Job request: 12087

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Ali 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
ifn2ygjopba67tzr failed generate_notebook_hospitalisation_prediction_lrti
y4yctmlfbncvkray succeeded generate_notebook_hospitalisation_prediction_ot_externa
4jhn3i6rivbmtxkf succeeded generate_notebook_hospitalisation_prediction_otmedia
rzf5bidu7r7j26xy failed generate_notebook_hospitalisation_prediction_sinusitis
axol6a7icvh7fj5b failed generate_notebook_hospitalisation_prediction_urti
tc3tqslzt7vrbxci failed generate_notebook_hospitalisation_prediction_uti

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 200000

actions:

  generate_study_population_hospitalisation_urti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_urti --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_urti.csv.gz

  generate_study_population_hospitalisation_lrti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_lrti --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_lrti.csv.gz

  generate_study_population_hospitalisation_uti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_uti --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_uti.csv.gz

  generate_study_population_hospitalisation_sinusitis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_sinusitis --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_sinusitis.csv.gz

  generate_study_population_hospitalisation_ot_externa:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_ot_externa --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_ot_externa.csv.gz

  generate_study_population_hospitalisation_otmedia:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_otmedia --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_otmedia.csv.gz

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

  generate_notebook_hospitalisation_prediction_lrti:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_lrti.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_lrti --ExecutePreprocessor.timeout=86400
    # needs: [generate_study_population_hospitalisation_lrti,generate_study_population_bmi]
    needs: [generate_study_population_hospitalisation_lrti]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_lrti/hospitalisation_prediction_lrti.html 
        figures: output/hospitalisation_prediction_lrti/*

  generate_notebook_hospitalisation_prediction_uti:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_uti.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_uti --ExecutePreprocessor.timeout=86400
    # needs: [generate_study_population_hospitalisation_uti,generate_study_population_bmi]
    needs: [generate_study_population_hospitalisation_uti]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_uti/hospitalisation_prediction_uti.html 
        figures: output/hospitalisation_prediction_uti/*

  generate_notebook_hospitalisation_prediction_sinusitis:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_sinusitis.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_sinusitis --ExecutePreprocessor.timeout=86400
    # needs: [generate_study_population_hospitalisation_sinusitis,generate_study_population_bmi]
    needs: [generate_study_population_hospitalisation_sinusitis]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_sinusitis/hospitalisation_prediction_sinusitis.html 
        figures: output/hospitalisation_prediction_sinusitis/*

  generate_notebook_hospitalisation_prediction_ot_externa:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_ot_externa.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_ot_externa --ExecutePreprocessor.timeout=86400
    # needs: [generate_study_population_hospitalisation_ot_externa,generate_study_population_bmi]
    needs: [generate_study_population_hospitalisation_ot_externa]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_ot_externa/hospitalisation_prediction_ot_externa.html 
        figures: output/hospitalisation_prediction_ot_externa/*

  generate_notebook_hospitalisation_prediction_otmedia:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction_otmedia.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction_otmedia --ExecutePreprocessor.timeout=86400
    # needs: [generate_study_population_hospitalisation_otmedia,generate_study_population_bmi]
    needs: [generate_study_population_hospitalisation_otmedia]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_otmedia/hospitalisation_prediction_otmedia.html 
        figures: output/hospitalisation_prediction_otmedia/*

  generate_notebook_hosp_plots:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hosp_plots.ipynb --execute --to html --output-dir=/workspace/output/hosp_plots --ExecutePreprocessor.timeout=86400
    needs: [generate_notebook_hospitalisation_prediction_urti,generate_notebook_hospitalisation_prediction_lrti,generate_notebook_hospitalisation_prediction_uti,generate_notebook_hospitalisation_prediction_sinusitis,generate_notebook_hospitalisation_prediction_otmedia,generate_notebook_hospitalisation_prediction_ot_externa]
    outputs:
      moderately_sensitive:
        notebook: output/hosp_plots/hosp_plots.html 
        figures: output/hosp_plots/*

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:59:35

Config

  • Backend:
    TPP
  • Workspace:
    hospitalisation_pred
  • Branch:
    hosp_pred
  • Creator:
    ali-fahmi
  • Force run dependencies:
    False
  • Git Commit Hash:
    a646676
  • Requested actions:
    • generate_notebook_hospitalisation_prediction_urti
    • generate_notebook_hospitalisation_prediction_lrti
    • generate_notebook_hospitalisation_prediction_uti
    • generate_notebook_hospitalisation_prediction_sinusitis
    • generate_notebook_hospitalisation_prediction_ot_externa
    • generate_notebook_hospitalisation_prediction_otmedia