Job request: 1665

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 Service Restoration Observatory 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
4sbadfcqyciyunec failed generate_study_population
rzebg5dnzvuda65u failed generate_study_population_ethnicity
ruzgqqh5xerdo7sd failed join_ethnicity
sqf6jbvlno2brype succeeded generate_study_population_practice_count
wso3hgggmizs6acu failed generate_measures
2zodsryp7trisley failed generate_measure_ethnicity
bg5lhpojjm7yq6al failed get_patient_count
p3gpkvvgxcb7n3ya failed create_notebook
s2sqt2ybd4h5w3is failed generate_notebook

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 10000

actions:

  # convert_codelist:
  #   run: python:latest python analysis/convert_codelist.py
  #   outputs:
  #     highly_sensitive:
  #       cohort: codelists/opensafely-pulse-oximetry-converted.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-01 to 2021-02-01 by week" --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 --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_*.csv

  generate_measure_ethnicity:
    run: python:latest python analysis/generate_measure_ethnicity.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure: output/measure_ethnicity.csv

  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json

  create_notebook:
    run: python:latest python analysis/create_notebook.py
    needs: [get_patient_count, join_ethnicity]
    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, generate_measures, generate_measure_ethnicity, generate_study_population_practice_count, generate_study_population, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/SRO_Notebook.html

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:12:44

Config

  • Backend:
    TPP
  • Workspace:
    sro-pulse-oximetry-2
  • Branch:
    template
  • Creator:
    LFISHER7
  • Force run dependencies:
    False
  • Git Commit Hash:
    4cf71b3
  • Requested actions:
    • run_all