Metadata-Version: 2.0
Name: cosmosid-cli
Version: 0.0.9
Summary: Command line client and Python 3 libraries for CosmosID API
Home-page: https://www.cosmosid.com/
Author: CosmosID
Author-email: support@cosmosid.com
License: MIT
Description-Content-Type: UNKNOWN
Keywords: API Client for CosmosID
Platform: UNKNOWN
Classifier: Environment :: Console
Requires-Python: ~=3.2
Requires-Dist: requests (==2.17)
Requires-Dist: cliff (==2.8.0)
Requires-Dist: six
Requires-Dist: boto3 (==1.4.2)
Requires-Dist: s3transfer (==0.1.10)
Requires-Dist: tzlocal (==1.4)

Cosmos ID
=================

Command line interface (CLI) and Python 3 client library for interacting with the CosmosID API. 
Only works with Python 3, Python 2.7 is not supported yet.

Requirements
------------

OS Packages
~~~~~~~~~~~

-  python3
-  python3-pip

Python package
~~~~~~~~~~~~~~

-  boto3
-  cliff
-  s3transfer
-  requests

Installation
============

This package provides: \* core Python 3 client library; \* a simple CLI
for interacting with the CosmosID that uses the core library;

Basic installation
------------------

The CLI with the core Python library may be installed using ``pip3``. \*
simply run from console ``sudo pip3 install cosmosid_cli``

    Note: pip3 and setuptools should be upgraded to latest version. 
    Please update those packages on you workstation regarding to your 
    OS update process before setup cosmosid cli.
    .. code:: shell
        E.g. for Ubuntu 14.04 perform following steps:
        $ sudo apt-get update
        $ sudo apt-get upgrade
        $ sudo -H pip3 install -U pip setuptools 

Using the CosmosId CLI
=====================

The CosmosID CLI supports authentication via CosmosId API Key.
Your API key can be found on the `CosmosID profile page`_. To
automatically authenticate via CosmosId API Key you should create
credential file ``~/.cosmosid`` and store your API Key into it in the
following format:

.. code:: json

    {"api_key": "<your api key string>"}

You can directly use your CosmosId API Key, rather than storing it in a
credential file. To use API Key authentication, pass your key as an
argument to the ``cosmosid`` command:

.. code:: shell

    cosmosid --api_key=YOUR_API_KEY <command>

Commands
--------

There are several types of commands supported by the CosmosID CLI \*1. Commands for retrieving data to terminal (output) from CosmosID cloud - files, analysis.\*2. Commands for uploading metagenomics or amplicon samples to 
CosmosID cloud for analysis - uploads.\*3. Commands for retrieving the reports archive from CosmosID cloud - reports

    Note: Each command has options. To get usage information for each CosmosID CLI 
    command, the user can simply run ``cosmosid <command> --help``

