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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

If you had have previously installed CosmosID CLI just upgrade CLI to latest version. .. code:: shell

$ sudo -H pip3 install --upgrade cosmosid_cli

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:

{"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:

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:

#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 Cosmosid 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.

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. The CosmosID CLI supports uploading multiple Single-Read and Paired-End samples. For Paired-End samples, the CLI automatically parse and merge samples in pairs if the samples follow the naming conventions like: xxx_R1.fastq and xxx_R2.fastq OR xxx_R1_001.fastq and xxx_R2_001.fastq. Note: Paired-End samples require "fastq" format

To upload all samples from folder run cosmosid upload command with path to folder specified by --dir/-d parameter > Note: This command respects Paired-End samples grouping with the same rules as for regular upload

#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:

#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