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Job request: 11561

Organisation:
PHC, University of Oxford
Workspace:
mainroute_cancer
ID:
evjhihwr2pgc3jva
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Emma Mi 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_2wwcolorectal_cohort
    Status:
    Status: Failed
    Job identifier:
    asv5mj7vunapgoyj
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    describe
    Status:
    Status: Failed
    Job identifier:
    me4px5eoclliyuds
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  
  generate_2wwcolorectal_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2wwcolorectal
    outputs:
      highly_sensitive:
        cohort: output/input_2wwcolorectal.csv

  describe:
    run: python:latest python analysis/report_2wwcolorectal.py
    needs: [generate_2wwcolorectal_cohort]
    outputs:
      moderately_sensitive:
        all_figure: output/colorectal_cancer_10.jpg
        all_figure2: output/colorectal_cancer_11.jpg
        all_figure3: output/colorectal_cancer_12.jpg
        all_figure4: output/colorectal_cancer_13.jpg
        all_figure5: output/colorectal_cancer_14.jpg
        all_figure6: output/colorectal_cancer_15.jpg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:38

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

Job request

Status
Failed
Backend
TPP
Workspace
mainroute_cancer
Requested by
Emma Mi
Branch
main
Force run dependencies
Yes
Git commit hash
6e12e6b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request