Metadata-Version: 2.1
Name: cwl-utils
Version: 0.22
Summary: UNKNOWN
Home-page: https://github.com/common-workflow-language/cwl-utils
Author: Common workflow language working group
Author-email: common-workflow-language@googlegroups.com
License: Apache 2.0
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        cwl-utils
        ---------
        
        Python Utilities and Autogenerated Classes for loading and parsing `CWL
        v1.0 <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_0.py>`__,
        `CWL
        v1.1 <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_1.py>`__,
        and `CWL
        v1.2 <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_2.py>`__
        documents.
        
        Requires Python 3.6+
        
        Installation
        ------------
        
        ::
        
           pip3 install cwl-utils
        
        To install from source::
        
           git clone https://github.com/common-workflow-language/cwl-utils.git
           cd cwl-utils
           pip3 install .
        
        Usage
        -----
        
        Pull the all referenced software container images
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ``cwl-docker-extract`` is useful to cache or pre-pull all software
        container images referenced in a CWL CommandLineTool or CWL Workflow
        (including all referenced CommandLineTools and sub-Workflows and so on).
        
        The default behaviour is to use the Docker engine to download and save
        the software container images in Docker format.
        
        .. code:: bash
        
           cwl-docker-extract DIRECTORY path_to_my_workflow.cwl
        
        Or you can use the Singularity software container engine to download and
        save the software container images and convert them to the Singularity
        format at the same time.
        
        .. code:: bash
        
           cwl-docker-extract --singularity DIRECTORY path_to_my_workflow.cwl
        
        
        Print all referenced software packages
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ``cwl-cite-extract`` prints all software packages found (recursively) in the
        specified CWL document.
        
        Currently the package name and any listed specs and version field are printed
        for all ``SoftwareRequirement`` s found.
        
        .. code:: bash
        
           cwl-cite-extract path_to_my_workflow.cwl
        
        
        Replace CWL Expressions with concrete steps
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ``cwl-expression-refactor`` refactors CWL documents so that any CWL Expression
        evaluations are separate steps (either CWL ExpressionTools or CWL CommandLineTools.)
        This allows execution by CWL engines that do not want to support inline expression
        evaluation outside of concrete steps, or do not want to directly support CWL's
        optional ``InlineJavascriptRequirement`` at all.
        
        
        .. code:: bash
        
           cwl-expression-refactor directory/path/to/save/outputs path_to_my_workflow.cwl [more_workflows.cwl]
        
        Split a packed CWL document
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ``cwl-graph-split`` splits a packed CWL document file into multiple files.
        
        Packed CWL documents use the $graph construct to contain multiple CWL Process
        objects (Workflow, CommandLineTool, ExpressionTool, Operation). Typically
        packed CWL documents contain a CWL Workflow under the name "main" and the
        workflow steps (including any sub-workflows).
        
        .. code:: bash
        
           cwl-graph-split --outdir optional/directory/path/to/save/outputs path_to_my_workflow.cwl
        
        Normalize a CWL document
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        ``cwl-normalizer`` normalizes one or more CWL document so that for each document,
        a JSON format CWL document is produces with it and all of its dependencies packed
        together, upgrading to CWL v1.2, as needed. Can optionally refactor CWL
        Expressions into separate steps in the manner of cwl-expression-refactor.
        
        .. code:: bash
        
           cwl-normalizer directory/path/to/save/outputs path_to_my_workflow.cwl [more_workflows.cwl]
        
        
        Using the CWL Parsers
        ~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
           from pathlib import Path
           from ruamel import yaml
           import sys
        
           from cwl_utils.parser import load_document_by_uri, save
        
           # File Input - This is the only thing you will need to adjust or take in as an input to your function:
           cwl_file = Path("testdata/md5sum.cwl")  # or a plain string works as well
        
           # Import CWL Object
           cwl_obj = load_document_by_uri(cwl_file)
        
           # View CWL Object
           print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))
        
           # Export CWL Object into a built-in typed object
           saved_obj = save(cwl_obj)
           print(f"Export of the loaded CWL object: {saved_obj}.")
        
        Development
        -----------
        
        Regenerate parsers
        ~~~~~~~~~~~~~~~~~~
        
        To regenerate install the ``schema_salad`` package and run:
        
        ``cwl_utils/parser/cwl_v1_0.py`` was created via
        ``schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/CommonWorkflowLanguage.yml --codegen-parser-info "org.w3id.cwl.v1_0" > cwl_utils/parser/cwl_v1_0.py``
        
        ``cwl_utils/parser/cwl_v1_1.py`` was created via
        ``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/CommonWorkflowLanguage.yml --codegen-parser-info "org.w3id.cwl.v1_1" > cwl_utils/parser/cwl_v1_1.py``
        
        ``cwl_utils/parser/cwl_v1_2.py`` was created via
        ``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/CommonWorkflowLanguage.yml --codegen-parser-info "org.w3id.cwl.v1_2" > cwl_utils/parser/cwl_v1_2.py``
        
        Release
        ~~~~~~~
        
        To release CWLUtils, bump the version in ``cwl_utils/__meta__.py``, and
        tag that commit with the new version. The
        `gh-action-pypi-publish <https://github.com/pypa/gh-action-pypi-publish>`__
        should release that tag.
        
        
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Typing :: Typed
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: pretty
