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        "author": "mpkocher natechols",
        "author_email": "mkocher@pacificbiosciences.com",
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        "description": "pbcommand High Level Overview\n=============================\n\nco-owners:\n\n[mpkocher](https://github.com/mpkocher)\n\n[natechols](https://github.com/natechols)\n\nPacBio Officially Supported Library. Note the APIs are still in flux and not yet 1.0.0.\n\n[Full Docs](http://pbcommand.readthedocs.org/en/latest/)\n\n[![Circle CI](https://circleci.com/gh/PacificBiosciences/pbcommand.svg?style=svg)](https://circleci.com/gh/PacificBiosciences/pbcommand)\n\nPacBio library for common utils, models, and tools to interface with pbsmrtpipe workflow engine.\n\nTo integrate with the pbsmrtpipe workflow engine you must to be able to generate a **Tool Contract** and to be able to run from a **Resolved Tool Contract**.\n\nA **Tool Contract** contains the metadata of the exe, such as the file types of inputs, outputs and options.\n\nExample [Tool Contract Json](https://github.com/PacificBiosciences/pbcommand/blob/master/tests/data/dev_example_dev_txt_app_tool_contract.json) (and [Avro Schema](https://github.com/PacificBiosciences/pbcommand/blob/master/pbcommand/schemas/tool_contract.avsc))\n\nExample [Resolved Tool Contract Json](https://github.com/PacificBiosciences/pbcommand/blob/master/tests/data/resolved_tool_contract_dev_app.json) (and [Avro Schema](https://github.com/PacificBiosciences/pbcommand/blob/master/pbcommand/schemas/resolved_tool_contract.avsc))\n\nThere are two principle use cases, first wrapping/calling python functions that have been defined in external python packages, or scripts. Second, creating a CLI tool that supports emitting tool contracts, running resolved tool contracts and complete argparse style CLI.\n\nExample from **pbcommand.cli.examples**\n\n```python\n\nimport sys\nimport logging\n\nfrom pbcommand.models import FileTypes\nfrom pbcommand.cli import registry_builder, registry_runner\n\nlog = logging.getLogger(__name__)\n\nregistry = registry_builder(\"pbcommand\", \"python -m pbcommand.cli.examples.dev_quick_hello_world \")\n\n\ndef _example_main(input_files, output_files, **kwargs):\n    # Simple Function that should imported from your library code\n    # write mock output files for testing purposes, otherwise the End-to-End test will fail\n    xs = output_files if isinstance(output_files, (list, tuple)) else [output_files]\n    for x in xs:\n        with open(x, 'w') as writer:\n            writer.write(\"Mock data\\n\")\n    return 0\n\n\n@registry(\"dev_qhello_world\", \"0.2.1\", FileTypes.FASTA, FileTypes.FASTA, nproc=1, options=dict(alpha=1234))\ndef run_rtc(rtc):\n    return _example_main(rtc.task.input_files[0], rtc.task.output_files[0], nproc=rtc.task.nproc)\n\n\n@registry(\"dev_fastq2fasta\", \"0.1.0\", FileTypes.FASTQ, FileTypes.FASTA)\ndef run_rtc(rtc):\n    return _example_main(rtc.task.input_files[0], rtc.task.output_files[0])\n\n\nif __name__ == '__main__':\n    sys.exit(registry_runner(registry, sys.argv[1:]))\n\n```\n\nA driver is the commandline interface that the workflow engine will call.\n\nThe driver will be called with \"${exe} /path/to/resolved_tool_contract.json\"\n\nThe tool contracts can be emitted to a directory and used in [pbsmrtpipe](https://github.com/PacificBiosciences/pbsmrtpipe).\n\n```bash\n$> python -m pbcommand.cli.examples.dev_quick_hello_world -o /path/to/my-tool-contracts\n```\n\n\nCreating a Full Commandline Tool with TC/RTC and argparse support\n-----------------------------------------------------------------\n\nThree Steps\n- define Parser\n- add running from argparse and running from Resolved ToolContract funcs to call your main\n- add call to driver\n\nImport or define your main function.\n\n```python\ndef run_my_main(fasta_in, fasta_out, min_length):\n    # do stuff. Main should return an int exit code\n    return 0\n```\n\nDefine a function that will add inputs, outputs and options to your parser.