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Job request: 5741

Organisation:
University of Manchester
Workspace:
hosp_pred_popul
ID:
hyxp6nx5rdlchqwd
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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: 3000

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 --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/hospitalisation_data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/hospitalisation_data/input_hospitalisation_*.csv.gz

  # generate_study_population_elderly:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_elderly 
  #     --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_elderly.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
        
  # describe_elderly_agedis:
  #   run: r:latest analysis/tables/gen_csv_age_check.R
  #   needs: [generate_study_population_elderly]
  #   outputs:
  #     moderately_sensitive:
  #       agetable: output/age_quant.csv

  # describe:
  #   run: r:latest analysis/plot/overall_ab_prescribing.R
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       cohort: output/overall.png
  #       boxplot: output/overallbox.png

  # describe_percentile:
  #   run: r:latest analysis/plot/overall_ab_prescribing_2575percentile.R
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       percentile: output/overall_25th_75th_percentile.png

  # describe_starpu:
  #   run: r:latest analysis/plot/starpu_ab_prescribing.R
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       cohort: output/starpuline.png
  #       boxplot: output/starpubox.png
  
  #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/*
  
  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/*

  # describe_infection_ab_UTI:
  #   run: r:latest analysis/plot/infection_ab_UTI.R
  #   needs: [generate_study_population, generate_measures]
  #   outputs:
  #      moderately_sensitive:
  #       plot: output/UTI.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 69:22:11

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

Job information

Status
Failed
Backend
TPP
Workspace
hosp_pred_popul
Requested by
ali
Branch
hospitalisation
Force run dependencies
No
Git commit hash
79905f3
Requested actions
  • generate_study_population_hospitalisation

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