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+/rcsb.db-1.709.tar.gz
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+%global _empty_manifest_terminate_build 0
+Name:		python-rcsb.db
+Version:	1.709
+Release:	1
+Summary:	RCSB Python Database Access and Loading Utility Classes
+License:	Apache 2.0
+URL:		https://github.com/rcsb/py-rcsb_db
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/fe/d1/79bfb9b2a3c3578d96d3690ea020dadb8d7469b6e526c1b22c5e6b4b427d/rcsb.db-1.709.tar.gz
+BuildArch:	noarch
+
+
+%description
+# RCSB DB
+
+## A collection of Python Database Utility Classes
+
+[![Build Status](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_apis/build/status/rcsb.py-rcsb_db?branchName=master)](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_build/latest?definitionId=12&branchName=master)
+
+## Introduction
+
+This module contains a collection of utility classes for processing and loading PDB repository and
+derived data content using relational and document database servers.  One target data store for
+these tools is a document database used to exchange content within the RCSB PDB data pipeline.
+
+### Installation
+
+Download the library source software from the project repository:
+
+```bash
+
+git clone --recurse-submodules https://github.com/rcsb/py-rcsb_db.git
+
+```
+
+Optionally, run test suite (Python versions 2.7, 3.6, and 3.7) using
+[setuptools](https://setuptools.readthedocs.io/en/latest/) or
+[tox](http://tox.readthedocs.io/en/latest/example/platform.html):
+
+```bash
+python setup.py test
+
+or simply run
+
+tox
+```
+
+Installation is via the program [pip](https://pypi.python.org/pypi/pip).  To run tests
+from the source tree, the package must be installed in editable mode (i.e. -e):
+
+```bash
+pip install -e .
+```
+
+#### Installing in Ubuntu Linux (tested in 18.04)
+
+You will need a few packages, before `pip install .` can work:
+
+```bash
+
+sudo apt install default-libmysqlclient-dev flex bison
+
+```
+
+### Installing on macOS
+
+To use and develop this package on macOS requires a number of packages that are not
+distributed as part of the base macOS operating system.
+The following steps provide one approach to creating the development environment for this
+package.  First, install the Apple [XCode](https://developer.apple.com/xcode/) package and associate command-line tools.
+This will provide essential compilers and supporting tools.  The [HomeBrew](https://brew.sh/) package
+manager provides further access to a variety of common open source services and tools.
+Follow the instructions provided by at the [HomeBrew](https://brew.sh/) site to
+install this system.   Once HomeBrew is installed, you can further install the
+[MariaDB](https://mariadb.com/kb/en/library/installing-mariadb-on-macos-using-homebrew/) and
+[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 `schema_update_cli` is provided for generating operational schema from
+PDBx/mmCIF dictionary metadata.  Schema are encoded for the ExDB  API (rcsb), and
+for the document schema encoded in JSON and BSON formats.  The latter schema can be used to
+validate the loadable document objects produced for the collections served by MongoDB.
+
+```bash
+ => schema_update_cli  --help
+usage: schema_update_cli [-h] [--update_chem_comp_ref]
+                         [--update_chem_comp_core_ref]
+                         [--update_bird_chem_comp_ref]
+                         [--update_bird_chem_comp_core_ref]
+                         [--update_bird_ref] [--update_bird_family_ref]
+                         [--update_pdbx] [--update_pdbx_core]
+                         [--update_repository_holdings]
+                         [--update_entity_sequence_clusters]
+                         [--update_data_exchange] [--update_ihm_dev]
+                         [--update_drugbank_core] [--update_config_all]
+                         [--update_config_deployed] [--update_config_test]
+                         [--config_path CONFIG_PATH]
+                         [--config_name CONFIG_NAME]
+                         [--cache_path SCHEMA_CACHE_PATH]
+                         [--schema_types SCHEMA_TYPES]
+                         [--schema_levels SCHEMA_LEVELS] [--debug] [--mock]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --update_chem_comp_ref
+                        Update schema for Chemical Component reference
+                        definitions
+  --update_chem_comp_core_ref
+                        Update core schema for Chemical Component reference
+                        definitions
+  --update_bird_chem_comp_ref
+                        Update schema for Bird Chemical Component reference
+                        definitions
+  --update_bird_chem_comp_core_ref
+                        Update core schema for Bird Chemical Component
+                        reference definitions
+  --update_bird_ref     Update schema for Bird reference definitions
+  --update_bird_family_ref
+                        Update schema for Bird Family reference definitions
+  --update_pdbx         Update schema for PDBx entry data
+  --update_pdbx_core    Update schema for PDBx core entry/entity data
+  --update_repository_holdings
+                        Update schema for repository holdings
+  --update_entity_sequence_clusters
+                        Update schema for entity sequence clusters
+  --update_data_exchange
+                        Update schema for data exchange status
+  --update_ihm_dev      Update schema for I/HM dev entry data
+  --update_drugbank_core
+                        Update DrugBank schema
+  --update_config_all   Update using configuration settings (e.g.
+                        DATABASE_NAMES_ALL)
+  --update_config_deployed
+                        Update using configuration settings (e.g.
+                        DATABASE_NAMES_DEPLOYED)
+  --update_config_test  Update using configuration settings (e.g.
+                        DATABASE_NAMES_TEST)
+  --config_path CONFIG_PATH
+                        Path to configuration options file
+  --config_name CONFIG_NAME
+                        Configuration section name
+  --cache_path CACHE_PATH
+                        Schema cache directory path
+  --schema_types SCHEMA_TYPES
+                        Schema encoding (rcsb|json|bson) (comma separated)
+  --schema_levels SCHEMA_LEVELS
+                        Schema validation level (full|min) (comma separated)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for dependencies and
+                        testing
+________________________________________________________________________________
+
+```
+
+For example, the following command will generate the JSON and BSON schema for the collections in the
+pdbx_core schema.
+
+```bash
+schema_update_cli  --mock --schema_types json,bson \
+                   --schema_level full  \
+                   --update_pdbx_core   \
+                   --cache_path . \
+                   --config_path ./rcsb/db/config/exdb-config-example.yml  \
+                   --config_name site_info_configuration
+```
+
+A convenience CLI `exdb_repo_load_cli` is provided to support loading PDB repositories
+containing entry and chemical reference data content types in the form of document collections
+compatible with MongoDB.
+
+```bash
+exdb_repo_load_cli --help
+
+usage: exdb_repo_load_cli [-h] [--full] [--replace] [--load_chem_comp_ref]
+                          [--load_chem_comp_core_ref]
+                          [--load_bird_chem_comp_ref]
+                          [--load_bird_chem_comp_core_ref] [--load_bird_ref]
+                          [--load_bird_family_ref] [--load_entry_data]
+                          [--load_pdbx_core] [--load_pdbx_core_merge]
+                          [--load_pdbx_core_entry] [--load_pdbx_core_entity]
+                          [--load_pdbx_core_entity_monomer]
+                          [--load_pdbx_core_assembly] [--load_ihm_dev]
+                          [--config_path CONFIG_PATH]
+                          [--config_name CONFIG_NAME] [--db_type DB_TYPE]
+                          [--document_style DOCUMENT_STYLE]
+                          [--read_back_check] [--schema_level SCHEMA_LEVEL]
+                          [--load_file_list_path LOAD_FILE_LIST_PATH]
+                          [--fail_file_list_path FAIL_FILE_LIST_PATH]
+                          [--save_file_list_path SAVE_FILE_LIST_PATH]
+                          [--num_proc NUM_PROC] [--chunk_size CHUNK_SIZE]
+                          [--file_limit FILE_LIMIT]
+                          [--prune_document_size PRUNE_DOCUMENT_SIZE]
+                          [--debug] [--mock] [--cache_path CACHE_PATH]
+                          [--rebuild_cache] [--rebuild_schema]
+                          [--vrpt_repo_path VRPT_REPO_PATH]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --full                Fresh full load in a new tables/collections
+  --replace             Load with replacement in an existing table/collection
+                        (default)
+  --load_chem_comp_ref  Load Chemical Component reference definitions (public
+                        subset)
+  --load_chem_comp_core_ref
+                        Load Chemical Component Core reference definitions
+                        (public subset)
+  --load_bird_chem_comp_ref
+                        Load Bird Chemical Component reference definitions
+                        (public subset)
+  --load_bird_chem_comp_core_ref
+                        Load Bird Chemical Component Core reference
+                        definitions (public subset)
+  --load_bird_ref       Load Bird reference definitions (public subset)
+  --load_bird_family_ref
+                        Load Bird Family reference definitions (public subset)
+  --load_entry_data     Load PDBx entry data (current released subset)
+  --load_pdbx_core      Load all PDBx core collections (current released
+                        subset)
+  --load_pdbx_core_merge
+                        Load all PDBx core collections with merged content
+                        (current released subset)
+  --load_pdbx_core_entry
+                        Load PDBx core entry (current released subset)
+  --load_pdbx_core_entity
+                        Load PDBx core entity (current released subset)
+  --load_pdbx_core_entity_monomer
+                        Load PDBx core entity monomer (current released
+                        subset)
+  --load_pdbx_core_assembly
+                        Load PDBx core assembly (current released subset)
+  --load_ihm_dev        Load I/HM DEV model data (current released subset)
+  --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)
+  --document_style DOCUMENT_STYLE
+                        Document organization (rowwise_by_name_with_cardinalit
+                        y|rowwise_by_name|columnwise_by_name|rowwise_by_id|row
+                        wise_no_name
+  --read_back_check     Perform read back check on all documents
+  --schema_level SCHEMA_LEVEL
+                        Schema validation level (full|min default=None)
+  --load_file_list_path LOAD_FILE_LIST_PATH
+                        Input file containing load file path list (override
+                        automatic repository scan)
+  --fail_file_list_path FAIL_FILE_LIST_PATH
+                        Output file containing file paths that fail to load
+  --save_file_list_path SAVE_FILE_LIST_PATH
+                        Save repo file paths from automatic file system scan
+                        in this path
+  --num_proc NUM_PROC   Number of processes to execute (default=2)
+  --chunk_size CHUNK_SIZE
+                        Number of files loaded per process
+  --file_limit FILE_LIMIT
+                        Load file limit for testing
+  --prune_document_size PRUNE_DOCUMENT_SIZE
+                        Prune large documents to this size limit (MB)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --cache_path CACHE_PATH
+                        Cache path for resource files
+  --rebuild_cache       Rebuild cached resource files
+  --rebuild_schema      Rebuild schema on-the-fly if not cached
+  --vrpt_repo_path VRPT_REPO_PATH
+                        Path to validation report repository
+________________________________________________________________________________
+```
+
+Part of the schema definition process supported by this module involves refining
+the dictionary metadata with more specific data typing and coverage details.
