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Job request: 23965

Organisation:
Bennett Institute
Workspace:
covid-vaccine-history
ID:
jqd572s7l4iiosgl
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:
    extract_varying
    Status:
    Status: Succeeded
    Job identifier:
    boybtyxxq2jb7ahv
  • Action:
    process
    Status:
    Status: Succeeded
    Job identifier:
    gm77g3jkau4su7pi
  • Action:
    report_history
    Status:
    Status: Succeeded
    Job identifier:
    gh3qozxvlzajjy26
  • Action:
    report_snapshot_20201208
    Status:
    Status: Succeeded
    Job identifier:
    chlewjsl4mbo6tjx
  • Action:
    report_snapshot_20210906
    Status:
    Status: Failed
    Job identifier:
    o567byfhsg4eaci4
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    report_snapshot_20220401
    Status:
    Status: Failed
    Job identifier:
    jcgcyteo53rehbgs
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    report_snapshot_20220912
    Status:
    Status: Failed
    Job identifier:
    qxda7nj6ou5gn44r
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    report_snapshot_20230403
    Status:
    Status: Failed
    Job identifier:
    ylrr74vdsyn3iomf
    Error:
    nonzero_exit: Job exited with an error: Job ran out of memory (limit was 128.00GB)
  • Action:
    report_snapshot_20230911
    Status:
    Status: Failed
    Job identifier:
    nnecw66ftjmuatva
    Error:
    nonzero_exit: Job exited with an error: Job ran out of memory (limit was 128.00GB)
  • Action:
    report_snapshot_20240401
    Status:
    Status: Failed
    Job identifier:
    jkh627cztgdleuy3
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    report_snapshot_20241003
    Status:
    Status: Failed
    Job identifier:
    upec4srrrjr3nlui
    Error:
    nonzero_exit: Job exited with an error: Job ran out of memory (limit was 128.00GB)

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  extract_fixed:
    run: ehrql:v1 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:v1 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
      moderately_sensitive:
        txt: output/process/*.txt

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

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

 # 2020-12-08
  extract_snapshot_20201208:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_snapshot.py
      --output output/extracts/extract_snapshot_20201208.arrow
      -- 20201208
    outputs:
      highly_sensitive:
        cohort: output/extracts/extract_snapshot_20201208.arrow

  report_snapshot_20201208:
    run: r:latest analysis/report_snapshot.R 20201208
    needs: [extract_snapshot_20201208, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20201208/*.csv
        png: output/report_snapshot_20201208/*.png
        txt: output/report_snapshot_20201208/*.txt

 # 2021-09-06
  extract_snapshot_20210906:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_snapshot.py
      --output output/extracts/extract_snapshot_20210906.arrow
      -- 20210906
    outputs:
      highly_sensitive:
        cohort: output/extracts/extract_snapshot_20210906.arrow

  report_snapshot_20210906:
    run: r:latest analysis/report_snapshot.R 20210906
    needs: [extract_snapshot_20210906, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20210906/*.csv
        png: output/report_snapshot_20210906/*.png
        txt: output/report_snapshot_20210906/*.txt

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

  report_snapshot_20220401:
    run: r:latest analysis/report_snapshot.R 20220401
    needs: [extract_snapshot_20220401, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20220401/*.csv
        png: output/report_snapshot_20220401/*.png
        txt: output/report_snapshot_20220401/*.txt

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

  report_snapshot_20220912:
    run: r:latest analysis/report_snapshot.R 20220912
    needs: [extract_snapshot_20220912, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20220912/*.csv
        png: output/report_snapshot_20220912/*.png
        txt: output/report_snapshot_20220912/*.txt

 # 2023-04-03
  extract_snapshot_20230403:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_snapshot.py
      --output output/extracts/extract_snapshot_20230403.arrow
      -- 20230403
    outputs:
      highly_sensitive:
        cohort: output/extracts/extract_snapshot_20230403.arrow

  report_snapshot_20230403:
    run: r:latest analysis/report_snapshot.R 20230403
    needs: [extract_snapshot_20230403, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20230403/*.csv
        png: output/report_snapshot_20230403/*.png
        txt: output/report_snapshot_20230403/*.txt

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

  report_snapshot_20230911:
    run: r:latest analysis/report_snapshot.R 20230911
    needs: [extract_snapshot_20230911, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20230911/*.csv
        png: output/report_snapshot_20230911/*.png    
        txt: output/report_snapshot_20230911/*.txt

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

  report_snapshot_20240401:
    run: r:latest analysis/report_snapshot.R 20240401
    needs: [extract_snapshot_20240401, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20240401/*.csv
        png: output/report_snapshot_20240401/*.png  
        txt: output/report_snapshot_20240401/*.txt

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

  report_snapshot_20241003:
    run: r:latest analysis/report_snapshot.R 20241003
    needs: [extract_snapshot_20241003, process]
    outputs:
      moderately_sensitive:
        csv: output/report_snapshot_20241003/*.csv
        png: output/report_snapshot_20241003/*.png    
        txt: output/report_snapshot_20241003/*.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 1993:35:59

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-vaccine-history
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
0ee0c1f
Requested actions
  • extract_varying
  • process
  • report_history
  • report_snapshot_20201208
  • report_snapshot_20210906
  • report_snapshot_20220401
  • report_snapshot_20220912
  • report_snapshot_20230403
  • report_snapshot_20230911
  • report_snapshot_20240401
  • report_snapshot_20241003

Code comparison

Compare the code used in this job request