Metadata-Version: 1.1
Name: ndexsignorloader
Version: 0.2.0
Summary: Loads SIGNOR data into NDEx
Home-page: https://github.com/ndexcontent/ndexsignorloader
Author: Chris Churas
Author-email: contact@ndexbio.org
License: BSD license
Description: ==========================
        NDEx Signor Content Loader
        ==========================
        
        
        .. image:: https://img.shields.io/pypi/v/ndexsignorloader.svg
                :target: https://pypi.python.org/pypi/ndexsignorloader
        
        .. image:: https://img.shields.io/travis/ndexcontent/ndexsignorloader.svg
                :target: https://travis-ci.org/ndexcontent/ndexsignorloader
        
        .. image:: https://coveralls.io/repos/github/ndexcontent/ndexsignorloader/badge.svg?branch=master
                :target: https://coveralls.io/github/ndexcontent/ndexsignorloader?branch=master
        
        .. image:: https://readthedocs.org/projects/ndexsignorloader/badge/?version=latest
                :target: https://ndexsignorloader.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        Python application that loads Signor data into NDEx_
        
        This tool downloads data files from Signor_ and performs the following operations:
        
        **1\)** The text files are loaded into a network using this loadplan_
        
        **2\)** The edge attribute **direct** is set to **True** if value is **'t'** otherwise its set to **False**
        
        **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**
        
        **4\)** The **compartment** node attribute is set to **cytoplasm** if its not set (which is case for all nodes in **FULL-Human, Full-Rat, and Full-Mouse** networks)
        
        **5\)** 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.
        
        **6\)** 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 **compartment** node attribute. The ordering is as follows:
        
        * **extracellular** are placed at the top
        * **receptor** are below **extracellular**
        * **cytoplasm** are placed in the middle
        * **factor** are below **cytoplasm**
        * **phenotypeList** are placed at the bottom
        
        **7\)** The following network attributes are set
        
        * **name** is set to data from Signor service **getPathwayData.php?pathway=** (except for the full networks which have a more generic description)
        * **author** is set to data from Signor service **getPathwayData.php?pathway=** (unless its empty in which case its not added to network)
        * **organism** is set to **Human, 9606, Homo sapiens** (except for Full Rat and Mouse networks)
        * **prov:wasGeneratedBy** is set to ndexsignorloader <VERSION> (example: ndexsignorloader 1.0.0)
        * **prov:wasDerivedFrom** set to URL to download data file (or in case of full networks its set to Signor site)
        * **version** is set to Abbreviated day-month-year (example: 05-Jun-2019)
        * **description** is taken from Signor service **getPathwayData.php?pathway=**
        * **rightsHolder** is set to **Prof. Gianni Cesareni**
        * **rights** is set to **Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)**
        * **reference** is set to citation for **SIGNOR: a database of causal relationships between biological entities**
        * **labels** is set to data from Signor service **getPathwayData.php?pathway=** (not set for full networks)
        * **type** is set to a list with **pathway** and if known type of pathway
        * **__normalizationversion** is set to **0.1**
        
        Dependencies
        ------------
        
        * `ndex2 <https://pypi.org/project/ndex2>`_
        * `ndexutil <https://pypi.org/project/ndexutil>`_
        
        Compatibility
        -------------
        
        * Python 3.3+
        
        Installation
        ------------
        
        .. code-block::
        
           git clone https://github.com/ndexcontent/ndexsignorloader
           cd ndexsignorloader
           make dist
           pip install dist/ndexloadsignor*whl
        
        
        Run **make** command with no arguments to see other build/deploy options including creation of Docker image 
        
        .. code-block::
        
           make
        
        Output:
        
        .. code-block::
        
           clean                remove all build, test, coverage and Python artifacts
           clean-build          remove build artifacts
           clean-pyc            remove Python file artifacts
           clean-test           remove test and coverage artifacts
           lint                 check style with flake8
           test                 run tests quickly with the default Python
           test-all             run tests on every Python version with tox
           coverage             check code coverage quickly with the default Python
           docs                 generate Sphinx HTML documentation, including API docs
           servedocs            compile the docs watching for changes
           testrelease          package and upload a TEST release
           release              package and upload a release
           dist                 builds source and wheel package
           install              install the package to the active Python's site-packages
           dockerbuild          build docker image and store in local repository
           dockerpush           push image to dockerhub
        
        
        Configuration
        -------------
        
        The **ndexloadsignor.py** requires a configuration file in the following format be created.
        The default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with
        :code:`--conf` flag.
        
        **Format of configuration file**
        
        .. code-block::
        
            [<value in --profile (default ndexsignorloader)>]
        
            user = <NDEx username>
            password = <NDEx password>
            server = <NDEx server(omit http) ie public.ndexbio.org>
        
        **Example configuration file**
        
        .. code-block::
        
            [ndexsignorloader_dev]
        
            user = joe123
            password = somepassword123
            server = dev.ndexbio.org
        
        
        Needed files
        ------------
        
        **TODO:** Add description of needed files
        
        
        Usage
        -----
        
        For information invoke :code:`ndexloadsignor.py -h`
        
        **Example usage**
        
        **TODO:** Add information about example usage
        
        .. code-block::
        
           ndexloadsignor.py # TODO Add other needed arguments here
        
        
        Via Docker
        ~~~~~~~~~~~~~~~~~~~~~~
        
        **Example usage**
        
        **TODO:** Add information about example usage
        
        
        .. code-block::
        
           docker run -v `pwd`:`pwd` -w `pwd` coleslawndex/ndexsignorloader:0.1.0 ndexloadsignor.py --conf conf # TODO Add other needed arguments here
        
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        .. _NDEx: http://www.ndexbio.org
        .. _Signor: https://signor.uniroma2.it/
        .. _loadplan: https://github.com/ndexcontent/ndexsignorloader/blob/master/ndexsignorloader/loadplan.json
        .. _style.cx: https://github.com/ndexcontent/ndexsignorloader/blob/master/ndexsignorloader/style.cx
        
        
        =======
        History
        =======
        
        0.2.0 (2019-06-28)
        ------------------
        
        * Changed prov:wasDerivedFrom network attribute to just signor website URL for full networks
        
        * Removed author network attribute if no value is found
        
        * Removed labels attribute for full networks 
        
        0.1.0 (2019-06-27)
        ------------------
        
        * First release on PyPI.
        
Keywords: ndexsignorloader
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
