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Job request: 8863

Organisation:
Bennett Institute
Workspace:
hypertension-sro
ID:
h6tjrlybgslugurq
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

  • Action:
    join_measures
    Status:
    Status: Succeeded
    Job identifier:
    a7xbzek3w3rqn66c
  • Action:
    check_data
    Status:
    Status: Succeeded
    Job identifier:
    64xwkgnspr37kmdp
  • Action:
    join_deciles
    Status:
    Status: Succeeded
    Job identifier:
    knws4ennfcoeer2u

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 "2019-03-01 to 2022-04-01 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 "2019-03-01 to 2022-04-01 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 "2019-03-01 to 2022-04-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp007_*.feather

  join_ethnicity:
    run: >
      cohort-joiner:v0.0.27
        --lhs output/indicators/input_hyp*.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]
    outputs:
      highly_sensitive:
        cohort: output/indicators/joined/input_hyp*.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_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]
    outputs:
      moderately_sensitive:
        deciles_charts: output/indicators/joined/deciles_chart_*_*_practice_rate.png
        deciles_tables: output/indicators/joined/deciles_table_*_*_practice_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_10_01.csv
        skim_txt: output/indicators/joined/data_check/skim_df_hyp*_2020_10_01.txt
        table_date_diff_csv: output/indicators/joined/data_check/tab_hyp*_num_bp_date_diff_2020_10_01.csv
        plot_date_diff: output/indicators/joined/data_check/plot_hyp*_num_bp_date_diff_2020_10_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]
    outputs:
      moderately_sensitive:
        measure_csv: output/indicators/joined/measures/measures_hyp*.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: 00:04:06

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

Job request

Status
Succeeded
Backend
TPP
Workspace
hypertension-sro
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
f4260f9
Requested actions
  • check_data
  • join_measures
  • join_deciles

Code comparison

Compare the code used in this job request