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Job request: 5772

Organisation:
Bennett Institute
Workspace:
vaccine-effectiveness-hospital-admissions-validation
ID:
q27h5ywdbdairl7o
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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_prim_cov
    Status:
    Status: Failed
    Job identifier:
    o6b5i2thwuxt6vuu
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    yfjsxbpel26sglhf
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_results
    Status:
    Status: Failed
    Job identifier:
    mmsz6w7kv3basbmi
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
 
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_study_population_prim_cov:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prim_cov
    outputs:
      highly_sensitive:
        cohort: output/input_prim_cov.csv

  generate_results:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/generate_results.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population, generate_study_population_prim_cov]
    outputs:
      moderately_sensitive:
        notebook: output/generate_results.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 51:07:50

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

Job request

Status
Failed
Backend
TPP
Workspace
vaccine-effectiveness-hospital-admissions-validation
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
f89d841
Requested actions
  • generate_study_population
  • generate_study_population_prim_cov
  • generate_results

Code comparison

Compare the code used in this job request