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    "info": {
        "author": "Michael Franklin",
        "author_email": "michael.franklin@petermac.org",
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        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
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            "Topic :: Scientific/Engineering"
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        "description": "# python-wdlgen\n\n[![Build Status](https://travis-ci.org/illusional/python-wdlgen.svg?branch=master)](https://travis-ci.org/illusional/python-wdlgen)\n[![PyPI version](https://badge.fury.io/py/illusional.wdlgen.svg)](https://badge.fury.io/py/illusional.wdlgen)\n \n[Workflow Description Language](http://www.openwdl.org) is way to describe tasks and workflows in a \"_human readable and writable way_\". It was initially developed and offered by [Broad Institute](https://software.broadinstitute.org/) to be paired with their workflow engine [Cromwell](https://cromwell.readthedocs.io/en/stable/), however it has since been made open source with other engines such as [Toil](http://toil.readthedocs.io/en/3.14.0/running/wdl.html) and [DNAnexus\\*](https://github.com/dnanexus/dxWDL).\n\n\n### WARNING\n\nThis module now only generates developmental WDL, this includes Directories and wrapping all inputs in an input block. \nTo use this generated WDL, you must use a version of **Cromwell higher than 37**. \n\nThis module automatically includes `version development` in the Workflow and Task outputs. \nThe guides below may not reflect the current version of this repository, but will be updated soon.\n\nThis syntax is based on the [Developmental Workflow Description Language specification](https://github.com/openwdl/wdl/blob/master/versions/development/SPEC.md).\n\n___\n\n## Motiviation\n\nI needed an easy way to generate some _BASIC_ WDL through some in memory objects, and I was using ([a fork](https://github.com/illusional/python-cwlgen) of) [common-workflow-language/python-cwlgen](https://github.com/common-workflow-language/python-cwlgen), I figured I could open this up to see what use it has.\n\n## Installation\n\n```\npip install illusional.wdlgen\n```\n\n## General support\n\nThis software is provided as-is, without warranty of any kind ... and so on.\n\nIt's a pretty dumb wrapper that uses string interpolation to generate the structure. It wouldn't handle automatically escaping illegal characters.\n\nGenerally it supports:\n\n- Types - All types are represented as a `WdlType`, which can either be a [`PrimitiveType`](https://github.com/openwdl/wdl/blob/master/versions/1.0/SPEC.md#types), or an `ArrayType` (see [goal](#goals)). Also supports the postfix quantifiers.\n\n- Workflow creation (`wdlgen.Workflow`)\n\t- manual imports (`wdlgen.Workflow.WorkflowImport`)\n\t- inputs (`wdlgen.Input`)\n\t- outputs (`wdlgen.Output`)\n\t- calls:\n\t\t- general call (`wdlgen.WorkflowCall`)\n\t\t- scatter (`wdlgen.WorkflowScatter(WorkflowCall[])`)\n\n- Task creation (`wdlgen.Task`) - This is based similar to how [CWL constructs its commands](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool).\n\t- inputs: `wdlgen.Input`\n\t- outputs: `wdlgen.Output`\n\t- runtime: `wdlgen.Task.Runtime`\n\t- command: `wdlgen.Task.Command`\n\t\t- arguments: `wdlgen.Task.Command.Argument`\n\t\t- inputs: `wdlgen.Task.Command.Input`\n\n## How to use\n\nThis will give you a _brief_ overview on how to _use_ python-wdlgen. Goals are to improve the write a proper documentation spec, but if you have a moderate understanding of workflows in either CWL or WDL, this code will hopefully be fairly intuitive.\n\nEvery class inherits from a `WDLBase` which means it must have a `get_string()` method which returns the string representation of the class, calling this on any children it may have.\n\n### Types\n\nAll types are represented as a WDLType, which has a parse method. It's a little overkill in some cases, but makes managing attributes a bit easier.\n\n```python\nparsed_string = wdlgen.WdlType.parse(\"String\")\t# WdlType<PrimitiveType<String>>\nparsed_op_str = wdlgen.WdlType.parse(\"String?\") # WdlType<PrimtiveType<String>>\nparsed_array = wdlgen.WDLType.parse(\"File[]\")\t# WdlType<ArrayType<File>>\nparsed_ar_oq = wdlgen.WdlType(parse(\"Int?[]+\"))\t# WdlType<ArrayType<Int?