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Update unzip: Include file extensions into designation tokens #227

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Merged
kostrykin merged 7 commits into from
Apr 11, 2026
Merged

Update unzip: Include file extensions into designation tokens #227

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e70f249
Disable `GIA301` check
kostrykin Apr 10, 2026
d2b51cb
Reproduce #223 in test
kostrykin Apr 10, 2026
6203039
Update `discover_datasets` pattern to suggestion from @martinherrerias
kostrykin Apr 10, 2026
183fee2
Merge branch 'master' into dev/unzip3
kostrykin Apr 10, 2026
d08441e
Fix pattern
kostrykin Apr 10, 2026
89bf737
Merge branch 'dev/unzip3' of github.com:kostrykin/galaxy-image-analys…
kostrykin Apr 10, 2026
45dde8d
Bump @VERSION_SUFFIX@
kostrykin Apr 10, 2026
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Binary file added tools/unzip/test-data/input2.zip
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41 changes: 30 additions & 11 deletions tools/unzip/unzip.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<macros>
<import>creators.xml</import>
<token name="@TOOL_VERSION@">6.0</token>
<token name="@VERSION_SUFFIX@">4</token>
<token name="@VERSION_SUFFIX@">5</token>
<token name="@PROFILE@">22.01</token>
<xml name="regex_sanitizer">
<sanitizer>
Expand Down Expand Up @@ -102,7 +102,7 @@
<filter>extract_options['target'] == 'single'</filter>
</data>
<collection name="unzipped" type="list" label="${tool.name} on ${on_string} all files as collection">
<discover_datasets directory="out" pattern="(?P&lt;designation&gt;\.*[^\.]+)\.?(?P&lt;ext&gt;.*)" visible="false" format="auto"/>
<discover_datasets directory="out" pattern="^(?P&lt;designation&gt;\.*[^\.]+(?:\.?(?P&lt;ext&gt;.*)))$" visible="false" format="auto"/>
<filter>extract_options['target'] != 'single'</filter>
</collection>
</outputs>
Expand All @@ -121,8 +121,8 @@
<param name="target" value="all"/>
</conditional>
<output_collection name="unzipped" type="list" count="2">
<element name="input" file="input.png" ftype="png" compare="sim_size"/>
<element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
<element name="input.png" file="input.png" ftype="png" compare="sim_size"/>
<element name="res.tiff" file="res.tiff" ftype="tiff" compare="sim_size"/>
</output_collection>
</test>
<!-- Binary files without file extension -->
Expand All @@ -145,8 +145,8 @@
<output_collection name="unzipped" type="list" count="4">
<element name="binaries_yelp" file="yelp" compare="sim_size"/>
<element name="binaries_yes" file="yes" compare="sim_size"/>
<element name="images_input" file="input.png" ftype="png" compare="sim_size"/>
<element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>
<element name="images_input.png" file="input.png" ftype="png" compare="sim_size"/>
<element name="images_res.tiff" file="res.tiff" ftype="tiff" compare="sim_size"/>
</output_collection>
</test>
<test expect_num_outputs="1">
Expand All @@ -163,8 +163,8 @@
<param name="target" value="all"/>
</conditional>
<output_collection name="unzipped" type="list" count="2">
<element name="input" file="input.png" ftype="png" compare="sim_size"/>
<element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
<element name="input.png" file="input.png" ftype="png" compare="sim_size"/>
<element name="res.tiff" file="res.tiff" ftype="tiff" compare="sim_size"/>
</output_collection>
</test>
<!-- ZIP containing dotfiles and non-dotfiles -->
Expand All @@ -184,7 +184,7 @@
<has_size value="0"/>
</assert_contents>
</element>
<element name="subdir_"><!-- The suffix `.dotfile` is recognized as the extension -->
<element name="subdir_.dotfile">
<assert_contents>
<has_size value="0"/>
</assert_contents>
Expand Down Expand Up @@ -222,8 +222,27 @@
<param name="keep_regex" value="./images/.*"/>
</conditional>
<output_collection name="unzipped" type="list" count="2">
<element name="images_input" file="input.png" ftype="png" compare="sim_size"/>
<element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>
<element name="images_input.png" file="input.png" ftype="png" compare="sim_size"/>
<element name="images_res.tiff" file="res.tiff" ftype="tiff" compare="sim_size"/>
</output_collection>
</test>
<!-- ZIP with two files with same stem name: https://github.com/BMCV/galaxy-image-analysis/issues/223 -->
<test expect_num_outputs="1">
<param name="input_file" value="input2.zip" ftype="zip"/>
<conditional name="extract_options">
<param name="target" value="all"/>
</conditional>
<output_collection name="unzipped" type="list" count="2">
<element name="input_file.tsv" ftype="tsv">
<assert_contents>
<has_line line="b"/>
</assert_contents>
</element>
<element name="input_file.txt" ftype="txt">
<assert_contents>
<has_line line="a"/>
</assert_contents>
</element>
</output_collection>
</test>
</tests>
Expand Down
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