Skip to content

Job request: 16267

Organisation:
Bennett Institute
Workspace:
isaric-exploration
ID:
nm5p2ufq3yq26c4c
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

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

  ## # # # # # # # # # # # # # # # # # # # 
  ## End 
  ## # # # # # # # # # # # # # # # # # # #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:05:00

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

Job request

Status
Succeeded
Backend
TPP
Workspace
isaric-exploration
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
f5440bc
Requested actions
  • extract_isaric_admission1
  • process_isaric

Code comparison

Compare the code used in this job request