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Job request: 4597

Organisation:
Bennett Institute
Workspace:
med-safety-poc
ID:
l4t7zyewhseuwogt
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Lisa Hopcroft 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:
    add_practice_ids
    Status:
    Status: Failed
    Job identifier:
    sr3eyoya77t4p5bw
    Error:
    Docker image ghcr.io/opensafely-core/python:latest is not currently available
  • Action:
    generate_plots
    Status:
    Status: Failed
    Job identifier:
    7rpnlw23vpqt2m4g
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    fcmsx5wz6pws5ohv
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 5000

actions:

  # generate_study_population_ce1:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_ce1_for_ce2 --index-date-range "2020-01-01 to 2020-12-01 by month"
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/ce1/input_ce1_for_ce2_*.csv

  generate_study_population_ce2:
    run: cohortextractor-v2:latest generate_cohort --cohort-definition analysis/study_definition_ce2.py --output output/ce2/input_ce2_*.csv --dummy-data-file output/ce1/input_expanded_ce1_for_ce2_*.csv
    outputs:
      highly_sensitive:
        cohort: output/ce2/input_ce2_*.csv


  validate_cohort_v2:
    run: cohortextractor-v2:latest validate_cohort databricks --cohort-definition analysis/study_definition_ce2.py --output output/ce2/sql/generated_sql_*.sql
    outputs:
      moderately_sensitive:
        cohort: output/ce2/sql/generated_sql_*.sql


  add_practice_ids:
    run: python:latest python analysis/add_practice_ids.py
    needs: [generate_study_population_ce2]
    outputs:
      moderately_sensitive:
        cohort: output/ce2/input_expanded_*.csv


  generate_measures:
    run: cohortextractor-v2:latest generate_measures --cohort-definition analysis/study_definition_ce2.py --output output/ce2/measure_ce2_*.csv --input=output/ce2/input_ce2_*.csv
    needs: [add_practice_ids]
    outputs:
        moderately_sensitive:
          measure_csv: output/ce2/measure_ce2_*.csv


  # generate_report:
  #   run: cohort-report:v2.0.2 output/ce1/input_2019-09-01.feather
  #   needs: [generate_study_population_ce1]
  #   config:
  #     output_path: output/ce1/cohort_reports_outputs
  #   outputs:
  #     moderately_sensitive:
  #       reports: output/ce1/cohort_reports_outputs/*.html

    
  generate_plots:
    run: python:latest python analysis/plot_measures.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        counts: output/ce2/figures/plot_*.jpeg

Timeline

  • Created:

  • Finished:

  • Runtime:

These timestamps are generated and stored using the UTC timezone on the NHSD-REF backend.

Job request

Status
Failed
Backend
NHSD REF
Workspace
med-safety-poc
Requested by
Lisa Hopcroft
Branch
main
Force run dependencies
No
Git commit hash
0da31e9
Requested actions
  • add_practice_ids
  • generate_measures
  • generate_plots

Code comparison

Compare the code used in this job request