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Job request: 20466

Organisation:
University of Bristol
Workspace:
vaccine-counts
ID:
3jd7ip3khieqbsn2
View repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    html_snapshot
    Status:
    Status: Succeeded
    Job identifier:
    wjmnicjuksypnzck

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:11

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vaccine-counts
Requested by
Ed Parker
Branch
main
Force run dependencies
No
Git commit hash
2a8c753
Requested actions
  • html_snapshot

Code comparison

Compare the code used in this Job Request