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Mostly more cosmetics, but remove codebuild status which isn't workin…
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…g (probably because the build is not public).
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netsettler committed Sep 6, 2023
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:target: https://cgap-portal.readthedocs.io/en/latest/
:alt: Documentation Status

.. image:: https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiMWtFYjJTeXkzcXZVYkpmbkd3VUlOQ0pSTnlLRGloVENJcitGS1g1RTV1THgxQkc3M2tDY0NFUFUxOXRBeS92dUNtbXdRZU5YWEkzbUhaMm1lUlNDZ2NZPSIsIml2UGFyYW1ldGVyU3BlYyI6Ijl6OUZkY3JvaWlyZDduUnEiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=master
:alt: CodeBuild Status


Welcome to CGAP!
================

CGAP is the Computational Genome Analysis Platform.

We are a team of scientists, clinicians, and developers
who aim to streamline the clinical genetics workflow.

Expand All @@ -37,7 +36,7 @@ who aim to streamline the clinical genetics workflow.
* CGAP is an open source system under continuous development.
For documentation, see
`the CGAP Portal page at ReadTheDocs
<https://cgap-portal.readthedocs.io/en/latest/>`_.
<https://cgap-portal.readthedocs.io/en/latest/>`_.

* For information about governance and other policies, see
`the CGAP Governance repository
Expand All @@ -49,19 +48,19 @@ Repository Structure

These are some important files and directories you might want to be aware of:

* ``.github/workflows/`` contains Github Action Workflows
* ``bin/`` contains a few legacy scripts, though most are in ``scripts/``
* ``deploy/docker`` contains containerization related scripts/configuration
* ``docs/ contains`` documentation
* ``scripts/`` contains misc scripts
* ``src/encoded/`` where the code is
* ``.dockerignore`` specifies paths ignored by the Dockerfile
* ``Dockerfile`` contains the Docker build instructions for the cgap-portal - see ``docker-production.rst``
* ``Makefile`` contains macros for common build operations - see ``make info``
* ``docker-compose.yml`` builds the new local deployment - see ``docker-local.rst``
* ``package.json`` and ``package-lock.json`` specify the front-end dependencies
* ``pyproject.toml`` and ``poetry.lock`` specify the back-end dependencies
* ``setup_eb.py`` performs final installation setup
* ``.dockerignore`` specifies paths ignored by the Dockerfile
* ``.github/workflows/`` contains Github Action Workflows
* ``bin/`` contains a few legacy scripts, though most are in ``scripts/``
* ``deploy/docker`` contains containerization related scripts/configuration
* ``docker-compose.yml`` builds the new local deployment (see ``docker-local.rst``)
* ``Dockerfile`` contains the Docker build instructions for the cgap-portal (see ``docker-production.rst``)
* ``docs/ contains`` documentation
* ``Makefile`` contains macros for common build operations (see ``make info``)
* ``package.json`` and ``package-lock.json`` specify the front-end dependencies
* ``pyproject.toml`` and ``poetry.lock`` specify the back-end dependencies
* ``scripts/`` contains misc scripts
* ``setup_eb.py`` performs final installation setup
* ``src/encoded/`` where the code is


Navigating core functionality (src/encoded/)
Expand All @@ -70,16 +69,16 @@ Navigating core functionality (src/encoded/)
Top level files are modules that make up the core functionality of the back-end. Some modules differ greatly from or do
not even exist in fourfront. Directories are outlined below.

* ``annotations/`` contains mapping table and ingestion related metadata
* ``commands/`` contains Python commands that can be run on the system from the command line
* ``docs/`` contains ReadTheDocs documentation
* ``ingestion/`` contains ingestion related code, such as mapping table intake and VCF processing
* ``schemas/`` contains the metadata schemas
* ``search/`` contains the search/filter_set APIs
* ``static/`` contains front-end code
* ``tests/`` contains back-end unit tests and insert data
* ``types/`` contains metadata type definitions
* ``upgrade/`` contains collection schema version upgraders
* ``annotations/`` contains mapping table and ingestion related metadata
* ``commands/`` contains Python commands that can be run on the system from the command line
* ``docs/`` contains ReadTheDocs documentation
* ``ingestion/`` contains ingestion related code, such as mapping table intake and VCF processing
* ``schemas/`` contains the metadata schemas
* ``search/`` contains the search/filter_set APIs
* ``static/`` contains front-end code
* ``tests/`` contains back-end unit tests and insert data
* ``types/`` contains metadata type definitions
* ``upgrade/`` contains collection schema version upgraders


Related Repositories
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Note that ``cgap-portal`` is bound on supporting functionality
in numerous libaries, but importantly:

* **dcicsnovault**
[`pypi library <https://pypi.org/project/dcicsnovault/>`_]
[`source repo <https://github.com/4dn-dcic/snovault>`_]
* **dcicsnovault**
[`pypi library <https://pypi.org/project/dcicsnovault/>`_]
[`source repo <https://github.com/4dn-dcic/snovault>`_]

* **dcicutils**
[`pypi library <https://pypi.org/project/dcicutils/>`_]
[`source repo <https://github.com/4dn-dcic/utils>`_]
* **dcicutils**
[`pypi library <https://pypi.org/project/dcicutils/>`_]
[`source repo <https://github.com/4dn-dcic/utils>`_]

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