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    "info": {
        "author": "CosmosID",
        "author_email": "support@cosmosid.com",
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        "classifiers": [
            "Environment :: Console",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
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        "description": "# Cosmos ID\n\n Command line interface (CLI) and Python 3 client library for interacting with the CosmosID API. Only works with Python [3.6,3.7,3.8,3.9,3.10].\n## Requirements\n\n### OS Packages\n\n* python3\n* python3-pip\n\n### Python package\n\n* poetry\n\n# Installation\n\nThis package provides:\n\n* core Python 3 client library;\n* a simple CLI for interacting with the CosmosID that uses the core library;\n\n## Basic installation\n\nThe CLI with the core Python library can be installed using `pip3`.\n\n* simply run from console `sudo pip3 install cosmosid_cli`\n\n> 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.\n>\n> ```shell\n> E.g. for Ubuntu 14.04 perform following steps:\n> $ sudo apt-get update\n> $ sudo apt-get upgrade\n> $ sudo -H pip3 install -U pip setuptools\n>```\n>\n> If you had have previously installed CosmosID CLI just upgrade CLI\n> to latest version.\n>\n> ```shell\n> $ sudo -H pip3 install --upgrade cosmosid_cli\n> ```\n\nTo install package locally from folder with source files do the following:\n\n* install `poetry` check the [doc](https://python-poetry.org/docs/#osx--linux--bashonwindows-install-instructions)\n* `cd cosmosid-cli/package/`\n* `poetry install`\n\n# Using the CosmosID CLI\n\nThe CosmosID CLI supports authentication via CosmosID API Key.\nYour API key can be found on the [CosmosID profile page](https://app.cosmosid.com/settings).\nTo automatically authenticate via CosmosID API Key you should create\ncredential file `~/.cosmosid` and store your API Key into it in\nthe following format:\n\n```json\n{\"api_key\": \"<your api key string>\"}\n```\n\nYou 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:\n\n```shell\ncosmosid --api_key=YOUR_API_KEY <command>\n```\n\nCLI supports  files of following extensions: 'fasta', 'fna', 'fasta.gz', 'fastq', 'fq', 'fastq.gz', 'bam', 'sra'\n\n## Commands\n\nThere are several types of commands supported by the CosmosID CLI\n\n1. Commands for retrieving data to terminal (output) from CosmosID cloud - files, runs, analysis.\n2. Commands for uploading metagenomics or amplicon samples to\n   CosmosID cloud for analysis - uploads.\n3. Commands for retrieving the reports archive from CosmosID cloud - reports\n\n> Note: Each command has options. To get usage information for each CosmosID CLI command, the user can simply run `cosmosid <command> --help`\n\n### Retrieve Files\n\nThe 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\nor unquote or partly quote output values - all, minimal, none, non-numeric (by default only non-numeric values are quoted)\n\nExample of output for the --help options for the <files> command:\n\n```shell\n$ cosmosid files --help\nusage: cosmosid files [-h] [-f {csv,json,table,value,yaml}] [-c COLUMN]\n                      [--noindent] [--max-width <integer>] [--fit-width]\n                      [--print-empty] [--quote {all,minimal,none,nonnumeric}]\n                      [--parent PARENT]\n                      [--order {type,name,id,status,size,created}] [--up]\n\nShow files in a given directory.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --parent PARENT, -p PARENT\n                        ID of the parent directory. Default: Root\n  --order {type,name,id,status,reads,created}, -o {type,name,id,status,size,created}\n                        field for ordering\n  --up                  order direction\n\noutput formatters:\n  output formatter options\n\n  -f {csv,json,table,value,yaml}, --format {csv,json,table,value,yaml}\n                        the output format, defaults to table\n  -c COLUMN, --column COLUMN\n                        specify the column(s) to include, can be repeated\n\njson formatter:\n  --noindent            whether to disable indenting the JSON\n\ntable formatter:\n  --max-width <integer>\n                        Maximum display width, 1 to disable. You can also use\n                        the CLIFF_MAX_TERM_WIDTH environment variable, but the\n                        parameter takes precedence.\n\n  --fit-width       Fit the table to the display width. Implied if --max-\n                        width greater than 0. Set the environment variable\n                        CLIFF_FIT_WIDTH=1 to always enable\n\n --print-empty     Print empty table if there is no data to show.\n\nCSV Formatter:\n  --quote {all,minimal,none,nonnumeric} when to include quotes, defaults to nonnumeric\n```\n\nTo retrieve files (samples) stored in CosmosID simply run the `cosmosid` command with a `files` subcommand. For example:\n\n```shell\n#to get contents of your CosmosID root folder\ncosmosid files\n\n#to get contents of appropriate folder use its id as argument\ncosmosid files --parent=<folder_id>\n\n#to get ordered list simply use the ordering argument with field name with/without order direction\ncosmosid files --parent=<folder_id> --order size --up\n```\n\n### Retrieve Sample Runs\n\nAn each file (sample) stored in CosmosID has one or more Sample Run(s) associated with it.