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Job request: 6851

Organisation:
University of Manchester
Workspace:
hosp_pred_urti_2019
ID:
qlwosattrdlma6dn
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 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: 10000

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_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation --index-date-range "2019-01-01 to 2019-03-01 by month" --output-dir=output/hospitalisation_data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_*.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_measures:
  #   run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
  #   needs: [generate_study_population]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measure_*.csv
         
  #generate_notebook_starpu:
  #  run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
  #  needs: [generate_measures]
  #  outputs:
  #    moderately_sensitive:
  #      notebook: output/hospitalisation_risk/starpu.html 
  #      figures: output/hospitalisation_risk/*
        #tables: output/tables/*
        #csvs: output/*/* # two possible subfolders
        #text: output/text/*

  # 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_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]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/hospitalisation_prediction_uti/hospitalisation_prediction_uti.html 
  #       figures: output/hospitalisation_prediction_uti/*

  # describe_hospitalisation_reading_csv_urti:
  #   run: r:latest analysis/hospitalisation_reading_csv_urti.R
  #   needs: [generate_study_population_hospitalisation_1, generate_study_population_hospitalisation_2, generate_study_population_hospitalisation_3, generate_study_population_hospitalisation_4]
  #   outputs:
  #      moderately_sensitive:
  #       rds1: output/hospitalisation_data/data2019.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_1, generate_study_population_hospitalisation_2]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_prediction_urti/hospitalisation_prediction_urti.html 
        figures: output/hospitalisation_prediction_urti/*
  
  # generate_notebook_hospitalisation_prediction:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_prediction.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_prediction --ExecutePreprocessor.timeout=86400
  #   needs: [generate_study_population_hospitalisation]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/hospitalisation_prediction/hospitalisation_prediction.html 
  #       figures: output/hospitalisation_prediction/*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:30:57

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

Job information

Status
Failed
Backend
TPP
Workspace
hosp_pred_urti_2019
Requested by
ali
Branch
hospitalisation
Force run dependencies
No
Git commit hash
9ca023e
Requested actions
  • generate_notebook_hospitalisation_prediction_urti

Code comparison

Compare the code used in this Job Request