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Job request: 3813

Organisation:
Bennett Institute
Workspace:
hba1c-levels-report
ID:
arvwjo2uhwhw7mgt
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robin Park 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: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-06-01 by month" --output-dir=output/data #--output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.csv
        
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data #--output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.csv
        
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.csv
        
  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure_*.csv
        
  generate_abnormal_nb:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/abnormal_results.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/abnormal_results.html
        
  generate_levels_nb:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/hba1c_levels.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/hba1c_levels.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:17

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

Job request

Status
Succeeded
Backend
TPP
Workspace
hba1c-levels-report
Requested by
Robin Park
Branch
master
Force run dependencies
No
Git commit hash
c6892f8
Requested actions
  • generate_abnormal_nb

Code comparison

Compare the code used in this job request