Metadata-Version: 2.1
Name: ndexutil
Version: 0.8.0
Summary: Unsupported NDEx utilities
Home-page: https://github.com/ndexbio/ndexutils
Author: The NDEx Project
Author-email: contact@ndexbio.org
License: BSD
Keywords: network analysis biology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Dist: ndex2 (<=4.0.0,>=3.3.0)
Requires-Dist: requests
Requires-Dist: requests-toolbelt
Requires-Dist: networkx
Requires-Dist: urllib3 (>=1.16)
Requires-Dist: pandas
Requires-Dist: mygene
Requires-Dist: enum34
Requires-Dist: jsonschema
Requires-Dist: biothings-client
Requires-Dist: enum ; python_version == "2.6" or python_version == "2.7"

ndexutil
==========

.. _NDEx: https://ndexbio.org
.. _NDEx CX: https://www.home.ndexbio.org/data-model/

**Warning: This repository is for development and features may change.
Please use this at your own risk.**

.. image:: https://img.shields.io/pypi/v/ndexutil.svg
        :target: https://pypi.python.org/pypi/ndexutil

.. image:: https://img.shields.io/travis/ndexbio/ndexutil.svg
        :target: https://travis-ci.org/ndexbio/ndexutil

.. image:: https://coveralls.io/repos/github/ndexbio/ndexutils/badge.svg?branch=master
        :target: https://coveralls.io/github/ndexbio/ndexutils?branch=master

.. image:: https://readthedocs.org/projects/ndexutils/badge/?version=latest
        :target: https://ndexutil.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

Dependencies
------------

* `ndex2 <https://pypi.org/project/ndex2>`_
* `networkx <https://pypi.org/project/networkx>`_
* `biothings_client <https://pypi.org/project/biothings-client>`_
* `requests <https://pypi.org/project/requests>`_
* `requests-toolbelt <https://pypi.org/project/requests_toolbelt>`_
* `pandas <https://pypi.org/project/pandas>`_
* `mygene <https://pypi.org/project/mygene>`_
* `enum34 <https://pypi.org/project/enum34>`_
* `jsonschema <https://pypi.org/project/jsonschema>`_
* `urllib3 <https://pypi.org/project/urllib3>`_

Compatibility
-------------

* Python 3.5+

Installation
------------

.. code-block::

   git clone https://github.com/ndexbio/ndexutils
   cd ndexutils
   make dist
   pip install dist/ndexutil*whl

OR via `PyPI <https://pypi.org/ndexutils>`_

.. code-block::

   pip install ndexutil

ndexmisctools.py
-----------------

**WARNING:** Please consider this tool alpha and probably contains errors/bugs and could cause data corruption or loss. You have been warned

**ndexmisctools.py** lets caller perform some operations on `NDEx`_ via the
command line.
This tool follows format of ``ndexmisctools.py <COMMAND> <args>``

For more information run ``ndexmisctools.py --help`` and ``ndexmisctools.py <COMMAND> --help``

**COMMANDS**:

* **copynetwork** - copies `NDEx`_ network between accounts and even servers

  For copying the source and destination credentials must be stored in the configuration (default ``~/.ndexutils.conf``)
  and be formatted as follows:

  .. code-block::

   [mycopyprofile]
   source_user=bob
   source_password=6ea8f0ab0b2e
   source_server=public.ndexbio.org
   dest_user=smith
   dest_password=4efe9cd8
   dest_server=public.ndexbio.org

  The following command copies the network ``9025480b-6fbc-4efe-9cd8-b575ce49dfda`` from source credentials defined in configuration to dest

  .. code-block::

    ndexmisctools.py --profile mycopyprofile copynetwork --uuid 9025480b-6fbc-4efe-9cd8-b575ce49dfda


* **networkattribupdate** - updates network attributes on network in `NDEx`_

  **WARNING:** Currently **name, version, and description** CANNOT be updated with this command.

  Credentials must be stored in the configuration (default ``~/.ndexutils.conf``)
  and be formatted as follows:

