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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 the authorised researcher Milan Wiedemann 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:

  # 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 request

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