Metadata-Version: 2.1
Name: bento-lib
Version: 2.2.0
Summary: A set of common utilities and helpers for Bento platform services.
Home-page: https://github.com/bento-platform/bento_lib
Author: David Lougheed
Author-email: david.lougheed@mail.mcgill.ca
License: LGPLv3
Description: # Bento Library (for Python Bento microservices)
        
        ![Test Status](https://github.com/bento-platform/bento_lib/workflows/Test/badge.svg)
        ![Lint Status](https://github.com/bento-platform/bento_lib/workflows/Lint/badge.svg)
        [![codecov](https://codecov.io/gh/bento-platform/bento_lib/branch/master/graph/badge.svg)](https://codecov.io/gh/bento-platform/bento_lib)
        [![PyPI version](https://badge.fury.io/py/bento-lib.svg)](https://badge.fury.io/py/bento-lib)
        
        Common utilities and helpers for Bento platform services.
        
        
        ## Running Tests
        
        ```bash
        python3 -m tox
        ```
        
        
        ## Releasing
        
        
        ### 1. Release Checklist
        
          * [ ] All tests pass and test coverage has not been reduced
        
          * [ ] Package version has been updated (following semver) in 
            `bento_lib/package.cfg`
            
          * [ ] The latest changes have been merged from the `develop` branch into the
            `master` branch
            
          * [ ] 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
        
        The `bento_lib` project uses [semantic versioning](https://semver.org/) 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
        upon upgrading.
        
        
        ### 2. Releasing from the Command Line
        
        ```bash
        # 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/*
        ```
        
        
        ## Modules
        
        ### `auth`
        
        `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`
        
        `drs` provides utilities for fetching data and record metadata from 
        GA4GH-compatible DRS services, and Bento's own implementation (which has some 
        non-standard extensions.)
        
        ### `events`
        
        `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 `bento.`.
        
        ### `schemas`
        
        `schemas` contains common JSON schemas which may be useful to a variety of
        different Bento services.
        
        `schemas.bento` contains Bento-specific schemas, and `schemas.ga4gh` contains
        GA4GH-standardized schemas (possibly not exactly to spec.)
        
        ### `search`
        
        `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
        `psycopg2`-provided
        [intermediate representation (IR)](https://www.psycopg.org/docs/sql.html) 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`
        
        `utils` contains miscellaneous utilities commonly required by Bento services.
        
        ### `workflows`
        
        `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.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: flask
Provides-Extra: django
