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Job request: 26007

Organisation:
Bennett Institute
Workspace:
covid-vaccine-history
ID:
qjpv577j7tmadbwe
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Martina Pesce 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:
    extract_fixed
    Status:
    Succeeded
    Job identifier:
    pfaafl6hqmv4bs5a
  • Action:
    extract_snapshot_20201207
    Status:
    Succeeded
    Job identifier:
    bek4ucoib74cu4pc
  • Action:
    extract_snapshot_20210906
    Status:
    Succeeded
    Job identifier:
    u5rfxnuozju23jse
  • Action:
    extract_snapshot_20220321
    Status:
    Succeeded
    Job identifier:
    otzcrout2ryzd3eu
  • Action:
    extract_snapshot_20220829
    Status:
    Succeeded
    Job identifier:
    mhb4qoiwmpw7k3ap
  • Action:
    extract_snapshot_20230403
    Status:
    Succeeded
    Job identifier:
    wmkbiiuj4sjamwel
  • Action:
    extract_snapshot_20230828
    Status:
    Succeeded
    Job identifier:
    uoejcmhpwyea4654
  • Action:
    extract_snapshot_20240415
    Status:
    Succeeded
    Job identifier:
    tdomli46kxqeaxye
  • Action:
    extract_snapshot_20240930
    Status:
    Succeeded
    Job identifier:
    73jjisgtwkhdmuvg
  • Action:
    extract_snapshot_20250331
    Status:
    Succeeded
    Job identifier:
    phbnuwxyuhsz4usi
  • Action:
    extract_snapshot_20250929
    Status:
    Succeeded
    Job identifier:
    be2fumdfqr4n7hub
  • Action:
    extract_varying
    Status:
    Succeeded
    Job identifier:
    q6hazu2qmcg32jvs
  • Action:
    prepare
    Status:
    Succeeded
    Job identifier:
    k6p45efx6vpjj5zp
  • Action:
    vax_data_quality
    Status:
    Failed
    Job identifier:
    gb2xz4yu63dacylb
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    report_history
    Status:
    Succeeded
    Job identifier:
    6jfyq7vsygvwsd6n
  • Action:
    report_snapshot_20201207
    Status:
    Succeeded
    Job identifier:
    zgnntqrmnftu4gbq
  • Action:
    report_snapshot_20210906
    Status:
    Succeeded
    Job identifier:
    xfzepghs37jni3lb
  • Action:
    report_snapshot_20220321
    Status:
    Succeeded
    Job identifier:
    qmeficorhx5oe3wm
  • Action:
    report_snapshot_20220829
    Status:
    Succeeded
    Job identifier:
    3jiyjra5gnvj7dji
  • Action:
    report_snapshot_20230403
    Status:
    Succeeded
    Job identifier:
    dqkrgjgs3ujlyiee
  • Action:
    report_snapshot_20230828
    Status:
    Succeeded
    Job identifier:
    rrs7cpv566umx26x
  • Action:
    report_snapshot_20240415
    Status:
    Succeeded
    Job identifier:
    ykiuz5udghpplk4o
  • Action:
    report_snapshot_20240930
    Status:
    Succeeded
    Job identifier:
    r4hwnprar6frz2y7
  • Action:
    report_snapshot_20250331
    Status:
    Running
    Job identifier:
    ujqk6ek6fw6gnmaf
  • Action:
    report_snapshot_20250929
    Status:
    Running
    Job identifier:
    5cvq5bt2rbc573rz

Pipeline

Show project.yaml 
version: '4.0'

actions:

  extract_fixed:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_fixed.py
      --output output/1-extract/extract_fixed.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_fixed.arrow
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_fixed.arrow

  extract_varying:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_varying.py
      --output output/1-extract/extract_varying:arrow
      #--dummy-data-file analysis/1-extract/dummy-data/dummy_varying.arrow
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_varying/*.arrow

  vax_data_quality:
    run: r:v2 analysis/2-prepare/vax_data_quality.R
    needs: [extract_varying]
    outputs:
      moderately_sensitive:
        csv: output/2-prepare/vax_data_quality/*.csv
        #txt: output/2-prepare/vax_data_quality/*.txt

  prepare:
    run: r:v2 analysis/2-prepare/prepare.R
    needs: [extract_fixed, extract_varying]
    outputs:
      highly_sensitive:
        arrow: output/2-prepare/prepare/*.arrow
      moderately_sensitive:
        #csv: output/2-prepare/prepare/*.csv
        txt: output/2-prepare/prepare/*.txt

# report vaccine history over entire observational period ---
  report_history:
    run: r:v2 analysis/3-history/report_history.R
    needs: [prepare]
    outputs:
      moderately_sensitive:
        csv: output/3-history/report_history/*.csv
        png: output/3-history/report_history/*.png

