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Aquainfra importer #108

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merged 17 commits into from
May 14, 2024
Merged

Aquainfra importer #108

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4d0ef81
init data source tool for downoading aquainfra content
MarkusKonk Apr 10, 2024
3848025
refinements
MarkusKonk Apr 10, 2024
ec07676
add data_source.py
MarkusKonk Apr 10, 2024
fc08f16
Update tools/aquainfra_importer/aquainfra_importer.xml
MarkusKonk Apr 10, 2024
8e981bb
update importer outputs
MarkusKonk May 14, 2024
c10fcd3
add new line at the end of file
MarkusKonk May 14, 2024
732d80f
some linting
MarkusKonk May 14, 2024
102f0d4
some linting
MarkusKonk May 14, 2024
cca63b1
some linting
MarkusKonk May 14, 2024
b062963
some linting
MarkusKonk May 14, 2024
767c137
some linting
MarkusKonk May 14, 2024
f4ee9cd
some linting
MarkusKonk May 14, 2024
e69555e
some linting
MarkusKonk May 14, 2024
edfc53b
some linting
MarkusKonk May 14, 2024
3269e75
some linting
MarkusKonk May 14, 2024
a99ee59
some linting
MarkusKonk May 14, 2024
5b72400
Update tools/aquainfra_importer/aquainfra_importer.xml
bgruening May 14, 2024
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11 changes: 11 additions & 0 deletions tools/aquainfra_importer/.shed.yml
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categories:
- Ecology
owner: ecology
remote_repository_url: https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer
homepage_url: https://github.com/AquaINFRA/galaxy
long_description: |
A data source tool for downloading datasets via the AquaINFRA Interaction Platform.
type: unrestricted
auto_tool_repositories:
name_template: "{{ tool_id }}"
description_template: "Data source tool for content provided in AquaINRA: {{ tool_name }}."
13 changes: 13 additions & 0 deletions tools/aquainfra_importer/aquainfra_importer.xml
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<tool id="aquainfra_importer" name="AquaINFRA Importer" tool_type="data_source" version="1.0" profile="22.05">
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<description>downloads content via the AquaINFRA interaction platform</description>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit '$output'
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When installing from the toolshed, this will only work if you also provide the data_source.py script together with the .xml because this literally expects the .xml and the .py file in the same directory.
If you haven't customized anything you can just copy over https://github.com/galaxyproject/galaxy/blob/dev/tools/data_source/data_source.py here.

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Thanks for the quick review. I just added the file to PR.

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Cool, I'm now checking things on my own instance to see how it behaves :-)

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but the aquainfra part of this is not implemented yet? or should it be?

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Yeah, I wasn't sure what to do first. The problem is that only very very few datasets have metadata including a direct download link. Most don't have a link or redirect to the website of the data provider where you need to accept conditions or login or similar. Ideally the "Import to Galaxy" Button would be on the website of the data provider but I don't see that happen in the near future.
Give me some time to update the platform and I will show you an example record to test the import to Galaxy.

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]]></command>
<inputs action="https://aquainfra.dev.52north.org/" check_values="false" method="get">
<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
<param name="tool_id" type="hidden" value="aquainfra_importer" />
</inputs>
<outputs>
<data name="output" format="zip" label="resource"/>
</outputs>
</tool>