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Job request: 17343

Organisation:
Bennett Institute
Workspace:
qof-blood-pressure
ID:
6h3ci5fbaar76l57
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Milan Wiedemann requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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:

  # Generate ethnicity study population
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv
  
  generate_study_population_bp002_1y_lookback:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_bp002_1y_lookback
      --index-date-range "2019-03-01 to 2023-03-31 by month" 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_bp002_1y*.csv
  
  generate_study_population_bp002_5y_lookback:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_bp002_5y_lookback 
      --index-date-range "2019-03-01 to 2023-03-31 by month" 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_bp002_5y*.csv
  
  join_ethnicity:
    run: >
      cohort-joiner:v0.0.12 
        --lhs output/input_bp002*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/joined
    needs: [generate_study_population_ethnicity, generate_study_population_bp002_1y_lookback, generate_study_population_bp002_5y_lookback]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_bp002*.csv

  generate_measures_bp002_1y_lookback:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_bp002_1y_lookback 
       --output-dir=output/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_bp002_1y*_rate.csv

  generate_measures_bp002_5y_lookback:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_bp002_5y_lookback 
       --output-dir=output/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_bp002_5y*_rate.csv

  generate_deciles_charts:
    run: >
      deciles-charts:v0.0.15
        --input-files output/joined/measure_*.csv
        --output-dir output/joined/
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_bp002_1y_lookback, generate_measures_bp002_5y_lookback]
    outputs:
      moderately_sensitive:
        deciles_charts: output/joined/deciles_chart_*_*_practice_breakdown_rate.png
        deciles_tables: output/joined/deciles_table_*_*_practice_breakdown_rate.csv
      
  join_measures:
    run: r:latest analysis/join_measures.R
    needs: [generate_measures_bp002_1y_lookback, generate_measures_bp002_5y_lookback]
    outputs:
      moderately_sensitive:
        bp002_achievement_csv: output/joined/measures/measures_bp002_achievem.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 38:47:05

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

Job information

Status
Succeeded
Backend
TPP
Workspace
qof-blood-pressure
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
Yes
Git commit hash
9720aa2
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request