{ "info": { "author": "The NDEx Project", "author_email": "contact@ndexbio.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "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", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: Scientific/Engineering :: Medical Science Apps." ], "description": "ndex-python-utilities\n======================\n\n**Warning: This repository is for development and features may change.\nPlease use this at your own risk.**\n\n.. image:: https://img.shields.io/pypi/v/ndexutils.svg\n :target: https://pypi.python.org/pypi/ndexutils\n\n.. image:: https://img.shields.io/travis/ndexbio/ndexutils.svg\n :target: https://travis-ci.org/ndexbio/ndexutils\n\n.. image:: https://coveralls.io/repos/github/ndexbio/ndexutils/badge.svg?branch=master\n :target: https://coveralls.io/github/ndexbio/ndexutils?branch=master\n\n.. image:: https://readthedocs.org/projects/ndexutils/badge/?version=latest\n :target: https://ndexutils.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\nDependencies\n------------\n\n* `ndex2 `_\n* `networkx `_\n* `ndexutil `_\n* `biothings_client `_\n* `requests `_\n* `requests-toolbelt `_\n* `pandas `_\n* `mygene `_\n* `enum34 `_\n* `jsonschema `_\n* `urllib3 `_\n\nCompatibility\n-------------\n\n* Python 3.5+\n\nInstallation\n------------\n\n.. code-block::\n\n git clone https://github.com/ndexbio/ndexutils\n cd ndexutils\n make dist\n pip install dist/ndexutil*whl\n\nOR via `PyPI `_\n\n.. code-block::\n\n pip install ndexutil\n\nndexmisctools.py\n-----------------\n\n**WARNING:** Please consider this tool alpha and probably contains errors/bugs and could cause data corruption or loss. You have been warned\n\n**ndexmisctools.py** lets caller perform some operations on NDEx via the\ncommand line.\nThis tool follows format of ``ndexmisctools.py ``\n\nFor more information run ``ndexmisctools.py --help`` and ``ndexmisctools.py --help``\n\n**COMMANDS**:\n\n* **copynetwork** - copies NDEx network between accounts and even servers\n\n For copying the source and destination credentials must be stored in the configuration (default ``~/.ndexutils.conf``)\n and be formatted as follows:\n\n .. code-block::\n\n [mycopyprofile]\n source_user=bob\n source_password=6ea8f0ab0b2e\n source_server=public.ndexbio.org\n dest_user=smith\n dest_password=4efe9cd8\n dest_server=public.ndexbio.org\n\n The following command copies the network ``9025480b-6fbc-4efe-9cd8-b575ce49dfda`` from source credentials defined in configuration to dest\n\n .. code-block::\n\n ndexmisctools.py --profile mycopyprofile copynetwork --uuid 9025480b-6fbc-4efe-9cd8-b575ce49dfda\n\n\n* **networkattribupdate** - updates network attributes on network in NDEx\n\n **WARNING:** Currently **name, version, and description** CANNOT be updated with this command.\n\n Credentials must be stored in the configuration (default ``~/.ndexutils.conf``)\n and be formatted as follows:\n\n .. code-block::\n\n [myattrib]\n user=bob\n password=6ea8f0ab0b2e\n server=public.ndexbio.org\n\n The following command updates **foo** network attribute on the network ``9025480b-6fbc-4efe-9cd8-b575ce49dfda``\n\n .. code-block::\n\n ndexmisctools.py --profile myattrib networkattribupdate --uuid 9025480b-6fbc-4efe-9cd8-b575ce49dfda --name foo --type string --value 'my new value'\n\n\n* **systemproperty** - updates showcase, visibility, and indexing for single network or all networks in networkset in NDEx\n\n **NOTE:** ``--showcase`` has no effect if network visibility is ``private``\n\n Credentials must be stored in the configuration (default ``~/.ndexutils.conf``)\n and be formatted as follows:\n\n .. code-block::\n\n [myattrib]\n user=bob\n password=6ea8f0ab0b2e\n server=public.ndexbio.org\n\n The following command enables showcase and sets indexing to `meta` for network with id ``9025480b-6fbc-4efe-9cd8-b575ce49dfda``\n\n .. code-block::\n\n ndexmisctools.py --profile myattrib systemproperty --uuid 9025480b-6fbc-4efe-9cd8-b575ce49dfda --showcase --indexlevel meta\n\n The following command sets visibility to `public` for all networks in networkset with id ``e9580d43-ec14-4be8-9977-9de88e1d410a``\n\n .. code-block::\n\n ndexmisctools.py --profile myattrib systemproperty --networksetid e9580d43-ec14-4be8-9977-9de88e1d410a --visibility public\n\n\nTSV Loader\n----------\n\nThis module contains the Tab Separated Variable Loader (TSV Loader) which generates\nan `NDEx CX `_ file from a tab separated\ntext file of edge data and attributes.\n\nTo load data a load plan must be created. This plan tells the loader how to map the\ncolumns in the file to nodes, and edges. This load plan needs to validate against\n`this load plan JSON schema `_\n\n**Example TSV file**\n\n.. code-block::\n\n SOURCE TARGET WEIGHT\n ABCD AAA1 0.555\n GGGG BBBB 0.305\n\n**SOURCE** is the source node, **TARGET** is target node\n\nA schema that could be:\n\n.. code-block::\n\n {\n \"source_plan\":\n {\n \"node_name_column\": \"SOURCE\"\n },\n \"target_plan\":\n {\n \"node_name_column\": \"TARGET\"\n },\n \"edge_plan\":\n {\n \"default_predicate\": \"unknown\",\n \"property_columns\": [\n {\n \"column_name\": \"WEIGHT\",\n \"attribute_name\": \"weight\",\n \"data_type\": \"double\"\n }\n ]\n }\n }\n\n\n\nExample below assumes the following:\n\n* **./loadplan.json** is the load plan in JSON format\n* **./style.cx** is a `NDEx CX `_ with a style.\n\n.. code-block::\n\n import ndex2\n from ndexutil.tsv.streamtsvloader import StreamTSVLoader\n\n # using ndex2 client library read CX file as NiceCXNetwork object\n style_network = ndex2.create_nice_cx_from_file('./style.cx')\n\n loader = StreamTSVLoader('./loadplan.json', style_network)\n with open('./input.tsv', 'r') as tsvfile:\n with open('./output.cx', 'w') as outfile:\n loader.write_cx_network(tsvfile, outfile)\n\n\nCredits\n-------\n\n\n\n=======\nHistory\n=======\n\n0.7.0 2019-09-11\n-----------------\n\n* Added new command to **ndexmisctools.py** named *systemproperty* that lets\n caller update showcase, visibility, and indexing for a single network or\n all networks in a networkset in NDEx\n\n0.6.1 2019-07-12\n----------------\n\n* Fixed bug where **ndexmisctools.py** *networkattributeupdate* was creating\n duplicate network attributes for name, description, and value. This is\n due to server bug. 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separate aspect\n\n0.2.0 2019-04-01\n----------------\n\n* StreamTSVLoader class added which enables loading of TSV data into\n in streaming format to handle loading of large networks\n\n\n\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/ndexbio/ndexutils", "keywords": "network analysis biology", "license": "BSD", "maintainer": "", "maintainer_email": "", "name": "ndexutil", "package_url": "https://pypi.org/project/ndexutil/", "platform": "", "project_url": "https://pypi.org/project/ndexutil/", "project_urls": { "Homepage": "https://github.com/ndexbio/ndexutils" }, "release_url": "https://pypi.org/project/ndexutil/0.7.0/", "requires_dist": [ "ndex2 (<=4.0.0,>=3.3.0)", "requests", "requests-toolbelt", "networkx", "urllib3 (>=1.16)", "pandas", "mygene", "enum34", "jsonschema", "biothings-client", "enum ; python_version == \"2.6\" or python_version == \"2.7\"" 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