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Bugfixes, and one fast report #453

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Bugfixes, and one fast report #453

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MattWellie
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@MattWellie MattWellie commented Oct 30, 2024

Fixes

Miah has spotted a couple of bugs

  • the arguments to the PED -> PhenoPacket converter need correction
  • the HTML generator script doesn't tolerate an output path outside of the current directory

Proposed Changes

  • correction to the ped conversion arguments
  • use os.makedirs based on the target location, not the current location

Report Fixes

  • for the CPG pipeline, we need to create the main document: The CPG pipeline will only register outputs in metamist if the exact file has been created, so we always make that, then optionally do splitting.
  • the jinja template engine is now started up with trim_blocks and lstrip_blocks - these arguments stop jinja from inserting empty lines in the HTMLs we produce. These account for over half the file length in lines, but their removal didn't speed anything up
  • I've also fixed the clinvar hyperlink - I was creating a hyperlink with no content if the allele doesn't have a clinvar entry. This removal also didn't meaningfully speed things up, but it's silly.
  • This includes a complete GPT-4 inspired revolution on the report - now it's paginated, with a spectacular performance upgrade.
  • Sample/Family rows are now collapsible using this functionality

still required

  • now that we don't need to split report, we can try to reconcile this new jquery with the original child table functionality

Checklist

  • Related Issue created
  • Tests covering new change
  • Linting checks pass

@MattWellie MattWellie changed the title Bugfixes, and even more reports Bugfixes, and one fast report Oct 31, 2024
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something like this would be useful to combine the child-row details with the main view, but DataTables seems to be less straightforward than it was using TableSorter
e.g. https://datatables.net/dev/accessibility/DataTables_1_10/examples/api/row_details.html ?

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