A set of common utilities and helpers for Bento platform services.
Bento Library (for Python Bento microservices)
Common utilities and helpers for Bento platform services.
python3 -m tox
1. Release Checklist
All tests pass and test coverage has not been reduced
Package version has been updated (following semver) in
The latest changes have been merged from the
developbranch into the
A release has been created, tagged in the format of
v#.#.#and named in the format of
Version #.#.#, listing any changes made, in the GitHub releases page tagged from the master branch!
1A. Note on Versioning
bento_lib project uses semantic versioning for
releasing. If the API is broken in any way, including minor differences in the
way a function behaves given an identical set of parameters (excluding bugfixes
for unintentional behaviour), the MAJOR version must be incremented. In this
way, we guarantee that projects relying on this API do not accidentally break
2. Releasing from the Command Line
# IF NECESSARY: Install twine OUTSIDE of the virtual environment python3 -m pip install twine # Switch to the correct branch and make sure it's up to date git checkout master git pull # If needed, enter the project virtual environment source env/bin/activate # Remove existing build files rm -rf build/ dist/ bento_lib.egg-info/ # Build the new package python3 setup.py sdist bdist_wheel # In between these steps - test out the package... make sure everything works # before uploading it to production PyPI. # Upload it to PyPI twine upload dist/*
auth provides Python service decorators and Django / DRF backends for dealing
with the Bento container authentication headers (derived from
lua-resty-openidc, set by the internal container NGINX instance.)
drs provides utilities for fetching data and record metadata from
GA4GH-compatible DRS services, and Bento's own implementation (which has some
events facilitates JSON-serialized message-passing between Bento
microservices. Serialized objects can be at most 512 MB.
Events should have a lower-case type which is type-insensitively unique and adequately describes the associated data.
All Bento channels are prefixed with
schemas contains common JSON schemas which may be useful to a variety of
different Bento services.
schemas.bento contains Bento-specific schemas, and
GA4GH-standardized schemas (possibly not exactly to spec.)
search contains definitions, validators, and transformations for the query
syntax for Bento, as well as a transpiler to the
psycopg2 PostgreSQL IR.
The query syntax for Bento takes advantage of JSON schemas augmented with additional properties about the field's accessibility and, in the case of Postgres, how the field maps to a table column (or JSON column sub-field.)
search.data_structure contains code for evaluating a Bento query against a
Python data structure.
search.operations contains constants representing valid search operations one
can allow against particular fields from within an augmented JSON schema.
search.postgres contains a "transpiler" from the Bento query syntax to the
intermediate representation (IR) for
PostgreSQL, allowing safe queries against a Postgres database.
search.queries provides definitions for the Bento query AST and some helper
methods for creating and processing ASTs.
utils contains miscellaneous utilities commonly required by Bento services.
workflows contains common code used for handling workflow metadata processing
and response generation, as well as code associated with Bento's ingestion
routines across the different data services.
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