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    "info": {
        "author": "Chris Churas",
        "author_email": "contact@ndexbio.org",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
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        "description": "==========================\nNDEx Signor Content Loader\n==========================\n\n\n.. image:: https://img.shields.io/pypi/v/ndexsignorloader.svg\n        :target: https://pypi.python.org/pypi/ndexsignorloader\n\n.. image:: https://img.shields.io/travis/ndexcontent/ndexsignorloader.svg\n        :target: https://travis-ci.org/ndexcontent/ndexsignorloader\n\n.. image:: https://coveralls.io/repos/github/ndexcontent/ndexsignorloader/badge.svg?branch=master\n        :target: https://coveralls.io/github/ndexcontent/ndexsignorloader?branch=master\n\n.. image:: https://readthedocs.org/projects/ndexsignorloader/badge/?version=latest\n        :target: https://ndexsignorloader.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\nPython application that loads Signor data into NDEx_\n\nThis tool downloads data files from Signor_ and performs the following operations:\n\n**1\\)** The text files are loaded into a network using this loadplan_\n\n**2\\)** The edge attribute **direct** is set to **True** if value is **'t'** otherwise its set to **False**\n\n**3\\)** Using values in the **databasea** and **databaseb** data files, the **represents** field found on each node is prefixed with **uniprot:** if the database value is **UNIPROT** and **signor:** if the database value is **SIGNOR**\n\n**4\\)** The **location** node attribute is set to **cytoplasm** if its not set (which is case for all nodes in **Signor Complete - Human, Signor Complete - Rat, and Signor Complete - Mouse** networks)\n\n**5\\)** The **location** node attribute with value **phenotypeList** is set to empty string\n\n**6\\)** Any negative or non-numeric citations are removed from the **citation** edge attribute (There were multiple cases of -1 and **Other**). In addition, a specific PMC:## is updated to its pubmed id.\n\n**7\\)** **IF --edgecollapse** flag is set on commandline, then edges between same nodes are collapsed if they have same **interaction** with attributes stored in lists with exception of **direct** which is a bool. The pubmed id is prepended (as html link) to each **sentence** attribute entry.\n        In addition, a network attribute named **notes** is added with following text: **Edges have been collapsed with attributes converted to lists with exception of direct attribute**\n\n**8\\)** The layout of the network is created using the spring layout, but with additional logic that positions nodes in a vertical based on value of the **location** node attribute. The ordering is as follows:\n\n* **extracellular** are placed at the top\n* **receptor** are below **extracellular**\n* **cytoplasm** are placed in the middle\n* **factor** are below **cytoplasm**\n* If attribute is empty, nodes are placed at the bottom\n\n**9\\)** The following network attributes are set\n\n* **name** is set to data from Signor service **getPathwayData.php?pathway=** (except for the full/complete networks which have a more generic description)\n* **author** is set to data from Signor service **getPathwayData.php?pathway=** (unless its empty in which case its not added to network)\n* **organism** is set to **Human, 9606, Homo sapiens** (except for **Signor Complete - Rat, and Signor Complete - Mouse** networks)\n* **prov:wasGeneratedBy** is set to ndexsignorloader <VERSION> (example: ndexsignorloader 1.0.0)\n* **prov:wasDerivedFrom** set to URL to download data file (or in case of full networks its set to Signor site)\n* **version** is set to Abbreviated day-month-year (example: 05-Jun-2019)\n* **description** is taken from Signor service **getPathwayData.php?pathway=**\n* **rightsHolder** is set to **Prof. Gianni Cesareni**\n* **rights** is set to **Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)**\n* **reference** is set to citation for **SIGNOR: a database of causal relationships between biological entities**\n* **labels** is set to data from Signor service **getPathwayData.php?pathway=** (not set for full networks)\n* **type** is set to a list with **pathway** and if known type of pathway\n* **__normalizationversion** is set to **0.1**\n\nDependencies\n------------\n\n* `ndex2 <https://pypi.org/project/ndex2>`_\n* `ndexutil <https://pypi.org/project/ndexutil>`_\n\nCompatibility\n-------------\n\n* Python 3.4+\n\nInstallation\n------------\n\n.. code-block::\n\n   git clone https://github.com/ndexcontent/ndexsignorloader\n   cd ndexsignorloader\n   make dist\n   pip install dist/ndexloadsignor*whl\n\n\nRun **make** command with no arguments to see other build/deploy options including creation of Docker image \n\n.. code-block::\n\n   make\n\nOutput:\n\n.. code-block::\n\n   clean                remove all build, test, coverage and Python artifacts\n   clean-build          remove build artifacts\n   clean-pyc            remove Python file artifacts\n   clean-test           remove test and coverage artifacts\n   lint                 check style with flake8\n   test                 run tests quickly with the default Python\n   test-all             run tests on every Python version with tox\n   coverage             check code coverage quickly with the default Python\n   docs                 generate Sphinx HTML documentation, including API docs\n   servedocs            compile the docs watching for changes\n   testrelease          package and upload a TEST release\n   release              package and upload a release\n   dist                 builds source and wheel package\n   install              install the package to the active Python's site-packages\n   dockerbuild          build docker image and store in local repository\n   dockerpush           push image to dockerhub\n\n\nConfiguration\n-------------\n\nThe **ndexloadsignor.py** requires a configuration file in the following format be created.\nThe default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with\n:code:`--conf` flag.\n\n**Format of configuration file**\n\n.. code-block::\n\n    [<value in --profile (default ndexsignorloader)>]\n\n    user = <NDEx username>\n    password = <NDEx password>\n    server = <NDEx server(omit http) ie public.ndexbio.org>\n\n**Example configuration file**\n\n.. code-block::\n\n    [ndexsignorloader_dev]\n\n    user = joe123\n    password = somepassword123\n    server = dev.ndexbio.org\n\n\nUsage\n-----\n\nFor information invoke :code:`ndexloadsignor.py -h`\n\n**Example usage**\n\n**TODO:** Add information about example usage\n\n.. code-block::\n\n   mkdir signor\n   ndexloadsignor.py signor/\n\n\nVia Docker\n~~~~~~~~~~~~~~~~~~~~~~\n\n**Example usage**\n\n**TODO:** Add information about example usage\n\n\n.. code-block::\n\n   docker run -v `pwd`:`pwd` -w `pwd` coleslawndex/ndexsignorloader:1.0.0 ndexloadsignor.py --conf conf # TODO Add other needed arguments here\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _NDEx: http://www.ndexbio.org\n.. _Signor: https://signor.uniroma2.it/\n.. _loadplan: https://github.com/ndexcontent/ndexsignorloader/blob/master/ndexsignorloader/loadplan.json\n.. _style.cx: https://github.com/ndexcontent/ndexsignorloader/blob/master/ndexsignorloader/style.cx\n\n\n=======\nHistory\n=======\n\n1.0.0 (2019-07-30)\n-------------------\n\n* **--edgecollapse** flag added which collapses all edges putting all attributes\n  minus **direct** into lists. For **sentence** attribute each entry the\n  list is now prepended with href link to citation labeled pubmed:#### In addition,\n  if **--edgecollapse** flag is set then a **notes** network attribute is added to\n  let user know.\n\n* **--style** can also accept NDEx UUID for network style. Network needs to be on  same\n  server set in **--profile**\n\n0.3.0 (2019-07-29)\n-------------------\n\n* Added commandline flag **--visibility** that lets user dictate whether NEW networks are public or private (default is public)\n\n* Signor Full Human, Signor Full Rat, and Signor Full Mouse networks have been renamed\n  to Signor Complete - Human, Signor Complete - Rat, Signor Complete - Mouse\n\n* On edges, replaced location attribute value of phenotypesList with empty string NSU-75\n\n* Added __iconurl network attribute and renamed type network attribute to networkType\n\n0.2.0 (2019-06-28)\n------------------\n\n* Changed prov:wasDerivedFrom network attribute to just signor website URL for full networks\n\n* Removed author network attribute if no value is found\n\n* Removed labels attribute for full networks \n\n0.1.0 (2019-06-27)\n------------------\n\n* First release on PyPI.\n\n\n",
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