Skip to content

Job request: 8141

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
lmtbsi4u7ukp5cci
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 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.

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:

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

Job request

Status
Failed 
JobRequestError: execute_validation_analyses failed on a previous run and must be re-run
Backend
TPP
Workspace
ethnicity-short-data-report-notebook
Requested by
Colm Andrews
Branch
notebook
Force run dependencies
No
Git commit hash
dc1b03b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request