Job request: 5027

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 Blood Pressure - Quality and Outcomes Framework (QOF) 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

ID Status Action
i264bg7wtg75ntlv succeeded generate_study_population
p7lt46qivvji6bg4 succeeded generate_study_population_ethnicity
v4gil7mcbuadsiyp succeeded join_ethnicity
qjm6ng7yaeim7dh7 succeeded generate_study_population_practice_count
itak5tgoagwuwiyz succeeded generate_measures
i4qlt5tusp7xbd2x succeeded calculate_rates
cuh5zsw6avpkmfhc succeeded create_notebook
grucosavhglde56f succeeded generate_notebook
hi5ay2y2pd6dztb7 succeeded run_tests

Pipeline

Show Hide 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
  
  create_notebook:
    run: python:latest python analysis/create_notebook.py
    outputs:
      moderately_sensitive:
        notebook: analysis/SRO_Notebook.ipynb

  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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 13:12:15

Config

  • Backend:
    TPP
  • Workspace:
    blood-pressure-qof
  • Branch:
    master
  • Creator:
    milanwiedemann
  • Force run dependencies:
    False
  • Git Commit Hash:
    260e155
  • Requested actions:
    • run_all