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Job request: 7223

Organisation:
Bennett Institute
Workspace:
test-interactive
ID:
ux2ay4szqs3iyl3d
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Lucy Bridges 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_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_eth, 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:23

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
Lucy Bridges
Branch
main
Force run dependencies
No
Git commit hash
e8e47d2
Requested actions
  • generate_codelist_report

Code comparison

Compare the code used in this Job Request