+A scanning tools is provided to collect and organize these details for the
+other ETL tools in this package.  The following convenience CLI, `repo_scan_cli`,
+is provided to scan supported PDB repository content and update data type and coverage details.
+
+```bash
+repo_scan_cli --help
+
+usage: repo_scan_cli [-h] [--scanType SCANTYPE]
+                     [--scan_chem_comp_ref | --scan_chem_comp_core_ref | --scan_bird_chem_comp_ref | --scan_bird_chem_comp_core_ref | --scan_bird_ref | --scan_bird_family_ref | --scan_entry_data | --scan_ihm_dev]
+                     [--config_path CONFIG_PATH] [--config_name CONFIG_NAME]
+                     [--input_file_list_path INPUT_FILE_LIST_PATH]
+                     [--output_file_list_path OUTPUT_FILE_LIST_PATH]
+                     [--fail_file_list_path FAIL_FILE_LIST_PATH]
+                     [--scan_data_file_path SCAN_DATA_FILE_PATH]
+                     [--coverage_file_path COVERAGE_FILE_PATH]
+                     [--type_map_file_path TYPE_MAP_FILE_PATH]
+                     [--num_proc NUM_PROC] [--chunk_size CHUNK_SIZE]
+                     [--file_limit FILE_LIMIT] [--debug] [--mock]
+                     [--working_path WORKING_PATH]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --scanType SCANTYPE   Repository scan type (full|incr)
+  --scan_chem_comp_ref  Scan Chemical Component reference definitions (public
+                        subset)
+  --scan_chem_comp_core_ref
+                        Scan Chemical Component Core reference definitions
+                        (public subset)
+  --scan_bird_chem_comp_ref
+                        Scan Bird Chemical Component reference definitions
+                        (public subset)
+  --scan_bird_chem_comp_core_ref
+                        Scan Bird Chemical Component Core reference
+                        definitions (public subset)
+  --scan_bird_ref       Scan Bird reference definitions (public subset)
+  --scan_bird_family_ref
+                        Scan Bird Family reference definitions (public subset)
+  --scan_entry_data     Scan PDB entry data (current released subset)
+  --scan_ihm_dev        Scan PDBDEV I/HM entry data (current released subset)
+  --config_path CONFIG_PATH
+                        Path to configuration options file
+  --config_name CONFIG_NAME
+                        Configuration section name
+  --input_file_list_path INPUT_FILE_LIST_PATH
+                        Input file containing file paths to scan
+  --output_file_list_path OUTPUT_FILE_LIST_PATH
+                        Output file containing file paths scanned
+  --fail_file_list_path FAIL_FILE_LIST_PATH
+                        Output file containing file paths that fail scan
+  --scan_data_file_path SCAN_DATA_FILE_PATH
+                        Output working file storing scan data (Pickle)
+  --coverage_file_path COVERAGE_FILE_PATH
+                        Coverage map (JSON) output path
+  --type_map_file_path TYPE_MAP_FILE_PATH
+                        Type map (JSON) output path
+  --num_proc NUM_PROC   Number of processes to execute (default=2)
+  --chunk_size CHUNK_SIZE
+                        Number of files loaded per process
+  --file_limit FILE_LIMIT
+                        Load file limit for testing
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --working_path WORKING_PATH
+                        Working path for temporary files
+________________________________________________________________________________
+
+```
+
+The following CLI provides a preliminary access to ETL functions for processing
+derived content types such as sequence comparative data.
+
+```bash
+etl_exec_cli --help
+usage: etl_exec_cli [-h] [--full] [--etl_entity_sequence_clusters]
+                    [--etl_repository_holdings] [--data_set_id DATA_SET_ID]
+                    [--sequence_cluster_data_path SEQUENCE_CLUSTER_DATA_PATH]
+                    [--sandbox_data_path SANDBOX_DATA_PATH]
+                    [--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]
+                    [--prune_document_size PRUNE_DOCUMENT_SIZE] [--debug]
+                    [--mock] [--cache_path CACHE_PATH] [--rebuild_cache]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --full                Fresh full load in a new tables/collections (Default)
+  --etl_entity_sequence_clusters
+                        ETL entity sequence clusters
+  --etl_repository_holdings
+                        ETL repository holdings
+  --data_set_id DATA_SET_ID
+                        Data set identifier (default= 2018_14 for current
+                        week)
+  --sequence_cluster_data_path SEQUENCE_CLUSTER_DATA_PATH
+                        Sequence cluster data path (default set by
+                        configuration
+  --sandbox_data_path SANDBOX_DATA_PATH
+                        Date exchange sandboxPath data path (default set by
+                        configuration
+  --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
+  --prune_document_size PRUNE_DOCUMENT_SIZE
+                        Prune large documents to this size limit (MB)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --cache_path CACHE_PATH
+                        Path containing cache directories
+  --rebuild_cache       Rebuild cached resource files
+________________________________________________________________________________
+
+```
+
+### Examples
+
+If you are working in the source repository, then you can run the CLI commands in the following manner.
+The following examples load data in the mock repositories in source distribution assuming you have a local
+default installation of MongoDb (no user/pw assigned).
+
+To run the command-line interface `exdb_repo_load_cli` outside of the source distribution, you will need to
+create a configuration file with the appropriate path details and authentication credentials.
+
+For instance, to perform a fresh/full load of all of the chemical component definitions in the mock repository:
+
+```bash
+
+cd rcsb/db/scripts
+python RepoLoadExec.py --full  --load_chem_comp_ref  \
+                      --config_path ../config/exdb-config-example.yml \
+                      --config_name site_info_configuration \
+                      --fail_file_list_path failed-cc-path-list.txt \
+                      --read_back_check
+```
+
+The following illustrates, a full load of the mock structure data repository followed by a reload with replacement of
+this same data.
+
+```bash
+
+cd rcsb/db/scripts
+python RepoLoadExec.py  --mock --full  --load_entry_data \
+                     --config_path ../config/exdb-config-example.yml \
+                     --config_name site_info_configuration \
+                     --save_file_list_path  LATEST_PDBX_LOAD_LIST.txt \
+                     --fail_file_list_path failed-entry-path-list.txt
+
+python RepoLoadExec.py --mock --replace  --load_entry_data \
+                      --config_path ../config/exdb-config-example.yml \
+                      --config_name site_info_configuration \
+                      --load_file_list_path  LATEST_PDBX_LOAD_LIST.txt \
+                      --fail_file_list_path failed-entry-path-list.txt
+```
+
+### Configuration Example
+
+RCSB/PDB repository path details are stored as configuration options.
+An example configuration file included in this package is shown below.
+This example is references dictionary resources and mock repository data
+provided in the package in `rcsb/mock-data/*`. Example configuration details are
+stored in rcsb/db/config/exdb-config-example.yml.The `site_info_configuration` section
+in this file provides database server connection details and common path details.
+This is followed by sections specifying the dictionaries, helper functions, and
+configuration used to define the schema for the each supported content type
+(e.g., pdbx_core, chem_comp_core, bird_chem_comp_core,.. ).
