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rocoto

The uw mode for realizing and validating Rocoto XML documents.

.. literalinclude:: rocoto/help.cmd
   :language: text
   :emphasize-lines: 1

.. literalinclude:: rocoto/help.out
   :language: text

realize

In uw terminology, to realize a configuration file is to transform it from its raw form into its final, usable state. In the case of uw rocoto, that means transforming a structured UW YAML file into a :rocoto:`Rocoto XML<>` file. The structured YAML language required by UW closely follows the XML language defined by Rocoto.

More information about the structured UW YAML file for Rocoto can be found :any:`here<defining_a_workflow>`.

.. literalinclude:: rocoto/realize-help.cmd
   :language: text
   :emphasize-lines: 1

.. literalinclude:: rocoto/realize-help.out
   :language: text

Examples

The examples in this section use a UW YAML file rocoto.yaml with contents:

.. literalinclude:: rocoto/rocoto.yaml
   :language: yaml

  • To realize a UW YAML input file to stdout in Rocoto XML format:

    .. literalinclude:: rocoto/realize-exec-stdout.cmd
   :language: text
   :emphasize-lines: 1

    .. literalinclude:: rocoto/realize-exec-stdout.out
   :language: xml

  • To realize a UW YAML input file to a file named rocoto.xml:

    .. literalinclude:: rocoto/realize-exec-file.cmd
   :language: text
   :emphasize-lines: 2

    .. literalinclude:: rocoto/realize-exec-file.out
   :language: text

  • To read the UW YAML from stdin and write the XML to stdout:

    .. literalinclude:: rocoto/realize-exec-stdin-stdout.cmd
   :language: text
   :emphasize-lines: 1

    .. literalinclude:: rocoto/realize-exec-stdin-stdout.out
   :language: xml

  • To see verbose log output (Rocoto XML and some output elided for brevity):

    .. literalinclude:: rocoto/realize-exec-stdout-verbose.cmd
   :language: text
   :emphasize-lines: 2

    .. literalinclude:: rocoto/realize-exec-stdout-verbose.out
   :language: xml

validate

.. literalinclude:: rocoto/validate-help.cmd
   :language: text
   :emphasize-lines: 1

.. literalinclude:: rocoto/validate-help.out
   :language: text

Examples

The examples in this section use a Rocoto XML file rocoto-good.xml with contents:

.. literalinclude:: rocoto/rocoto-good.xml
   :language: xml

  • To validate XML from stdin:

    .. literalinclude:: rocoto/validate-good-stdin.cmd
   :language: text
   :emphasize-lines: 1

    .. literalinclude:: rocoto/validate-good-stdin.out
   :language: text

  • To validate XML from file rocoto-good.xml:

    .. literalinclude:: rocoto/validate-good-file.cmd
   :language: text
   :emphasize-lines: 1

    .. literalinclude:: rocoto/validate-good-file.out
   :language: text

  • When the XML is invalid:

    In this example, the <command> line was removed from rocoto-good.xml to create rocoto-bad.xml.

    .. literalinclude:: rocoto/validate-bad-file.cmd
   :language: text
   :emphasize-lines: 1

    .. literalinclude:: rocoto/validate-bad-file.out
   :language: text

    To decode the three ERROR:RELAXNGV messages, it is easiest to read from the bottom up. They say:

    • At line 9 column 0 (i.e. <string>:9:0), the element (i.e. <task>) failed to validate.
    • The sequence of interleaved elements under <task> was invalid.
    • A <command> element was expected, but it wasn't found.