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Job request: 1081

Organisation:
Bennett Institute
Workspace:
sro-pulse-oximetry
ID:
sbbire6pkot7zfft
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:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-01 to 2021-01-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/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/measures
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv: output/measures/measure_*.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


  generate_plots:
    run: python:latest python analysis/generate_plots.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        figure1: output/figures/population_rates.jpeg
        figure2: output/figures/sex_rates.jpeg
        figure3: output/figures/region_rates.jpeg
        figure4: output/figures/age_rates.jpeg
  
 
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/pulse_oximetry_SRO.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_patient_count, generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        notebook: output/pulse_oximetry_SRO.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:28:16

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

Job information

Status
Failed
Backend
TPP
Workspace
sro-pulse-oximetry
Requested by
Louis Fisher
Branch
master
Force run dependencies
Yes
Git commit hash
825e710
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request