 # report detailed vaccine history at specific snapshots in time ----

 # 2020-12-07
  extract_snapshot_20201207:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20201207.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20201207.arrow
      --
      --snapshot_date 20201207
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20201207.arrow

  report_snapshot_20201207:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20201207
    needs: [extract_snapshot_20201207, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20201207/*.csv
        png: output/4-snapshot/report_snapshot_20201207/*.png
        txt: output/4-snapshot/report_snapshot_20201207/*.txt

 # 2021-09-06
  extract_snapshot_20210906:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20210906.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20210906.arrow
      --
      --snapshot_date 20210906
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20210906.arrow

  report_snapshot_20210906:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20210906
    needs: [extract_snapshot_20210906, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20210906/*.csv
        png: output/4-snapshot/report_snapshot_20210906/*.png
        txt: output/4-snapshot/report_snapshot_20210906/*.txt

 # 2022-03-21
  extract_snapshot_20220321:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20220321.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20220321.arrow
      --
      --snapshot_date 20220321
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20220321.arrow

  report_snapshot_20220321:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20220321
    needs: [extract_snapshot_20220321, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20220321/*.csv
        png: output/4-snapshot/report_snapshot_20220321/*.png
        txt: output/4-snapshot/report_snapshot_20220321/*.txt

 # 2022-08-29
  extract_snapshot_20220829:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20220829.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20220829.arrow
      --
      --snapshot_date 20220829
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20220829.arrow

  report_snapshot_20220829:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20220829
    needs: [extract_snapshot_20220829, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20220829/*.csv
        png: output/4-snapshot/report_snapshot_20220829/*.png
        txt: output/4-snapshot/report_snapshot_20220829/*.txt

 # 2023-04-03
  extract_snapshot_20230403:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20230403.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20230403.arrow
      --
      --snapshot_date 20230403
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20230403.arrow

  report_snapshot_20230403:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20230403
    needs: [extract_snapshot_20230403, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20230403/*.csv
        png: output/4-snapshot/report_snapshot_20230403/*.png
        txt: output/4-snapshot/report_snapshot_20230403/*.txt

 # 2023-08-28
  extract_snapshot_20230828:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20230828.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20230828.arrow
      --
      --snapshot_date 20230828
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20230828.arrow

  report_snapshot_20230828:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20230828
    needs: [extract_snapshot_20230828, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20230828/*.csv
        png: output/4-snapshot/report_snapshot_20230828/*.png
        txt: output/4-snapshot/report_snapshot_20230828/*.txt

 # 2024-04-15
  extract_snapshot_20240415:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20240415.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20240415.arrow
      --
      --snapshot_date 20240415
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20240415.arrow

  report_snapshot_20240415:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20240415
    needs: [extract_snapshot_20240415, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20240415/*.csv
        png: output/4-snapshot/report_snapshot_20240415/*.png
        txt: output/4-snapshot/report_snapshot_20240415/*.txt

 # 2024-09-30
  extract_snapshot_20240930:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20240930.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20240930.arrow
      --
      --snapshot_date 20240930
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20240930.arrow

  report_snapshot_20240930:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20240930
    needs: [extract_snapshot_20240930, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20240930/*.csv
        png: output/4-snapshot/report_snapshot_20240930/*.png
        txt: output/4-snapshot/report_snapshot_20240930/*.txt

 # 2025-03-31
  extract_snapshot_20250331:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20250331.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20250331.arrow
      --
      --snapshot_date 20250331
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20250331.arrow

  report_snapshot_20250331:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20250331
    needs: [extract_snapshot_20250331, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20250331/*.csv
        png: output/4-snapshot/report_snapshot_20250331/*.png
        txt: output/4-snapshot/report_snapshot_20250331/*.txt

# 2025-09-29

  extract_snapshot_20250929:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20250929.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20250929.arrow
      --
      --snapshot_date 20250929
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20250929.arrow

  report_snapshot_20250929:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20250929
    needs: [extract_snapshot_20250929, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20250929/*.csv
        png: output/4-snapshot/report_snapshot_20250929/*.png
        txt: output/4-snapshot/report_snapshot_20250929/*.txt

Timeline

  • Created:

  • Started:

  • Runtime: 370:56:42

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

Job request

Status
Running
Backend
TPP
Workspace
covid-vaccine-history
Requested by
Martina Pesce
Branch
main
Force run dependencies
Yes
Git commit hash
a2b3565
Requested actions
  • extract_fixed
  • extract_varying
  • vax_data_quality
  • prepare
  • report_history
  • extract_snapshot_20201207
  • report_snapshot_20201207
  • extract_snapshot_20210906
  • report_snapshot_20210906
  • extract_snapshot_20220321
  • report_snapshot_20220321
  • extract_snapshot_20220829
  • report_snapshot_20220829
  • extract_snapshot_20230403
  • report_snapshot_20230403
  • extract_snapshot_20230828
  • report_snapshot_20230828
  • extract_snapshot_20240415
  • report_snapshot_20240415
  • extract_snapshot_20240930
  • report_snapshot_20240930
  • extract_snapshot_20250331
  • report_snapshot_20250331
  • extract_snapshot_20250929
  • report_snapshot_20250929

Code comparison

Compare the code used in this job request