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Job request: 9511

Organisation:
University of Nottingham
Workspace:
postopcovid
ID:
prihlynq53jglqkq
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: 100000

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.RData
  
  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.RData

  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_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_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
        model_adjusted: output/postopcovidmodel.csv
        model_adjusted_waves: output/postopcovidmodelwaves.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: output/postopcovid_adjusted_sub.RData
        model_adjusted: output/postopcovidmodelsub.csv
        model_adjusted_waves: output/postopcovidmodelwavessub.csv

  table_postopcovid_tv:      
    run: r:latest analysis/Table_postopcovid_tv.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_tv: output/postopcovid_tv.RData
        model_VTE_tv: output/postopVTEmodelsplit.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]
    outputs:
      moderately_sensitive:
        table_tv: output/postopcovid_tv_sub.RData
        model_VTE_tv: output/postopVTEmodelsplitsub.csv
        model_COVID_tv: 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
        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: output/postoplos_sub.RData
        model_los: 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
        model_VTE: output/postopVTEmodel.csv
        
  table_postopVTE_sub:      
    run: r:latest analysis/Table_postopVTE_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_VTE: output/postopVTE_sub.RData
        model_VTE: output/postopVTEmodelsub.csv
        
  table_postopmortality:      
    run: r:latest analysis/Table_postopmortality.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_mortality: output/postopmortality.RData
        model_mortality: output/postopdiedmodel.csv
        
  table_postopmortality_sub:      
    run: r:latest analysis/Table_postopmortality_sub.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_mortality: output/postopmortality_sub.RData
        model_mortality: output/postopdiedmodelsub.csv

  analysis_crude:
    run: r:latest analysis/analysis_crude.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        km_figures: output/*_km.png
        crude_tables: output/*_counts.csv

  analysis_adjusted:
    run: r:latest analysis/analysis_adjusted.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        covid_cox_models: output/*_model.csv
        finalfit_tables: output/*_model.html
        
  report:
    run: r:latest -e 'rmarkdown::render("analysis/Results.rmd", output_dir = "/workspace/output/",knit_root_dir = "/workspace",)'    
    needs: [generate_study_population, data_manage, 
    flowchart,
    table_demo,
    table_postopcovid_crude,
    table_postopcovid_adjusted,
    table_postopcovid_tv,
    table_postopLOS,
    table_postopVTE,
    table_postopmortality,
    table_postopcovid_crude_sub,
    table_postopcovid_adjusted_sub,
    table_postopcovid_tv_sub,
    table_postopLOS_sub,
    table_postopVTE_sub,
    table_postopmortality_sub]
    outputs:
      moderately_sensitive:
        results_report: output/Results.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:56:29

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
c250fb5
Requested actions
  • 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
  • report

Code comparison

Compare the code used in this Job Request