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Job request: 3001

Organisation:
Bennett Institute
Workspace:
breakthrough-covid-master
ID:
4cgjcwqd7d5grsp4
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

  • Action:
    generate_study_population
    Status:
    Status: Succeeded
    Job identifier:
    qb2y5gwkjfoymrdu
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    yqwbvsm3mzixammp
  • Action:
    table_1
    Status:
    Status: Failed
    Job identifier:
    5hemsum2wgbscspb
  • Action:
    data_summaries
    Status:
    Status: Succeeded
    Job identifier:
    bsobnmpo7wfv66zl
  • Action:
    figure_1
    Status:
    Status: Succeeded
    Job identifier:
    bqf7j4pwxaf6gkpq
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    gyxsxtjwyouiejtu

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

  # Data summaries ----
  data_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/markdown/data_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:
        svg: output/figures/cumulative_incidence_positive_test.svg
  
  # # Table 2 ----
  # table_2:
  #   run: r:latest analysis/table_2.R
  #   needs: [data_process]
  #   outputs:
  #     moderately_sensitive:
  #       table: output/tables/table2*.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 08:08:26

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

Job information

Status
Failed
Backend
TPP
Workspace
breakthrough-covid-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
0e21d1b
Requested actions
  • generate_study_population
  • data_process
  • data_properties
  • data_summaries
  • table_1
  • figure_1

Code comparison

Compare the code used in this Job Request