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Job request: 2038

Organisation:
Bennett Institute
Workspace:
sro-measures-demographics
ID:
umypxtgmpp2i5gwh
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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: 1000
   
    
actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/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/input*.csv

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count.csv

#   generate_measures:
#       run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
#       needs: [generate_study_population]
#       outputs:
#         moderately_sensitive:
#           measure_csv: output/measure_*.csv

#   generate_measure_ethnicity:
#     run: python:latest python analysis/generate_measure_ethnicity.py
#     needs: [join_ethnicity]
#     outputs:
#       moderately_sensitive:
#         measure: output/measure_*_ethnicity.csv
  
#   get_practice_count:
#     run: python:latest python analysis/get_practice_count.py
#     needs: [generate_study_population_practice_count]
#     outputs:
#       moderately_sensitive:
#         text: output/practice_count.json
  
#   get_patient_count:
#     run: python:latest python analysis/get_patients_counts.py
#     needs: [generate_study_population]
#     outputs:
#       moderately_sensitive:
#         text: output/patient_count.json
        


   
  
#   generate_notebook:
#     run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
#     needs: [generate_measures, get_practice_count, get_patient_count, generate_measure_ethnicity, join_ethnicity]
#     outputs:
#       moderately_sensitive:
#         notebook: output/sentinel_measures.html
     
#   generate_notebook_demographics:
#     run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_demographics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
#     needs: [generate_measures, get_practice_count, get_patient_count, generate_measure_ethnicity, join_ethnicity]
#     outputs:
#       moderately_sensitive:
#         notebook: output/sentinel_measures_demographics.html
     
  # generate_notebook_practice:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_by_practice.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_measures, get_practice_count, get_patient_count]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/sentinel_measures_by_practice.html
  #       csvs: output/*_check.csv

#   get_event_summary:
#     run: python:latest python analysis/get_event_summary.py
#     needs: [generate_study_population]
#     outputs:
#       moderately_sensitive:
#         text: output/*_event_summary.csv

#   run_tests:
#     run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
#     outputs:
#       moderately_sensitive:
#         log: output/pytest.xml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 13:28:25

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

Job information

Status
Succeeded
Backend
TPP
Workspace
sro-measures-demographics
Requested by
Louis Fisher
Branch
demographics-notebook
Force run dependencies
No
Git commit hash
af3c0a9
Requested actions
  • generate_study_population
  • generate_study_population_ethnicity
  • join_ethnicity
  • generate_study_population_practice_count

Code comparison

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