+
+```yaml
+site_info_configuration:
+  # Site specific path and server configuration options - (REFERENCING DEVELOPMENT RESOURCES)
+  #
+  CONFIG_SUPPORT_TOKEN: CONFIG_SUPPORT_TOKEN_ENV
+  #
+  # Database server connection details
+  #
+  MONGO_DB_HOST: localhost
+  MONGO_DB_PORT: "27017"
+  _MONGO_DB_USER_NAME: ""
+  _MONGO_DB_PASSWORD: ""
+  MYSQL_DB_HOST_NAME: localhost
+  MYSQL_DB_PORT_NUMBER: "3306"
+  _MYSQL_DB_USER_NAME: wrIzBGtCsQmkjc7tbEPQ3oEaOnpvivXaKcQsvXD6kn4KHMvA7LCL4O9GlAI=
+  _MYSQL_DB_PASSWORD: qXPp32Z6DhNVMwo9fQIK5+KB13c1Jd43E3Bn6LmJcSyXc0NAt4H/hwo/xglYpmELV5Vqaw==
+  _MYSQL_DB_PASSWORD_ALT: s6mNxq3FIwZLrLiIeHpDZQcuVxfQqrR3gA+dEMOGgHwsjrJV5da08H74RmnNRus74Q==
+  MYSQL_DB_DATABASE_NAME: mysql
+  CRATE_DB_HOST: localhost
+  CRATE_DB_PORT: "4200"
+  COCKROACH_DB_HOST: localhost
+  COCKROACH_DB_PORT: "26257"
+  COCKROACH_DB_NAME: system
+  _COCKROACH_DB_USER_NAME: HR2ez8iLbEpvN+hXKIQS3qa6/QpiFRpf/WvrfHiwfjcL09E+iWTQJhsxTsw=
+  #
+  # Primary repository data and related computed repository data paths
+  #
+  BIRD_REPO_PATH: MOCK_BIRD_REPO
+  BIRD_FAMILY_REPO_PATH: MOCK_BIRD_FAMILY_REPO
+  BIRD_CHEM_COMP_REPO_PATH: MOCK_BIRD_CC_REPO
+  CHEM_COMP_REPO_PATH: MOCK_CHEM_COMP_REPO
+  PDBX_REPO_PATH: MOCK_PDBX_SANDBOX
+  RCSB_EXCHANGE_SANDBOX_PATH: MOCK_EXCHANGE_SANDBOX
+  IHM_DEV_REPO_PATH: MOCK_IHM_REPO
+  VRPT_REPO_PATH: MOCK_VALIDATION_REPORTS
+  VRPT_REPO_PATH_ENV: VRPT_REPO_PATH_ALT
+  #
+  RCSB_EDMAP_LIST_PATH: MOCK_EXCHANGE_SANDBOX/status/edmaps.json
+  #
+  RCSB_SEQUENCE_CLUSTER_DATA_PATH: cluster_data/mmseqs_clusters_current
+  SIFTS_SUMMARY_DATA_PATH: sifts-summary
+  # -------------------------------------------------------------------------------------------
+  #   -- Below are common across current deployments -
+  #
+  # Supporting and integrated resource data cache directory names
+  #
+  #DRUGBANK_CACHE_DIR: DrugBank
+  _DRUGBANK_AUTH_USERNAME: 0qrpNd4OhGuVsJqEpcsAVEovZ0hl6QkgxmbTy3bPssd06Z9tuM6bJqgsWwmFCd0JnjIMIEWyKPMmF1pI5g==
+  _DRUGBANK_AUTH_PASSWORD: lA/K132i8DOtLdMHfm3gpNqprZ6ABKjsCRxfcXIMnxpKQzBv/B6dmC7x1vRO86JhqdT0b84=
+  DRUGBANK_MOCK_URL_TARGET: DrugBank/full_database.zip
+  #
+  #ATC_CACHE_DIR: atc
+  #CHEM_COMP_CACHE_DIR: chem_comp
+  NCBI_TAXONOMY_CACHE_DIR: NCBI
+  ENZYME_CLASSIFICATION_CACHE_DIR: ec
+  STRUCT_DOMAIN_CLASSIFICATION_CACHE_DIR: domains_struct
+  SIFTS_SUMMARY_CACHE_DIR: sifts_summary
+  DICTIONARY_CACHE_DIR: dictionaries
+  DATA_TYPE_INFO_CACHE_DIR: data_type_and_coverage
+  REPO_UTIL_CACHE_DIR: repo_util
+  EXDB_CACHE_DIR: exdb
+  CITATION_REFERENCE_CACHE_DIR: cit_ref
+  #
+  #
+  PROVENANCE_INFO_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/provenance/rcsb_extend_provenance_info.json
+  PROVENANCE_INFO_CACHE_DIR: provenance
+  #
+  SCHEMA_DEFINITION_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/schema_definitions
+  SCHEMA_DEFINITION_CACHE_DIR: schema_definitions
+  JSON_SCHEMA_DEFINITION_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/json_schema_definitions
+  JSON_SCHEMA_DEFINITION_CACHE_DIR: json_schema_definitions
+  #
+  # Helper class binding and mappings
+  #
+  DICT_METHOD_HELPER_MODULE_PATH_MAP:
+    rcsb.utils.dictionary.DictMethodEntryHelper: rcsb.utils.dictionary.DictMethodEntryHelper
+    rcsb.utils.dictionary.DictMethodChemRefHelper: rcsb.utils.dictionary.DictMethodChemRefHelper
+    rcsb.utils.dictionary.DictMethodEntityHelper: rcsb.utils.dictionary.DictMethodEntityHelper
+    rcsb.utils.dictionary.DictMethodAssemblyHelper: rcsb.utils.dictionary.DictMethodAssemblyHelper
+    rcsb.utils.dictionary.DictMethodEntityInstanceHelper: rcsb.utils.dictionary.DictMethodEntityInstanceHelper
+  # ------ ------ ------ ------ ------ ------ ------ -------
+  # ADDED rcsb.db V0.966 Source dictionary locators -
+  #
+  PDBX_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/mmcif_pdbx_v5_next.dic
+  RCSB_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/dist/rcsb_mmcif_ext.dic
+  IHMDEV_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/ihm-extension.dic
+  FLR_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/flr-extension.dic
+  VRPT_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/vrpt_mmcif_ext.dic
+  VRPT_DICT_MAPPING_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/vrpt_dictmap.json
+  # ------ ------ ------ ------ ------ ------ ------ ------ ------
+  # Added in rcsb.db V0.966 - Data type details and type mapping
+  APP_DATA_TYPE_INFO_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/data_type_and_coverage/app_data_type_mapping.cif
+  INSTANCE_DATA_TYPE_INFO_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/data_type_and_coverage
+  #
+  CONTENT_DEF_HELPER_MODULE: rcsb.db.helpers.ContentDefinitionHelper
+  DOCUMENT_DEF_HELPER_MODULE: rcsb.db.helpers.DocumentDefinitionHelper
+  CONFIG_APPEND_LOCATOR_PATHS:
+    - https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/config/exdb-config-schema.yml
+# ------ ------ ------ ------ ------ ------ ------ ------ ------
+#  Added V1.001 for stash storage server
+#  -- This is a placeholder configuration to support remote testing --
+#  local|server
+  STASH_MODE: local
+  STASH_LOCAL_BASE_PATH: stash-storage
+  #
+  STASH_SERVER_URL: https://raw.githubusercontent.com
+  STASH_SERVER_FALLBACK_URL: https://raw.githubusercontent.com
+  _STASH_SERVER_BASE_PATH: bIo7kGc2w6Oel0QNr7Pc/4bFfDQayhPxddnGHynP6yudxc44QYuAFoTFdOqY2ZzsM2DEk56r26MfG66bEQ42lp38guy837xwzN1Vgu+r9zvAm11HXEA=
+  REFERENCE_SEQUENCE_ALIGNMETS: PDB
+##
+```
+
+
+%package -n python3-rcsb.db
+Summary:	RCSB Python Database Access and Loading Utility Classes
+Provides:	python-rcsb.db
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-rcsb.db
+# RCSB DB
+
+## A collection of Python Database Utility Classes
+
+[![Build Status](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_apis/build/status/rcsb.py-rcsb_db?branchName=master)](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_build/latest?definitionId=12&branchName=master)
+
+## Introduction
+
+This module contains a collection of utility classes for processing and loading PDB repository and
+derived data content using relational and document database servers.  One target data store for
+these tools is a document database used to exchange content within the RCSB PDB data pipeline.
+
+### Installation
+
+Download the library source software from the project repository:
+
+```bash
+
+git clone --recurse-submodules https://github.com/rcsb/py-rcsb_db.git
+
+```
+
+Optionally, run test suite (Python versions 2.7, 3.6, and 3.7) using
+[setuptools](https://setuptools.readthedocs.io/en/latest/) or
+[tox](http://tox.readthedocs.io/en/latest/example/platform.html):
+
+```bash
+python setup.py test
+
+or simply run
+
+tox
+```
+
+Installation is via the program [pip](https://pypi.python.org/pypi/pip).  To run tests
+from the source tree, the package must be installed in editable mode (i.e. -e):
+
+```bash
+pip install -e .
+```
+
+#### Installing in Ubuntu Linux (tested in 18.04)
+
+You will need a few packages, before `pip install .` can work:
+
+```bash
+
+sudo apt install default-libmysqlclient-dev flex bison
+
+```
+
+### Installing on macOS
+
+To use and develop this package on macOS requires a number of packages that are not
+distributed as part of the base macOS operating system.
+The following steps provide one approach to creating the development environment for this
+package.  First, install the Apple [XCode](https://developer.apple.com/xcode/) package and associate command-line tools.
+This will provide essential compilers and supporting tools.  The [HomeBrew](https://brew.sh/) package
+manager provides further access to a variety of common open source services and tools.
+Follow the instructions provided by at the [HomeBrew](https://brew.sh/) site to
+install this system.   Once HomeBrew is installed, you can further install the
+[MariaDB](https://mariadb.com/kb/en/library/installing-mariadb-on-macos-using-homebrew/) and
+[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 `schema_update_cli` is provided for generating operational schema from
+PDBx/mmCIF dictionary metadata.  Schema are encoded for the ExDB  API (rcsb), and
+for the document schema encoded in JSON and BSON formats.  The latter schema can be used to
+validate the loadable document objects produced for the collections served by MongoDB.
