Skip to content

Commit

Permalink
Merge pull request #18605 from bernt-matthias/xsd-data-action
Browse files Browse the repository at this point in the history 
[24.1] xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion
  • Loading branch information
@mvdbeek
mvdbeek authored Jul 31, 2024
2 parents fe6d2e3 + 262b4b6 commit 745913d
Show file tree
Hide file tree
Showing 4 changed files with 100 additions and 69 deletions.
2 changes: 1 addition & 1 deletion doc/schema_template.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ $tag:tool|outputs|data|actions|action://complexType[@name='Action']
$tag:tool|outputs|data|actions|action|option://complexType[@name='ActionsOption']
$tag:tool|outputs|data|discover_datasets://complexType[@name='OutputDiscoverDatasets']
$tag:tool|outputs|collection://complexType[@name='OutputCollection']
$tag:tool|outputs|collection|data://complexType[@name='OutputCollectionDataElement']
$tag:tool|outputs|collection|data://complexType[@name='OutputCollectionData']
$tag:tool|outputs|collection|filter://complexType[@name='OutputFilter']
$tag:tool|outputs|collection|discover_datasets://complexType[@name='OutputCollectionDiscoverDatasets']
$tag:tool|tests://complexType[@name='Tests']
Expand Down
99 changes: 34 additions & 65 deletions lib/galaxy/tool_util/xsd/galaxy.xsd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5827,15 +5827,24 @@ on Human (hg18)``.
<xs:attributeGroup ref="OutputDataAttributes"/>
</xs:complexType>

<!-- Allowed tags included in collection-data -->
<xs:group name="OutputCollectionDataElement">
<xs:choice>
<xs:element name="actions" type="Actions" />
<xs:element name="change_format" type="ChangeFormat" />
</xs:choice>
</xs:group>

<!-- Allowed tags included in collection -->
<xs:group name="OutputCollectionElement">
<xs:choice>
<xs:element name="data" type="OutputCollectionDataElement" />
<xs:element name="data" type="OutputCollectionData" />
<xs:element name="discover_datasets" type="OutputCollectionDiscoverDatasets" />
<xs:element name="filter" type="OutputFilter" />
</xs:choice>
</xs:group>

<xs:complexType name="OutputCollectionDataElement">
<xs:complexType name="OutputCollectionData">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Expand All @@ -5844,7 +5853,7 @@ define the elements of a collection statically. See also [Planemo's documentatio
]]></xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
<xs:group ref="OutputCollectionDataElement" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
<xs:attributeGroup ref="OutputCommon" />
<xs:attributeGroup ref="OutputDataAttributes" />
Expand Down Expand Up @@ -6002,23 +6011,7 @@ Therefore a filter for such a variable looks like the following example.
</xs:simpleContent>
</xs:complexType>

<xs:complexType name="OutputDiscoverDatasets">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Describe datasets to dynamically collect after the job complete.
There are many simple tools with examples of this element distributed with
Galaxy, including:
* [multi_output.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output.xml)
* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_assign_primary.xml)
* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_configured.xml)
More information can be found on Planemo's documentation for
[multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
]]></xs:documentation>
</xs:annotation>
<xs:attributeGroup name="OutputDiscoverDatasetsCommon">
<xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort must not be set.</xs:documentation>
Expand Down Expand Up @@ -6069,6 +6062,26 @@ More information can be found on Planemo's documentation for
<xs:documentation xml:lang="en">Indication if this dataset is visible in output history. This defaults to ``false``, but probably shouldn't - be sure to set to ``true`` if that is your intention.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:attributeGroup>

