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Job request: 21063

Organisation:
University of Bristol
Workspace:
vaccine-counts
ID:
zmf27t3jb7mcpg5o
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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

  • Action:
    process
    Status:
    Status: Succeeded
    Job identifier:
    qzoruqehcbb6uol3
  • Action:
    report
    Status:
    Status: Succeeded
    Job identifier:
    dw3irn35cnqtqket

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  extract_fixed:
    run: ehrql:v0 generate-dataset analysis/dataset_definition_fixed.py
      --output output/extracts/extract_fixed.arrow
      --dummy-data-file lib/dummydata/dummyinput_fixed.arrow
    outputs:
      highly_sensitive:
        cohort: output/extracts/extract_fixed.arrow

  extract_varying:
    run: ehrql:v0 generate-dataset analysis/dataset_definition_varying.py
      --output output/extracts/extract_varying.arrow
      --dummy-data-file lib/dummydata/dummyinput_varying.arrow
    outputs:
      highly_sensitive:
        cohort: output/extracts/extract_varying.arrow


  process:
    run: r:latest analysis/process.R
    needs: [extract_fixed, extract_varying]
    outputs:
      highly_sensitive:
        rds: output/process/*.rds

  report:
    run: r:latest analysis/report.R
    needs: [process]
    outputs:
      moderately_sensitive:
        csv: output/report/*.csv
        png: output/report/*.png

  # Additional actions for snapshot
  extract_snapshot:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_snapshot
        --skip-existing
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_snapshot.csv.gz

  process_snapshot:
    run: r:latest analysis/snapshot_process.R
    needs: [extract_snapshot]
    outputs:
      highly_sensitive:
        rds: output/snapshot/processed_snapshot.rds

  report_snapshot:
    run: r:latest analysis/snapshot_report.R
    needs: [process_snapshot]
    outputs:
      highly_sensitive:
        rds: output/snapshot_report/snapshot_summary.rds
      moderately_sensitive:
        csv: output/snapshot_report/snapshot_summary.csv
    
  html_snapshot:
    run: r:latest -e 'rmarkdown::render("analysis/vaccine_snapshot_report.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/snapshot_report")'
    needs: [process_snapshot, report_snapshot]
    outputs:
      moderately_sensitive:
        html: output/snapshot_report/vaccine_snapshot_report.html
        png: output/snapshot_report/*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:41:33

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

Job request

Status
Succeeded
Backend
TPP
Workspace
vaccine-counts
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
ebbb74c
Requested actions
  • process
  • report

Code comparison

Compare the code used in this job request