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[23.0] Allow duplicate labels in linter if outputs contain filters #15933

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merged 4 commits into from
Jul 25, 2023
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[23.0] Allow duplicate labels in linter if outputs contain filters #15933

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af797d9
fix linter: duplicated label check
bernt-matthias Apr 13, 2023
2775005
make duplicated label a warning
bernt-matthias May 9, 2023
c684e0b
also warn in case of a filter
bernt-matthias May 9, 2023
da8fc06
more black
bernt-matthias Jul 25, 2023
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9 changes: 8 additions & 1 deletion lib/galaxy/tool_util/linters/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,14 @@ def lint_output(tool_xml, lint_ctx):

label = output.attrib.get("label", "${tool.name} on ${on_string}")
if label in labels:
lint_ctx.error(f"Tool output [{name}] uses duplicated label '{label}'", node=output)
filter_node = output.find(".//filter")
if filter_node is not None:
lint_ctx.warn(
f"Tool output [{name}] uses duplicated label '{label}', double check if filters imply disjoint cases",
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What case triggered this ?

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Just had it here: galaxyproject/tools-iuc#5291 .. but found it acceptable in this case to use different labels. Can't remember a really good example.

Point is that we (probably?) need to allow for the possibility to have two outputs that are never outputed together (i.e. they use disjoint filters). Then it might OK to allow for the same label. For instance if from_work_dir needs to be different when a flag is set or not set.

Since it seemed pretty hard (or impossible) to check the filters if they are disjoint I thought that its best to just check if there is a filter.

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Then it might OK to allow for the same label. For instance if from_work_dir needs to be different when a flag is set or not set.

I'd move the output to the right place or use the same output name, which is much friendlier for predicting what outputs will be generated. I think a warning is just the right level here.

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If we make this a warning then the outcome (IUC wise) would be the same (galaxyproject/tools-iuc#5260), ie. the PR workflow would fail.

But, given your idea to skip linting for the push to master/main we could just raise the fail level to error for the merge.

Just tell me your preference (warning / info) and I will change it.

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@mvdbeek mvdbeek May 9, 2023 •
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warning is the right level IMO, galaxyproject/tools-iuc#5291 was improved by the new label and I think in many / all instances there are tweaks that would make the tool better as in either more userfriendly or more predictable

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How about this example @mvdbeek: galaxyproteomics/tools-galaxyp#721 ?

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I'm sorry, can you point out what I should look at there ?

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There is an output dataset and an output collection which are mutually exclusive. They have the same name which I find acceptable in this case.

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ok, so you're also saying it should be a warning ?

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Yes, according to my intuition of the meaning of "warning".

node=output,
)
else:
lint_ctx.warn(f"Tool output [{name}] uses duplicated label '{label}'", node=output)
labels.add(label)

format_set = False
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18 changes: 14 additions & 4 deletions test/unit/tool_util/test_tool_linters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -566,6 +566,12 @@
<outputs>
<data name="valid_name" format="fasta"/>
<data name="valid_name" format="fasta"/>
<data name="another_valid_name" format="fasta" label="same label may be OK if there is a filter">
<filter>a condition</filter>
</data>
<data name="yet_another_valid_name" format="fasta" label="same label may be OK if there is a filter">
<filter>another condition</filter>
</data>
</outputs>
</tool>
"""
Expand Down Expand Up @@ -1492,13 +1498,17 @@ def test_outputs_discover_tool_provided_metadata(lint_ctx):
def test_outputs_duplicated_name_label(lint_ctx):
tool_source = get_xml_tool_source(OUTPUTS_DUPLICATED_NAME_LABEL)
run_lint(lint_ctx, outputs.lint_output, tool_source)
assert "2 outputs found." in lint_ctx.info_messages
assert "4 outputs found." in lint_ctx.info_messages
assert len(lint_ctx.info_messages) == 1
assert not lint_ctx.valid_messages
assert not lint_ctx.warn_messages
assert len(lint_ctx.warn_messages) == 2
assert "Tool output [valid_name] uses duplicated label '${tool.name} on ${on_string}'" in lint_ctx.warn_messages
assert (
"Tool output [yet_another_valid_name] uses duplicated label 'same label may be OK if there is a filter', double check if filters imply disjoint cases"
in lint_ctx.warn_messages
)
assert "Tool output [valid_name] has duplicated name" in lint_ctx.error_messages
assert "Tool output [valid_name] uses duplicated label '${tool.name} on ${on_string}'" in lint_ctx.error_messages
assert len(lint_ctx.error_messages) == 2
assert len(lint_ctx.error_messages) == 1


def test_stdio_default_for_default_profile(lint_ctx):
Expand Down
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