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Job request: 9261

Organisation:
University of Manchester
Workspace:
hospitalisation_pred
ID:
g4spj7mpozvbesfv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher ali 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: 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_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/*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:14:16

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

Job request

Status
Failed
Backend
TPP
Workspace
hospitalisation_pred
Requested by
ali
Branch
hosp_pred
Force run dependencies
No
Git commit hash
1bcc67f
Requested actions
  • generate_notebook_hospitalisation_prediction_urti
  • generate_notebook_hospitalisation_prediction_lrti
  • generate_notebook_hospitalisation_prediction_sinusitis

Code comparison

Compare the code used in this job request