+
+```bash
+ => schema_update_cli  --help
+usage: schema_update_cli [-h] [--update_chem_comp_ref]
+                         [--update_chem_comp_core_ref]
+                         [--update_bird_chem_comp_ref]
+                         [--update_bird_chem_comp_core_ref]
+                         [--update_bird_ref] [--update_bird_family_ref]
+                         [--update_pdbx] [--update_pdbx_core]
+                         [--update_repository_holdings]
+                         [--update_entity_sequence_clusters]
+                         [--update_data_exchange] [--update_ihm_dev]
+                         [--update_drugbank_core] [--update_config_all]
+                         [--update_config_deployed] [--update_config_test]
+                         [--config_path CONFIG_PATH]
+                         [--config_name CONFIG_NAME]
+                         [--cache_path SCHEMA_CACHE_PATH]
+                         [--schema_types SCHEMA_TYPES]
+                         [--schema_levels SCHEMA_LEVELS] [--debug] [--mock]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --update_chem_comp_ref
+                        Update schema for Chemical Component reference
+                        definitions
+  --update_chem_comp_core_ref
+                        Update core schema for Chemical Component reference
+                        definitions
+  --update_bird_chem_comp_ref
+                        Update schema for Bird Chemical Component reference
+                        definitions
+  --update_bird_chem_comp_core_ref
+                        Update core schema for Bird Chemical Component
+                        reference definitions
+  --update_bird_ref     Update schema for Bird reference definitions
+  --update_bird_family_ref
+                        Update schema for Bird Family reference definitions
+  --update_pdbx         Update schema for PDBx entry data
+  --update_pdbx_core    Update schema for PDBx core entry/entity data
+  --update_repository_holdings
+                        Update schema for repository holdings
+  --update_entity_sequence_clusters
+                        Update schema for entity sequence clusters
+  --update_data_exchange
+                        Update schema for data exchange status
+  --update_ihm_dev      Update schema for I/HM dev entry data
+  --update_drugbank_core
+                        Update DrugBank schema
+  --update_config_all   Update using configuration settings (e.g.
+                        DATABASE_NAMES_ALL)
+  --update_config_deployed
+                        Update using configuration settings (e.g.
+                        DATABASE_NAMES_DEPLOYED)
+  --update_config_test  Update using configuration settings (e.g.
+                        DATABASE_NAMES_TEST)
+  --config_path CONFIG_PATH
+                        Path to configuration options file
+  --config_name CONFIG_NAME
+                        Configuration section name
+  --cache_path CACHE_PATH
+                        Schema cache directory path
+  --schema_types SCHEMA_TYPES
+                        Schema encoding (rcsb|json|bson) (comma separated)
+  --schema_levels SCHEMA_LEVELS
+                        Schema validation level (full|min) (comma separated)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for dependencies and
+                        testing
+________________________________________________________________________________
+
+```
+
+For example, the following command will generate the JSON and BSON schema for the collections in the
+pdbx_core schema.
+
+```bash
+schema_update_cli  --mock --schema_types json,bson \
+                   --schema_level full  \
+                   --update_pdbx_core   \
+                   --cache_path . \
+                   --config_path ./rcsb/db/config/exdb-config-example.yml  \
+                   --config_name site_info_configuration
+```
+
+A convenience CLI `exdb_repo_load_cli` is provided to support loading PDB repositories
+containing entry and chemical reference data content types in the form of document collections
+compatible with MongoDB.
+
+```bash
+exdb_repo_load_cli --help
+
+usage: exdb_repo_load_cli [-h] [--full] [--replace] [--load_chem_comp_ref]
+                          [--load_chem_comp_core_ref]
+                          [--load_bird_chem_comp_ref]
+                          [--load_bird_chem_comp_core_ref] [--load_bird_ref]
+                          [--load_bird_family_ref] [--load_entry_data]
+                          [--load_pdbx_core] [--load_pdbx_core_merge]
+                          [--load_pdbx_core_entry] [--load_pdbx_core_entity]
+                          [--load_pdbx_core_entity_monomer]
+                          [--load_pdbx_core_assembly] [--load_ihm_dev]
+                          [--config_path CONFIG_PATH]
+                          [--config_name CONFIG_NAME] [--db_type DB_TYPE]
+                          [--document_style DOCUMENT_STYLE]
+                          [--read_back_check] [--schema_level SCHEMA_LEVEL]
+                          [--load_file_list_path LOAD_FILE_LIST_PATH]
+                          [--fail_file_list_path FAIL_FILE_LIST_PATH]
+                          [--save_file_list_path SAVE_FILE_LIST_PATH]
+                          [--num_proc NUM_PROC] [--chunk_size CHUNK_SIZE]
+                          [--file_limit FILE_LIMIT]
+                          [--prune_document_size PRUNE_DOCUMENT_SIZE]
+                          [--debug] [--mock] [--cache_path CACHE_PATH]
+                          [--rebuild_cache] [--rebuild_schema]
+                          [--vrpt_repo_path VRPT_REPO_PATH]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --full                Fresh full load in a new tables/collections
+  --replace             Load with replacement in an existing table/collection
+                        (default)
+  --load_chem_comp_ref  Load Chemical Component reference definitions (public
+                        subset)
+  --load_chem_comp_core_ref
+                        Load Chemical Component Core reference definitions
+                        (public subset)
+  --load_bird_chem_comp_ref
+                        Load Bird Chemical Component reference definitions
+                        (public subset)
+  --load_bird_chem_comp_core_ref
+                        Load Bird Chemical Component Core reference
+                        definitions (public subset)
+  --load_bird_ref       Load Bird reference definitions (public subset)
+  --load_bird_family_ref
+                        Load Bird Family reference definitions (public subset)
+  --load_entry_data     Load PDBx entry data (current released subset)
+  --load_pdbx_core      Load all PDBx core collections (current released
+                        subset)
+  --load_pdbx_core_merge
+                        Load all PDBx core collections with merged content
+                        (current released subset)
+  --load_pdbx_core_entry
+                        Load PDBx core entry (current released subset)
+  --load_pdbx_core_entity
+                        Load PDBx core entity (current released subset)
+  --load_pdbx_core_entity_monomer
+                        Load PDBx core entity monomer (current released
+                        subset)
+  --load_pdbx_core_assembly
+                        Load PDBx core assembly (current released subset)
+  --load_ihm_dev        Load I/HM DEV model data (current released subset)
+  --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)
+  --document_style DOCUMENT_STYLE
+                        Document organization (rowwise_by_name_with_cardinalit
+                        y|rowwise_by_name|columnwise_by_name|rowwise_by_id|row
+                        wise_no_name
+  --read_back_check     Perform read back check on all documents
+  --schema_level SCHEMA_LEVEL
+                        Schema validation level (full|min default=None)
+  --load_file_list_path LOAD_FILE_LIST_PATH
+                        Input file containing load file path list (override
+                        automatic repository scan)
+  --fail_file_list_path FAIL_FILE_LIST_PATH
+                        Output file containing file paths that fail to load
+  --save_file_list_path SAVE_FILE_LIST_PATH
+                        Save repo file paths from automatic file system scan
+                        in this path
+  --num_proc NUM_PROC   Number of processes to execute (default=2)
+  --chunk_size CHUNK_SIZE
+                        Number of files loaded per process
+  --file_limit FILE_LIMIT
+                        Load file limit for testing
+  --prune_document_size PRUNE_DOCUMENT_SIZE
+                        Prune large documents to this size limit (MB)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --cache_path CACHE_PATH
+                        Cache path for resource files
+  --rebuild_cache       Rebuild cached resource files
+  --rebuild_schema      Rebuild schema on-the-fly if not cached
+  --vrpt_repo_path VRPT_REPO_PATH
+                        Path to validation report repository
+________________________________________________________________________________
+```
+
+Part of the schema definition process supported by this module involves refining
+the dictionary metadata with more specific data typing and coverage details.
+A scanning tools is provided to collect and organize these details for the
+other ETL tools in this package.  The following convenience CLI, `repo_scan_cli`,
+is provided to scan supported PDB repository content and update data type and coverage details.
+
+```bash
+repo_scan_cli --help
+
+usage: repo_scan_cli [-h] [--scanType SCANTYPE]
+                     [--scan_chem_comp_ref | --scan_chem_comp_core_ref | --scan_bird_chem_comp_ref | --scan_bird_chem_comp_core_ref | --scan_bird_ref | --scan_bird_family_ref | --scan_entry_data | --scan_ihm_dev]
+                     [--config_path CONFIG_PATH] [--config_name CONFIG_NAME]
+                     [--input_file_list_path INPUT_FILE_LIST_PATH]
+                     [--output_file_list_path OUTPUT_FILE_LIST_PATH]
+                     [--fail_file_list_path FAIL_FILE_LIST_PATH]
+                     [--scan_data_file_path SCAN_DATA_FILE_PATH]
+                     [--coverage_file_path COVERAGE_FILE_PATH]
+                     [--type_map_file_path TYPE_MAP_FILE_PATH]
+                     [--num_proc NUM_PROC] [--chunk_size CHUNK_SIZE]
+                     [--file_limit FILE_LIMIT] [--debug] [--mock]
+                     [--working_path WORKING_PATH]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --scanType SCANTYPE   Repository scan type (full|incr)
+  --scan_chem_comp_ref  Scan Chemical Component reference definitions (public
+                        subset)
+  --scan_chem_comp_core_ref
+                        Scan Chemical Component Core reference definitions
+                        (public subset)
+  --scan_bird_chem_comp_ref
+                        Scan Bird Chemical Component reference definitions
+                        (public subset)
+  --scan_bird_chem_comp_core_ref
+                        Scan Bird Chemical Component Core reference
+                        definitions (public subset)
+  --scan_bird_ref       Scan Bird reference definitions (public subset)
+  --scan_bird_family_ref
+                        Scan Bird Family reference definitions (public subset)
+  --scan_entry_data     Scan PDB entry data (current released subset)
+  --scan_ihm_dev        Scan PDBDEV I/HM entry data (current released subset)
+  --config_path CONFIG_PATH
+                        Path to configuration options file
+  --config_name CONFIG_NAME
+                        Configuration section name
+  --input_file_list_path INPUT_FILE_LIST_PATH
+                        Input file containing file paths to scan
+  --output_file_list_path OUTPUT_FILE_LIST_PATH
+                        Output file containing file paths scanned
+  --fail_file_list_path FAIL_FILE_LIST_PATH
+                        Output file containing file paths that fail scan
+  --scan_data_file_path SCAN_DATA_FILE_PATH
+                        Output working file storing scan data (Pickle)
+  --coverage_file_path COVERAGE_FILE_PATH
+                        Coverage map (JSON) output path
+  --type_map_file_path TYPE_MAP_FILE_PATH
+                        Type map (JSON) output path
+  --num_proc NUM_PROC   Number of processes to execute (default=2)
+  --chunk_size CHUNK_SIZE
+                        Number of files loaded per process
+  --file_limit FILE_LIMIT
+                        Load file limit for testing
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --working_path WORKING_PATH
+                        Working path for temporary files
+________________________________________________________________________________
+
+```
+
+The following CLI provides a preliminary access to ETL functions for processing
+derived content types such as sequence comparative data.
