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Job request: 9803

Organisation:
Bennett Institute
Workspace:
pathology-comparators-main
ID:
u6iu77ec7us7et5b
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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: 10000

actions:

  
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-10-01 to 2021-10-08 by week" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_report:
    run: cohort-report:v3.0.0 output/input_2021-10-01.feather
    needs: [generate_study_population]
    config:
      output_path: output/cohort_reports_outputs
    outputs:
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input_2021-10-01.html

  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv_1: output/measure_*_rate.csv
          measure_csv_2: output/measure_*_rate_by_region.csv
          measure_csv_3: output/measure_*_rate_by_comparator.csv
          measure_csv_4: output/measure_*_rate_by_value.csv
          # note the weekly files are not stored, only the compiled file
  
  calculate_rates:
      run: python:latest python analysis/rate_calculations.py
      needs: [generate_measures]
      outputs:
        moderately_sensitive:
          tables: output/*_per_test.csv

  
  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/SRO_Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [create_notebook, calculate_rates, generate_study_population_practice_count]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/SRO_Notebook.html

  # run_tests:
  #   run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
  #   outputs:
  #     moderately_sensitive:
  #       log: output/pytest.xml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:44:33

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pathology-comparators-main
Requested by
Helen Curtis
Branch
master
Force run dependencies
No
Git commit hash
fe489b7
Requested actions
  • generate_study_population
  • generate_report
  • generate_measures

Code comparison

Compare the code used in this Job Request