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Job request: 3168

Organisation:
Bennett Institute
Workspace:
breakthrough-covid-master
ID:
scjh4h5pdmlj2egk
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:
    table_3
    Status:
    Status: Failed
    Job identifier:
    qe7m63jvig6fywdb
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    table_1
    Status:
    Status: Succeeded
    Job identifier:
    4byaoxtas2not6qc
  • Action:
    figure_1
    Status:
    Status: Succeeded
    Job identifier:
    4pdsqrmf5qrgn4hg
  • Action:
    table_2
    Status:
    Status: Failed
    Job identifier:
    sj46hi27helvqpzl
    Error:
    nonzero_exit: Job exited with an error code

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
        
  # 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: 00:12:17

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

Job request

Status
Failed
Backend
TPP
Workspace
breakthrough-covid-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
af49439
Requested actions
  • table_1
  • figure_1
  • table_2
  • table_3

Code comparison

Compare the code used in this job request