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Job request: 8146

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
j7ousvzd744uynd2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    split_codelist
    Status:
    Status: Succeeded
    Job identifier:
    ywwlk6ydquhm4bds
  • Action:
    generate_study_population
    Status:
    Status: Succeeded
    Job identifier:
    yinnb5r233wersba
  • Action:
    generate_dataset_report
    Status:
    Status: Succeeded
    Job identifier:
    diio2qoywum6ucyk
  • Action:
    execute_validation_analyses_16
    Status:
    Status: Failed
    Job identifier:
    zn4wudgzq3w55h2n
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    generate_report_ethnicity
    Status:
    Status: Failed
    Job identifier:
    zw5exanpg6zhuves
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    execute_validation_analyses
    Status:
    Status: Failed
    Job identifier:
    ho4xhefwkkpy476k
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_report_ethnicity_16
    Status:
    Status: Failed
    Job identifier:
    d5uun5db5aacsqog
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  split_codelist:
    run: r:latest analysis/00_trim_snomed_codelist.r
    outputs:
      highly_sensitive:
        data: codelists/ethnicity_*.csv

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

  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

  execute_validation_analyses:
    run: python:latest python analysis/validation_script.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/phenotype_validation_ethnicity/5/tables/*.csv
        figures: output/phenotype_validation_ethnicity/5/figures/*.png
  
  execute_validation_analyses_16:
    run: python:latest python analysis/validation_script_16.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/phenotype_validation_ethnicity/16/tables/*.csv
        figures: output/phenotype_validation_ethnicity/16/figures/*.png

  generate_report_ethnicity:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/report_ethnicity_rp.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_ethnicity_rp.html

  generate_report_ethnicity_16:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/report_ethnicity_rp_16.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [execute_validation_analyses_16]
    outputs:
      moderately_sensitive:
        notebook: output/report_ethnicity_rp_16.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:25:59

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

Job information

Status
Failed
Backend
TPP
Workspace
ethnicity-short-data-report-notebook
Requested by
Colm Andrews
Branch
notebook
Force run dependencies
Yes
Git commit hash
dc1b03b
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request