Retrieve Files
~~~~~~~~~~~~~~

The commands for retrieving data have options for output format. The user can get data into the terminal (or another output) in a different format - csv, json, table, value, yaml (table is default), and specify the column(s) to show. In additional there are CSV format options, user can quote
or unquote or partly quote output values - all, minimal, none, non-numeric (by default only non-numeric values are quoted)

Example of output for the ``--help`` options for the ``<files>`` command:
.. code:: shell
    $ cosmosid files --help
    usage: cosmosid files [-h] [-f {csv,json,table,value,yaml}] [-c COLUMN]
                      [--noindent] [--max-width <integer>] [--fit-width]
                      [--print-empty] [--quote {all,minimal,none,nonnumeric}]
                      [--parent PARENT]
                      [--order {type,name,id,status,size,created}] [--up]

    Show files in a given directory.

    optional arguments:
      -h, --help            show this help message and exit
      --parent PARENT, -p PARENT
                            ID of the parent directory. Default: Root
      --order {type,name,id,status,size,created}, -o {type,name,id,status,size,created}
                            field for ordering
      --up                  order direction

    output formatters:
      output formatter options

      -f {csv,json,table,value,yaml}, --format {csv,json,table,value,yaml}
                        the output format, defaults to table
      -c COLUMN, --column COLUMN
                        specify the column(s) to include, can be repeated

    json formatter:
      --noindent            whether to disable indenting the JSON

    table formatter:
      --max-width <integer>
                            Maximum display width, <1 to disable. You can also use
                            the CLIFF_MAX_TERM_WIDTH environment variable, but the
                            parameter takes precedence.

      --fit-width       Fit the table to the display width. Implied if --max-
                            width greater than 0. Set the environment variable
                            CLIFF_FIT_WIDTH=1 to always enable

     --print-empty     Print empty table if there is no data to show.

    CSV Formatter:
      --quote {all,minimal,none,nonnumeric} when to include quotes, defaults to nonnumeric


To retrieve files (samples) stored in CosmosID simply run the
``cosmosid`` command with a ``files`` subcommand. For example:

.. code:: shell

    #to get contents of your CosmosId root folder
    cosmosid files

    #to get contents of appropriate folder use its id as argument
    cosmosid files --parent <folder_id>

    #to get ordered list simply use the ordering argument with field name with/without order direction
    cosmosid files --parent <folder_id> --order size --up

Upload files
~~~~~~~~~~~~

The CosmosId CLI supports uploading sample files into CosmosID for
analysis. CosmosId supports following file types: *.fastq, .fasta, .fas,
.fa, .seq, .fsa, .fq, .fna, .gz*
CosmosId supports following types of analysis: \* Metagenomics. \* Amplicon - 16s (only 16S supported for now)

    Note: you can get usage help for each command and arguments of
    Mcosmosid CLI to simply runnig ``cosmosid --help`` or
    ``cosmosid <command> --help``
    To upload sample file to CosmosID run ``cosmosid`` command with
    ``upload`` subcommand.  By default samples will be uploaded into
    root folder. To upload sample into specific *existing* folder
    you must use id of the folder as parameter.

.. code:: shell

    #to upload one sample file for Metagenomics analysis
    cosmosid upload --file <path to file> --type metagenomics

    #to upload multiple sample files
    cosmosid upload -f <path to file-1> -f <path to file-2>

    #to upload sample file into specific folder for Amplicon 16s analysis
    cosmosid upload --file <path to file-1> --parent <folder id> --type amplicon-16s

    Note: uploading of a big file takes time, please be patient

Once file has been uploaded to CosmosID the analyzing process will
automatically begin. You can check the result of metagenomics analysis on the page
`CosmosID Samples`_
Amplicon analysis results available only from CosmosID CLI for now.

Retrieving Analysis Results
~~~~~~~~~~~~~~~~~~~~~~~~~~~

To retrieve analysis results for a specified file in CosmosID simply run
``cosmosid`` command with ``analysis`` subcommand. For example:

.. code:: shell

    #to get list of analysis for a given file id
    cosmosid analysis --id <file ID>

    #to get ordered list of analysis for a given file id simly use ordering argument with field name with/without order direction
    cosmosid analysis --id <file ID> --order created --up

    Note: There is no analysis results for Amplicon 16s sample. Use report generation 
    instead of get list of analysis for Amplicon 16s

Generate Analysis Report Archive
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The CosmosId CLI supports retrieving analysis reports archives from
CosmosID for a given ``File ID`` and saving the archive to a
given file.

To retrieve an analysis report archive with TSV files run the
``cosmosid`` command with ``reports`` subcommand. \`\`\`shell #to create
analysis report archive and save it in current directory with name
equivalent to file name in CosmosID cosmosid reports –id

to create analysis report archive and save it into given directory
==================================================================

cosmosid reports –id –dir ~/cosmosid/reports

to create analysis report archive and save it into given local file
===================================================================

cosmosid reports –id –output /tmp/analysis\_report.zip

.. _CosmosID Samples: https://app.cosmosid.com/samples
.. _CosmosID profile page: https://app.cosmosid.com/settings

