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Job request: 7227

Organisation:
Bennett Institute
Workspace:
bmi-short-data-report
ID:
gkdf7xlw43bfnbs4
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robin Park 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: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input.feather

  preprocess_inputs:
    run: python:latest python analysis/preprocess_inputs.py --output-format feather
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/data/input_processed.feather

  generate_cohort_report:
    run: cohort-report:v3.0.0 output/data/input_processed.feather
    needs: [preprocess_inputs]
    config:
      output_path: output/cohort_reports_outputs
    outputs: 
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input_processed.html

  generate_report_bmi:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/report_bmi.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [preprocess_inputs]
    outputs:
      moderately_sensitive:
        notebook: output/report_bmi.html

  generate_report_height_weight:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/report_height_weight.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [preprocess_inputs]
    outputs:
      moderately_sensitive:
        notebook: output/report_height_weight.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:45

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

Job request

Status
Succeeded
Backend
TPP
Workspace
bmi-short-data-report
Requested by
Robin Park
Branch
main
Force run dependencies
No
Git commit hash
1409ea2
Requested actions
  • generate_report_height_weight

Code comparison

Compare the code used in this job request