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# RCSB DB ## A collection of Python Database Utility Classes [](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]