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Job request: 8721

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
pqbofjpg7qrm7i2m
View repo View project.yaml

This page shows the technical details of what happened when 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 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

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/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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:16:53

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
No
Git commit hash
82a4ad4
Requested actions
  • execute_simple_validation_analyses
  • execute_simple_validation_analyses_16

Code comparison

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