Metadata-Version: 1.2
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
Description: 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
Keywords: API Client for CosmosID
Platform: UNKNOWN
Classifier: Environment :: Console
Requires-Python: ~=3.2
