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Job request: 1727

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination-wip-branch
ID:
zindyszjclnrryjh

This page shows the technical details of what happened when authorised researcher Millie Green requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

  • Action:
    cox_models_sub
    Status:
    Status: Succeeded
    Job identifier:
    2h3zm5yhf4mzfg4w

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_all:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        
  # Summarise data
  data_properties_all:
    run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
    needs: [data_process_all]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt
        
  # Practice ID summaries
  practice_id:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries_practices.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        html: output/Data_summaries_practices.html
        
  # Models
  cox_models:
    run: r:latest analysis/R/Scripts/02_Models.R
    needs: [generate_study_population, data_process_all]
    outputs:
      highly_sensitive :
        models: output/models/testing/mod*.rds
        
  cox_models_sub:
    run: r:latest analysis/R/Scripts/02_Models_sub_test.R
    needs: [generate_study_population, data_process_all]
    outputs:
      highly_sensitive :
        models: output/models/testing/mod_test*.rds
        

  # Models 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_all, cox_models]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/Model_comparisons.html
        
  # Models
  cox_model_final:
    run: r:latest analysis/R/Scripts/03_Final_model.R
    needs: [generate_study_population, data_process_all]
    outputs:
      highly_sensitive :
        models: output/models/mod*.rds
      moderately_sensitive:
        tables: output/models/tab*.html
        data: output/models/tab*.csv
        plots: output/models/plot*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:02

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Millie Green
Branch
wip
Force run dependencies
No
Git commit hash
8a46e8c
Requested actions
  • cox_models_sub

Code comparison

Compare the code used in this Job Request