Metadata-Version: 2.1
Name: opentargets-validator
Version: 0.6.0
Summary: Evidence validation at targetvalidation.org
Home-page: https://github.com/opentargets/validator
Author: OpenTargets Core Team <support@targetvalidation.org>
Author-email: support@targetvalidation.org
License: Apache License, Version 2.0
Download-URL: https://github.com/opentargets/validator/archive/0.6.0.tar.gz
Description: [![PyPI version](https://badge.fury.io/py/opentargets-validator.svg)](https://badge.fury.io/py/opentargets-validator)
        
        [![Build Status](https://travis-ci.org/opentargets/validator.svg?branch=master)](https://travis-ci.org/opentargets/validator)
        
        [![codecov](https://codecov.io/gh/opentargets/validator/branch/master/graph/badge.svg)](https://codecov.io/gh/opentargets/validator)
        
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        # opentargets-validator
        
        Evidence string validator.
        
        ## Purpose
        
        This tool is intended to validate JSON files that have a single JSON object per line. This is the format that is required from the [data sources](https://docs.targetvalidation.org/data-sources/data-sources) that provide us with evidence for our target-disease associations. 
        
        The validator will check the expected structure, defined in a JSON schema which must be provided via a `--schema` argument. 
        
        Be aware that this is *not* a general-purpose JSON validator, and use of "pretty-printed" JSON will cause errors. 
        
        ## Schema URLs
        The Open Targets JSON schema is located at https://github.com/opentargets/json_schema. Note that you should *not* use `master` as this may change any time, instead use the latest available tag, e.g. `1.6.3`. If you are a data provider, you will always receive an email from Open Targets with information about what JSON schema version to use. Also, when specifying the schema to the validator you have to use the "raw" GitHub URL:
        
        `https://raw.githubusercontent.com/opentargets/json_schema/1.6.3/opentargets.json`
        
        ## How to install it
        
        The easiest way is with pip:
        
        ```sh
        pip install -U opentargets-validator
        ```
        
        It supports both Python 2 and Python 3.
        
        ## How to use it
        
        You have two options:
        - pass a filename or URL as a positional argument
        - read from stdin (e.g. a shell pipe)
        
        ### Read from stdin
        
        ```sh
        cat file.json | opentargets_validator --schema https://raw.githubusercontent.com/opentargets/json_schema/{tag_version}/opentargets.json
        ```
        
        ### Read from positional argument
        
        This can automatically decompress gzip'ed files. Compression will be detected via filename e.g. ending with `.json.gz`.
        
        Examples of acceptable paths are:
        - https://file/location/name.json
        - https://file/location/name.json.gz
        - file://relative/local/file.json
        - file:///absolute/file.json
        - location/file.json
        
        ```sh
        opentargets_validator --schema https://raw.githubusercontent.com/opentargets/json_schema/{tag_version}/opentargets.json https://where/myfile/is/located.json
        ```
        
        ## Note
        
        There used to be a `--log-lines` argument that could be used to exit early when a certain number of errors occored. This is no longer supported, and with parallelization improvements it is rarely necessary in practice.
        
        Evidence lines are checked for uniqueness by calculating the hash of the `unique_association_fields` field. This can be done in the validator using the `--hash` argument.
        
        ## How to develop 
        
        Within a [virtualenv](https://virtualenv.pypa.io/en/latest/) you can install with:
        
        ```sh
        pip install -e .[dev]
        ```
        
        and you can run the tests with:
        
        ```sh
        pytest --cov=opentargets_validator --cov-report term tests/ --fulltrace
        ```
        
        This repository has [Travis integration](https://travis-ci.com/opentargets/validator) and [CodeCov integration](https://codecov.io/gh/opentargets/validator) .
        
        Releases are put on [PyPI](https://pypi.org/project/opentargets-validator) automatically via Travis from GitHub tags.
        
Keywords: opentargets,bioinformatics,python2
Platform: any
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown; charset=UTF-8
Provides-Extra: dev
