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Add q2view display application. #1

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Jan 17, 2019
Merged

Add q2view display application. #1

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dcebe05
Add q2view display application.
blankenberg Aug 21, 2018
4b2ceb6
Update q2view_display.loc.sample
blankenberg Aug 21, 2018
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8 changes: 6 additions & 2 deletions config/datatypes_conf.xml.sample
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Expand Up @@ -189,8 +189,12 @@
<datatype extension="nrrd" type="galaxy.datatypes.images:Nrrd" mimetype="image/nrrd"/>
<datatype extension="nhdr" type="galaxy.datatypes.images:Nrrd" subclass="true"/>
<datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="true"/>
<datatype extension="qza" type="galaxy.datatypes.qiime2:Qiime2Artifact" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="qzv" type="galaxy.datatypes.qiime2:Qiime2Visualization" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="qza" type="galaxy.datatypes.qiime2:Qiime2Artifact" mimetype="application/octet-stream" display_in_upload="true">
<display file="qiime/qiime2/q2view.xml"/>
</datatype>
<datatype extension="qzv" type="galaxy.datatypes.qiime2:Qiime2Visualization" mimetype="application/octet-stream" display_in_upload="true">
<display file="qiime/qiime2/q2view.xml"/>
</datatype>
<datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true"/>
<datatype extension="tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<!-- Proteomics Datatypes -->
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5 changes: 5 additions & 0 deletions config/tool_data_table_conf.xml.sample
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Expand Up @@ -105,4 +105,9 @@
<columns>value, name, url</columns>
<file path="tool-data/intermine_simple_display.loc" />
</table>
<!-- q2view servers -->
<table name="q2view_display" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, url</columns>
<file path="tool-data/q2view_display.loc" />
</table>
</tables>
7 changes: 7 additions & 0 deletions display_applications/qiime/qiime2/q2view.xml
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@@ -0,0 +1,7 @@
<?xml version="1.0"?>
<display id="q2view" version="1.0.0" name="view at">
<dynamic_links from_data_table="q2view_display" skip_startswith="#" id="value" name="name">
<url>${ url % { 'q2view_file_url_qp': $q2view_file.qp } }</url>
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How does this work? Is the url % { mapping something (like URI-encoding) over the object? Or are we assigning into a scope of some sort?

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url comes from the 'url' column of the q2view_display.loc.sample file. This is just doing standard dictionary-based string replacement.

The .qp attribute of $q2view_file calls urllib.parse.quote_plus on the URL generated for q2view_file.

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This is just doing standard dictionary-based string replacement.

oh. duh! Thanks!

The .qp attribute of $q2view_file calls urllib.parse.quote_plus on the URL generated for q2view_file.

Ah, neat!

<param type="data" name="q2view_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
</dynamic_links>
</display>
3 changes: 3 additions & 0 deletions tool-data/q2view_display.loc.sample
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# Table used for listing QIIME2View display servers
#<unique_id> <display_name> <url>
main_q2view qiime2view https://view.qiime2.org/visualization/?type=html&src=%(q2view_file_url_qp)s