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Job request: 2735

Organisation:
Bennett Institute
Workspace:
breakthrough-covid-master
ID:
u6kv6f6bhpe7pw54
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: Failed
    Job identifier:
    korqdewwvynwcugf
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    jmhjuu4emizs5bck
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_1
    Status:
    Status: Failed
    Job identifier:
    qx2r34kouhik6hqp
    Error:
    dependency_failed: Not starting as dependency failed

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:
        data: output/data/data_all.rds
        
  # 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:
        table: output/tables/table2.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:06

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

Job request

Status
Failed
Backend
EMIS
Workspace
breakthrough-covid-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
28285fe
Requested actions
  • generate_study_population
  • data_process
  • table_1

Code comparison

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