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Job request: 4233

Organisation:
Bennett Institute
Workspace:
hba1c-levels
ID:
7mpjnzpeuaujq3ts
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 #--output-format=feather
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.csv

  generate_data_description:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/data_description.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/data_description.html

  generate_charts:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/charts.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/charts.html

  # cohort_report:
  #   run: cohort-report:v2.0.1 output/data/input_joined.feather
  #   needs: [join_ethnicity]
  #   config:
  #     output_path: output/data
  #   outputs:
  #     moderately_sensitive:
  #       cohort_report: output/data/descriptives_input_joined.html
        
  # 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:

  • Finished:

  • Runtime:

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

Job request

Status
Succeeded
Backend
TPP
Workspace
hba1c-levels
Requested by
Robin Park
Branch
study-def
Force run dependencies
No
Git commit hash
7744ae7
Requested actions
  • generate_charts

Code comparison

Compare the code used in this job request