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Job request: 1665

Organisation:
Bennett Institute
Workspace:
sro-pulse-oximetry-2
ID:
kyb2vfyyyp4s5bbk
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 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

Pipeline

Show 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:12:44

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Failed
Backend
TPP
Workspace
sro-pulse-oximetry-2
Requested by
Louis Fisher
Branch
template
Force run dependencies
No
Git commit hash
4cf71b3
Requested actions
  • run_all

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