsb.utils.seq >= 0.82
-rcsb.utils.seqalign >= 0.31
 rcsb.utils.targets >= 0.82
 rcsb.utils.struct >= 0.47
 rcsb.utils.taxonomy >= 0.43
 rcsb.utils.dictionary >= 1.27
-rcsb.workflow >= 0.46
-statistics; python_version < "3.0"

{rcsb_exdb-1.27 → rcsb_exdb-1.28}/setup.py

@@ -47,7 +47,6 @@ setup(
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
     ],
-    entry_points={"console_scripts": ["exdb_exec_cli=rcsb.exdb.cli.ExDbExec:main"]},
     #
     install_requires=packagesRequired[1:],
     packages=find_packages(exclude=["rcsb.mock-data", "rcsb.exdb.tests-anal", "rcsb.exdb.tests-*", "tests.*"]),
@@ -57,7 +56,7 @@ setup(
     },
     #
     test_suite="rcsb.exdb.tests",
-    tests_require=["tox"],
+    tests_require=["tox", "rcsb.utils.citation >= 0.22"],
     #
     # Not configured ...
     extras_require={"dev": ["check-manifest"], "test": ["coverage"]},

rcsb_exdb-1.27/rcsb/exdb/cli/ExDbExec.py

@@ -1,239 +0,0 @@
-##
-# File: ExDbExec.py
-# Date: 22-Apr-2019  jdw
-#
-#  Execution wrapper  --  for extract and load operations -
-#
-#  Updates:
-#   4-Sep-2019 jdw add Tree and Drugbank loaders
-#  14-Feb-2020 jdw change over to ReferenceSequenceAnnotationProvider/Adapter
-#   9-Mar-2023 dwp Lower refChunkSize to 10 (UniProt API having trouble streaming XML responses)
-#  25-Apr-2024 dwp Add arguments and logic to support CLI usage from weekly-update workflow;
-#                  Add support for logging output to a specific file
-#  20-Aug-2024 dwp Add load_target_cofactors operation; change name of upd_targets_cofactors to upd_targets
-#  22-Oct-2024 dwp Add ccd_img_gen and ccd_file_gen operations
-#                  (latter will only be used briefly, as will stop generating SDF and Mol2 files in Dec 2024)
-##
-__docformat__ = "google en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Apache 2.0"
-
-import os
-import sys
-import argparse
-import logging
-
-from rcsb.utils.config.ConfigUtil import ConfigUtil
-from rcsb.exdb.wf.ExDbWorkflow import ExDbWorkflow
-
-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", stream=sys.stdout)
-logger = logging.getLogger()
-
-
-def main():
-    parser = argparse.ArgumentParser()
-    #
-    parser.add_argument(
-        "--op",
-        default=None,
-        required=True,
-        help="Loading operation to perform",
-        choices=[
-            "etl_chemref",  # ETL integrated chemical reference data
-            "etl_uniprot_core",  # ETL UniProt core reference data
-            "etl_tree_node_lists",  # ETL tree node lists
-            "upd_ref_seq",  # Update reference sequence assignments
-            "upd_neighbor_interactions",
-            "upd_uniprot_taxonomy",
-            "upd_targets",
-            "load_target_cofactors",
-            "upd_pubchem",
-            "upd_entry_info",
-            "upd_glycan_idx",
-            "upd_resource_stash",
-            "ccd_img_gen",
-            "ccd_file_gen",
-        ]
-    )
-    parser.add_argument(
-        "--load_type",
-        default="full",
-        help="Type of load ('full' for complete and fresh single-worker load, 'replace' for incremental and multi-worker load)",
-        choices=["full", "replace"],
-    )
-    #
-    parser.add_argument("--config_path", default=None, help="Path to configuration options file")
-    parser.add_argument("--config_name", default="site_info_remote_configuration", help="Configuration section name")
-    parser.add_argument("--cache_path", default=None, help="Cache path for resource files")
-    parser.add_argument("--num_proc", default=2, help="Number of processes to execute (default=2)")
-    parser.add_argument("--chunk_size", default=10, help="Number of files loaded per process")
-    parser.add_argument("--max_step_length", default=500, help="Maximum subList size (default=500)")
-    parser.add_argument("--db_type", default="mongo", help="Database server type (default=mongo)")
-    parser.add_argument("--document_limit", default=None, help="Load document limit for testing")
-    #
-    parser.add_argument("--rebuild_cache", default=False, action="store_true", help="Rebuild cached resource files")
-    parser.add_argument("--rebuild_sequence_cache", default=False, action="store_true", help="Rebuild cached resource files for reference sequence updates")
-    parser.add_argument("--provider_types_exclude", default=None, help="Resource provider types to exclude")
-    parser.add_argument("--use_filtered_tax_list", default=False, action="store_true", help="Use filtered list for taxonomy tree loading")
-    parser.add_argument("--disable_read_back_check", default=False, action="store_true", help="Disable read back check on all documents")
-    parser.add_argument("--debug", default=False, action="store_true", help="Turn on verbose logging")
-    parser.add_argument("--mock", default=False, action="store_true", help="Use MOCK repository configuration for testing")
-    parser.add_argument("--log_file_path", default=None, help="Path to runtime log file output.")
