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Apply metadata setter for default to conditionals #7197

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Apply metadata setter for default to conditionals #7197

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59c9687
Apply metadata setter for default to conditionals
pvanheus Jan 9, 2019
a8729fa
* Add test, fix W293 whitespace lint warning
pvanheus Jan 10, 2019
e55cc42
fix formatting
pvanheus Feb 7, 2019
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17 changes: 16 additions & 1 deletion lib/galaxy/tools/actions/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -743,10 +743,25 @@ def set_metadata_defaults(self, output, dataset, tool, on_text, trans, incoming,
<action name="column_names" type="metadata" default="${','.join([input.name for input in $individual_inputs ])}" />
</actions>
</data>

or

<actions>
<conditional name="format">
<when value="something_good">
<action type="metadata" name="column_names" default="one,two,three" />
</when>
</conditional>
</actions>
"""
if output.actions:
action_list = output.actions.actions
for action in output.actions.actions:
if action.tag == "metadata" and action.default:
if action.tag == "conditional":
for case in action.cases:
action_list.extend(case.actions)
for action in action_list:
if action.tag == "metadata" and hasattr(action, "default") and action.default:
metadata_new_value = fill_template(action.default, context=params).split(",")
dataset.metadata.__setattr__(str(action.name), metadata_new_value)

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30 changes: 30 additions & 0 deletions test/functional/tools/metadata_column_names_conditional.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
<tool id="metadata_columns_conditional" name="metadata_columns_conditional" version="1.0.0">
<description>Tests whether metadata is being set correctly.</description>
<command><![CDATA[
cp '$input' '$output'
]]></command>
<inputs>
<param name="input" type="data" multiple="false" />
<param name="variable" type="integer" value="1" size="1" />
</inputs>
<outputs>
<data format="tabular" name="output">
<actions>
<conditional name="variable">
<when value="1">
<action name="column_names" type="metadata" default="First,${input.name}" />
</when>
</conditional>
</actions>
</data>
</outputs>
<tests>
<test>
<param name="input" value="2.tabular" />
<param name="variable" value="1" />
<output name="output">
<metadata name="column_names" value="First,2.tabular"/>
</output>
</test>
</tests>
</tool>
1 change: 1 addition & 0 deletions test/functional/tools/samples_tool_conf.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
<tool file="metadata_bcf.xml" />
<tool file="metadata_biom1.xml" />
<tool file="metadata_column_names.xml" />
<tool file="metadata_column_names_conditional.xml" />
<tool file="strict_shell.xml" />
<tool file="strict_shell_default_off.xml" />
<tool file="detect_errors_aggressive.xml" />
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