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Job request: 1425

Organisation:
Bennett Institute
Workspace:
hospital-admissions-validation
ID:
e4r5mw7zbpos4r2c
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 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_descriptives:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_descriptives
    outputs:
      highly_sensitive:
        cohort: output/input_descriptives.csv
  
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
  
  generate_results:
    run: python:latest python analysis/generate_results.py
    needs: [generate_study_population, generate_study_population_descriptives]
    outputs:
      moderately_sensitive:
        ae_attendance_count_dict: output/num_ae_attendances.json
        hosp_dict: output/emergency_hospitalisation.json
        ae_dict: output/ae.json
        any_ae_dict: output/ae_any.json
        all_ae_dict: output/ae_all.json
        discharge_csv: output/discharge_destination.csv
        performance_dict: output/model_performance.json
        sensitivity_dict: output/sensitivity.json
        model_csvs: output/model_*.csv
  
  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/results.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_study_population]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/results.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
GitError: Error fetching commit 979fdff47f90dec4097c23bb57eb0a5867c3d229 from https://github.com/opensafely/vaccine-effectiveness-hospital-admissions-validation
Backend
TPP
Workspace
hospital-admissions-validation
Requested by
Louis Fisher
Branch
secondary
Force run dependencies
No
Git commit hash
979fdff
Requested actions
  • generate_results

Code comparison

Compare the code used in this job request