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Job request: 10351

Organisation:
University of Nottingham
Workspace:
postopcovid
ID:
pmlcl7cgivkaraxq
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 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: 50000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  data_manage:
    run: r:latest analysis/data_manage.R
    needs: [generate_study_population]
    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_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_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_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: 13:13:13

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

Job request

Status
Succeeded
Backend
TPP
Workspace
postopcovid
Requested by
Colin Crooks
Branch
main
Force run dependencies
No
Git commit hash
787c9f6
Requested actions
  • data_manage
  • data_manage_postdisch_week
  • flowchart
  • table_demo
  • table_postopcovid_crude
  • table_postopcovid_crude_sub
  • table_postopcovid_adjusted
  • table_postopcovid_adjusted_sub
  • table_postopcovid_tv
  • table_postopcovid_tv_sub
  • table_postopLOS
  • table_postopLOS_sub
  • table_postopVTE
  • table_postopVTE_sub
  • table_postopmortality
  • table_postopmortality_sub
  • table_postopreadmit
  • table_postopreadmit_sub
  • report

Code comparison

Compare the code used in this job request