3dbeacons api - #8253
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moved this to Triage/Discuss
in Galaxy Tool Developers SIG Board
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The linting step fails during checking: The first one seems to pop up because bio.tools is down atm. The second one I don't understand. |
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please add this file as <required_files> in the Galaxy tool.
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Like this:
<required_files>
<include path="api_wrapper_3dbeacons.py"/>
</required_files>
With no type so a normal path is assumed as default?
| <xref type="bio.tools">3d-beacons</xref> | ||
| </xrefs> | ||
| <requirements> | ||
| <requirement type="package" version="3.13">python</requirement> |
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| <requirement type="package" version="3.13">python</requirement> |
requests will get you python
| <when value="single"> | ||
| <param name="qualifier" type="text" value="" optional="false" | ||
| label="Qualifier" help="ID/ AC to search for"/> | ||
| <param name="provider" type="select" optional="true" |
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can you select multiple providers?
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Nope, only a single one. I would love to see a real provider selection, but the 3D-Beacons API only uses the last one in the parameter list.
| <param name="provider" type="select" optional="true" | ||
| label="Provider"> | ||
| <help><![CDATA[ | ||
| Request from provider only. If none is selected, query all providers. |
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None is not an option, and optional=false
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I change the text to "If no provider is selected...". Works in planemo serve if I do not select any provider. Then the query includes all providers.
| ]]></help> | ||
| <expand macro="provider_options"/> | ||
| </param> | ||
| <param name="exclude_provider" type="select" optional="true" |
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can you exclude multiple providers?
Should exclude providers have priority over include_providers? Means you skip them even if the user has choosen then in include_providers ... so that you avoid the error message?
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No, only single provider. So in case include_provider == exclude_provider the 3D-Beacons API 404s, the error in front of that saves an unnecessary API call. I know the error is a bit awkward and your suggestion will prevent it. So I'm going to implement it but give priority to include_provider because with no provider, there would never be a result.
| <expand macro="provider_options"/> | ||
| </param> | ||
| <param name="template" type="text" value="" optional="true" | ||
| label="Template"> |
| ]]></help> | ||
| <validator type="regex" message="Template must be a 4-character PDB ID (e.g., '1ake') optionally followed by assembly and chain (e.g., '1ake.1.A', '1ake1A').">^[a-zA-Z0-9]{4}([._-]?\d+[._-]?[A-Za-z])?$</validator> | ||
| </param> | ||
| <param name="sequence_range" type="text" value="" optional="true" |
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you can do that, or use two integer params. Two integer params make a better API that can be validated with pydatic
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How do I make sure that both, start & end are set, as soon as one value is provided? I don't see how I can check "if start is not None and end is None: ERROR" outside of the command element. <validator> can not see values outside of its own <param> scope, right?
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@bienchen can you please remind me why we can not add a real world test? Your outputs with nested lists look complicated and would really need some real tests. |
In the SWISS-MODEL. wrapper, we skipped that because the API could be down or change and the test would fail because of that, not because of an error in the tool integration. If you think that testing is more important here than possible API issues, I can add a test. Recommendations what to test? single & batch mode or just batch mode because it has the more complex output? |
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Yes, I think testing is important, especially that your outputs do have the correct shape etc ... the collections look complicated and should be tested imho. I hope the API is most time up :) |
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