+
+```bash
+etl_exec_cli --help
+usage: etl_exec_cli [-h] [--full] [--etl_entity_sequence_clusters]
+                    [--etl_repository_holdings] [--data_set_id DATA_SET_ID]
+                    [--sequence_cluster_data_path SEQUENCE_CLUSTER_DATA_PATH]
+                    [--sandbox_data_path SANDBOX_DATA_PATH]
+                    [--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]
+                    [--prune_document_size PRUNE_DOCUMENT_SIZE] [--debug]
+                    [--mock] [--cache_path CACHE_PATH] [--rebuild_cache]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --full                Fresh full load in a new tables/collections (Default)
+  --etl_entity_sequence_clusters
+                        ETL entity sequence clusters
+  --etl_repository_holdings
+                        ETL repository holdings
+  --data_set_id DATA_SET_ID
+                        Data set identifier (default= 2018_14 for current
+                        week)
+  --sequence_cluster_data_path SEQUENCE_CLUSTER_DATA_PATH
+                        Sequence cluster data path (default set by
+                        configuration
+  --sandbox_data_path SANDBOX_DATA_PATH
+                        Date exchange sandboxPath data path (default set by
+                        configuration
+  --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
+  --prune_document_size PRUNE_DOCUMENT_SIZE
+                        Prune large documents to this size limit (MB)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --cache_path CACHE_PATH
+                        Path containing cache directories
+  --rebuild_cache       Rebuild cached resource files
+________________________________________________________________________________
+
+```
+
+### Examples
+
+If you are working in the source repository, then you can run the CLI commands in the following manner.
+The following examples load data in the mock repositories in source distribution assuming you have a local
+default installation of MongoDb (no user/pw assigned).
+
+To run the command-line interface `exdb_repo_load_cli` outside of the source distribution, you will need to
+create a configuration file with the appropriate path details and authentication credentials.
+
+For instance, to perform a fresh/full load of all of the chemical component definitions in the mock repository:
+
+```bash
+
+cd rcsb/db/scripts
+python RepoLoadExec.py --full  --load_chem_comp_ref  \
+                      --config_path ../config/exdb-config-example.yml \
+                      --config_name site_info_configuration \
+                      --fail_file_list_path failed-cc-path-list.txt \
+                      --read_back_check
+```
+
+The following illustrates, a full load of the mock structure data repository followed by a reload with replacement of
+this same data.
+
+```bash
+
+cd rcsb/db/scripts
+python RepoLoadExec.py  --mock --full  --load_entry_data \
+                     --config_path ../config/exdb-config-example.yml \
+                     --config_name site_info_configuration \
+                     --save_file_list_path  LATEST_PDBX_LOAD_LIST.txt \
+                     --fail_file_list_path failed-entry-path-list.txt
+
+python RepoLoadExec.py --mock --replace  --load_entry_data \
+                      --config_path ../config/exdb-config-example.yml \
+                      --config_name site_info_configuration \
+                      --load_file_list_path  LATEST_PDBX_LOAD_LIST.txt \
+                      --fail_file_list_path failed-entry-path-list.txt
+```
+
+### Configuration Example
+
+RCSB/PDB repository path details are stored as configuration options.
+An example configuration file included in this package is shown below.
+This example is references dictionary resources and mock repository data
+provided in the package in `rcsb/mock-data/*`. Example configuration details are
+stored in rcsb/db/config/exdb-config-example.yml.The `site_info_configuration` section
+in this file provides database server connection details and common path details.
+This is followed by sections specifying the dictionaries, helper functions, and
+configuration used to define the schema for the each supported content type
+(e.g., pdbx_core, chem_comp_core, bird_chem_comp_core,.. ).
+
+```yaml
+site_info_configuration:
+  # Site specific path and server configuration options - (REFERENCING DEVELOPMENT RESOURCES)
+  #
+  CONFIG_SUPPORT_TOKEN: CONFIG_SUPPORT_TOKEN_ENV
+  #
+  # Database server connection details
+  #
+  MONGO_DB_HOST: localhost
+  MONGO_DB_PORT: "27017"
+  _MONGO_DB_USER_NAME: ""
+  _MONGO_DB_PASSWORD: ""
+  MYSQL_DB_HOST_NAME: localhost
+  MYSQL_DB_PORT_NUMBER: "3306"
+  _MYSQL_DB_USER_NAME: wrIzBGtCsQmkjc7tbEPQ3oEaOnpvivXaKcQsvXD6kn4KHMvA7LCL4O9GlAI=
+  _MYSQL_DB_PASSWORD: qXPp32Z6DhNVMwo9fQIK5+KB13c1Jd43E3Bn6LmJcSyXc0NAt4H/hwo/xglYpmELV5Vqaw==
+  _MYSQL_DB_PASSWORD_ALT: s6mNxq3FIwZLrLiIeHpDZQcuVxfQqrR3gA+dEMOGgHwsjrJV5da08H74RmnNRus74Q==
+  MYSQL_DB_DATABASE_NAME: mysql
+  CRATE_DB_HOST: localhost
+  CRATE_DB_PORT: "4200"
+  COCKROACH_DB_HOST: localhost
+  COCKROACH_DB_PORT: "26257"
+  COCKROACH_DB_NAME: system
+  _COCKROACH_DB_USER_NAME: HR2ez8iLbEpvN+hXKIQS3qa6/QpiFRpf/WvrfHiwfjcL09E+iWTQJhsxTsw=
+  #
+  # Primary repository data and related computed repository data paths
+  #
+  BIRD_REPO_PATH: MOCK_BIRD_REPO
+  BIRD_FAMILY_REPO_PATH: MOCK_BIRD_FAMILY_REPO
+  BIRD_CHEM_COMP_REPO_PATH: MOCK_BIRD_CC_REPO
+  CHEM_COMP_REPO_PATH: MOCK_CHEM_COMP_REPO
+  PDBX_REPO_PATH: MOCK_PDBX_SANDBOX
+  RCSB_EXCHANGE_SANDBOX_PATH: MOCK_EXCHANGE_SANDBOX
+  IHM_DEV_REPO_PATH: MOCK_IHM_REPO
+  VRPT_REPO_PATH: MOCK_VALIDATION_REPORTS
+  VRPT_REPO_PATH_ENV: VRPT_REPO_PATH_ALT
+  #
+  RCSB_EDMAP_LIST_PATH: MOCK_EXCHANGE_SANDBOX/status/edmaps.json
+  #
+  RCSB_SEQUENCE_CLUSTER_DATA_PATH: cluster_data/mmseqs_clusters_current
+  SIFTS_SUMMARY_DATA_PATH: sifts-summary
+  # -------------------------------------------------------------------------------------------
+  #   -- Below are common across current deployments -
+  #
+  # Supporting and integrated resource data cache directory names
+  #
+  #DRUGBANK_CACHE_DIR: DrugBank
+  _DRUGBANK_AUTH_USERNAME: 0qrpNd4OhGuVsJqEpcsAVEovZ0hl6QkgxmbTy3bPssd06Z9tuM6bJqgsWwmFCd0JnjIMIEWyKPMmF1pI5g==
+  _DRUGBANK_AUTH_PASSWORD: lA/K132i8DOtLdMHfm3gpNqprZ6ABKjsCRxfcXIMnxpKQzBv/B6dmC7x1vRO86JhqdT0b84=
+  DRUGBANK_MOCK_URL_TARGET: DrugBank/full_database.zip
+  #
+  #ATC_CACHE_DIR: atc
+  #CHEM_COMP_CACHE_DIR: chem_comp
+  NCBI_TAXONOMY_CACHE_DIR: NCBI
+  ENZYME_CLASSIFICATION_CACHE_DIR: ec
+  STRUCT_DOMAIN_CLASSIFICATION_CACHE_DIR: domains_struct
+  SIFTS_SUMMARY_CACHE_DIR: sifts_summary
+  DICTIONARY_CACHE_DIR: dictionaries
+  DATA_TYPE_INFO_CACHE_DIR: data_type_and_coverage
+  REPO_UTIL_CACHE_DIR: repo_util
+  EXDB_CACHE_DIR: exdb
+  CITATION_REFERENCE_CACHE_DIR: cit_ref
+  #
+  #
+  PROVENANCE_INFO_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/provenance/rcsb_extend_provenance_info.json
+  PROVENANCE_INFO_CACHE_DIR: provenance
+  #
+  SCHEMA_DEFINITION_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/schema_definitions
+  SCHEMA_DEFINITION_CACHE_DIR: schema_definitions
+  JSON_SCHEMA_DEFINITION_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/json_schema_definitions
+  JSON_SCHEMA_DEFINITION_CACHE_DIR: json_schema_definitions
+  #
+  # Helper class binding and mappings
+  #
+  DICT_METHOD_HELPER_MODULE_PATH_MAP:
+    rcsb.utils.dictionary.DictMethodEntryHelper: rcsb.utils.dictionary.DictMethodEntryHelper
+    rcsb.utils.dictionary.DictMethodChemRefHelper: rcsb.utils.dictionary.DictMethodChemRefHelper
+    rcsb.utils.dictionary.DictMethodEntityHelper: rcsb.utils.dictionary.DictMethodEntityHelper
+    rcsb.utils.dictionary.DictMethodAssemblyHelper: rcsb.utils.dictionary.DictMethodAssemblyHelper
+    rcsb.utils.dictionary.DictMethodEntityInstanceHelper: rcsb.utils.dictionary.DictMethodEntityInstanceHelper
+  # ------ ------ ------ ------ ------ ------ ------ -------
+  # ADDED rcsb.db V0.966 Source dictionary locators -
+  #
+  PDBX_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/mmcif_pdbx_v5_next.dic
+  RCSB_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/dist/rcsb_mmcif_ext.dic
+  IHMDEV_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/ihm-extension.dic
+  FLR_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/flr-extension.dic
+  VRPT_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/vrpt_mmcif_ext.dic
+  VRPT_DICT_MAPPING_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/vrpt_dictmap.json
+  # ------ ------ ------ ------ ------ ------ ------ ------ ------
+  # Added in rcsb.db V0.966 - Data type details and type mapping
+  APP_DATA_TYPE_INFO_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/data_type_and_coverage/app_data_type_mapping.cif
+  INSTANCE_DATA_TYPE_INFO_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/data_type_and_coverage
+  #
+  CONTENT_DEF_HELPER_MODULE: rcsb.db.helpers.ContentDefinitionHelper
+  DOCUMENT_DEF_HELPER_MODULE: rcsb.db.helpers.DocumentDefinitionHelper
+  CONFIG_APPEND_LOCATOR_PATHS:
+    - https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/config/exdb-config-schema.yml
+# ------ ------ ------ ------ ------ ------ ------ ------ ------
+#  Added V1.001 for stash storage server
+#  -- This is a placeholder configuration to support remote testing --
+#  local|server
+  STASH_MODE: local
+  STASH_LOCAL_BASE_PATH: stash-storage
+  #
+  STASH_SERVER_URL: https://raw.githubusercontent.com
+  STASH_SERVER_FALLBACK_URL: https://raw.githubusercontent.com
+  _STASH_SERVER_BASE_PATH: bIo7kGc2w6Oel0QNr7Pc/4bFfDQayhPxddnGHynP6yudxc44QYuAFoTFdOqY2ZzsM2DEk56r26MfG66bEQ42lp38guy837xwzN1Vgu+r9zvAm11HXEA=
+  REFERENCE_SEQUENCE_ALIGNMETS: PDB
+##
+```
+
+
+%package help
+Summary:	Development documents and examples for rcsb.db
+Provides:	python3-rcsb.db-doc
+%description help
+# RCSB DB
+
+## A collection of Python Database Utility Classes
+
+[![Build Status](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_apis/build/status/rcsb.py-rcsb_db?branchName=master)](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_build/latest?definitionId=12&branchName=master)
+
+## Introduction
+
+This module contains a collection of utility classes for processing and loading PDB repository and
+derived data content using relational and document database servers.  One target data store for
+these tools is a document database used to exchange content within the RCSB PDB data pipeline.
+
+### Installation
+
+Download the library source software from the project repository:
+
+```bash
+
+git clone --recurse-submodules https://github.com/rcsb/py-rcsb_db.git
+
+```
+
+Optionally, run test suite (Python versions 2.7, 3.6, and 3.7) using
+[setuptools](https://setuptools.readthedocs.io/en/latest/) or
+[tox](http://tox.readthedocs.io/en/latest/example/platform.html):
+
+```bash
+python setup.py test
+
+or simply run
+
+tox
+```
+
+Installation is via the program [pip](https://pypi.python.org/pypi/pip).  To run tests
+from the source tree, the package must be installed in editable mode (i.e. -e):
+
+```bash
+pip install -e .
+```
+
+#### Installing in Ubuntu Linux (tested in 18.04)
+
+You will need a few packages, before `pip install .` can work:
+
+```bash
+
+sudo apt install default-libmysqlclient-dev flex bison
+
+```
+
+### Installing on macOS
+
+To use and develop this package on macOS requires a number of packages that are not
+distributed as part of the base macOS operating system.
+The following steps provide one approach to creating the development environment for this
+package.  First, install the Apple [XCode](https://developer.apple.com/xcode/) package and associate command-line tools.
+This will provide essential compilers and supporting tools.  The [HomeBrew](https://brew.sh/) package
+manager provides further access to a variety of common open source services and tools.
+Follow the instructions provided by at the [HomeBrew](https://brew.sh/) site to
+install this system.   Once HomeBrew is installed, you can further install the
+[MariaDB](https://mariadb.com/kb/en/library/installing-mariadb-on-macos-using-homebrew/) and
+[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 `schema_update_cli` is provided for generating operational schema from
+PDBx/mmCIF dictionary metadata.  Schema are encoded for the ExDB  API (rcsb), and
+for the document schema encoded in JSON and BSON formats.  The latter schema can be used to
+validate the loadable document objects produced for the collections served by MongoDB.
+
+```bash
+ => schema_update_cli  --help
+usage: schema_update_cli [-h] [--update_chem_comp_ref]
+                         [--update_chem_comp_core_ref]
+                         [--update_bird_chem_comp_ref]
+                         [--update_bird_chem_comp_core_ref]
+                         [--update_bird_ref] [--update_bird_family_ref]
+                         [--update_pdbx] [--update_pdbx_core]
+                         [--update_repository_holdings]
+                         [--update_entity_sequence_clusters]
+                         [--update_data_exchange] [--update_ihm_dev]
+                         [--update_drugbank_core] [--update_config_all]
+                         [--update_config_deployed] [--update_config_test]
+                         [--config_path CONFIG_PATH]
+                         [--config_name CONFIG_NAME]
+                         [--cache_path SCHEMA_CACHE_PATH]
+                         [--schema_types SCHEMA_TYPES]
+                         [--schema_levels SCHEMA_LEVELS] [--debug] [--mock]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --update_chem_comp_ref
+                        Update schema for Chemical Component reference
+                        definitions
+  --update_chem_comp_core_ref
+                        Update core schema for Chemical Component reference
+                        definitions
+  --update_bird_chem_comp_ref
+                        Update schema for Bird Chemical Component reference
+                        definitions
+  --update_bird_chem_comp_core_ref
+                        Update core schema for Bird Chemical Component
+                        reference definitions
+  --update_bird_ref     Update schema for Bird reference definitions
+  --update_bird_family_ref
+                        Update schema for Bird Family reference definitions
+  --update_pdbx         Update schema for PDBx entry data
+  --update_pdbx_core    Update schema for PDBx core entry/entity data
+  --update_repository_holdings
+                        Update schema for repository holdings
+  --update_entity_sequence_clusters
+                        Update schema for entity sequence clusters
+  --update_data_exchange
+                        Update schema for data exchange status
+  --update_ihm_dev      Update schema for I/HM dev entry data
+  --update_drugbank_core
+                        Update DrugBank schema
+  --update_config_all   Update using configuration settings (e.g.
+                        DATABASE_NAMES_ALL)
+  --update_config_deployed
+                        Update using configuration settings (e.g.
+                        DATABASE_NAMES_DEPLOYED)
+  --update_config_test  Update using configuration settings (e.g.
+                        DATABASE_NAMES_TEST)
+  --config_path CONFIG_PATH
+                        Path to configuration options file
+  --config_name CONFIG_NAME
+                        Configuration section name
+  --cache_path CACHE_PATH
+                        Schema cache directory path
+  --schema_types SCHEMA_TYPES
+                        Schema encoding (rcsb|json|bson) (comma separated)
+  --schema_levels SCHEMA_LEVELS
+                        Schema validation level (full|min) (comma separated)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for dependencies and
+                        testing
+________________________________________________________________________________
+
+```
+
+For example, the following command will generate the JSON and BSON schema for the collections in the
+pdbx_core schema.
+
+```bash
+schema_update_cli  --mock --schema_types json,bson \
+                   --schema_level full  \
+                   --update_pdbx_core   \
+                   --cache_path . \
+                   --config_path ./rcsb/db/config/exdb-config-example.yml  \
+                   --config_name site_info_configuration
+```
+
+A convenience CLI `exdb_repo_load_cli` is provided to support loading PDB repositories
+containing entry and chemical reference data content types in the form of document collections
+compatible with MongoDB.
