Job request: 10316

Organisation:: Bennett Institute
Workspace:: antidepressant-prescribing-lda
ID:: blujghuxgxebt26d

This page shows the technical details of what happened when the authorised researcher Christine Cunningham 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:

generate_study_population_register

Status:

Status: Succeeded

Job identifier:

5c4vzwmjizby6u37
Action:

join_cohorts_qof

Status:

Status: Succeeded

Job identifier:

xncv4pib5fruhwyf
Action:

generate_measures_register

Status:

Status: Succeeded

Job identifier:

ga7kaqzmjmrnzy4z

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 10000

actions:

  ####################
  # Cohort Generation
  ####################

  # Since this runs on everyone, we can reuse for both studies 
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  # Generate depression register by month
  generate_study_population_register:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_register --index-date-range "2020-01-01 to 2020-04-01 by month" --output-format=csv.gz --output-dir output/qof
    outputs:
      highly_sensitive:
        cohort: output/qof/input_register_*.csv.gz

  # Generate dep003 by month
  generate_study_population_dep003:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dep003 --index-date-range "2020-01-01 to 2020-04-01 by month" --output-format=csv.gz --output-dir output/qof
    outputs:
      highly_sensitive:
        cohort: output/qof/input_dep003_*.csv.gz

  # Generate prescription variables by month
  generate_study_population_lda:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_lda --index-date-range "2020-01-01 to 2022-04-01 by month" --output-format=csv.gz --output-dir output/lda
    outputs:
      highly_sensitive:
        cohort: output/lda/input_lda_*.csv.gz

  # Generate dataset report
  generate_dataset_report:
    run: >
      dataset-report:v0.0.19
        --input-files output/qof/input_*.csv.gz
        --output-dir output/qof/
    needs: [generate_study_population_register, generate_study_population_dep003]
    outputs:
      moderately_sensitive:
        dataset_report: output/qof/input_*.html

  ####################
  # Join ethnicity to all generated input files
  # Efficiency fix https://github.com/opensafely/research-template
  # BUT BEWARE STALE DATA
  ###################

  join_cohorts_qof:
    run: >
      cohort-joiner:v0.0.18
        --lhs output/qof/input_*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/qof/joined
    needs: [generate_study_population_ethnicity, generate_study_population_register, generate_study_population_dep003]
    outputs:
      highly_sensitive:
        cohort: output/qof/joined/input_*.csv.gz

  join_cohorts_lda:
    run: >
      cohort-joiner:v0.0.18
        --lhs output/lda/input_*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/lda/joined
    needs: [generate_study_population_ethnicity, generate_study_population_lda]
    outputs:
      highly_sensitive:
        cohort: output/lda/joined/input_*.csv.gz

  ####################
  # Python testing
  ####################
  test_input:
    run: >
            python:latest python analysis/test_input.py
            --input-files output/qof/joined/input_*.csv.gz
            --output-dir output/qof/joined/python
    needs: [join_cohorts_qof]
    outputs:
      moderately_sensitive:
        cohort: output/qof/joined/python/test_*.*

  ####################
  # Measures
  ####################

  # Output the summary values by date
  generate_measures_register:
      run: cohortextractor:latest generate_measures --study-definition study_definition_register --output-dir=output/qof/joined
      needs: [join_cohorts_qof]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/qof/joined/measure_register_*_rate.csv

  join_measures_register:
      run: python:latest python analysis/join_and_round.py
           --input-list output/qof/joined/measure_register_total_rate.csv
           --input-list output/qof/joined/measure_register_age_band_rate.csv
           --input-list output/qof/joined/measure_register_carehome_rate.csv
           --input-list output/qof/joined/measure_register_ethnicity_rate.csv
           --input-list output/qof/joined/measure_register_imd_rate.csv
           --input-list output/qof/joined/measure_register_learning_disability_rate.csv
           --input-list output/qof/joined/measure_register_region_rate.csv
           --input-list output/qof/joined/measure_register_sex_rate.csv
           --output-dir output/qof/joined/summary
           --output-name "measure_register.csv"
      needs: [generate_measures_register]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/qof/joined/summary/measure_register.csv

  generate_measures_dep003:
      run: cohortextractor:latest generate_measures --study-definition study_definition_dep003 --output-dir=output/qof/joined
      needs: [join_cohorts_qof]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/qof/joined/measure_dep003_*_rate.csv

  generate_measures_lda:
      run: cohortextractor:latest generate_measures --study-definition study_definition_lda --output-dir=output/lda/joined
      needs: [join_cohorts_lda]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/lda/joined/measure_*_rate.csv

  #############################
  # Plotting
  #############################
  generate_qof_deciles_charts:
    run: >
            deciles-charts:v0.0.15
            --input-files output/qof/joined/measure_*_practice_rate.csv
            --output-dir output/qof/joined
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_register, generate_measures_dep003]
    outputs:
      moderately_sensitive:
        cohort: output/qof/joined/deciles_*_*.*

  generate_qof_groups:
    run: >
            python:latest python analysis/group_charts.py
            --input-files output/qof/joined/measure_*.csv
            --output-dir output/qof/joined
            --date-lines "2019-03-31" "2020-03-31" "2021-03-31"
            --scale "percentage"
    needs: [generate_measures_register, generate_measures_dep003]
    outputs:
      moderately_sensitive:
        cohort: output/qof/joined/group_chart_*.png

  generate_lda_groups:
    run: >
            python:latest python analysis/group_charts.py
            --input-files output/lda/joined/measure_*.csv
            --output-dir output/lda/joined
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
    needs: [generate_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/joined/group_chart_*.png

  generate_table1:
    run: >
            python:latest python analysis/table1.py
            --input-dir output/lda/joined
            --output-dir output/lda/joined
            --measure-attribute "antidepressant_any"
    needs: [generate_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/joined/table1.csv

  #############################
  # Display
  #############################
  generate_report:
    run: >
            python:latest python analysis/report.py
            --input-dir output/qof/joined
            --output-dir output/qof/joined
            --resource-dir analysis/resources
    needs: [generate_qof_deciles_charts, generate_qof_groups]
    outputs:
      moderately_sensitive:
        cohort: output/qof/joined/report.html

Timeline

Created: 2 years, 4 months ago 18 Jul 2022 15:12:16 UTC
Started: 2 years, 4 months ago 18 Jul 2022 20:07:52 UTC
Finished: 2 years, 4 months ago 19 Jul 2022 02:07:17 UTC
Runtime: 05:58:48

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

Job information

Status: Succeeded
Backend: TPP
Workspace: antidepressant-prescribing-lda
Requested by: Christine Cunningham
Branch: main
Force run dependencies: No
Git commit hash: cdaf6a3
Requested actions: generate_study_population_register

join_cohorts_qof

generate_measures_register

Code comparison

Compare the code used in this Job Request