Job request: 4876

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Louis Fisher requested one or more actions to be run against real patient data in the Mechanical Valve Anticoag 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
nhyz3ebigkpx2zog succeeded generate_measures
fzrhz4n36o6rrv4j succeeded generate_notebook
o6w5bvv77ghfleef succeeded generate_study_population
faamd34zjdw7ipx2 succeeded join_ethnicity
n2wbql5zwjbzhobi succeeded patient_count

Pipeline

Show Hide project.yaml
version: "3.0"

expectations:
  population_size: 15000

actions:
  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

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-12-01 by month" --output-dir=output --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/input*.csv


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

  patient_count:
    run: python:latest python analysis/get_patient_count.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        csv: output/patient_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

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity, generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/notebook.html
        figures: output/measure_*.jpeg
        total_csv: output/doac_rate_total.csv
        csvs: output/current_doac_*.csv

  recent_data:
    run: python:latest python analysis/recent_data.py
    needs: [generate_notebook]
    outputs:
      moderately_sensitive:
        csv: output/doac_rate_total_recent.csv

  # # to be run locally
  combine:
    run: python:latest python analysis/combined_analysis.py
    outputs:
      moderately_sensitive:
        measure_csv: released_outputs/combined_rate.csv
        count: released_outputs/count.jpeg
        count_with_mean: released_outputs/count_with_mean.jpeg
        rate: released_outputs/rate.jpeg

  # # to be run locally
  generate_report_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report_notebook.ipynb --execute --to html --output-dir=/workspace/released_outputs --ExecutePreprocessor.timeout=86400 --no-input
    needs: [combine]
    outputs:
      moderately_sensitive:
        notebook: released_outputs/report_notebook.html

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 15:37:29

Config

  • Backend:
    EMIS
  • Workspace:
    mechanical-valve-anticoag-updated
  • Branch:
    updates
  • Creator:
    LFISHER7
  • Force run dependencies:
    False
  • Git Commit Hash:
    1c8884b
  • Requested actions:
    • generate_study_population
    • join_ethnicity
    • patient_count
    • generate_measures
    • generate_notebook