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Job request: 24864

Organisation:
Bennett Institute
Workspace:
covid-vaccine-history
ID:
e3ykxv24idrff2oa
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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:
    extract_fixed
    Status:
    Status: Succeeded
    Job identifier:
    2ovhwkz3u26wwxbx
  • Action:
    extract_varying
    Status:
    Status: Succeeded
    Job identifier:
    fyjalug4bnpmsigk
  • Action:
    prepare
    Status:
    Status: Succeeded
    Job identifier:
    nyz76ztcqo5yrq63
  • Action:
    report_history
    Status:
    Status: Succeeded
    Job identifier:
    ho3q43atlk3vxl3a

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

  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 ----

 # 2020-12-08
  extract_snapshot_20201208:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20201208.arrow
      --dummy-data-file analysis/1-extract/dummy-data/dummy_snapshot_20201208.arrow
      --
      --snapshot_date 20201208
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20201208.arrow

  report_snapshot_20201208:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20201208
    needs: [extract_snapshot_20201208, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20201208/*.csv
        png: output/4-snapshot/report_snapshot_20201208/*.png
        txt: output/4-snapshot/report_snapshot_20201208/*.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

 # 2022-04-01
  extract_snapshot_20220401:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20220401.arrow
      --
      --snapshot_date 20220401
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20220401.arrow

  report_snapshot_20220401:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20220401
    needs: [extract_snapshot_20220401, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20220401/*.csv
        png: output/4-snapshot/report_snapshot_20220401/*.png
        txt: output/4-snapshot/report_snapshot_20220401/*.txt

 # 2022-09-12
  extract_snapshot_20220912:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20220912.arrow
      --
      --snapshot_date 20220912
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20220912.arrow

  report_snapshot_20220912:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20220912
    needs: [extract_snapshot_20220912, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20220912/*.csv
        png: output/4-snapshot/report_snapshot_20220912/*.png
        txt: output/4-snapshot/report_snapshot_20220912/*.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
      --
      --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

 # 2023-09-11
  extract_snapshot_20230911:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20230911.arrow
      --
      --snapshot_date 20230911
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20230911.arrow

  report_snapshot_20230911:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20230911
    needs: [extract_snapshot_20230911, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20230911/*.csv
        png: output/4-snapshot/report_snapshot_20230911/*.png
        txt: output/4-snapshot/report_snapshot_20230911/*.txt

 # 2024-04-01
  extract_snapshot_20240401:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20240401.arrow
      --
      --snapshot_date 20240401
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20240401.arrow

  report_snapshot_20240401:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20240401
    needs: [extract_snapshot_20240401, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20240401/*.csv
        png: output/4-snapshot/report_snapshot_20240401/*.png
        txt: output/4-snapshot/report_snapshot_20240401/*.txt

 # 2024-10-03
  extract_snapshot_20241003:
    run: ehrql:v1 generate-dataset analysis/1-extract/dataset_definition_snapshot.py
      --output output/1-extract/extract_snapshot_20241003.arrow
      --
      --snapshot_date 20241003
    outputs:
      highly_sensitive:
        cohort: output/1-extract/extract_snapshot_20241003.arrow

  report_snapshot_20241003:
    run: r:v2 analysis/4-snapshot/report_snapshot.R 20241003
    needs: [extract_snapshot_20241003, prepare]
    outputs:
      moderately_sensitive:
        csv: output/4-snapshot/report_snapshot_20241003/*.csv
        png: output/4-snapshot/report_snapshot_20241003/*.png
        txt: output/4-snapshot/report_snapshot_20241003/*.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:49:57

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-history
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
86d9ecf
Requested actions
  • extract_fixed
  • extract_varying
  • prepare
  • report_history

Code comparison

Compare the code used in this Job Request