+
+```bash
+exdb_repo_load_cli --help
+
+usage: exdb_repo_load_cli [-h] [--full] [--replace] [--load_chem_comp_ref]
+                          [--load_chem_comp_core_ref]
+                          [--load_bird_chem_comp_ref]
+                          [--load_bird_chem_comp_core_ref] [--load_bird_ref]
+                          [--load_bird_family_ref] [--load_entry_data]
+                          [--load_pdbx_core] [--load_pdbx_core_merge]
+                          [--load_pdbx_core_entry] [--load_pdbx_core_entity]
+                          [--load_pdbx_core_entity_monomer]
+                          [--load_pdbx_core_assembly] [--load_ihm_dev]
+                          [--config_path CONFIG_PATH]
+                          [--config_name CONFIG_NAME] [--db_type DB_TYPE]
+                          [--document_style DOCUMENT_STYLE]
+                          [--read_back_check] [--schema_level SCHEMA_LEVEL]
+                          [--load_file_list_path LOAD_FILE_LIST_PATH]
+                          [--fail_file_list_path FAIL_FILE_LIST_PATH]
+                          [--save_file_list_path SAVE_FILE_LIST_PATH]
+                          [--num_proc NUM_PROC] [--chunk_size CHUNK_SIZE]
+                          [--file_limit FILE_LIMIT]
+                          [--prune_document_size PRUNE_DOCUMENT_SIZE]
+                          [--debug] [--mock] [--cache_path CACHE_PATH]
+                          [--rebuild_cache] [--rebuild_schema]
+                          [--vrpt_repo_path VRPT_REPO_PATH]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --full                Fresh full load in a new tables/collections
+  --replace             Load with replacement in an existing table/collection
+                        (default)
+  --load_chem_comp_ref  Load Chemical Component reference definitions (public
+                        subset)
+  --load_chem_comp_core_ref
+                        Load Chemical Component Core reference definitions
+                        (public subset)
+  --load_bird_chem_comp_ref
+                        Load Bird Chemical Component reference definitions
+                        (public subset)
+  --load_bird_chem_comp_core_ref
+                        Load Bird Chemical Component Core reference
+                        definitions (public subset)
+  --load_bird_ref       Load Bird reference definitions (public subset)
+  --load_bird_family_ref
+                        Load Bird Family reference definitions (public subset)
+  --load_entry_data     Load PDBx entry data (current released subset)
+  --load_pdbx_core      Load all PDBx core collections (current released
+                        subset)
+  --load_pdbx_core_merge
+                        Load all PDBx core collections with merged content
+                        (current released subset)
+  --load_pdbx_core_entry
+                        Load PDBx core entry (current released subset)
+  --load_pdbx_core_entity
+                        Load PDBx core entity (current released subset)
+  --load_pdbx_core_entity_monomer
+                        Load PDBx core entity monomer (current released
+                        subset)
+  --load_pdbx_core_assembly
+                        Load PDBx core assembly (current released subset)
+  --load_ihm_dev        Load I/HM DEV model data (current released subset)
+  --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)
+  --document_style DOCUMENT_STYLE
+                        Document organization (rowwise_by_name_with_cardinalit
+                        y|rowwise_by_name|columnwise_by_name|rowwise_by_id|row
+                        wise_no_name
+  --read_back_check     Perform read back check on all documents
+  --schema_level SCHEMA_LEVEL
+                        Schema validation level (full|min default=None)
+  --load_file_list_path LOAD_FILE_LIST_PATH
+                        Input file containing load file path list (override
+                        automatic repository scan)
+  --fail_file_list_path FAIL_FILE_LIST_PATH
+                        Output file containing file paths that fail to load
+  --save_file_list_path SAVE_FILE_LIST_PATH
+                        Save repo file paths from automatic file system scan
+                        in this path
+  --num_proc NUM_PROC   Number of processes to execute (default=2)
+  --chunk_size CHUNK_SIZE
+                        Number of files loaded per process
+  --file_limit FILE_LIMIT
+                        Load file limit for testing
+  --prune_document_size PRUNE_DOCUMENT_SIZE
+                        Prune large documents to this size limit (MB)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --cache_path CACHE_PATH
+                        Cache path for resource files
+  --rebuild_cache       Rebuild cached resource files
+  --rebuild_schema      Rebuild schema on-the-fly if not cached
+  --vrpt_repo_path VRPT_REPO_PATH
+                        Path to validation report repository
+________________________________________________________________________________
+```
+
+Part of the schema definition process supported by this module involves refining
+the dictionary metadata with more specific data typing and coverage details.
+A scanning tools is provided to collect and organize these details for the
+other ETL tools in this package.  The following convenience CLI, `repo_scan_cli`,
+is provided to scan supported PDB repository content and update data type and coverage details.
+
+```bash
+repo_scan_cli --help
+
+usage: repo_scan_cli [-h] [--scanType SCANTYPE]
+                     [--scan_chem_comp_ref | --scan_chem_comp_core_ref | --scan_bird_chem_comp_ref | --scan_bird_chem_comp_core_ref | --scan_bird_ref | --scan_bird_family_ref | --scan_entry_data | --scan_ihm_dev]
+                     [--config_path CONFIG_PATH] [--config_name CONFIG_NAME]
+                     [--input_file_list_path INPUT_FILE_LIST_PATH]
+                     [--output_file_list_path OUTPUT_FILE_LIST_PATH]
+                     [--fail_file_list_path FAIL_FILE_LIST_PATH]
+                     [--scan_data_file_path SCAN_DATA_FILE_PATH]
+                     [--coverage_file_path COVERAGE_FILE_PATH]
+                     [--type_map_file_path TYPE_MAP_FILE_PATH]
+                     [--num_proc NUM_PROC] [--chunk_size CHUNK_SIZE]
+                     [--file_limit FILE_LIMIT] [--debug] [--mock]
+                     [--working_path WORKING_PATH]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --scanType SCANTYPE   Repository scan type (full|incr)
+  --scan_chem_comp_ref  Scan Chemical Component reference definitions (public
+                        subset)
+  --scan_chem_comp_core_ref
+                        Scan Chemical Component Core reference definitions
+                        (public subset)
+  --scan_bird_chem_comp_ref
+                        Scan Bird Chemical Component reference definitions
+                        (public subset)
+  --scan_bird_chem_comp_core_ref
+                        Scan Bird Chemical Component Core reference
+                        definitions (public subset)
+  --scan_bird_ref       Scan Bird reference definitions (public subset)
+  --scan_bird_family_ref
+                        Scan Bird Family reference definitions (public subset)
+  --scan_entry_data     Scan PDB entry data (current released subset)
+  --scan_ihm_dev        Scan PDBDEV I/HM entry data (current released subset)
+  --config_path CONFIG_PATH
+                        Path to configuration options file
+  --config_name CONFIG_NAME
+                        Configuration section name
+  --input_file_list_path INPUT_FILE_LIST_PATH
+                        Input file containing file paths to scan
+  --output_file_list_path OUTPUT_FILE_LIST_PATH
+                        Output file containing file paths scanned
+  --fail_file_list_path FAIL_FILE_LIST_PATH
+                        Output file containing file paths that fail scan
+  --scan_data_file_path SCAN_DATA_FILE_PATH
+                        Output working file storing scan data (Pickle)
+  --coverage_file_path COVERAGE_FILE_PATH
+                        Coverage map (JSON) output path
+  --type_map_file_path TYPE_MAP_FILE_PATH
+                        Type map (JSON) output path
+  --num_proc NUM_PROC   Number of processes to execute (default=2)
+  --chunk_size CHUNK_SIZE
+                        Number of files loaded per process
+  --file_limit FILE_LIMIT
+                        Load file limit for testing
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --working_path WORKING_PATH
+                        Working path for temporary files
+________________________________________________________________________________
+
+```
+
+The following CLI provides a preliminary access to ETL functions for processing
+derived content types such as sequence comparative data.
+
+```bash
+etl_exec_cli --help
+usage: etl_exec_cli [-h] [--full] [--etl_entity_sequence_clusters]
+                    [--etl_repository_holdings] [--data_set_id DATA_SET_ID]
+                    [--sequence_cluster_data_path SEQUENCE_CLUSTER_DATA_PATH]
+                    [--sandbox_data_path SANDBOX_DATA_PATH]
+                    [--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]
+                    [--prune_document_size PRUNE_DOCUMENT_SIZE] [--debug]
+                    [--mock] [--cache_path CACHE_PATH] [--rebuild_cache]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --full                Fresh full load in a new tables/collections (Default)
+  --etl_entity_sequence_clusters
+                        ETL entity sequence clusters
+  --etl_repository_holdings
+                        ETL repository holdings
+  --data_set_id DATA_SET_ID
+                        Data set identifier (default= 2018_14 for current
+                        week)
+  --sequence_cluster_data_path SEQUENCE_CLUSTER_DATA_PATH
+                        Sequence cluster data path (default set by
+                        configuration
+  --sandbox_data_path SANDBOX_DATA_PATH
+                        Date exchange sandboxPath data path (default set by
+                        configuration
+  --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
+  --prune_document_size PRUNE_DOCUMENT_SIZE
+                        Prune large documents to this size limit (MB)
+  --debug               Turn on verbose logging
+  --mock                Use MOCK repository configuration for testing
+  --cache_path CACHE_PATH
+                        Path containing cache directories
+  --rebuild_cache       Rebuild cached resource files
+________________________________________________________________________________
+
+```
+
+### Examples
+
+If you are working in the source repository, then you can run the CLI commands in the following manner.
+The following examples load data in the mock repositories in source distribution assuming you have a local
+default installation of MongoDb (no user/pw assigned).
+
+To run the command-line interface `exdb_repo_load_cli` outside of the source distribution, you will need to
+create a configuration file with the appropriate path details and authentication credentials.
+
+For instance, to perform a fresh/full load of all of the chemical component definitions in the mock repository:
+
+```bash
+
+cd rcsb/db/scripts
+python RepoLoadExec.py --full  --load_chem_comp_ref  \
+                      --config_path ../config/exdb-config-example.yml \
+                      --config_name site_info_configuration \
+                      --fail_file_list_path failed-cc-path-list.txt \
+                      --read_back_check
+```
+
+The following illustrates, a full load of the mock structure data repository followed by a reload with replacement of
+this same data.
