Implement tool markdown reports. #19054
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bgruening
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Oct 26, 2024
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Very cool idea. @neoformit maybe something for the Alphafold tool?
Yep, this could be a nice addition to the HTML output. We met last week with the structural biology community who were mostly interested in collating output metrics/plots for interpretation of model confidence. An Md report would make a nice job of pulling that together. |
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mvdbeek
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| dataset_instance = self.hda_manager.get_accessible(dataset_id, trans.user) | ||
| self.hda_manager.ensure_dataset_on_disk(trans, dataset_instance) | ||
| file_path = trans.app.object_store.get_filename(dataset_instance.dataset) | ||
| raw_content = open(file_path).read() |
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Can you limit this to something like 10KB ? Also the with handler is a good idea.
mvdbeek
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Nov 21, 2024
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It’s probably too late, but I’m wondering if we can release the tool_markdown in version 24.2. Or is there a specific reason to wait for version 25.0? @jmchilton |
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Many tools produce HTML and we do our best to support those but they are less than ideal. We cannot safely trust those HTML files to be rendered after they have been imported - probably even rendering the HTML of "safe tools" will catch up with us at some point. The ability to be able to safely render these Markdown components even after an export and re-import makes them more reproducible IMO. Once implemented, it will be much easier to compose these chunks and embed them into workflow reports also and even in the PDF version of those reports - where we couldn't really do much with HTML at all I believe.
I've included two test tools. One that links to and display the outputs of the tool and a second one that utilizes "extra files" content of the report itself - if the tool would like to included data in the report that shouldn't be a formal output of the tool. I've discovered some limitations around extra files rendering and I've included some bug fixes to get the existing components to work. There is still work to be done around these components but I think that is independent of this task.
The next steps include documenting which directives are available to tools (some don't make sense like workflow_license), better reporting when there are errors, and allowing the embed of these outputs into workflow and page reports after the fact.
xref #19039
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