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Job request: 4228

Organisation:
Bennett Institute
Workspace:
hba1c-levels
ID:
da6pci6zz6mgvrhv
View repo View project.yaml

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

  # 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:

  • Started:

  • Finished:

  • Runtime: 03:27:36

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

Job information

Status
Succeeded
Backend
TPP
Workspace
hba1c-levels
Requested by
Robin Park
Branch
study-def
Force run dependencies
Yes
Git commit hash
3766595
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request