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New wrapper module & changes in logs reporting #322

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merged 19 commits into from
Oct 9, 2024

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@Shettland Shettland commented Oct 8, 2024

This PR includes a new module temporarily called "wrapper" which executes download, read-lab-metadata and validate processes consecutively for each downloaded set of samples. This simplifies the processing workflow as all the provided metadata is validated and a report is generated including all the errors found for each sample which can be sent via email to the corresponding submitter.

Along with this new module come several changes in related modules:

  • Those log_summary messages which previously included any field from the schema now include the label instead, as it's what the submitter will see in the xlsx template.
  • The excel log report created by logs-to-excel now has a cell size adjustment step for large messages
  • Multiple error handlings for merge_logs() and create_logs_excel() methods in log_summary.py

Closes #302

@Shettland Shettland changed the title TEMPORAL TITLE: WRAPPER PR New wrapper module & changes in logs reporting Oct 8, 2024
@Shettland Shettland merged commit a80cfb9 into BU-ISCIII:develop Oct 9, 2024
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