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Job request: 8848

Organisation:
Bennett Institute
Workspace:
hypertension-sro
ID:
b3aqcpawcqzavw3n
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

  • Action:
    join_ethnicity
    Status:
    Status: Succeeded
    Job identifier:
    vpnycp3w5itxxjgj

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:45:01

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
b4cfb65
Requested actions
  • join_ethnicity

Code comparison

Compare the code used in this Job Request