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Job request: 15935

Organisation:
Bennett Institute
Workspace:
isaric-exploration
ID:
6ltjozmjievy2oll
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

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 1000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create-project.R 
  ## Edit and run create-project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract admission date 
  ## # # # # # # # # # # # # # # # # # # # 

  extract_isaric_admission1:
    run: databuilder:v0 generate-dataset 'analysis/dataset_definition_isaric.py'
      --dummy-tables 'dummy-tables/' --output 'output/admissions/isaric_admission1.csv.gz'
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/isaric_admission1.csv.gz

  process_isaric:
    run: r:latest analysis/process_isaric.R
    needs:
    - extract_isaric_admission1
    outputs:
      highly_sensitive:
        rds: output/admissions/processed_isaric.rds
      moderately_sensitive:
        txt: output/admissions/isaric_raw_skim.txt

  extract_sus_methodA_admission1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission1.csv.gz --param admission_number=1
      --param admission_method=A
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission1.csv.gz

  extract_sus_methodA_admission2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission2.csv.gz --param admission_number=2
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission1
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission2.csv.gz

  extract_sus_methodA_admission3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission3.csv.gz --param admission_number=3
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission2
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission3.csv.gz

  extract_sus_methodA_admission4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission4.csv.gz --param admission_number=4
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission3
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission4.csv.gz

  extract_sus_methodA_admission5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission5.csv.gz --param admission_number=5
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission4
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission5.csv.gz

  extract_sus_methodB_admission1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission1.csv.gz --param admission_number=1
      --param admission_method=B
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission1.csv.gz

  extract_sus_methodB_admission2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission2.csv.gz --param admission_number=2
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission1
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission2.csv.gz

  extract_sus_methodB_admission3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission3.csv.gz --param admission_number=3
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission2
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission3.csv.gz

  extract_sus_methodB_admission4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission4.csv.gz --param admission_number=4
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission3
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission4.csv.gz

  extract_sus_methodB_admission5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission5.csv.gz --param admission_number=5
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission4
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission5.csv.gz

  extract_sus_methodC_admission1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission1.csv.gz --param admission_number=1
      --param admission_method=C
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission1.csv.gz

  extract_sus_methodC_admission2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission2.csv.gz --param admission_number=2
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission1
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission2.csv.gz

  extract_sus_methodC_admission3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission3.csv.gz --param admission_number=3
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission2
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission3.csv.gz

  extract_sus_methodC_admission4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission4.csv.gz --param admission_number=4
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission3
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission4.csv.gz

  extract_sus_methodC_admission5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission5.csv.gz --param admission_number=5
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission4
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission5.csv.gz

  process_sus:
    run: r:latest analysis/process_sus.R
    needs:
    - extract_sus_methodA_admission1
    - extract_sus_methodA_admission2
    - extract_sus_methodA_admission3
    - extract_sus_methodA_admission4
    - extract_sus_methodA_admission5
    - extract_sus_methodB_admission1
    - extract_sus_methodB_admission2
    - extract_sus_methodB_admission3
    - extract_sus_methodB_admission4
    - extract_sus_methodB_admission5
    - extract_sus_methodC_admission1
    - extract_sus_methodC_admission2
    - extract_sus_methodC_admission3
    - extract_sus_methodC_admission4
    - extract_sus_methodC_admission5
    outputs:
      highly_sensitive:
        rds: output/admissions/processed_sus*.rds

  validation:
    run: r:latest analysis/validation.R
    needs:
    - process_isaric
    - process_sus
    outputs:
      moderately_sensitive:
        csv: output/validation/*.csv

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  ## End 
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Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:04:59

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

Job information

Status
Failed
Backend
TPP
Workspace
isaric-exploration
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
31c1719
Requested actions
  • extract_sus_methodB_admission1
  • extract_sus_methodB_admission2
  • extract_sus_methodB_admission3
  • extract_sus_methodB_admission4
  • extract_sus_methodB_admission5
  • process_sus

Code comparison

Compare the code used in this Job Request