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Job request: 7559

Organisation:
Bennett Institute
Workspace:
test-interactive
ID:
6nom2b2bvkajkv2h
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  
  generate_study_population:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition
        --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather
        
  generate_study_population_monthly:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_monthly
        --output-format=feather
        --index-date-range "2021-01-01 to 2021-12-01 by month"
    outputs:
      highly_sensitive:
        cohort: output/input_monthly_*.feather
    
  generate_study_population_weekly:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_weekly
        --output-format=feather
        --index-date-range "2021-01-01 to 2021-12-24 by week" 
    outputs:
      highly_sensitive:
        cohort: output/input_weekly_*.feather

  generate_weekly_summary_table:
    run: python:latest python analysis/weekly_summary.py
    needs: [generate_study_population_weekly]
    outputs:
      moderately_sensitive:
        table: output/weekly_count.csv

  generate_study_counts_bp:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_counts_bp
        --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_counts_bp.feather

  generate_study_counts_eth:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_counts_eth
        --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_counts_eth.feather

  generate_study_counts_aaa:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_counts_aaa
        --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_counts_aaa.feather

  generate_top_5_table:
    run: python:latest python analysis/top_codes_table.py
    needs: [generate_study_counts_bp, generate_study_counts_aaa]
    outputs:
      moderately_sensitive:
        table: output/top_5_code_table_*.csv

  generate_codelist_report:
    run: >
      cohortextractor:latest generate_codelist_report
        --output-dir=output
        --codelist-path=codelists/opensafely-systolic-blood-pressure-qof.csv
        --start-date=2021-01-01
        --end-date=2021-12-31
    outputs:
      moderately_sensitive:
        table: output/counts_per_*.csv
        list_sizes: output/list_sizes.csv

  generate_measures:
    run: python:latest python analysis/generate_measures.py
    needs: [generate_codelist_report]
    outputs:
      moderately_sensitive:
        measure: output/measure_counts_per_week_practice.csv

  generate_deciles_charts:
    run: >
      deciles-charts:v0.0.15
        --input-files output/measure_counts_per_week_practice.csv
        --output-dir output
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/deciles_*_*.*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:06

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

Job information

Status
Failed
Backend
TPP
Workspace
test-interactive
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
7e57c37
Requested actions
  • generate_codelist_report
  • generate_measures
  • generate_deciles_charts

Code comparison

Compare the code used in this Job Request