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Job request: 9465

Organisation:
University of Nottingham
Workspace:
postopcovid
ID:
xxmzw2tf2igjs5s7
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

  • Action:
    report
    Status:
    Status: Failed
    Job identifier:
    2crpd3cxiak6z4iz
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    analysis_adjusted
    Status:
    Status: Succeeded
    Job identifier:
    cqzf43nmfqzabbws

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_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_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

  table_postopLOS:      
    run: r:latest analysis/Table_postoplos.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_los: output/postoplos.RData
        
  table_postopVTE:      
    run: r:latest analysis/Table_postopVTE.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        table_VTE: output/postopVTE.RData
        
  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, table_demo,table_postopcovid_crude,table_postopcovid_adjusted,table_postopcovid_tv,table_postopLOS,table_postopVTE,flowchart]
    outputs:
      moderately_sensitive:
        results_report: output/Results.html
        bootstrap_km: output/bootstrap.RData

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:02:42

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

Job request

Status
Failed
Backend
TPP
Workspace
postopcovid
Requested by
Colin Crooks
Branch
main
Force run dependencies
No
Git commit hash
f548e94
Requested actions
  • analysis_adjusted
  • report

Code comparison

Compare the code used in this job request