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Job request: 5467

Workspace:
blood-pressure-qof
ID:
fylzfh5ao4zqe3ta
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Milan Wiedemann requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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 "2019-09-01 to 2022-03-31 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --index-date-range "2019-09-01 to 2022-03-31 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count_*.csv

  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*_rate.csv
  
  calculate_rates:
      run: python:latest python analysis/rate_calculations.py
      needs: [generate_measures]
      outputs:
        moderately_sensitive:
          tables: output/rate_table_*.csv
          child_code_table: output/child_code_table.csv
          plots: output/plot_*.png
          decile_chart: output/decile_chart.png
  
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/qof_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [calculate_rates, generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        notebook: output/qof_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:

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

Job information

Status
Succeeded
Backend
TPP
Workspace
blood-pressure-qof
Requested by
Milan Wiedemann
Branch
master
Force run dependencies
No
Git commit hash
ae436b8
Requested actions
  • calculate_rates
  • generate_notebook