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RCSB ExDB Assets

A collection data assets supporting RCSB Exchange Database Utility Classes

Introduction

This module contains a collection of configuration, dictionary and data assets supporting processing and loading of both PDB repository and derived data content using relational and document database stores.

Updating and Generating Schemas

The process of updating schemas involves two main steps: (1) Updating the relevant dictionary definitions, and (2) Generating the schema files based on the updated dictionary files.

Updating Dictionary Files

All dictionary files used for schemas are found under the dictionary_files directory. The final "production-level" dictionary files are stored under dictionary_files/dist, which are composed from merging a set of the smaller component dictionary files together (e.g., those under base and extension).

Accordingly, the general set of steps for updating the dictionary files are as follows:

  1. Update the relevant dictionary file under dictionary_files. This could either be the base core dictionary file (dictionary_files/base/rcsb_mmcif_ext-core.dic) or an extensions dictionary file (dictionary_files/extensions/*).
    • Also be sure to update the version information at the top of the file
  2. Update the base header dictionary file: dictionary_files/base/rcsb_mmcif_ext-header.dic
    • This simply involves updating the version and description of changes
  3. Generate the dist dictionary by running the Build.sh script:
    • From the dictionary_files directory, run: ./scripts/Build.sh rcsb_mmcif_ext local

Generating Schema Files

Once the dictionary files are updated, the schema files can be generated.

Before generating the schema files, several things should be configured/set-up first:

  1. Make sure the configuration file, ./config/exdb-config-example.yml, exists and points to local py-rcsb_exdb_assets directory tree
  2. Make sure the schema_update_cli command is installed.
    • If not, get it by installing the rcsb.db package: pip install rcsb.db

Once the above are confirmed, the general steps for generating the schema files are as follows:

  1. Make any necessary changes to the schema configuration file: ./config/exdb-config-schema.yml
    • Even if no direct schema changes are necessary, be sure to update the version number (major.minor.patch) of the corresponding collection schema that is being updated based on the dictionary updates, e.g.:
pdbx_core:
  - NAME: pdbx_core_entry
    VERSION: 9.0.1
  1. From the top directory of py-rcsb_exdb_assets, run the schema generation command (adjusting the arguments as necessary):
    • This will create a directory CACHE with the new schema files found under CACHE/json_schema_definitions/ and CACHE/schema_definitions/
# First run it for 'pdbx_core' schemas:
schema_update_cli   --encoding_types rcsb,json,bson --validation_levels full,min  --update_pdbx_core  --cache_path CACHE --config_path ./config/exdb-config-example.yml --config_name site_info_configuration

# Next run it for 'pdbx_comp_model_core' schemas:
schema_update_cli   --encoding_types rcsb,json,bson --validation_levels full,min  --update_pdbx_comp_model_core  --cache_path CACHE --config_path ./config/exdb-config-example.yml --config_name site_info_configuration
  1. Copy the newly generated schema files into corresponding directories in py-rcsb_exdb_assets:
    • cp CACHE/json_schema_definitions/* json_schema_definitions/
    • cp CACHE/schema_definitions/* schema_definitions/
  2. Create a PR to this repository (py-rcsb_exdb_assets) with the new dictionary and schema files