-    #
-    # Arguments specific for op == 'upd_ref_seq'
-    parser.add_argument("--ref_chunk_size", default=10, help="Max chunk size for reference sequence updates (for op 'upd_ref_seq')")
-    parser.add_argument("--min_missing", default=0, help="Minimum number of allowed missing reference sequences (for op 'upd_ref_seq')")
-    parser.add_argument("--min_match_primary_percent", default=None, help="Minimum reference sequence match percentage (for op 'upd_ref_seq')")
-    parser.add_argument("--test_mode", default=False, action="store_true", help="Test mode for reference sequence updates (for op 'upd_ref_seq')")
-    #
-    # Arguments specific for op == 'ccd_img_gen' or 'ccd_file_gen'
-    parser.add_argument("--cc_output_path", default=None, help="The base local directory path where chemical component files (image, coordinates) are written (for op 'ccd_img_gen')")
-    parser.add_argument("--cc_cache_path", default=None, help="The base local directory path where chemical component cache data are written (for op 'ccd_img_gen')")
-    parser.add_argument("--oe_license_path", default=None, help="Path to OpenEye license file")
-    #
-    # Arguments buildExdbResources
-    parser.add_argument("--rebuild_all_neighbor_interactions", default=False, action="store_true", help="Rebuild all neighbor interactions from scratch (default is incrementally)")
-    parser.add_argument("--cc_file_prefix", default="cc-full", help="File name discriminator for index sets")
-    parser.add_argument("--cc_url_target", default=None, help="target url for chemical component dictionary resource file (default: None=all public)")
-    parser.add_argument("--bird_url_target", default=None, help="target url for bird dictionary resource file (cc format) (default: None=all public)")
-    #
-    args = parser.parse_args()
-    #
-    try:
-        op, commonD, loadD = processArguments(args)
-    except Exception as err:
-        logger.exception("Argument processing problem %s", str(err))
-        raise ValueError("Argument processing problem") from err
-    #
-    #
-    # Log input arguments
-    loadLogD = {k: v for d in [commonD, loadD] for k, v in d.items() if k != "inputIdCodeList"}
-    logger.info("running load op %r on loadLogD %r:", op, loadLogD)
-    #
-    # Run the operation
-    okR = False
-    exWf = ExDbWorkflow(**commonD)
-    if op in ["etl_chemref", "etl_uniprot_core", "etl_tree_node_lists", "upd_ref_seq"]:
-        okR = exWf.load(op, **loadD)
-    elif op in [
-        "upd_neighbor_interactions",
-        "upd_uniprot_taxonomy",
-        "upd_targets",
-        "load_target_cofactors",
-        "upd_pubchem",
-        "upd_entry_info",
-        "upd_glycan_idx",
-        "upd_resource_stash",
-    ]:
-        okR = exWf.buildExdbResource(op, **loadD)
-    elif op in [
-        "ccd_img_gen",
-        "ccd_file_gen",
-    ]:
-        okR = exWf.generateCcdFiles(op, **loadD)
-    else:
-        logger.error("Unsupported op %r", op)
-    #
-    logger.info("Operation %r completed with status %r", op, okR)
-    #
-    if not okR:
-        logger.error("Operation %r failed with status %r", op, okR)
-        raise ValueError("Operation %r failed" % op)
-
-
-def processArguments(args):
-    # Logging details
-    logFilePath = args.log_file_path
-    debugFlag = args.debug
-    if debugFlag:
-        logger.setLevel(logging.DEBUG)
-    else:
-        logger.setLevel(logging.INFO)
-    if logFilePath:
-        logDir = os.path.dirname(logFilePath)
