Job request: 8721

View Repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

ID Status Action
5u7tuacjtse4xkag succeeded execute_simple_validation_analyses
hsaxlcsjf2wy2udv failed execute_simple_validation_analyses_16

Pipeline

Show Hide 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/registered/tables/*.csv
        figures: output/phenotype_validation_ethnicity/5/registered/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/registered/tables/*.csv
        figures: output/phenotype_validation_ethnicity/16/registered/figures/*.png

  generate_report_ethnicity:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/report_ethnicity_rp_registered.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_registered.html

  generate_report_ethnicity_16:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/report_ethnicity_rp_16_registered.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_registered.html
  

  execute_simple_validation_analyses:
    run: python:latest python analysis/simple_validation_script.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/phenotype_validation_ethnicity/5/registered/tables/simple*.csv
        figures: output/phenotype_validation_ethnicity/5/registered/figures/h*.png
  
  execute_simple_validation_analyses_16:
    run: python:latest python analysis/simple_validation_script_16.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/phenotype_validation_ethnicity/16/registered/tables/simple*.csv
        figures: output/phenotype_validation_ethnicity/16/registered/figures/h*.png

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 06:16:53

Config

  • Backend:
    TPP
  • Workspace:
    ethnicity-short-data-report-notebook
  • Branch:
    notebook
  • Creator:
    andrewscolm
  • Force run dependencies:
    False
  • Git Commit Hash:
    82a4ad4
  • Requested actions:
    • execute_simple_validation_analyses
    • execute_simple_validation_analyses_16