\n\n```python\nfrom pbcommand.models import FileTypes\n\n\ndef add_args_and_options(p):\n    # FileType, label, name, description\n    p.add_input_file_type(FileTypes.FASTA, \"fasta_in\", \"Fasta File\", \"PacBio Spec'ed fasta file\")\n    # File Type, label, name, description, default file name\n    p.add_output_file_type(FileTypes.FASTA, \"fasta_out\", \"Filtered Fasta file\", \"Filtered Fasta file\", \"filter.fasta\")\n    # Option id, label, default value, name, description\n    # for the argparse, the read-length will be translated to --read-length and (accessible via args.read_length)\n    p.add_int(\"pbcommand.task_options.dev_read_length\", \"read-length\", 25, \"Length filter\", \"Min Sequence Length filter\")\n    return p\n```\n\nDefine Parser\n\n```python\nfrom pbcommand.models import TaskTypes, SymbolTypes, get_pbparser\n\n\ndef get_contract_parser():\n    tool_id = \"example_namespace.tasks.my_id\"\n    version = \"0.1.0\"  # or reuse __version__\n    display_name = \"My Example Tool\"\n    # Number of processors to use, can also be SymbolTypes.MAX_NPROC\n    nproc = 1\n    # Log file, tmp dir, tmp file. See ResourceTypes in models, ResourceTypes.TMP_DIR\n    resource_types = ()\n    # Commandline exe to call \"{exe}\" /path/to/resolved-tool-contract.json\n    driver_exe = \"python -m pbcommand.cli.example.dev_app --resolved-tool-contract \"\n    desc = \"Dev app for Testing that supports emitting tool contracts\"\n    is_distributed = False \n    # set to True if you want your task to be submitted to the cluster manager (e.g., SGE) if \n    # one is provided to the workflow engine.\n    p = get_pbparser(tool_id, version, display_name, desc, driver_exe, is_distributed=is_distributed, nproc=nproc, resource_types=resource_types)\n    add_args_and_options(p)\n    return p\n```\n        \n\nDefine a Wrapping layer to call your main from both the tool contract and raw argparse IO layer\n\n```python\ndef _args_runner(args):\n    # this is the args from parser.parse_args()\n    # the properties of args are defined as \"labels\" in the add_args_and_options func.\n    return run_my_main(args.fasta_in, args.fasta_out, args.read_length)\n\n    \ndef _resolved_tool_contract_runner(resolved_tool_contract):\n    \"\"\"\n    :type resolved_tool_contract: pbcommand.models.ResolvedToolContract\"\"\"\n    rtc = resolved_tool_contract\n    # all options are referenced by globally namespaced id. This allows tools to use other tools options\n    # e.g., pbalign to use blasr defined options.\n    return run_my_main(rtc.task.input_files[0], rtc.task.outputs[0], rtc.task.options[\"pbcommand.task_options.dev_read_length\"])\n```\n    \n    \n    \n    \nAdd running layer\n\n```python\nimport sys\nimport logging\nfrom pbcommand.utils import setup_log\nfrom pbcommand.cli import pbparser_runner\n\nlog = logging.getLogger(__name__)\n\n\ndef main(argv=sys.argv):\n    # New interface that supports running resolved tool contracts\n    log.info(\"Starting {f} version {v} pbcommand example dev app\".format(f=__file__, v=\"0.1.0\"))\n    return pbparser_runner(argv[1:], \n                           get_contract_parser(), \n                           _args_runner, # argparse runner func\n                           _resolved_tool_contract_runner, # tool contract runner func\n                           log, # log instance\n                           setup_log # setup log func\n                           )\nif __name__ == '__main__':\n    sys.exit(main())\n```\n\nNow you can run your tool via the argparse standard interface as well as emitting a **Tool Contract** to stdout from the commandline interface.\n\n```sh\n> python -m 'pbcommand.cli.examples.dev_app' --emit-tool-contract\n```\n\nAnd you can run the tool from a **Resolved Tool Contract**\n\n```sh\n> python -m pbcommand.cli.example.dev_app --resolved-tool-contract /path/to/resolved_contract.json\n```\n\nSee the dev apps in [\"pbcommand.cli.examples\"](https://github.com/PacificBiosciences/pbcommand/blob/master/pbcommand/cli/examples/dev_app.py) for a complete application (They require pbcore to be installed).\n\nIn addition to TC/RTC support, there's a complete argparse support for the task options. 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