Skip to content

Job request: 13372

Organisation:
DataLab
Workspace:
antidepressant-prescribing-lda
ID:
cbejqmpwezitgjch
View repo View project.yaml

This page shows the technical details of what happened when 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 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:

  ####################
  # Curation
  ####################
  generate_study_population_curation:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_curation --output-format=csv.gz --output-dir output/curation --index-date-range "2019-03-01 to 2019-03-01 by month"
    outputs:
      highly_sensitive:
        cohort: output/curation/input_curation_*.csv.gz

  generate_dataset_report_curation:
    run: >
      python:latest python analysis/dataset_report.py
        --input-files output/curation/input_curation_*.csv.gz
        --output-dir output/curation/
    needs: [generate_study_population_curation]
    outputs:
      moderately_sensitive:
        dataset_report: output/curation/input_curation_*.html

  ####################
  # 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 "2019-01-01 to 2022-07-01 by month" --output-format=csv.gz --output-dir output/lda/codelist_update
    outputs:
      highly_sensitive:
        cohort: output/lda/codelist_update/input_lda_*.csv.gz

  # Generate dataset report
  generate_dataset_report:
    run: >
      python:latest python analysis/dataset_report.py
        --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

  # Generate dataset report lda
  generate_dataset_report_lda:
    run: >
      python:latest python analysis/dataset_report.py
        --input-files output/lda/codelist_update/input_*.csv.gz
        --output-dir output/lda/codelist_update
    needs: [generate_study_population_lda]
    outputs:
      moderately_sensitive:
        dataset_report: output/lda/codelist_update/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/codelist_update/input_*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/lda/codelist_update/joined
    needs: [generate_study_population_ethnicity, generate_study_population_lda]
    outputs:
      highly_sensitive:
        cohort: output/lda/codelist_update/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/codelist_update/joined/
      needs: [join_cohorts_lda]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/lda/codelist_update/joined/measure_*_rate.csv

  join_measures_lda:
      run: python:latest python analysis/join_and_round.py
           --input-files output/lda/codelist_update/joined/measure_*.csv
           --output-dir output/lda/codelist_update/joined/summary
           --output-name "measure_lda.csv"
      needs: [generate_measures_lda]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/lda/codelist_update/joined/summary/measure_lda.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_all_prescribing:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --measures-pattern "*_all_total_rate"
            --output-dir output/lda/codelist_update/joined/summary
            --output-name "total_population_prescribing"
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
            --confidence-intervals
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/total_population_prescribing.png

  generate_lda_learning_disability_prescribing:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --measures-pattern "*_learning_disability_total_rate"
            --output-dir output/lda/codelist_update/joined/summary
            --output-name "learning_disability_prescribing"
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
            --confidence-intervals
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/learning_disability_prescribing.png

  generate_lda_autism_prescribing:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --measures-pattern "*_autism_total_rate"
            --output-dir output/lda/codelist_update/joined/summary
            --output-name "autism_prescribing"
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
            --confidence-intervals
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/autism_prescribing.png

  generate_lda_all_breakdowns:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --measures-pattern "antidepressant_*_all_breakdown_*_rate"
            --output-dir output/lda/codelist_update/joined/summary
            --output-name "any_antidepressant_by_demographic_group"
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
            --exclude-group "Unknown"
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/any_antidepressant_by_demographic_group.png

  generate_lda_learning_disability_breakdown:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --measures-pattern "antidepressant_*_learning_disability_breakdown_*_rate"
            --output-dir output/lda/codelist_update/joined/summary
            --output-name "learning_disability_any_antidepressant_by_demographic_group"
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
            --exclude-group "Unknown"
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/learning_disability_any_antidepressant_by_demographic_group.png

  generate_lda_autism_breakdown:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --measures-pattern "antidepressant_*_autism_breakdown_*_rate"
            --output-dir output/lda/codelist_update/joined/summary
            --output-name "autism_any_antidepressant_by_demographic_group"
            --date-lines "2020-03-16" "2020-12-02"
            --scale "rate"
            --exclude-group "Unknown"
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/autism_any_antidepressant_by_demographic_group.png

  generate_table1:
    run: >
            python:latest python analysis/table1.py
            --input-file output/lda/codelist_update/joined/summary/measure_lda.csv
            --output-dir output/lda/codelist_update/joined/summary
            --measures-pattern "antidepressant_any_*_breakdown_*_rate"
            --column-names "all" "learning_disability" "autism"
    needs: [join_measures_lda]
    outputs:
      moderately_sensitive:
        cohort: output/lda/codelist_update/joined/summary/table1.html

  #############################
  # 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:

  • Started:

  • Finished:

  • Runtime: 16:57:26

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

Job information

Status
Failed
Backend
TPP
Workspace
antidepressant-prescribing-lda
Requested by
Christine Cunningham
Branch
main
Force run dependencies
No
Git commit hash
0444509
Requested actions
  • generate_study_population_curation
  • generate_dataset_report_curation
  • generate_dataset_report
  • generate_dataset_report_lda