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Job request: 696

Organisation:
Bennett Institute
Workspace:
database-notebooks_full_master
ID:
xzrcpos26nt7of6c
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # note not possible to execute and save notebook in a single action with `--execute --to notebook` because of self-dependency
  # still possible to execute and save to html or md file

  characteristics_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-patient-characteristics.ipynb --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_population]
    outputs:
      moderately_sensitive:
        html: output/database-patient-characteristics.html

  database_builds_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-builds.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        html: output/database-builds.html
        
  database_schema_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-schema.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        html: output/database-schema.html
       
  characteristics_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-patient-characteristics.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        md: output/database-patient-characteristics.md
       
  database_builds_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-builds.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        md: output/database-builds.md
        png: output/database-builds_files/*.png
        
  database_schema_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-schema.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        md: output/database-schema.md

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:22:18

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

Job request

Status
Succeeded
Backend
TPP
Workspace
database-notebooks_full_master
Requested by
Will Hulme
Branch
master
Force run dependencies
No
Git commit hash
4f02ce7
Requested actions
  • generate_population

Code comparison

Compare the code used in this job request