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# cidc-schemas | Branch | Status | Maintainability | Test Coverage | Code Style | | ---------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------- | | [master](https://cimac-cidc.github.io/cidc-schemas/) |  | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/maintainability) | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/test_coverage) | <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a> | This repository contains formal definitions of the CIDC metadata model using [json-schema](https://json-schema.org/) syntax and vocabulary. ### View documentation at https://cimac-cidc.github.io/cidc-schemas/ ## Installation To install the latest released version, run: ```bash pip install cidc-schemas ``` ## Development ### Project Structure - **`cidc_schemas/`** - a python module for generating, validating, and reading manifest and assay templates. - **`schemas/`** - json specifications defining the CIDC metadata model. - `templates/` - schemas for generating and validating manifest and assay templates. - `assays/` - schemas for defining assay data models. - `artifacts/` - schemas for defining artifacts. - **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation. - **`template_examples/`** - example populated Excel files for template specifications in `schemas/templates`, and `.csv`s auto-generated from those `.xlsx`s that allow to transparently keep track of changes in them. - **`tests/`** - tests for the `cidc_schemas` module. - **`.githooks/`** - git hooks, e.g. for auto-generate `.csv`s in `template_examples/`. ### Developer Setup Install necessary dependencies. ```bash pip install -r requirements.dev.txt ``` Install and configure pre-commit hooks. ```bash pre-commit install ``` ### Running tests This repository has unit tests in the _tests_ folder. After installing dependencies the tests can be run via the command ```bash pytest tests ``` ### Building documentation To build the documentation, run the following commands: ```bash python setup.py install # install helpers from the cidc_schemas library python docs/generate_docs.py ``` This will output the generated html documents in `docs/docs`. If the updated docs are pushed up and merged into master, they will be viewable at https://cimac-cidc.github.io/cidc-schemas/. ## Using the Command-Line Interface This project comes with a command-line interface for validating schemas and generating/validating assay and manifest templates. ### Install the CLI Clone the repository and cd into it ```bash git clone git@github.com:CIMAC-CIDC/cidc-schemas.git cd cidc-schemas ``` Install the `cidc_schemas` package (this adds the `cidc_schemas` CLI to your console) ```bash python setup.py install ``` Run `cidc_schemas --help` to see available options. If you're making changes to the module and want those changes to be reflected in the CLI without reinstalling the `cidc_schemas` module every time, run ```bash python3 -m cidc_schemas.cli [args] ``` ### Generate templates Create a template for a given template configuration. ```bash cidc_schemas generate_template -m templates/manifests/pbmc_template.json -o pbmc.xlsx ``` ### Validate filled-out templates Check that a populated template file is valid with respect to a template specification. ```bash cidc_schemas validate_template -m templates/manifests/pbmc_template.json -x template_examples/pbmc_template.xlsx ``` ### Validate JSON schemas Check that a JSON schema conforms to the JSON Schema specifications. ```bash cidc_schemas validate_schema -f shipping_core.json ```