Job request: 4195

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
qmyvib3cvwmcavwy succeeded generate_measures
lnm27abdreude6ba succeeded generate_notebook
54ib525boavp5njs succeeded generate_study_population
v7pp5hmcb4mqppmv succeeded generate_study_population_ethnicity
tu2uahv7y3gizuk2 succeeded join_ethnicity
tgnj53yupa7o3vh7 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 "2019-09-01 to 2021-09-01 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
  
  # # 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: 08:40:32

Config

  • Backend:
    EMIS
  • Workspace:
    mechanical-valve-anticoag-updated
  • Branch:
    updates
  • Creator:
    LFISHER7
  • Force run dependencies:
    False
  • Git Commit Hash:
    3e0ec36
  • Requested actions:
    • generate_study_population_ethnicity
    • generate_study_population
    • join_ethnicity
    • patient_count
    • generate_measures
    • generate_notebook