Job request: 3029

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Chris Yeung requested one or more actions to be run against real patient data in the Graphnet-OpenSAFELY-Test 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
n4watsbidqtpbahs succeeded get_practice_count
hninjwl76civykx3 succeeded get_patient_count
3onleyjujgvxwimd succeeded generate_notebook
b2p6amwsewgkgmpl failed get_event_summary

Pipeline

Show Hide project.yaml 
version: '3.0'

expectations:
  population_size: 1000
   
    
actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-02-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --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: [generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*.csv
  
  get_practice_count:
    run: python:latest python analysis/get_practice_count.py
    needs: [generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        text: output/practice_count.json
  
  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json
        


        
  
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
     
  
  # generate_notebook_practice:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_by_practice.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_measures, get_practice_count, get_patient_count]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/sentinel_measures_by_practice.html
  #       csvs: output/*_check.csv

  get_event_summary:
    run: python:latest python analysis/get_event_summary.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/*_event_summary.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:11:17

Config

  • Backend:
    GRAPHNET
  • Workspace:
    sro-measure-cam-test
  • Branch:
    graphnet
  • Creator:
    chrisyeunggraphnet
  • Force run dependencies:
    False
  • Git Commit Hash:
    049f0cf
  • Requested actions:
    • get_practice_count
    • get_patient_count
    • generate_notebook
    • get_event_summary