  .. code-block::

    [myattrib]
    user=bob
    password=6ea8f0ab0b2e
    server=public.ndexbio.org

  The following command updates **foo** network attribute on the network ``9025480b-6fbc-4efe-9cd8-b575ce49dfda``

  .. code-block::

    ndexmisctools.py --profile myattrib networkattribupdate --uuid 9025480b-6fbc-4efe-9cd8-b575ce49dfda --name foo --type string --value 'my new value'


* **systemproperty** - updates showcase, visibility, and indexing for single network or all networks in networkset in `NDEx`_

  **NOTE:** ``--showcase`` has no effect if network visibility is ``private``

  Credentials must be stored in the configuration (default ``~/.ndexutils.conf``)
  and be formatted as follows:

  .. code-block::

    [myattrib]
    user=bob
    password=6ea8f0ab0b2e
    server=public.ndexbio.org

  The following command enables showcase and sets indexing to `meta` for network with id ``9025480b-6fbc-4efe-9cd8-b575ce49dfda``

  .. code-block::

    ndexmisctools.py --profile myattrib systemproperty --uuid 9025480b-6fbc-4efe-9cd8-b575ce49dfda --showcase --indexlevel meta

  The following command sets visibility to `public` for all networks in networkset with id ``e9580d43-ec14-4be8-9977-9de88e1d410a``

  .. code-block::

    ndexmisctools.py --profile myattrib systemproperty --networksetid e9580d43-ec14-4be8-9977-9de88e1d410a --visibility public

* **tsvloader** - Loads TSV files as networks into `NDEx`_

  The **tsvloader** command loads an edge list file in tab separated format (hence TSV) and using a load plan, loads that data as a network into `NDEx <https://ndexbio.org>`_.
  This tool attempts to mimic behavior of the older ``tsv_uploader.py`` script located here: https://github.com/ndexbio/load-content
  This new version uses the more memory efficient StreamTSVLoader.

  This command requires five positional parameters.
  The first three (``username`, ``password``, and ``server``) are credentials for
  `NDEx`_ server to upload the network.

  Any of these first three credential fields set to **'-'** will
  force this tool to obtain the information from (default ``~/.ndexutils.conf``) configuration file
  under the profile specified by the ``--profile`` field in this format:

  .. code-block::

      [<value of --profile>]
      user = <NDEx username>
      password = <NDEx password>
      server = <NDEx server ie public.ndexbio.org>

  The forth positional parameter ``tsv_file`` (see _`TSV Loader` section below) should be
  set to edge list file in tab separated format and the
  fifth or last positional parameter ``load_plan`` should be
  set to the load plan. The load plan is a JSON formatted text
  file that maps the columns to nodes, edges, and attributes
  in the network.

  By default this tool does not generate much output to
  standard out/error. For more verbosity add three to five ``-v`` parameters
  to left of command name **tsvloader** as seen in examples below.


  In example below the ``- - -`` tells the program to read the credentials
  from the configuration file

  .. code-block::

      ndexmisctools.py -vvvv tsvloader - - - datafile.tsv load.plan

  Here is an example where the name and description of the network is set
  and the ``-t`` specifies a template network used to get style and in this case
  since ``--copyattribs`` is set the network attributes (minus ``@context``) are
  also copied to the new network

  .. code-block::

      ndexmisctools.py -vvv tsvloader bob xx public.ndexbio.org \
                       datafile.tsv loadplan.json --uppercaseheader  \
                       -t dafe07ca-0676-11ea-93e0-525400c25d22 \
                       --name mynetwork --description 'some text' --copyattribs


  In this example an alternate header is prepended via the ``--header`` flag.

