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Job request: 1029

Organisation:
Bennett Institute
Workspace:
sro-pulse-oximetry
ID:
tmefs34ikgjqgqnb
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release 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 "2019-01-01 to 2021-01-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.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

  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]
    outputs:
      moderately_sensitive:
        notebook: output/pulse_oximetry_SRO.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:44:57

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sro-pulse-oximetry
Requested by
Louis Fisher
Branch
master
Force run dependencies
Yes
Git commit hash
5675c03
Requested actions
  • generate_study_population
  • generate_measures
  • generate_plots
  • generate_notebook
  • run_all

Code comparison

Compare the code used in this job request