-        if not os.path.isdir(logDir):
-            os.makedirs(logDir)
-        handler = logging.FileHandler(logFilePath, mode="a")
-        if debugFlag:
-            handler.setLevel(logging.DEBUG)
-        else:
-            handler.setLevel(logging.INFO)
-        formatter = logging.Formatter("%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s")
-        handler.setFormatter(formatter)
-        logger.addHandler(handler)
-    #
-    # Configuration details
-    configPath = args.config_path
-    configName = args.config_name
-    if not (configPath and configName):
-        logger.error("Config path and/or name not provided: %r, %r", configPath, configName)
-        raise ValueError("Config path and/or name not provided: %r, %r" % (configPath, configName))
-    mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") if args.mock else None
-    logger.info("Using configuration file %r (section %r)", configPath, configName)
-    cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=mockTopPath)
-    cfgObTmp = cfgOb.exportConfig()
-    logger.info("Length of config object (%r)", len(cfgObTmp))
-    if len(cfgObTmp) == 0:
-        logger.error("Missing or access issue for config file %r", configPath)
-        raise ValueError("Missing or access issue for config file %r" % configPath)
-    else:
-        del cfgObTmp
-    #
-    # Do any additional argument checking
-    op = args.op
-    if not op:
-        raise ValueError("Must supply a value to '--op' argument")
-    #
-    cachePath = args.cache_path if args.cache_path else "."
-    cachePath = os.path.abspath(cachePath)
-
-    if args.db_type != "mongo":
-        logger.error("Unsupported database type %r (must be 'mongo')", args.db_type)
-        raise ValueError("Unsupported database type %r (must be 'mongo')" % args.db_type)
-
-    # Now collect arguments into dictionaries
-    commonD = {
-        "configPath": configPath,
-        "configName": configName,
-        "cachePath": cachePath,
-        "mockTopPath": mockTopPath,
-        "debugFlag": debugFlag,
-        "rebuildCache": args.rebuild_cache,
-        "providerTypeExcludeL": args.provider_types_exclude,
-    }
-    loadD = {
-        "loadType": args.load_type,
-        "numProc": int(args.num_proc),
-        "chunkSize": int(args.chunk_size),
-        "maxStepLength": int(args.max_step_length),
-        "dbType": args.db_type,
-        "documentLimit": int(args.document_limit) if args.document_limit else None,
-        "readBackCheck": not args.disable_read_back_check,
-        "rebuildSequenceCache": args.rebuild_sequence_cache,
-        "useFilteredLists": args.use_filtered_tax_list,
-        "refChunkSize": int(args.ref_chunk_size),
-        "minMissing": int(args.min_missing),
-        "minMatchPrimaryPercent": float(args.min_match_primary_percent) if args.min_match_primary_percent else None,
-        "testMode": args.test_mode,
-        "rebuildAllNeighborInteractions": args.rebuild_all_neighbor_interactions,
-        "ccFileNamePrefix": args.cc_file_prefix,
-        "ccUrlTarget": args.cc_url_target,
-        "birdUrlTarget": args.bird_url_target,
-        "ccOutputPath": args.cc_output_path,
-        "ccCachePath": args.cc_cache_path,
-        "licenseFilePath": args.oe_license_path,
-    }
-
-    return op, commonD, loadD
-
-
-if __name__ == "__main__":
-    try:
-        main()
-    except Exception as e:
-        logger.exception("Run failed %s", str(e))
-        sys.exit(1)