Add results filtering #935
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lazappi
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Aug 19, 2025
rcannood
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Aug 19, 2025
Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>
lazappi
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Aug 19, 2025
rcannood
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* Add combine_output reporting component * Update process_task_results to combine outputs * Update get_task_info to new schema * Update get_method_info to new schema * Update get_metric_info to new schema * Update get_dataset_info to new schema * Update get_results to new schema Need to add metric execution info * Add metric resources to results component/schema * Update generate_qc to match new schema Add some new QC checks * Update combine_output to new schema * Update viash version and reference * Update process_results workflow to new components * Add render_report component * Add render_report to process results workflow * Handle missing values in generate_qc() This can happen when a method is disabled/skipped so there are no results to check * Handle missing controls in results report Skip scaling/results when there are no controls or give a warning when some controls failed * update common submodule * Strip quotes from descriptions/summaries * Add roles to author details * Add QC check for number of successful controls * Handle missing exit codes in report * Add schema validation to process_results workflow * Fix combine_output image version * Handle alternative field names in get_dataset_info * Handle v1 slots in get_method_info * Handle null author fields in report * Add missing information in control QC checks * Handle old doc URL location in get_method_info * Prefix component additional info in get_metric_info * Cleanup removed argument in get_results * Fix test script for generate_qc * Add authors to datasets, methods, metrics * schemas were moved to the common_resources repo * fix schema paths * set common submodule to different branch for testing * Fix resource * fix schema paths in the script * authors and references were moved into core * add a params placeholder for ease of use * show number of passed checks as well * fix result schema path * Add bibliography file * Add shared util functions * Use shared functions for authors and references * update submodule (#934) * Add scripts/create_resources/task_results_v4 * Update main reference Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Use temporary directory in render-report * Style reporting R scripts * add auto wf * add script to reprocess task results * Handle missing scaled scores in generate_qc * Set unknown error in get_results * fix script * Handle missing fields in old task info * Handle missing additional info in authors field * Fix typo in get_references_list() * Handle missing summary/label in get_task_info * Handle minimal dataset info in old results * Handle missing file size in get_dataset_info * Handle empty string in get_references_list() * Handle method info stored in functionality field * Move get_additional_info() to shared functions * Handle missing maximize in get_metric_info * Handle missing metric values in get_results * Properly handle workflow component in get_results * Handle metrics stored in functionality field * Give better error when dataset IDs don't map * Remove duplicate datasets in get_dataset_info * Handle infinite values in generate_qc * Add check that any valid scores are found * Adjust dataset process mapping * Handle source_urls in render_report * Fix additional info in get_method_info * Handle missing file size/date in report * Use regex to match DOI references * Fix empty scores check in report * Fix DOI regex * Handle DOIs without text citations * Warn about missing values for succeeded metrics * Improve controls check in report * update submodule * Add results filtering (#935) * introduce new component * implement component * format code * Update src/reporting/process_task_results/main.nf * Apply suggestions from code review Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> * add back previously removed arguments --------- Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
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Describe your changes
Filter results with include/exclude_datasets/methods/metrics
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)
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Proposed changes are described in the CHANGELOG.md
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