Pulsar and Zotero SRC Galaxy updates#58
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dometto
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dometto
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Really great addition, looks good to me apart from a few linting issues! And we should figure out why the tests continue to fail.
Question: I noticed that in the catalog item, the interactive parameter to configure Pulsar has default text in it by default. Is this test-Pulsar ignored by Galaxy, or actually added to the configuration?
Final question: if you add the Pulsar config, will Galaxy use it by default? Or can I somehow choose per job if it's run on Galaxy or Pulsar?
| _galaxy_pulsar_tool_mappings_input: "{{ src_galaxy_pulsar_tool_mappings | default('', true) }}" | ||
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| _galaxy_pulsar_configs_input: "{{ src_galaxy_pulsar_configs | default('', true) }}" | ||
| _galaxy_pulsar_tool_mappings_input: "{{ src_galaxy_pulsar_tool_mappings | default('', true) }}" |
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Looks identical to line 34, so remove one to fix the linter :)
| _galaxy_pulsar_configs_input: "{{ src_galaxy_pulsar_configs | default('', true) }}" | ||
| _galaxy_pulsar_tool_mappings_input: "{{ src_galaxy_pulsar_tool_mappings | default('', true) }}" | ||
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| _galaxy_pulsar_configs_input: "{{ src_galaxy_pulsar_configs | default('', true) }}" |
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Looks identical to line 33, so remove one to fix the linter :)
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| # Parse tool mappings | ||
| _galaxy_pulsar_tool_mappings: >- | ||
| {%- if _galaxy_pulsar_tool_mappings_input == '' or _galaxy_pulsar_tool_mappings_input == '[]' -%} |
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Maybe some documentation (in comments?) about why this parsing step is necessary would be useful: the regex itself is not super easy to read :)
Also note the linter's suggestion for improving the spacing
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The text is used as an example for users to know where to put the copied config from the pulsar instance. If they do not wish to use Pulsar, they have to remove the fields with the examples. Regarding the second question, now, every tool that you configure to use Pulsar will be redirected to there and will not be executed on Galaxy's side. I am currently working on tpv (see https://github.com/mirelaminkova/src-component-galaxy/tree/tpv) and when you provide Galaxy and Pulsar, it will decide, depending on the resources, where to be executed. This would also mean that I will most probably change the Galaxy and Pulsar config once again (or provide a new cat item, separate from this one). The Galaxy team has provided a db indicating how many resources a tool might need (https://gxy.io/tpv/db.yml). As for the linting and the molecule tests, I will take a look, thanks :) |
Ah ok! But this means that for 'default' Galaxy users who don't need Pulsar need to take a special action (remove the default config), or else their Galaxy will not work? That would be a bit unfortunate for the least technically minded users, they might find it a bit confusing to have to remove the default config. Or will Galaxy just use the local runner if the Pulsar config is invalid, so that there's no big problem if users forget to remove the default config? |
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It will not automatically use the Galaxy config, so indeed the users will have to remove the fields if they do not wish to work with Pulsar. I have not heard of any issues with this setup so far, but maybe I will change it in the future. |
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Hi,
I rolled out some updates to Galaxy: