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Job request: 3657

Organisation:
Bennett Institute
Workspace:
breakthrough-covid-master
ID:
n6maw4zvvumnlws7
View repo View project.yaml

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:
    table_1
    Status:
    Status: Succeeded
    Job identifier:
    i7gry7kw7f3ycbto
  • Action:
    simple_summaries
    Status:
    Status: Succeeded
    Job identifier:
    uo2ou5pcnu7ou4ch
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    yysurtpzvaqnazwq
  • Action:
    flow_chart
    Status:
    Status: Succeeded
    Job identifier:
    26g4uwqayru4zjmn
  • Action:
    figure_1
    Status:
    Status: Succeeded
    Job identifier:
    c7fls4jnk2dtcrft
  • Action:
    table_2
    Status:
    Status: Succeeded
    Job identifier:
    2jut5wmxwbhsacoj
  • Action:
    table_3
    Status:
    Status: Succeeded
    Job identifier:
    nqih366t4445gxkr

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
        
  # Figure 1 ----
  figure_1:
    run: r:latest analysis/cumulative_incidence.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        png: output/figures/figure1*.png
        svg: output/figures/figure1*.svg
  
  # Table 2 ----
  table_2:
    run: r:latest analysis/table_2.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table: output/tables/table2*.html
        
  # Table 3 ----
  table_3:
    run: r:latest analysis/table_3.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table: output/tables/table3*.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:21:46

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

Job information

Status
Succeeded
Backend
TPP
Workspace
breakthrough-covid-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
8e25885
Requested actions
  • flow_chart
  • data_properties
  • simple_summaries
  • table_1
  • figure_1
  • table_2
  • table_3

Code comparison

Compare the code used in this Job Request