\nTo retrieve sample run(s) associated with a file simply run the `cosmosid` command with `runs` subcommand. For example:\n\n```shell\n#to get runs associated with a speciffic file (sample)\ncosmosid runs --id=<file_id>\n```\n\n### Upload files\n\nThe CosmosID CLI supports uploading sample files into CosmosID for analysis.\nCosmosID supports the following file formats and extension names:\n.fasta, .fna, .fasta.gz, .fastq, .fq, .fastq.gz, bam, bam.gz, sra, sra.gz. (SRA files can be uploaded without extension)\n\nCosmosID supports the following types of analysis:\n\n* Metagenomics\n* Amplicon - 16S or ITS (only 16S and ITS supported for now)\n\n> Note: you can get usage help for each command and arguments of CosmosID CLI by simply runnig `cosmosid --help` or `cosmosid <command> --help`\n\nTo 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.\nThe 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\n\nTo upload all samples from folder run `cosmosid upload` command with path to folder specified by --dir/-d parameter\n> Note: This command respects Paired-End samples grouping with the same rules as for regular upload\n\nRunning example:\n\ncosmosid upload --type metagonomics -f /pathtofile/test1_R1.fastq -f /pathtofile/test1_R2.fastq -f  /pathtofile/test2.fasta\n\n```shell\n#to upload one sample file for Metagenomics analysis\ncosmosid upload --file <path to file> --type metagenomics\n\n#to upload sample file into specific folder for Amplicon 16s analysis\ncosmosid upload --file <path to file-1> --parent <folder id> --type amplicon-16s\n\n#to upload all files from folder\ncosmosid upload -d /home/user/samples/ --type metagenomics\n```\n\n> Note: uploading of a big file takes time, please be patient\n\nOnce file has been uploaded to CosmosID the analyzing process will automatically begin.\nYou can check the status of metagenomics analysis on the page [CosmosID Samples](https://app.cosmosid.com/samples).\nAmplicon analysis results available only from CosmosID CLI for now.\n\n### Retrieving Analysis Results\n\nAnalysis results can be retrieved from CosmosID by useing run id or file id. The latest run analysis results will be retrieved when file id used.\nTo retrieve analysis results for a specified run in CosmosID simply run `cosmosid` command with `analysis` subcommand. File  For example:\n\n```shell\n#to get list of analysis for the latest run of file\ncosmosid analysis --id=<file ID>\n\n#to get list of analysis for a given run id\ncosmosid analysis --run_id=<run ID>\n\n#to get ordered list of analysis for a given file id simply use ordering argument with field name with/without order direction\ncosmosid analysis --id=<file ID> --order created --up\n```\n\n> Note: There is no analysis results for Amplicon 16S and Amplicon ITS sample. Use report generation instead of getting list of analysis for Amplicon 16S and Amplicon ITS.\n\n### Generate Analysis Report Archive\n\nThe CosmosID CLI supports retrieving the archive of analysis reports from CosmosID for a given `File ID` with a given `Run ID` and saving the archive to a given file.\n\nTo retrieve an analysis report archive with TSV files run the `cosmosid` command with `reports` subcommand.\n\n```shell\n# to create analysis report archive for the latest run of sample and save it in\n# a current directory with a name equivalent to file name in CosmosID\ncosmosid reports --id=<file ID>\n\n# to create analysis report archive for the given run of sample and save it in\n# a current directory with a name equivalent to file name in CosmosID\ncosmosid reports --id=<file ID> --run_id=<run ID>\n\n# to create analysis report archive for the given run of sample and save it\n# in a given directory\ncosmosid reports --id=<file ID> --run_id=<run ID> --dir ~/cosmosid/reports\n\n# to create analysis report archive for the given run of sample and save it\n# into a given local file\ncosmosid reports --id=<file ID> --output /tmp/analysis_report.zip\n```\n\n### Retrieving Artifacts Results\n\nArtifacts results can be retrieved from CosmosID by using run id.\nTo retrieve artifacts results for a specified run in CosmosID simply run `cosmosid` command with `artifacts` subcommand. File  For example:\n\n```shell\n\n#to get list of artifacts for a given run id\ncosmosid artifacts --run_id=<run ID>\n\n##to create artifacts archive for the given run id of sample and store it to given path\ncosmosid artifacts --run_id=<run ID> --type=fastqc-zip --dir /home/user\n\n\n##to create artifacts archive for the given run id of sample and store it with given name in current dir\ncosmosid artifacts --run_id=<run ID> --type=fastqc-zip --output artifacts_report.zip\n\n##to create artifacts archive for the given run id of sample and store it with given name and given dir\ncosmosid artifacts --run_id=<run ID> --type=fastqc-zip --dir /home/user --output artifacts_report.zip\n\n#to get url to download the archive\ncosmosid artifacts --run_id=<run ID> --type=fastqc-zip --url\n```\n\n",
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