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Job request: 10480

Organisation:
University of Nottingham
Workspace:
postopcovid
ID:
e7gkodrojlqecaxn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colin Crooks 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: 50000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_study_population_COD:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_COD
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/input_COD.csv
        
  data_manage:
    run: r:latest analysis/data_manage.R
    needs: [generate_study_population,generate_study_population_COD]
    outputs:
      highly_sensitive:
        cohort: output/cohort_long.feather

  data_manage_postdisch_week:
    run: r:latest analysis/data_manage_postdisch_weeks.R
    needs: [generate_study_population,data_manage]
    outputs:
      highly_sensitive:
        cohort_splits: output/cohort_postdisch_week_splits.feather

  flowchart:      
    run: r:latest analysis/FlowChart.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        flowchart_data: output/flowchart.RData
        flowchart_fig: output/Flowchart.pdf
        
  table_demo:      
    run: r:latest analysis/Table_demo.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_demo: output/table_demo.csv

  table_postopcovid_crude:      
    run: r:latest analysis/Table_postopcovid_crude.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_crude: output/postopcovid_crude.RData
        table_crude_csv: output/postopcovid_crude.csv
        
  table_postopcovid_crude_sub:      
    run: r:latest analysis/Table_postopcovid_crude_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_crude: output/postopcovid_crude_sub.RData
        table_crude_csv: output/postopcovid_crude_sub.csv
       
  table_postopcovid_adjusted:      
    run: r:latest analysis/Table_postopcovid_adjusted.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_adjusted: output/postopcovid_adjusted.RData
        table_adjusted_csv: output/postopcovid_adjusted.csv
        model_adjusted: output/postopcovidmodel.csv
        model_adjusted_waves: output/postopcovidmodelwaves.csv
        plot_adjusted_waves: output/adjusted_waves_plot.png
       
  table_postopcovid_adjusted_per_op:      
    run: r:latest analysis/Table_postopcovid_adjusted_per_op.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_adjusted: output/postopcovid_adjusted_per_op.RData
        table_adjusted_csv: output/postopcovid_adjusted_per_op*.csv

  table_postopcovid_adjusted_bootstrap:      
    run: r:latest analysis/Table_postopcovid_adjusted_bootstrap.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        samples_adjusted: output/postopcovid_adjusted_bootstrappedIQR.RData
        summary_boot_adjusted_csv: output/postopcovid_adjusted_bootstrappedIQR.csv


  table_postopcovid_adjusted_bootstrap_sub:      
    run: r:latest analysis/Table_postopcovid_adjusted_bootstrap_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        samples_adjusted: output/postopcovid_adjusted_bootstrappedIQR_sub.RData
        summary_boot_adjusted_csv: output/postopcovid_adjusted_bootstrappedIQR_sub.csv

  table_postopcovid_adjusted_sub:      
    run: r:latest analysis/Table_postopcovid_adjusted_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_adjusted_sub: output/postopcovid_adjusted_sub.RData
        table_adjusted_sub_csv: output/postopcovid_adjusted_sub.csv
        model_adjusted_sub: output/postopcovidmodelsub.csv
        model_adjusted_waves_sub: output/postopcovidmodelwavessub.csv
        plot_adjusted_waves_sub: output/adjusted_waves_sub_plot.png

  table_postopcovid_tv:      
    run: r:latest analysis/Table_postopcovid_tv.R
    needs: [generate_study_population, data_manage,data_manage_postdisch_week]
    outputs:
      moderately_sensitive:
        table_tv: output/postopcovid_tv.RData
        table_tv_csv: output/postopcovid_tv.csv
        model_VTE_tv: output/postopVTEmodelsplit.csv
        table_tv_VTE_csv: output/postopcovid_VTE_tv.csv      
        model_COVID_tv: output/postopcovidmodelsplit.csv

  table_postopcovid_tv_daily:      
    run: r:latest analysis/Table_postopcovid_tv_continuous.R
    needs: [generate_study_population, data_manage,data_manage_postdisch_week]
    outputs:
      moderately_sensitive:
        table_tv_daily: output/postopcovid_tv_daily.RData
        table_tv_csv_daily: output/daily_postopcovid_tv.csv
        plot_tv_daily: output/dailyCovidRisk.pdf
        table_tv_VTE_csv_daily: output/daily_postopcovid_VTE_tv.csv    
        plot_tv_VTE_daily: output/dailyVTERisk.pdf

