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Job request: 24954

Organisation:
University of Manchester
Workspace:
openpregnosis_main
ID:
sxc5nsi543oif5nr
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Paolo Mazzone requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
  population_size: 1000

actions:
## Diagnostic analysis for event counts ##

  generate_diagnostic_event_counts:
    run: ehrql:v1 generate-dataset analysis/diagnostic_event_counts.py --output output/diagnostic_event_counts.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/diagnostic_event_counts.csv.gz

  analyze_diagnostic_event_counts:
    run: r:latest analysis/analyse_diagnostic.R
    needs: [generate_diagnostic_event_counts]
    outputs:
      moderately_sensitive:
        analysis_results: output/diagnostic_analysis_results.txt
        recommendations: output/event_count_recommendations.csv

## Main pregnancy event extraction ##

  generate_pregnancy_event_data:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/pregnancy_event_data.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/pregnancy_event_data.csv.gz

## Data processing and validation ##

  convert_stillbirth_episodes:
    run: r:latest analysis/convert_stillbirth_episodes.R
    needs: [generate_pregnancy_event_data]
    outputs:
      highly_sensitive:
        stillbirth_events_long: output/processed/stillbirth_events_long.csv
        stillbirth_pregnancies_wide: output/processed/stillbirth_pregnancies_wide.csv
        stillbirth_pregnancy_summary: output/processed/stillbirth_pregnancy_summary.csv

  convert_livebirth_episodes:
    run: r:latest analysis/convert_livebirth_episodes.R
    needs: [generate_pregnancy_event_data]
    outputs:
      highly_sensitive:
        livebirth_events_long: output/processed/livebirth_events_long.csv
        livebirth_pregnancies_wide: output/processed/livebirth_pregnancies_wide.csv
        livebirth_pregnancy_summary: output/processed/livebirth_pregnancy_summary.csv

  generate_delivery_validation_report:
    run: r:latest analysis/delivery_code_validation_report.R
    needs: [convert_stillbirth_episodes, convert_livebirth_episodes]
    outputs:
      highly_sensitive:
        validation_results: output/validation/delivery_validation_results.rds
        validation_summary: output/validation/delivery_validation_summary.txt
        validation_plots: output/validation/delivery_validation_plots.pdf

## Complete workflow ##

  run_all:
    run: echo:v1 "Complete pregnancy outcome analysis pipeline executed successfully" > output/pipeline_complete.txt
    needs: [analyze_diagnostic_event_counts, convert_stillbirth_episodes, convert_livebirth_episodes, generate_delivery_validation_report]
    outputs:
      highly_sensitive:
        complete_pipeline: output/pipeline_complete.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:55

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status
Succeeded
Backend
TPP
Workspace
openpregnosis_main
Requested by
Paolo Mazzone
Branch
main
Force run dependencies
No
Git commit hash
e1dd15a
Requested actions
  • generate_diagnostic_event_counts
  • analyze_diagnostic_event_counts

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