<xs:complexType name="OutputDiscoverDatasets">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Describe datasets to dynamically collect after the job complete.
There are many simple tools with examples of this element distributed with
Galaxy, including:
* [multi_output.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output.xml)
* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_assign_primary.xml)
* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_configured.xml)
More information can be found on Planemo's documentation for
[multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
]]></xs:documentation>
</xs:annotation>
<xs:attributeGroup ref="OutputDiscoverDatasetsCommon"/>
<xs:attribute name="assign_primary_output" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Replace the primary dataset described by the parameter ``data`` parameter with the first output discovered.</xs:documentation>
Expand All @@ -6092,51 +6105,7 @@ Galaxy, including:
]]></xs:documentation>
</xs:annotation>
<xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort_by must not be set.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pattern" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Regular expression used to find filenames and parse dynamic properties.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="directory" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Directory (relative to working directory) to search for files.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="recurse" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicates that the specified directory should be searched recursively for matching files.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="match_relative_path" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicates that the entire path of the discovered dataset relative to the specified directory should be available for matching patterns.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="format" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``ext``).</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ext" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``format``).</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="sort_by" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">A string `[reverse_][SORT_COMP_]SORTBY` describing the desired sort order of the collection elements. `SORTBY` can be `filename`, `name`, `designation`, `dbkey` and the optional `SORT_COMP` can be either `lexical` or `numeric`. Default is lexical sorting by filename.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="visible" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indication if this dataset is visible in the history. This defaults to ``false``, but probably shouldn't - be sure to set to ``true`` if that is your intention.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attributeGroup ref="OutputDiscoverDatasetsCommon"/>
</xs:complexType>
<xs:complexType name="Actions">
<xs:annotation>
Expand Down
44 changes: 42 additions & 2 deletions test/functional/tools/collection_creates_pair_format.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,28 @@
</command>
<inputs>
<param name="input1" type="data" label="Input" help="Input to be split." />
<param name="out_format" type="select" label="Output data type">
<option value="">do not change</option>
<option value="interval">interval</option>
</param>
</inputs>
<outputs>
<!-- format is specified separately for the elements, i.e. default format (fasta in this case) is ignored -->
<collection name="paired_output" format="fasta" type="paired" label="Split Pair">
<data name="forward" format="txt" />
<data name="forward" format="txt">
<change_format>
<when input="out_format" value="interval" format="interval" />
</change_format>
</data>
<data name="reverse" format_source="input1" from_work_dir="reverse.txt" />
</collection>
<!-- no format is specified separately for the elements, i.e. default format (fasta in this case) is used -->
<collection name="paired_output_default_format" format="fasta" type="paired" label="Split Pair">
<data name="forward" />
<data name="forward">
<change_format>
<when input="out_format" value="interval" format="interval" />
</change_format>
</data>
<data name="reverse" from_work_dir="reverse.txt" />
</collection>
</outputs>
Expand Down Expand Up @@ -48,5 +60,33 @@
</element>
</output_collection>
</test>
<test>
<param name="input1" ftype="bed" value="simple_lines_interleaved.txt" />
<param name="out_format" value="interval"/>
<output_collection name="paired_output" type="paired">
<element name="forward" ftype="interval">
<assert_contents>
<has_text_matching expression="^This is a line of text.\nThis is a line of text.\n$" />
</assert_contents>
</element>
<element name="reverse" ftype="bed">
<assert_contents>
<has_text_matching expression="^This is a different line of text.\nThis is a different line of text.\n$" />
</assert_contents>
</element>
</output_collection>
<output_collection name="paired_output_default_format" type="paired">
<element name="forward" ftype="interval">
<assert_contents>
<has_text_matching expression="^This is a line of text.\nThis is a line of text.\n$" />
</assert_contents>
</element>
<element name="reverse" ftype="fasta">
<assert_contents>
<has_text_matching expression="^This is a different line of text.\nThis is a different line of text.\n$" />
</assert_contents>
</element>
</output_collection>
</test>
</tests>
</tool>
24 changes: 23 additions & 1 deletion test/functional/tools/metadata_column_names.xml
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
<tool id="metadata_columns" name="metadata_columns" version="1.0.0">
<description>Tests whether metadata is being set correctly.</description>
<command><![CDATA[
cp '$input' '$output'
cp '$input' '$output';
cp '$input' '$paired_output.forward' ;
cp '$input' '$paired_output.reverse' ;
]]></command>
<inputs>
<param name="input" type="data" multiple="false" />
Expand All @@ -12,13 +14,33 @@
<action name="column_names" type="metadata" default="First,${input.name}" />
</actions>
</data>
<collection name="paired_output" format="tabular" type="paired" label="Split Pair">
<data name="forward">
<actions>
<action name="dbkey" type="metadata" default="hg38" />
</actions>
</data>
<data name="reverse">
<actions>
<action name="column_names" type="metadata" default="A,B,C" />
</actions>
</data>
</collection>
</outputs>
<tests>
<test>
<param name="input" value="2.tabular" />
<output name="output">
<metadata name="column_names" value="First,2.tabular"/>
</output>
<output_collection name="paired_output" type="paired">
<element name="forward" ftype="tabular" value="2.tabular">
<metadata name="dbkey" value="hg38"/>
</element>
<element name="reverse" ftype="tabular" value="2.tabular">
<metadata name="column_names" value="A,B,C"/>
</element>
</output_collection>
</test>
</tests>
</tool>

0 comments on commit 745913d

Please sign in to comment.