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Job request: 24318

Organisation:
Bennett Institute
Workspace:
tpp-database-history
ID:
yllpzngkblk3rujr
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Peter Inglesby 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:
    query
    Status:
    Status: Failed
    Job identifier:
    55k3ipkhathpozbh
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    aggregate
    Status:
    Status: Failed
    Job identifier:
    ogxxduagkq7trzwx
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    plot_from_2016
    Status:
    Status: Failed
    Job identifier:
    wmp7eyzsmo3j45vu
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    plot_from_2020
    Status:
    Status: Failed
    Job identifier:
    fjv4qvfsa44loiqf
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    plot_from_last_30_days
    Status:
    Status: Failed
    Job identifier:
    xbfhaitspp4hgfpv
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    render_report
    Status:
    Status: Failed
    Job identifier:
    3qoxe7zjiraz3arc
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  query:
    run: >
      sqlrunner:latest
        --dummy-data-file analysis/dummy_rows.csv.gz
        --output output/query/rows.csv.gz
        --log-file output/query/log.json
        analysis/query.sql
    outputs:
      highly_sensitive:
        rows: output/query/rows.csv.gz
      moderately_sensitive:
        log: output/query/log.json

  aggregate:
    needs: [query]
    run: python:latest python -m analysis.aggregate
    outputs:
      moderately_sensitive:
        aggregates: output/aggregate/*_by_*.csv

  plot_from_2016:
    needs: [query, aggregate]
    run: >
      python:latest python -m analysis.plot
        --from-date 2016-01-01
        --output output/plot_from_2016
    outputs:
      moderately_sensitive:
        plots: output/plot_from_2016/*.png
        metadata: output/plot_from_2016/metadata.json

  plot_from_2020:
    needs: [query, aggregate]
    run: >
      python:latest python -m analysis.plot
        --from-date 2020-02-01
        --output output/plot_from_2020
    outputs:
      moderately_sensitive:
        plots: output/plot_from_2020/*.png
        metadata: output/plot_from_2020/metadata.json

  plot_from_last_30_days:
    needs: [query, aggregate]
    run: >
      python:latest python -m analysis.plot
        --from-offset 30
        --output output/plot_from_last_30_days
    outputs:
      moderately_sensitive:
        plots: output/plot_from_last_30_days/*.png
        metadata: output/plot_from_last_30_days/metadata.json

  render_report:
    needs: [query, plot_from_2016, plot_from_2020, plot_from_last_30_days]
    run: python:latest python -m analysis.render_report
    outputs:
      moderately_sensitive:
        report: output/render_report/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:22:49

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

Job request

Status
Failed
Backend
TPP
Workspace
tpp-database-history
Requested by
Peter Inglesby
Branch
main
Force run dependencies
Yes
Git commit hash
6190dc3
Requested actions
  • run_all

Code comparison

Compare the code used in this job request