  table_postopcovid_tv_sub:      
    run: r:latest analysis/Table_postopcovid_tv_sub.R
    needs: [generate_study_population, data_manage,data_manage_postdisch_week]
    outputs:
      moderately_sensitive:
        table_tv_sub: output/postopcovid_tv_sub.RData
        table_tv_sub_csv: output/postopcovid_tv_sub.csv
        model_VTE_tv_sub: output/postopVTEmodelsplitsub.csv
        table_VTE_tv_sub_csv: output/postopcovid_VTE_tv_sub.csv
        model_COVID_tv_sub: output/postopcovidmodelsplitsub.csv
        
  table_postopcovid_tv_daily_sub:      
    run: r:latest analysis/Table_postopcovid_tv_continuous_sub.R
    needs: [generate_study_population, data_manage,data_manage_postdisch_week]
    outputs:
      moderately_sensitive:
        table_tv_daily_sub: output/postopcovid_tv_daily_sub.RData
        table_tv_csv_daily_sub: output/daily_postopcovid_tv_sub.csv
        plot_tv__daily_sub: output/dailyCovidRiskSub.pdf
        table_tv_VTE_csv_daily_sub: output/daily_postopcovid_VTE_tv_sub.csv    
        plot_tv_VTE_daily_sub: output/dailyVTERiskSub.pdf        
        
  table_postopLOS:      
    run: r:latest analysis/Table_postoplos.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_los: output/postoplos.RData
        table_los_csv: output/postoplos.csv
        model_los: output/postopLOSmodel.csv
        
  table_postopLOS_sub:      
    run: r:latest analysis/Table_postoplos_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_los_sub: output/postoplos_sub.RData
        table_los_sub_csv: output/postoplos_sub.csv
        model_los_sub: output/postopLOSmodel_sub.csv
        
  table_postopVTE:      
    run: r:latest analysis/Table_postopVTE.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_VTE: output/postopVTE.RData
        table_VTE_csv: output/postopVTE.csv
        model_VTE: output/postopVTEmodel.csv
        plot_VTE_waves: output/VTE_waves_plot.png
        
  table_postopVTE_sub:      
    run: r:latest analysis/Table_postopVTE_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_VTE_sub: output/postopVTE_sub.RData
        table_VTE_sub_csv: output/postopVTE_sub.csv        
        model_VTE_sub: output/postopVTEmodelsub.csv
        plot_VTE_sub_waves: output/VTE_waves_sub_plot.png
       
  table_postopmortality:      
    run: r:latest analysis/Table_postopmortality.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_mortality: output/postopmortality.RData
        table_mortality_csv: output/postopmortality.csv
        model_mortality: output/postopdiedmodel.csv
        plot_mortality: output/mortality_waves_plot.png
        
  table_postopmortality_sub:      
    run: r:latest analysis/Table_postopmortality_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_mortality_sub: output/postopmortality_sub.RData
        table_mortality_sub_csv: output/postopmortality_sub.csv
        model_mortality_sub: output/postopdiedmodelsub.csv
        plot_mortality_sub: output/mortality_waves_sub_plot.png
  
  table_postopreadmit:      
    run: r:latest analysis/Table_postop_readmit.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_readmit: output/postopreadmit.RData
        table_readmit_csv: output/postopreadmit.csv
        model_readmit: output/postopreadmitmodel.csv
        plot_readmit: output/readmit_waves_plot.png        
        
  table_postopreadmit_sub:      
    run: r:latest analysis/Table_postop_readmit_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_readmit_sub: output/postopreadmit_sub.RData
        table_readmit_sub_csv: output/postopreadmit_sub.csv
        model_readmit_sub: output/postopreadmitmodelsub.csv
        plot_readmit_sub: output/readmit_waves_sub_plot.png

  report:
    run: r:latest -e 'rmarkdown::render("analysis/Report.rmd", output_dir = "/workspace/output/",knit_root_dir = "/workspace",)'    
    needs: [generate_study_population, data_manage, data_manage_postdisch_week,
    flowchart,
    table_demo,
    table_postopcovid_crude,
    table_postopcovid_adjusted,
    table_postopcovid_tv,
    table_postopLOS,
    table_postopVTE,
    table_postopmortality,
    table_postopreadmit,
    table_postopcovid_crude_sub,
    table_postopcovid_adjusted_sub,
    table_postopcovid_tv_sub,
    table_postopLOS_sub,
    table_postopVTE_sub,
    table_postopmortality_sub,
    table_postopreadmit_sub]
    outputs:
      moderately_sensitive:
        results_report: output/Report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:28:57

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

Job information

Status
Failed
Backend
TPP
Workspace
postopcovid
Requested by
Colin Crooks
Branch
main
Force run dependencies
No
Git commit hash
66a4bae
Requested actions
  • table_postopcovid_adjusted_bootstrap
  • table_postopcovid_adjusted_bootstrap_sub
  • table_postopcovid_tv_daily
  • table_postopcovid_tv_daily_sub

Code comparison

Compare the code used in this Job Request