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Job request: 1810

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination-models
ID:
7om7lzfzav2efqce
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

  • Action:
    generate_study_population
    Status:
    Status: Succeeded
    Job identifier:
    kudl5ovdkoauu5zr
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    pzor63vg3ifelv3i
  • Action:
    data_summaries
    Status:
    Status: Succeeded
    Job identifier:
    tx2pwv3kqztw3tp3
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    ulymcqjtblgoapzn
  • Action:
    cox_models_sub
    Status:
    Status: Failed
    Job identifier:
    5w4w6i37vibcekeu
    Error:
    cancelled_by_user: Cancelled by user

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
        
  # Coxph 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
        
  # Coxme model
  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

  # 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, 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/final/mod*.rds
      moderately_sensitive:
        tables: output/models/final/tab*.html
        data: output/models/final/tab*.csv
        plots: output/models/final/plot*.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, cox_model_final]
    outputs:
      moderately_sensitive:
        html: output/Results_summary.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 23:38:55

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

Job request

Status
Failed
Backend
TPP
Workspace
factors-associated-with-covid-19-vaccination-models
Requested by
Millie Green
Branch
wip
Force run dependencies
No
Git commit hash
80423ac
Requested actions
  • generate_study_population
  • data_process
  • data_properties
  • data_summaries
  • cox_models_sub

Code comparison

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