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Job request: 25074

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
tocilizumab_sarilumab
ID:
ez4wgucu3vtgafvw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Bang Zheng 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:
    cox_subgroup2
    Status:
    Status: Failed
    Job identifier:
    hcwiafsod5stmiab
    Error:
    nonzero_exit: Job exited with an error

Pipeline

Show project.yaml 
version: '4.0'

actions:
  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/input.csv
    outputs:
      highly_sensitive:
        dataset: output/input.csv

  data_preparation:
    run: stata-mp:latest analysis/data_preparation_and_descriptives.do
    needs: [generate_dataset]
    outputs:
      highly_sensitive:
        dataset: output/main.dta
        dataset2: output/descriptives.xlsx
      moderately_sensitive:
        log: logs/data_preparation.log
        output: output/descriptives.csv
        
  cox_regression:
    run: stata-mp:latest analysis/cox.do
    needs: [data_preparation]
    outputs:
      highly_sensitive:
        dataset: output/cox.xlsx
      moderately_sensitive:
        log: logs/cox.log
        output1: output/cox.csv
        figure1: output/phtest.svg 
        figure2: output/psgraph.svg 
       

  cox_subgroup:
    run: stata-mp:latest analysis/cox_subgroup.do
    needs: [data_preparation]
    outputs:
      highly_sensitive:
        dataset: output/cox_subgroup.xlsx
      moderately_sensitive:
        log: logs/cox_subgroup.log
        output: output/cox_subgroup.csv

  cox_subgroup2:
    run: stata-mp:latest analysis/cox_subgroup2.do
    needs: [data_preparation]
    outputs:
      highly_sensitive:
        dataset: output/cox_subgroup2.xlsx
      moderately_sensitive:
        log: logs/cox_subgroup2.log
        output: output/cox_subgroup2.csv
        
  psw_check:
    run: stata-mp:latest analysis/psw_check.do
    needs: [data_preparation]
    outputs:
      highly_sensitive:
        dataset: output/psw_check.xlsx
      moderately_sensitive:
        log: logs/psw_check.log
        output: output/psw_check.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:06:26

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

Job request

Status
Failed
Backend
TPP
Workspace
tocilizumab_sarilumab
Requested by
Bang Zheng
Branch
main
Force run dependencies
No
Git commit hash
20887d4
Requested actions
  • cox_subgroup2

Code comparison

Compare the code used in this job request