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Job request: 17125

Organisation:
Bennett Institute
Workspace:
hypertension-sro
ID:
gdsratxa5pcreqhd
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: 10000

actions:

  # Study populations
  # Extract latests ethnicity record for cohort
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output/indicators 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_ethnicity.feather

  # Extract cohort for indicator HYP001 by month 
  generate_study_population_hyp001:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp001 
      --index-date-range "2019-04-01 to 2023-03-31 by month" 
      --output-dir=output/indicators
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp001_*.feather

  # Extract cohort for indicator HYP003 by month 
  generate_study_population_hyp003:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp003 
      --index-date-range "2019-04-01 to 2023-03-31 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp003_*.feather
  
  # Extract cohort for indicator HYP007 by month 
  generate_study_population_hyp007:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp007 
      --index-date-range "2019-04-01 to 2023-03-31 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp007_*.feather

  generate_study_population_bp002_1y_lookback:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_bp002_1y_lookback
      --index-date-range "2019-04-01 to 2023-03-31 by month" 
      --output-dir=output/indicators
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_bp002_1y*.feather
  
  join_ethnicity:
    run: >
      cohort-joiner:v0.0.27
        --lhs output/indicators/input_*.feather
        --rhs output/indicators/input_ethnicity.feather
        --output-dir output/indicators/joined
    needs: [generate_study_population_ethnicity, generate_study_population_hyp001, generate_study_population_hyp003, generate_study_population_hyp007, generate_study_population_bp002_1y_lookback]
    outputs:
      highly_sensitive:
        cohort: output/indicators/joined/input_*.feather

  # Measures
  # Generate measures for indicator HYP001 by month
  generate_measures_hyp001:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp001 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp001_*_rate.csv

 # Generate measures for indicator HYP003 by month
  generate_measures_hyp003:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp003 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp003_*_rate.csv

  # Generate measures for indicator HYP007 by month
  generate_measures_hyp007:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp007 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp007_*_rate.csv

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

  generate_deciles:
    run: >
      deciles-charts:v0.0.21
        --input-files output/indicators/joined/measure_*_*_rate.csv
        --output-dir output/indicators/joined/
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007, generate_measures_bp002_1y_lookback]
    outputs:
      moderately_sensitive:
        deciles_charts: output/indicators/joined/deciles_chart_*_*_practice_breakdown_rate.png
        deciles_tables: output/indicators/joined/deciles_table_*_*_practice_breakdown_rate.csv
  
  # check_data:
  #   run: r:latest analysis/check_bp_recording_values_dates.R
  #   needs: [join_ethnicity]
  #   outputs:
  #     moderately_sensitive:
  #       table_count_csv: output/indicators/joined/data_check/tab_hyp*_*_2020_03_01.csv
  #       skim_txt: output/indicators/joined/data_check/skim_df_hyp*_2020_03_01.txt
  #       table_date_diff_csv: output/indicators/joined/data_check/tab_hyp*_num_bp_date_diff_2020_03_01.csv
  #       plot_date_diff: output/indicators/joined/data_check/plot_hyp*_num_bp_date_diff_2020_03_01.png

  # # Join all measure files for each indicator
  join_measures:
    run: r:latest analysis/join_measures.R
    needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007, generate_measures_bp002_1y_lookback]
    outputs:
      moderately_sensitive:
        measure_csv: output/indicators/joined/measures/measures_*.csv

  # # Join all deciles (by practice) files for each indicator
  join_deciles:
    run: r:latest analysis/join_deciles.R
    needs: [generate_deciles]
    outputs:
      moderately_sensitive:
        measure_csv: output/indicators/joined/deciles/deciles_hyp_practice.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 18:25:24

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

Job information

Status
Succeeded
Backend
TPP
Workspace
hypertension-sro
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
0b7e7bf
Requested actions
  • generate_study_population_bp002_1y_lookback

Code comparison

Compare the code used in this Job Request