  **NOTE:** The ``--header`` flag does **NOT** remove an existing header

  .. code-block::

      ndexmisctools.py -vv --profile foo tsvloader - - public.ndexbio.org \
                       datafile.tsv loadplan.json \
                       --header 'col1	col2	col3' \
                       -t some_cx_file.cx \
                       -u 48a26aa0-0677-11ea-93e0-525400c25d22

  If successful ``0`` is returned otherwise there was an error.

.. _TSV_Loader: .

TSV Loader
----------

This module contains the Tab Separated Variable Loader (TSV Loader, see `ndexutil/streamtsvloader.py` module) which generates
an `NDEx CX`_ file from a tab separated
text file of edge data and attributes.

To load data a load plan must be created. This plan tells the loader how to map the
columns in the file to nodes, and edges. This load plan needs to validate against
`this load plan JSON schema <https://github.com/ndexbio/ndexutils/blob/master/ndexutil/tsv/loading_plan_schema.json>`_

**Example TSV file**

.. code-block::

    SOURCE  TARGET  WEIGHT
    ABCD    AAA1    0.555
    GGGG    BBBB    0.305

**SOURCE** is the source node, **TARGET** is target node

A schema that could be:

.. code-block::

    {
    "source_plan":
        {
            "node_name_column": "SOURCE"
        },
        "target_plan":
        {
            "node_name_column": "TARGET"
        },
        "edge_plan":
        {
            "default_predicate": "unknown",
            "property_columns": [
              {
                "column_name": "WEIGHT",
                "attribute_name": "weight",
                "data_type": "double"
              }
            ]
        }
    }



Example below assumes the following:

* **./loadplan.json** is the load plan in JSON format
* **./style.cx** is a `NDEx CX`_ with a style.

.. code-block::

    import ndex2
    from ndexutil.tsv.streamtsvloader import StreamTSVLoader

    # using ndex2 client library read CX file as NiceCXNetwork object
    style_network = ndex2.create_nice_cx_from_file('./style.cx')

    loader = StreamTSVLoader('./loadplan.json', style_network)
    with open('./input.tsv', 'r') as tsvfile:
        with open('./output.cx', 'w') as outfile:
            loader.write_cx_network(tsvfile, outfile)


Credits
-------



=======
History
=======

0.8.0 2019-11-15
------------------

* Fixed bug in StreamTSVLoader where 2 \@context network attributes were added to network if \@context was set in load plan and \@context was passed in the network attributes parameter for `write_cx_network()`

* Added new command to **ndexmisctools.py** named *tsvloader* that lets caller load TSV files as networks into NDEx

0.7.0 2019-09-11
-----------------

* Added new command to **ndexmisctools.py** named *systemproperty* that lets
  caller update showcase, visibility, and indexing for a single network or
  all networks in a networkset in NDEx

0.6.1 2019-07-12
----------------

* Fixed bug where **ndexmisctools.py** *networkattributeupdate* was creating
  duplicate network attributes for name, description, and value. This is
  due to server bug. To deal with this the code removes those entries when
  doing the network attribute update and forbids caller from trying to
  update those attributes

0.6.0 2019-07-10
----------------

* Added new commandline utility *ndexmisctools.py* which lets caller
  copy a network from one NDEx account to another and lets one update
  network attributes of a network in NDEx.
  WARNING: THIS IS AN UNTESTED ALPHA RELEASE AND MAY CONTAIN ERRORS

0.5.0 2019-06-06
----------------

* Added GeneSymbolSearcher class to loaderutils.py module

* Minor bug fix in NetworkIssueReport get_fullreport_as_string() where
  issue text is wrapped in str() in case its not a string 

0.4.0 2019-05-23
----------------

* Added loaderutils.py module with two new classes, NetworkIssueReport and
  an abstract class NetworkUpdator

0.3.0 2019-05-14
----------------

* tsv2nicecx2.convert_pandas_to_nice_cx_with_load_plan now loads @context
  data into a @context network attribute instead of a separate aspect

0.2.0 2019-04-01
----------------

* StreamTSVLoader class added which enables loading of TSV data into
  in streaming format to handle loading of large networks





