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Job request: 1959

Organisation:
Bennett Institute
Workspace:
faw_vaccine
ID:
lb56k6ljlmwibcpo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 1000000

actions:

  # Extract data for study population flow chart
  generate_study_population_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  # Calculate numbers for study population flow chart
  flow_chart:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/Study_definition_flow_chart.html
        
  # Extract study data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # Process data
  data_process:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_modelling.rds
        
  # Summarise data
  data_properties:
    run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt
        
  # More data summaries
  data_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/Data_summaries.html

  # # Coxph models
  # cox_models:
  #   run: r:latest analysis/R/Scripts/02a_models_coxph.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod*.rds
        
  # # Coxme model
  # coxme_model:
  #   run: r:latest analysis/R/Scripts/02b_models_coxme.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/testing/mod_test*.rds
  
  # # Model summaries
  # cox_models_summaries:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process, cox_models, coxme_model]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Model_comparisons.html
  
  # AFT vs Cox models feasibility
  aft_vs_cox_poc:
    run: r:latest analysis/R/Scripts/02c_models_cox_vs_aft_poc.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/testing/cox_vs_aft/mod*.rds
      moderately_sensitive:
        tables: output/models/testing/cox_vs_aft/table*.csv
        plots: output/models/testing/cox_vs_aft/plot*.svg

  # AFT models
  aft_vs_cox_models:
    run: r:latest analysis/R/Scripts/02d_models_cox_vs_aft.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/cox_vs_aft/mod*.rds
        
  # Model comparison
  aft_vs_cox_comparison:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Cox_vs_aft_model_comparison.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process, aft_vs_cox_models]
    outputs:
      moderately_sensitive:
        html: output/Cox_vs_aft_model_comparison.html
        
  # # Final (AFT) model
  # model_final:
  #   run: r:latest analysis/R/Scripts/03_Final_model.R
  #   needs: [generate_study_population, data_process]
  #   outputs:
  #     highly_sensitive :
  #       models: output/models/final/mod*.rds
      # moderately_sensitive:
      #   tables: output/models/final/tab*.html
      #   data: output/models/final/tab*.csv
      #   plots: output/models/final/plot*.svg
 
  # # Strata summaries
  # strata_summary:
  #   run: r:latest analysis/R/Scripts/04_Strata_Summary.R
  #   needs: [data_process, model_final]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/models/final/plot_strata*.svg
  
  # # Results summary
  # results_summary:
  #   run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Results_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
  #   needs: [generate_study_population, data_process, model_final]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Results_summary.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:25:05

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

Job request

Status
Succeeded
Backend
TPP
Workspace
faw_vaccine
Requested by
Millie Green
Branch
AFT
Force run dependencies
No
Git commit hash
f6dbc40
Requested actions
  • aft_vs_cox_models

Code comparison

Compare the code used in this job request