This page shows the technical details of what happened when authorised researcher Rachel Seeley requested one or more actions to be run against real patient data in the Direct Oral Anticoagulant (DOAC) prescribing during COVID-19 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.

Pipeline

Show Hide project.yaml
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2021-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_dose:
    run: python:latest python analysis/calculate_dose_scaled_back.py
    needs: [generate_study_population_1, generate_study_population_2]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather
  
  #generate_study_population_ethnicity:
  #run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=csv
  #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_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
    needs: [generate_dose]
    outputs: 
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/report.html
        plots: output/*.png

  #generate_dose_match:
  #run: python:latest python analysis/dose_match.py
  #needs: [generate_measures]
  #outputs:
  #moderately_sensitive:
  #figure: output/dose_match.png

State

State is inferred from the related Jobs.

Status: Failed

JobRequestError: generate_measures failed on a previous run and must be re-run

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: -

Config