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Job request: 7274

Organisation:
Bennett Institute
Workspace:
bmi-short-data-report
ID:
wlv6e2bsemr6zuzt
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Robin Park 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: 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_height_weight:
  #   run: python: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

  execute_validation_analyses:
    run: python:latest python analysis/report_functions.py
    needs: [preprocess_inputs]
    outputs:
      moderately_sensitive: 
        tables: output/tables/*.csv
        figures: output/figures/*.png
        
  generate_report_bmi:
    run: python:latest jupyter nbconvert /workspace/notebooks/report_bmi.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [execute_validation_analyses]
    outputs:
      moderately_sensitive:
        notebook: output/report_bmi.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:47:27

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

Job information

Status
Failed
Backend
TPP
Workspace
bmi-short-data-report
Requested by
Robin Park
Branch
main
Force run dependencies
No
Git commit hash
9e9ba4b
Requested actions
  • execute_validation_analyses
  • generate_report_bmi

Code comparison

Compare the code used in this Job Request