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Job request: 2262

Organisation:
Bennett Institute
Workspace:
sro-measures
ID:
zw4dbqb3am7d2dvk
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 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_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 --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather
        
  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_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.feather

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count.feather
        
  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
    
#   generate_measures:
#     run: python:latest python analysis/calculate_measures.py
#     needs: [join_ethnicity]
#     outputs:
#       moderately_sensitive:
#         measure: output/combined_measure_*.csv
    
#   generate_measures:
#       run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
#       needs: [join_ethnicity]
#       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
  
  
  

#   generate_notebook:
#     run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --template basic --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.html
  
#   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]
#     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]
#     outputs:
#       moderately_sensitive:
#         notebook: output/sentinel_measures_demographics.html
#         figures: output/*_*.png
     
  # 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: [join_ethnicity]
#     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: 14:09:21

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sro-measures
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
8f3f127
Requested actions
  • generate_study_population
  • get_patient_count
  • generate_study_population_ethnicity
  • join_ethnicity
  • generate_study_population_practice_count
  • get_practice_count

Code comparison

Compare the code used in this job request