Metadata-Version: 1.1
Name: ndexstringloader
Version: 0.1.0
Summary: Python Boilerplate contains all the boilerplate you need to create a Python NDEx Content Loader package.
Home-page: https://github.com/vrynkov/ndexstringloader
Author: Vladimir Rynkov
Author-email: vrynkov@ucsd.edu
License: BSD license
Description: ==========================
        NDEx STRING Content Loader
        ==========================
        
        
        .. image:: https://img.shields.io/pypi/v/ndexstringloader.svg
                :target: https://pypi.python.org/pypi/ndexstringloader
        
        .. image:: https://img.shields.io/travis/vrynkov/ndexstringloader.svg
                :target: https://travis-ci.org/vrynkov/ndexstringloader
        
        .. image:: https://readthedocs.org/projects/ndexstringloader/badge/?version=latest
                :target: https://ndexstringloader.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        
        
        Python Boilerplate contains all the boilerplate you need to create a Python NDEx Content Loader package.
        
        
        * Free software: BSD license
        * Documentation: https://ndexstringloader.readthedocs.io.
        
        
        Tools
        -----
        
        * **ndexloadstring.py** -- Loads STRING into NDEx_
        
        Dependencies
        ------------
        
        * `ndex2 3.1.0a1 <https://pypi.org/project/ndex2/3.1.0a1/>`_
        * `ndexutil 0.2.0a1 <https://pypi.org/project/ndexutil/0.2.0a1/>`_
        
        Compatibility
        -------------
        
        * Python 3.3+
        
        Installation
        ------------
        
        .. code-block::
        
           git clone https://github.com/vrynkov/ndexstringloader
           cd ndexstringloader
           make dist
           pip install dist/ndexloadstring*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 **ndexloadstring.py** requires a configuration file to be created.
        The default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with
        :code:`--conf` flag.
        
        **Configuration file**
        
        Networks listed in **[network_ids]** section need to be visible to the **user**
        
        .. code-block::
        
            [dev]
            user = joe123 
            password = somepassword123 
            server = dev.ndexbio.org 
            
            [prod]
            user = joe123 _prod
            password = somepassword123_prod 
            server = prod.ndexbio.org 
            
            [network_ids]
            style = 9c23e193-5d73-11e9-8c69-525400c25d22
            hi_confidence_style = 9c100b71-5d73-11e9-8c69-525400c25d22 
            full = a57b23c5-65fe-11e9-8c69-525400c25d22 
            hi_confidence = 311b0e5f-6570-11e9-8c69-525400c25d22 
        
            [source]
            ProteinLinksFile = https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz
            NamesFile = https://string-db.org/mapping_files/STRING_display_names/human.name_2_string.tsv.gz
            EntrezIdsFile = https://stringdb-static.org/mapping_files/entrez/human.entrez_2_string.2018.tsv.gz
            UniprotIdsFile = https://string-db.org/mapping_files/uniprot/human.uniprot_2_string.2018.tsv.gz
        
            [input]
            full_file_name = 9606.protein.links.full.v11.0.txt
            entrez_file = human.entrez_2_string.2018.tsv
            names_file = human.name_2_string.tsv
            uniprot_file = human.uniprot_2_string.2018.tsv
        
            [output]
            output_tsv_file_name = 9606.protein.links.full.v11.0.tsv.txt
            output_hi_conf_tsv_file_name = 9606.protein.links.full.v11.0.hi_conf.tsv.txt
        
        
        Needed files
        ------------
        
        Load plan is required for running this script.  **string_plan.json**  found at **ndexstringloader/ndexstringloader** can be used for this purpose.
        
        
        Usage
        -----
        
        For information invoke :code:`ndexloadstring.py -h`
        
        **Example usage**
        
        Here is how this command can be run for **dev** and **prod** targets:
        
        .. code-block::
        
           ndexloadstring.py --loadplan loadplan.json  --profile dev 
        
           ndexloadstring.py --loadplan loadplan.json  --profile prod 
        
        
        Via Docker
        ~~~~~~~~~~~~~~~~~~~~~~
        
        **Example usage**
        
        **TODO:** Add information about example usage
        
        
        .. code-block::
        
           docker run -v `pwd`:`pwd` -w `pwd` vrynkov/ndexstringloader:0.1.0 ndexloadstring.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
        
        
        =======
        History
        =======
        
        0.1.0 (2019-03-13)
        ------------------
        
        * First release on PyPI.
        
Keywords: ndexstringloader
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
