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Merge pull request #15825 from bernt-matthias/validation_metadata

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Add ability to assert metadata properties on input dataset parameters
This commit is contained in:
Marius van den Beek
2023-07-29 12:00:32 +02:00
committed by GitHub
parent 7cdb480595 6bd654cd20
commit fa64fc646d
7 changed files with 225 additions and 5 deletions
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test/functional/tools/metadata_check_eq.xml
+58
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@@ -0,0 +1,58 @@
<!-- functional tool test for the dataset_metadata_equal validator -->
<tool id="metadata_check_eq" name="metadata_check_eq" version="1.0.0" profile="23.1">
<description>Tests whether asserting metadata equals something works.</description>
<command><![CDATA[
#if $input or $input_negate
echo "sucess" >> '$output' &&
#end if
#if $input
echo "columns $input.metadata.columns" >> '$output' &&
echo "column_names $input.metadata.column_names" >> '$output'
#else
echo "columns $input_negate.metadata.columns" >> '$output' &&
echo "column_names $input_negate.metadata.column_names" >> '$output'
#end if
]]></command>
<inputs>
<param name="input" type="data" optional="true" multiple="false" format="tabular,csv">
<validator type="dataset_metadata_equal" metadata_name="columns" value_json="12" />
<validator type="dataset_metadata_equal" metadata_name="column_names" value_json="[&quot;Transaction_date&quot; ,&quot;Product&quot;, &quot;Price&quot;, &quot;Payment_Type&quot;, &quot;Name&quot;, &quot;City&quot;, &quot;State&quot;, &quot;Country&quot;, &quot;Account_Created&quot;, &quot;Last_Login&quot;, &quot;Latitude&quot;, &quot;Longitude&quot;]" />
</param>
<param name="input_negate" type="data" optional="true" multiple="false" format="tabular,csv">
<validator type="dataset_metadata_equal" metadata_name="columns" negate="true" value_json="12"/>
<validator type="dataset_metadata_equal" metadata_name="column_names" negate="true" value_json="[&quot;Transaction_date&quot; ,&quot;Product&quot;, &quot;Price&quot;, &quot;Payment_Type&quot;, &quot;Name&quot;, &quot;City&quot;, &quot;State&quot;, &quot;Country&quot;, &quot;Account_Created&quot;, &quot;Last_Login&quot;, &quot;Latitude&quot;, &quot;Longitude&quot;]" />
</param>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test expect_failure="true">
<param name="input" value="1.tabular" ftype="tabular" />
</test>
<test>
<param name="input" value="1.csv" ftype="csv" />
<output name="output">
<assert_contents>
<has_text text="sucess"/>
<has_text text="columns 12"/>
<has_text text="Transaction_date"/>
</assert_contents>
</output>
</test>
<test>
<param name="input_negate" value="1.tabular" ftype="tabular" />
<output name="output">
<assert_contents>
<has_text text="sucess"/>
<has_text text="columns 3"/>
<!-- tabular has no column names -->
<has_text text="Transaction_date" negate="true"/>
</assert_contents>
</output>
</test>
<test expect_failure="true">
<param name="input_negate" value="1.csv" ftype="csv" />
</test>
</tests>
</tool>
test/functional/tools/sample_tool_conf.xml
+1
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@@ -72,6 +72,7 @@
<tool file="metadata_bcf.xml" />
<tool file="metadata_bed.xml" />
<tool file="metadata_biom1.xml" />
<tool file="metadata_check_eq.xml" />
<tool file="metadata_column_names.xml" />
<tool file="strict_shell.xml" />
<tool file="strict_shell_default_off.xml" />