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Job request: 4678

Organisation:
Bennett Institute
Workspace:
updates-november
ID:
teqmfxtimlqfvv6o
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: 100000

actions:
  
  # Extract data ----
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv
        
  # Process data ----
  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_processed.rds
        
  # Inclusion/exclusion flow chart ----
  flow_chart:
    run: r:latest analysis/flow_chart.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        data: output/data/flowchart.csv

  # Data properties ----      
  data_properties:
    run: r:latest analysis/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt

  # Data summaries ----
  simple_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/simple_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/markdown/simple_summaries.html
  
  # Table 1 ----
  table_1:
    run: r:latest analysis/table_1.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table: output/tables/table1*.html
  
  # Table 2 ----
  table_2:
    run: r:latest analysis/table_2.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table1: output/tables/table2.html
        table2: output/tables/table2_redacted.html
  
  table_ckd:
    run: r:latest analysis/table_ckd.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table1: output/tables/table_ckd.html
        table2: output/tables/table_ckd_redacted.html

        
  # Figure 1 ----
  cummulative_incidence:
    run: r:latest analysis/cumulative_incidence.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        data: output/data/surv_data*.csv
        
  # Figure 2 ----
  figure_2:
    run: r:latest analysis/figure_2.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        png: output/figures/figure2*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:32:29

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

Job request

Status
Succeeded
Backend
TPP
Workspace
updates-november
Requested by
Millie Green
Branch
updates-november
Force run dependencies
No
Git commit hash
99d2605
Requested actions
  • generate_study_population

Code comparison

Compare the code used in this job request