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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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    generate_codelist_report
    Status:
    Status: Failed
    Job identifier:
    3mhthzn5f5nso7oe
    Error:
    nonzero_exit: Job exited with error code 1

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 request

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