> (+)>\n```\n\nYou can also construct these manually:\n```python\nparsed_string = WdlType(PrimitiveType(\"String\"))\nparsed_op_str = WdlType(PrimtiveType(\"String\", optional=True))\nparsed_array = WdlType(ArrayType(WdlType(PrimitiveType(\"File\"))))\nparsed_ar_q = WdlType(ArrayType(WdlType(PrimitiveType(\"Int\"), optional=True), requires_multiple=True))\n```\n\n### Input / Output\nInput: `wdlgen.Input(data_type: WdlType, name: str, expression: str = None)`\n\nOutput: `wdlgen.Output(data_type: WdlType, name: str, expression: str = None)`\n\nboth of which output something like:\n\t`{WdlType} {name} [= {expression}]`\n\n### Task\n\nA task is a collection of Inputs, Outputs and a Command that are identified by a _name_. Inputs and Outputs are as above. Note that you can use functions such as `stdout()` or other for the expression.\n\n> If you don't want to play by these rules, don't include any inputs or outputs and just provide your whole string to the initializer for command.\n\n```python\nt = wdlgen.Task(\"task_name\")\nt.inputs.append(wdlgen.Input(wdlgen.WdlType.parse(\"String\"), \"taskGreeting\"))\n# command in next section\nt.outputs.append(wdlgen.Output(wdlgen.WdlType.parse(\"File\"), \"standardOut\", \"stdout()\"))\n```\n\n#### Command\n\nThe command is broken up similar to how CWL breaks its command generation up, by itself it has a _base command_. Each component has a corresponding input (else use the `wdlgen.Task.Command.Argument` class), optionality, position, prefix (and whether the value should be separated from prefix; think `-o {val}` vs `outputDir={val}`) and potentially a default.\n\nConstruct a command like the following:\n```python\ncommand = wdlgen.Task.Command(\"echo\")\ncommand.inputs.append(wdlgen.Task.Command.CommandInput(\"taskGreeting\", optional=False, position=None, prefix=\"-a\", separate_value_from_prefix=True, default=None))\ncommand.inputs.append(wdlgen.Task.Command.CommandInput(\"otherInput\", optional=True, position=2, prefix=\"optional-param=\", separate_value_from_prefix=False, default=None))\n\n# t is the task\nt.command = command\nprint(command.get_string())\n```\n\nThis will result in the following WDL command:\n```bash\necho \\\n  -a ${taskGreeting} \\\n  ${\"optional-param=\" + otherInput}\n```\n\n#### Task output:\n\nThe combination of the task and command outputs:\n```wdl\nversion development\n\ntask task_name {\n  input {\n    String taskGreeting\n  }\n  command {\n    echo \\\n      -a ${taskGreeting} \\\n      ${\"optional-param=\" + otherInput}\n  }\n\n  output {\n    File standardOut = stdout()\n  }\n}\n```\n\n### Workflow\n\nYou should have moderate idea of the structure of WDL as there's no cleverness or abstraction done anywhere. Beware: there's also no checking attributes (to see if your `inputMap` actually corresponds to inputs).\n\nThe structure of a workflow is m\n\n```python\nw = wdlgen.Workflow(\"workflow_name\")\n\nw.imports.append(wdlgen.Workflow.WorkflowImport(\"tool_file\", \"\"))\nw.inputs.append(wdlgen.WdlType.parse(\"String\"), wdlgen.Input(\"inputGreeting\"))\n\n\ninputs_map = {\"taskGreeting\": \"inputGreeting\"}\nw.calls.append(wdlgen.WorkflowCall(\"Q.namspaced_task_identifier\", \"task_alias\", inputs_map))\nw.outputs.append(wdlgen.Output(wdlgen.WdlType.parse(\"File\"), \"standardOut\", \"task_alias.standardOut\")\n```\n\nWhich outputs:\n```wdl\nversion development\n\nimport \"tools/tool_file.wdl\"\n\nworkflow workflow_name {\n  input { \n    String inputGreeting\n  }\n  call Q.namspaced_task_identifier as task_alias {\n    input:\n      taskGreeting=inputGreeting\n  }\n  output {\n    File standardOut = task_alias.standardOut\n  }\n}\n```\n\n\n## Known limitations\n\nI'm not a fan of the string interpolation generation of WDL that this module does. I think trying to build an [Abstract syntax tree](https://en.wikipedia.org/wiki/Abstract_syntax_tree) and then there should be something that convert that into the DSL that WDL uses.\n\nYou could also cause syntax errors in generated WDL by providing illegal characters. \n\n## Goals\n\n- Improve code-level documentation.\n- Increase the testing coverage + quality of unit tests.\n- Better represent the WDL spec.\n- ~~Find an easier distribution / release method - such as PIP.~~\n- ~~Automate testing and delivery through TravisCI / CircleCI or similar.~~\n- Validate each value by [WDL's language specifications](https://github.com/openwdl/wdl/blob/master/versions/1.0/SPEC.md#language-specification).\n- Add support for structs\n\n### Long goals\n- Write a documentation site.\n- Make classes convert into AST and then into DSL.\n\n## Issues and Pull Requests\nFeel free to log issues and make pull requests. I make no guarantee to the existence or timeliness of replies.\n\n\nLinks:\n\n- WDL description: https://github.com/openwdl/wdl/blob/master/versions/1.0/SPEC.md",
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