+
+```bash
+
+cd rcsb/db/scripts
+python RepoLoadExec.py  --mock --full  --load_entry_data \
+                     --config_path ../config/exdb-config-example.yml \
+                     --config_name site_info_configuration \
+                     --save_file_list_path  LATEST_PDBX_LOAD_LIST.txt \
+                     --fail_file_list_path failed-entry-path-list.txt
+
+python RepoLoadExec.py --mock --replace  --load_entry_data \
+                      --config_path ../config/exdb-config-example.yml \
+                      --config_name site_info_configuration \
+                      --load_file_list_path  LATEST_PDBX_LOAD_LIST.txt \
+                      --fail_file_list_path failed-entry-path-list.txt
+```
+
+### Configuration Example
+
+RCSB/PDB repository path details are stored as configuration options.
+An example configuration file included in this package is shown below.
+This example is references dictionary resources and mock repository data
+provided in the package in `rcsb/mock-data/*`. Example configuration details are
+stored in rcsb/db/config/exdb-config-example.yml.The `site_info_configuration` section
+in this file provides database server connection details and common path details.
+This is followed by sections specifying the dictionaries, helper functions, and
+configuration used to define the schema for the each supported content type
+(e.g., pdbx_core, chem_comp_core, bird_chem_comp_core,.. ).
+
+```yaml
+site_info_configuration:
+  # Site specific path and server configuration options - (REFERENCING DEVELOPMENT RESOURCES)
+  #
+  CONFIG_SUPPORT_TOKEN: CONFIG_SUPPORT_TOKEN_ENV
+  #
+  # Database server connection details
+  #
+  MONGO_DB_HOST: localhost
+  MONGO_DB_PORT: "27017"
+  _MONGO_DB_USER_NAME: ""
+  _MONGO_DB_PASSWORD: ""
+  MYSQL_DB_HOST_NAME: localhost
+  MYSQL_DB_PORT_NUMBER: "3306"
+  _MYSQL_DB_USER_NAME: wrIzBGtCsQmkjc7tbEPQ3oEaOnpvivXaKcQsvXD6kn4KHMvA7LCL4O9GlAI=
+  _MYSQL_DB_PASSWORD: qXPp32Z6DhNVMwo9fQIK5+KB13c1Jd43E3Bn6LmJcSyXc0NAt4H/hwo/xglYpmELV5Vqaw==
+  _MYSQL_DB_PASSWORD_ALT: s6mNxq3FIwZLrLiIeHpDZQcuVxfQqrR3gA+dEMOGgHwsjrJV5da08H74RmnNRus74Q==
+  MYSQL_DB_DATABASE_NAME: mysql
+  CRATE_DB_HOST: localhost
+  CRATE_DB_PORT: "4200"
+  COCKROACH_DB_HOST: localhost
+  COCKROACH_DB_PORT: "26257"
+  COCKROACH_DB_NAME: system
+  _COCKROACH_DB_USER_NAME: HR2ez8iLbEpvN+hXKIQS3qa6/QpiFRpf/WvrfHiwfjcL09E+iWTQJhsxTsw=
+  #
+  # Primary repository data and related computed repository data paths
+  #
+  BIRD_REPO_PATH: MOCK_BIRD_REPO
+  BIRD_FAMILY_REPO_PATH: MOCK_BIRD_FAMILY_REPO
+  BIRD_CHEM_COMP_REPO_PATH: MOCK_BIRD_CC_REPO
+  CHEM_COMP_REPO_PATH: MOCK_CHEM_COMP_REPO
+  PDBX_REPO_PATH: MOCK_PDBX_SANDBOX
+  RCSB_EXCHANGE_SANDBOX_PATH: MOCK_EXCHANGE_SANDBOX
+  IHM_DEV_REPO_PATH: MOCK_IHM_REPO
+  VRPT_REPO_PATH: MOCK_VALIDATION_REPORTS
+  VRPT_REPO_PATH_ENV: VRPT_REPO_PATH_ALT
+  #
+  RCSB_EDMAP_LIST_PATH: MOCK_EXCHANGE_SANDBOX/status/edmaps.json
+  #
+  RCSB_SEQUENCE_CLUSTER_DATA_PATH: cluster_data/mmseqs_clusters_current
+  SIFTS_SUMMARY_DATA_PATH: sifts-summary
+  # -------------------------------------------------------------------------------------------
+  #   -- Below are common across current deployments -
+  #
+  # Supporting and integrated resource data cache directory names
+  #
+  #DRUGBANK_CACHE_DIR: DrugBank
+  _DRUGBANK_AUTH_USERNAME: 0qrpNd4OhGuVsJqEpcsAVEovZ0hl6QkgxmbTy3bPssd06Z9tuM6bJqgsWwmFCd0JnjIMIEWyKPMmF1pI5g==
+  _DRUGBANK_AUTH_PASSWORD: lA/K132i8DOtLdMHfm3gpNqprZ6ABKjsCRxfcXIMnxpKQzBv/B6dmC7x1vRO86JhqdT0b84=
+  DRUGBANK_MOCK_URL_TARGET: DrugBank/full_database.zip
+  #
+  #ATC_CACHE_DIR: atc
+  #CHEM_COMP_CACHE_DIR: chem_comp
+  NCBI_TAXONOMY_CACHE_DIR: NCBI
+  ENZYME_CLASSIFICATION_CACHE_DIR: ec
+  STRUCT_DOMAIN_CLASSIFICATION_CACHE_DIR: domains_struct
+  SIFTS_SUMMARY_CACHE_DIR: sifts_summary
+  DICTIONARY_CACHE_DIR: dictionaries
+  DATA_TYPE_INFO_CACHE_DIR: data_type_and_coverage
+  REPO_UTIL_CACHE_DIR: repo_util
+  EXDB_CACHE_DIR: exdb
+  CITATION_REFERENCE_CACHE_DIR: cit_ref
+  #
+  #
+  PROVENANCE_INFO_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/provenance/rcsb_extend_provenance_info.json
+  PROVENANCE_INFO_CACHE_DIR: provenance
+  #
+  SCHEMA_DEFINITION_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/schema_definitions
+  SCHEMA_DEFINITION_CACHE_DIR: schema_definitions
+  JSON_SCHEMA_DEFINITION_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/json_schema_definitions
+  JSON_SCHEMA_DEFINITION_CACHE_DIR: json_schema_definitions
+  #
+  # Helper class binding and mappings
+  #
+  DICT_METHOD_HELPER_MODULE_PATH_MAP:
+    rcsb.utils.dictionary.DictMethodEntryHelper: rcsb.utils.dictionary.DictMethodEntryHelper
+    rcsb.utils.dictionary.DictMethodChemRefHelper: rcsb.utils.dictionary.DictMethodChemRefHelper
+    rcsb.utils.dictionary.DictMethodEntityHelper: rcsb.utils.dictionary.DictMethodEntityHelper
+    rcsb.utils.dictionary.DictMethodAssemblyHelper: rcsb.utils.dictionary.DictMethodAssemblyHelper
+    rcsb.utils.dictionary.DictMethodEntityInstanceHelper: rcsb.utils.dictionary.DictMethodEntityInstanceHelper
+  # ------ ------ ------ ------ ------ ------ ------ -------
+  # ADDED rcsb.db V0.966 Source dictionary locators -
+  #
+  PDBX_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/mmcif_pdbx_v5_next.dic
+  RCSB_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/dist/rcsb_mmcif_ext.dic
+  IHMDEV_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/ihm-extension.dic
+  FLR_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/flr-extension.dic
+  VRPT_DICT_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/vrpt_mmcif_ext.dic
+  VRPT_DICT_MAPPING_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/dictionary_files/reference/vrpt_dictmap.json
+  # ------ ------ ------ ------ ------ ------ ------ ------ ------
+  # Added in rcsb.db V0.966 - Data type details and type mapping
+  APP_DATA_TYPE_INFO_LOCATOR: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/data_type_and_coverage/app_data_type_mapping.cif
+  INSTANCE_DATA_TYPE_INFO_LOCATOR_PATH: https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/data_type_and_coverage
+  #
+  CONTENT_DEF_HELPER_MODULE: rcsb.db.helpers.ContentDefinitionHelper
+  DOCUMENT_DEF_HELPER_MODULE: rcsb.db.helpers.DocumentDefinitionHelper
+  CONFIG_APPEND_LOCATOR_PATHS:
+    - https://raw.githubusercontent.com/rcsb/py-rcsb_exdb_assets/master/config/exdb-config-schema.yml
+# ------ ------ ------ ------ ------ ------ ------ ------ ------
+#  Added V1.001 for stash storage server
+#  -- This is a placeholder configuration to support remote testing --
+#  local|server
+  STASH_MODE: local
+  STASH_LOCAL_BASE_PATH: stash-storage
+  #
+  STASH_SERVER_URL: https://raw.githubusercontent.com
+  STASH_SERVER_FALLBACK_URL: https://raw.githubusercontent.com
+  _STASH_SERVER_BASE_PATH: bIo7kGc2w6Oel0QNr7Pc/4bFfDQayhPxddnGHynP6yudxc44QYuAFoTFdOqY2ZzsM2DEk56r26MfG66bEQ42lp38guy837xwzN1Vgu+r9zvAm11HXEA=
+  REFERENCE_SEQUENCE_ALIGNMETS: PDB
+##
+```
+
+
+%prep
+%autosetup -n rcsb.db-1.709
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-rcsb.db -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 1.709-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..213c8b4
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+d99129e425bf56f9cdedee3473adf800  rcsb.db-1.709.tar.gz