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Job request: 5099

Organisation:
University of Manchester
Workspace:
amr_population
ID:
u3jjriyb7vhmqazr
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: 1000

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_infection:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_infection --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_infection_*.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 --ExecutePreprocessor.timeout=86400
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/starpu.html 
  #       figures: output/*
  #       #tables: output/tables/*
  #       #csvs: output/*/* # two possible subfolders
  #       #text: output/text/*
  
  # describe_consultation_rate:
  #   run: r:latest analysis/plot/incident_consultation_age_stacked_barchart.R
  #   needs: [generate_measures]
  #   outputs:
  #      moderately_sensitive:
  #       bar1: output/consult_age_UTI.png
  #       bar2: output/consult_age_LRTI.png
  #       bar3: output/consult_age_URTI.png
  #       bar4: output/consult_age_sinusitis.png
  #       bar5: output/consult_age_ot_externa.png
  #       bar6: output/consult_age_otmedia.png
  #       bar7: output/consult_age_repeatedUTI.png
       


  # describe_consultation_prescribed:
  #   run: r:latest analysis/plot/consultation_prescibed_percentage.R
  #   needs: [generate_study_population]
  #   outputs:
  #      moderately_sensitive:
  #       bar1: output/prescribed_percentage_UTI.png
  #       csvs: output/uti_prescrib_check.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]
  #   outputs:
  #   moderately_sensitive:
  #       notebook: output/hospitalisation_risk/hospitalisation_analysis.html 
  #       figures: output/hospitalisation_risk/*
    
  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]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_risk/hospitalisation_analysis.html 
        figures: output/hospitalisation_risk/*

  # describe_prior_ab_12mb4:
  #   run: r:latest analysis/plot/ab_1yb4_stackedbar_2.R
  #   needs: [generate_study_population]
  #   outputs:
  #      moderately_sensitive:
  #       plot: output/AB_1yb4_line.jpeg
  #       plot_sex: output/AB_1yb4_SEX.jpeg
  #       count_table: output/prior_ab_by_month.csv      


  # describe_consultation_rate_all:
  #   run: r:latest analysis/plot/incident_consultation_by_age_infection.R
  #   needs: [generate_measures]
  #   outputs:
  #      moderately_sensitive:
  #       plot1: output/consult_age_1.jpeg
  #       plot2: output/consult_age_2.jpeg
  #       plot3: output/consult_all.jpeg
  #       csv1: output/consultation_rate.csv
  #       csv2: output/consultation_GP_rate.csv

  # describe_infection_prescribed_percent:
  #   run: r:latest analysis/plot/infection_prescibed_percent.R
  #   needs: [generate_measures]
  #   outputs:
  #      moderately_sensitive:
  #       plot1: output/infection_ab_precent_p1.jpeg
  #       plot2: output/infection_ab_precent_p2.jpeg
  #       plot3: output/infection_ab_precent_i1.jpeg
  #       plot4: output/infection_ab_precent_i2.jpeg
  #       plot5: output/infection_ab_precent_all.jpeg
  #       csv1: output/prescribed_infection_prevalent.csv
  #       csv2: output/prescribed_infection_incident.csv

  # describe_top10ABtypes_byInfection:
  #   run: r:latest analysis/plot/abtypes_top10.R
  #   needs: [generate_measures]
  #   outputs:
  #      moderately_sensitive:
  #       plot1: output/abtype_UTI.jpeg
  #       plot2: output/abtype_URTI.jpeg
  #       plot3: output/abtype_LRTI.jpeg
  #       plot4: output/abtype_sinusitis.jpeg
  #       plot5: output/abtype_ot_externa.jpeg
  #       plot6: output/abtype_otmedia.jpeg
  #       plot7: output/abtype_percent_UTI.jpeg
  #       plot8: output/abtype_percent_URTI.jpeg
  #       plot9: output/abtype_percent_LRTI.jpeg
  #       plot10: output/abtype_percent_sinusitis.jpeg
  #       plot11: output/abtype_percent_ot_externa.jpeg
  #       plot12: output/abtype_percent_otmedia.jpeg
  #       csv: output/abtype_top10_by_infection.csv
  
  # describe_top10ABtypes_total:
  #   run: r:latest analysis/plot/types_ab_prescriptions.R
  #   needs: [generate_study_population]
  #   outputs:
  #      moderately_sensitive:
  #       plot1: output/abtype_all_Rx.jpeg
  #       plot2: output/abtype_all_Rx_percent.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 107:07:24

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

Job information

Status
Failed
Backend
TPP
Workspace
amr_population
Requested by
ali
Branch
main
Force run dependencies
Yes
Git commit hash
aa4f078
Requested actions
  • generate_measures
  • generate_notebook_hospitalisation_analysis

Code comparison

Compare the code used in this Job Request