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Job request: 8925

Organisation:
Bennett Institute
Workspace:
bmi-short-data-report
ID:
7wc2bge3lhr3unoa
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robin Park 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:
    execute_validation_analyses
    Status:
    Status: Failed
    Job identifier:
    jfrkvstoalha73ou
    Error:
    nonzero_exit: Job exited with error code 137: Ran out of memory (limit for this job was 1e+02GB)
  • Action:
    generate_report_bmi
    Status:
    Status: Failed
    Job identifier:
    sptctkvhm5fx5gjy
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_event_counts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_eventcounts --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_eventcounts.feather

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input.feather

  preprocess_inputs:
    run: python:latest python analysis/preprocess_inputs.py --output-format feather
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/data/input_processed.feather

  execute_validation_analyses:
    run: python:latest python analysis/validation_script.py
    needs: [preprocess_inputs]
    outputs:
      moderately_sensitive: 
        tables: output/phenotype_validation_bmi/tables/*.csv
        figures: output/phenotype_validation_bmi/figures/*.png
        
  generate_report_bmi:
    run: python:latest jupyter nbconvert /workspace/notebooks/report_bmi.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [execute_validation_analyses]
    outputs:
      moderately_sensitive:
        notebook: output/report_bmi.html
        
  generate_report_eventcounts:
    run: python:latest jupyter nbconvert /workspace/notebooks/report_event_counts.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_event_counts]
    outputs:
      moderately_sensitive:
        notebook: output/report_event_counts.html

  generate_dataset_report:
    run: >
      dataset-report:v0.0.9
        --input-files output/data/input.feather
        --output-dir output/data
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        dataset_report: output/data/input.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 12:11:55

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

Job request

Status
Failed
Backend
TPP
Workspace
bmi-short-data-report
Requested by
Robin Park
Branch
main
Force run dependencies
No
Git commit hash
c359ed7
Requested actions
  • execute_validation_analyses
  • generate_report_bmi

Code comparison

Compare the code used in this job request