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Fix emphasize-lines with runcmd #280

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Merged
merged 4 commits into from
Oct 12, 2022
Merged

Fix emphasize-lines with runcmd #280

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a067825
Fix emphasize-lines with runcmd
kinow Oct 11, 2022
804c3cc
Update emphasize-lines in inputs.md
kinow Oct 11, 2022
8a15eba
Fix emphasize lines for the troubleshooting file
kinow Oct 11, 2022
4fd8724
tweak line emphasis
mr-c Oct 12, 2022
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13 changes: 12 additions & 1 deletion cwl/sphinx/runcmd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,9 +169,20 @@ def run(self):
r = match.group("replacement").replace("\\", "")
output = re.sub(p, r, output)

# Note: Sphinx's CodeBlock directive expects an array of command-line
# output lines: https://github.com/sphinx-doc/sphinx/blob/c51a88da8b7b40e8d8cbdb1fce85ca2346b2b59a/sphinx/directives/code.py#L114
# But the runcmd original code was simply wrapping a string
# containing \n in the text as a one-element array, e.g.
# ["cwltool --debug ...\ncwltool Version..."].
# That caused the output to be correctly rendered, but the
# emphasize-lines directive parameter to fail if the lines were
# anything greater than 0 (as the self.content array had 1 elem).
# See: https://github.com/common-workflow-language/user_guide/issues/269
output = output.split("\n")

# Set up our arguments to run the CodeBlock parent run function
self.arguments[0] = syntax
self.content = [output]
self.content = output
node = super(RunCmdDirective, self).run()

return node
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7 changes: 3 additions & 4 deletions src/topics/inputs.md
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Expand Up @@ -222,7 +222,7 @@ In the first example, you can't provide `itemA` without also providing `itemB`.

```{runcmd} cwltool record.cwl record-job2.yml
:working-directory: src/_includes/cwl/inputs
:emphasize-lines: 3, 9-10, 24
:emphasize-lines: 4, 10-11, 23
````

```{code-block} console
Expand All @@ -241,7 +241,7 @@ matching item (`itemC`) is added to the command line and remaining item (`itemD`

```{runcmd} cwltool record.cwl record-job3.yml
:working-directory: src/_includes/cwl/inputs
:emphasize-lines: 9-10, 24
:emphasize-lines: 9-10, 22
````

```{code-block} console
Expand All @@ -266,7 +266,6 @@ that accepts `null` (i.e. no value provided), or any value from an enum.
:language: cwl
:caption: "`exclusive-parameter-expressions.cwl`"
:name: exclusive-parameter-expressions.cwl
:emphasize-lines: 7, 21-23
```

Note how the JavaScript expression uses the value of the exclusive input parameter
Expand All @@ -284,7 +283,7 @@ output field (a `string`), resulting in failure when running your workflow.

```{runcmd} cwltool exclusive-parameter-expressions.cwl
:working-directory: src/_includes/cwl/inputs
:emphasize-lines: 6-10
:emphasize-lines: 5-10
```

To correct it, you must remember to use an or operator in your JavaScript expression
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4 changes: 2 additions & 2 deletions src/topics/troubleshooting.md
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Expand Up @@ -29,7 +29,7 @@ create the directory for you if it does not exist already):

```{runcmd} cwltool --cachedir /tmp/cachedir/ troubleshooting-wf1.cwl
:working-directory: src/_includes/cwl/troubleshooting
:emphasize-lines: 12-14, 19-21
:emphasize-lines: 13-15, 18-20
```

The workflow is in the `permanentFail` status due to `step_b` failing to execute the
Expand All @@ -53,7 +53,7 @@ Also note that the status of `step_b` is now of success.

```{runcmd} cwltool --cachedir /tmp/cachedir/ troubleshooting-wf1-stepb-fixed.cwl
:working-directory: src/_includes/cwl/troubleshooting
:emphasize-lines: 12, 16-18
:emphasize-lines: 12-16
```

In this example the workflow step `step_a` was not re-evaluated as it had been cached, and
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