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Job request: 1579

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination-test
ID:
wbuzjchvnh2zlsmj
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:
    atk7qpl6f6rr5lmh
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    data_process_all
    Status:
    Status: Failed
    Job identifier:
    tsxruyikn6doutop
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    cox_models
    Status:
    Status: Failed
    Job identifier:
    5e4vmaqg5b27i5bl
    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: 1000000

actions:

  # Extract data for study population flow chart
  generate_study_population_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  # Calculate numbers for study population flow chart
  flow_chart:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/Study_definition_flow_chart.html
        
  # Extract study data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # Process data
  data_process_all:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        
  # Models
  cox_models:
    run: r:latest analysis/R/Scripts/02_Models.R
    needs: [generate_study_population, data_process_all]
    outputs:
      moderately_sensitive:
        models: output/models/mod*.rds
        tables: output/models/tab*.html
        data: output/models/tab*.csv
        plots: output/models/plot*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:25:06

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

Job request

Status
Failed
Backend
TPP
Workspace
factors-associated-with-covid-19-vaccination-test
Requested by
Millie Green
Branch
wip
Force run dependencies
Yes
Git commit hash
4bed285
Requested actions
  • cox_models

Code comparison

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