{
    "info": {
        "author": "Daniel Domingo-Fern\u00e1ndez and Charles Tapley Hoyt",
        "author_email": "daniel.domingo.fernandez@scai.fraunhofer.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "ComPath |build| |coverage| |docs| |zenodo|\n==========================================\nAn integrative and extensible web application for exploring, analyzing, and curating pathway databases. ComPath is publicly available at https://compath.scai.fraunhofer.de/.\n\nThis package exposes the Bio2BEL pathway packages into a web application containing multiple built-in visualization and\nanalytics tools allowing for their analysis and comparison. By default, this packages wraps the following default\npackages:\n\n- `Bio2BEL KEGG <https://github.com/bio2bel/kegg>`_\n- `Bio2BEL Reactome <https://github.com/bio2bel/reactome>`_\n- `Bio2BEL WikiPathways <https://github.com/bio2bel/wikipathways>`_\n- `Bio2BEL MSig <https://github.com/bio2bel/msig>`_\n\nNew pathway/gene signatures resources can be added by forking the `ComPath Template Repository <https://github.com/compath/compath_template>`_.\n\nCitation\n--------\nIf you use ComPath in your work, please cite [1]_:\n\n.. [1] Domingo-Fern\u00e1ndez, D., *et al.* (2019). `ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases <https://doi.org/10.1038/s41540-018-0078-8>`_. *npj Syst Biol Appl.*, 5(1):3.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\n``compath`` can be installed easily from `PyPI <https://pypi.python.org/pypi/compath>`_ with the\nfollowing code in your favorite terminal:\n\n.. code-block:: sh\n\n    python3 -m pip install compath\n\nor from the latest code on `GitHub <https://github.com/compath/compath>`_ with:\n\n.. code-block:: sh\n\n    python3 -m pip install git+https://github.com/bio2bel/compath.git@master\n\nSetup\n-----\nEasiest\n~~~~~~~\nAfter installing ``compath``, run from the command line:\n\n.. code-block:: sh\n\n    python3 -m compath populate\n\nThis command populates all of the relevant Bio2BEL repositories for the default list, and if any optional ComPath\nrepositories have been registered with entry points, will also populated.\n\nFor Developers\n~~~~~~~~~~~~~~\nIf you just cloned the repo and installed it from the source code, you can run the sh script ``load_compath.sh`` by\ntyping :code:`sh load_compath.sh` in your terminal. This script will first install all packages and later populate the\ndatabase.\n\nIf you have already installed the packages, but not loaded the data. First, load\n`Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_ (see 'Mapping across gene/protein identifiers' section). Next, load all individual pathway database\npackages KEGG, Reactome, WikiPathways, and MSigDB  with :code:`python3 -m compath populate`. This command assumes that\nthese packages are already installed in your Python environment. You can check the packages installed by running\n:code:`python3 -m compath ls` in your terminal. Alternatively, you can populate each package independently by running:\n:code:`python3 -m bio2bel_kegg populate`, :code:`python3 -m bio2bel_reactome populate`,\n:code:`python3 -m bio2bel_wikipathways populate`, or :code:`python3 -m bio2bel_msig populate`.\n\nMapping across gene/protein identifiers\n---------------------------------------\nIn order to load the gene sets from default packages, ComPath assumes that `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_\nhas been already installed and populated. This package is required to perform the mapping from multiple Protein/Gene identifiers to HGNC symbols. The following steps are needed to install Bio2BEL HGNC:\n\n1. :code:`python3 -m pip install bio2bel_hgnc`\n2. :code:`python3 -m bio2bel_hgnc populate`\n\n\nRunning the Web Application\n---------------------------\nThe application can be run simply with\n\n.. code-block:: bash\n\n    python3 -m compath web\n\nThis command the Flask development server locally, by default on port 5000 (http://localhost:5000).\n\n\nCuration Interface\n------------------\nLoad mappings between pathways directly from the `ComPath Curation <https://github.com/compath/curation>`_ package.\n\n.. code-block:: sh\n\n    python3 -m compath load_mappings --connection=\"sqlite:////data/bio2bel.db\"\n\nLoad hierarchical mappings from a pathway database already containing that information (e.g., Reactome).\n\n.. code-block:: sh\n\n    python3 -m compath load_hierarchies --connection=\"sqlite:////data/bio2bel.db\"\n\n\nCreate a user.\n\n.. code-block:: sh\n\n    python3 -m compath manage --connection=\"sqlite:////data/bio2bel.db\" users make_user  'email' 'password'\n\nMake user admin.\n\n.. code-block:: sh\n\n    python3 -m compath manage --connection=\"sqlite:////data/bio2bel.db\" users make_admin 'email'\n\nDocker Instructions\n-------------------\n\nDeployment of ComPath with Docker\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n1. Build the container with compath as a name.\n\n.. code-block:: sh\n\n    docker build -t compath:0.0.1 .\n\n\n2. Create the data container in which the data will be located.\n\n.. code::\n\n    docker create -v /data --name compath-data compath:0.0.1\n\n\n\n3. Run docker container and connect it with the data container\n\n.. code::\n\n    docker run --name=compath --volumes-from compath-data --restart=always -d compath:0.0.1\n\n\n``For admin purposes and deploying ComPath inside Fraunhofer you can also run the following command``\n\n.. code-block:: sh\n\n    sh create_and_build_container.sh\n\nLoad Data\n~~~~~~~~~\n\nLoads the KEGG, Reactome, and WikiPathways modules into ComPath.\n\n.. code-block:: sh\n\n    docker exec -t -it compath /opt/compath/src/bin/load_data.sh\n\nRestart Container\n~~~~~~~~~~~~~~~~~\n\nRestarts the compath container\n\n.. code-block:: sh\n\n    docker restart compath\n\n\n.. |build| image:: https://travis-ci.org/ComPath/ComPath.svg?branch=master\n    :target: https://travis-ci.org/ComPath/ComPath\n    :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/ComPath/ComPath/coverage.svg?branch=master\n    :target: https://codecov.io/gh/ComPath/ComPath?branch=master\n    :alt: Coverage Status\n\n.. |docs| image:: http://readthedocs.org/projects/compath/badge/?version=latest\n    :target: https://compath.readthedocs.io/en/latest/\n    :alt: Documentation Status\n\n.. |climate| image:: https://codeclimate.com/github/compath/compath/badges/gpa.svg\n    :target: https://codeclimate.com/github/compath/compath\n    :alt: Code Climate\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/compath.svg\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/compath.svg\n    :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/compath.svg\n    :alt: MIT License\n\n.. |zenodo| image:: https://zenodo.org/badge/118578699.svg\n    :target: https://zenodo.org/badge/latestdoi/118578699",
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