Job request: 8725

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher ali-fahmi requested one or more actions to be run against real patient data in the BRIT Antibiotic Research 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

ID Status Action
n7lhjd3wq4cdjg34 failed generate_notebook_hospitalisation_prediction_urti

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 200000

actions:

  # generate_study_population:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/measures/input_*.csv.gz

  generate_study_population_hospitalisation:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation.csv.gz

  generate_study_population_bmi:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_bmi --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_bmi.csv.gz

  # generate_study_population_hospitalisation_2:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation --index-date-range "2019-04-01 to 2019-06-01 by month" --output-dir=output/hospitalisation_data --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/hospitalisation_data/input_hospitalisatio*.csv.gz

  # generate_study_population_hospitalisation_3:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation --index-date-range "2019-07-01 to 2019-09-01 by month" --output-dir=output/hospitalisation_data --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/hospitalisation_data/input_hospitalisati*.csv.gz

  # generate_study_population_hospitalisation_4:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation --index-date-range "2019-10-01 to 2019-12-01 by month" --output-dir=output/hospitalisation_data --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/hospitalisation_data/input_hospitalisat*.csv.gz

  # generate_notebook_hospitalisation_analysis:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_analysis.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
  #   needs: [generate_study_population_hospitalisation]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/hospitalisation_risk/hospitalisation_analysis.html 
  #       figures: output/hospitalisation_risk/*

  generate_notebook_hospitalisation_prediction_urti:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_urti_enc.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_urti --ExecutePreprocessor.timeout=86400
    needs: [generate_study_population_hospitalisation,generate_study_population_bmi]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_urti/hospitalisation_prediction_urti_enc.html 
        figures: output/hospitalisation_prediction_urti/*


  # generate_notebook_hospitalisation_prediction_urti_lr:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_urti_lr.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_urti --ExecutePreprocessor.timeout=86400
  #   needs: [generate_study_population_hospitalisation]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/hospitalisation_prediction_urti/hospitalisation_prediction_urti_lr.html 
  #       figures: output/hospitalisation_prediction_urti/*

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 25:39:04

Config

  • Backend:
    TPP
  • Workspace:
    hosp_simple
  • Branch:
    hospitalisation_simple
  • Creator:
    ali-fahmi
  • Force run dependencies:
    False
  • Git Commit Hash:
    71b3ff7
  • Requested actions:
    • generate_notebook_hospitalisation_prediction_urti