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Job request: 1782

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination-wip
ID:
56n5kbk5jqeh263v
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 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 
######################################

# 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: [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
        
  # Models
  cox_models:
    run: r:latest analysis/R/Scripts/02_Models.R
    needs: [generate_study_population, data_process]
    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]
    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, cox_models, cox_models_sub]
    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]
  #   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: 01:51:37

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

Job information

Status
Failed
Backend
TPP
Workspace
factors-associated-with-covid-19-vaccination-wip
Requested by
Millie Green
Branch
wip
Force run dependencies
No
Git commit hash
a92380a
Requested actions
  • cox_models_summaries

Code comparison

Compare the code used in this Job Request