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Job request: 2086

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination
ID:
url2qmyzfkymlf3f
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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:
    strata_summary
    Status:
    Status: Succeeded
    Job identifier:
    2phlk7a5ppi6qsme

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 (stratified cox) model
  model_final:
    run: r:latest analysis/R/Scripts/03_model_final.R
    needs: [generate_study_population, data_process]
    outputs:
      highly_sensitive :
        models: output/models/final/mod*.rds
 
  # 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
        csv: output/models/final/cmlhaz_quantiles.csv
  
  # # 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: [data_process, model_final]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Results_summary.html
        
  # Table and figure
  table_and_figure:
    run: r:latest analysis/R/Scripts/05_table_and_figure.R
    needs: [generate_study_population, data_process, model_final]
    outputs:
      moderately_sensitive:
        tables: output/models/final/tab*.csv
        plots: output/models/final/plot*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:04

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

Job request

Status
Succeeded
Backend
TPP
Workspace
factors-associated-with-covid-19-vaccination
Requested by
Will Hulme
Branch
master
Force run dependencies
No
Git commit hash
d075ec0
Requested actions
  • strata_summary

Code comparison

Compare the code used in this job request