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Job request: 2815

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag
ID:
24vq5hheykkfmpdb
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: 15000

actions:

  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
      
  generate_study_population_valve_replacement_start:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_valve_replacement --index-date-range "2018-01-01 to 2018-01-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_valve_replacement_*.csv

  generate_study_population_valve_replacement_end:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_valve_replacement --index-date-range "2018-12-31 to 2018-12-31 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_valve_replacement*.csv
  
  aortic_valve_count:
    run: python:latest python analysis/valve_type_count.py
    needs: [generate_study_population_valve_replacement_start, generate_study_population_valve_replacement_end]
    outputs:
      highly_sensitive:
        cohort: output/aortic_valve_count.json

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2021-05-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input*.csv
  
        
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/in*.csv
        
  patient_count:
    run: python:latest python analysis/get_patient_count.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        csv: output/patient_count.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_*_rate.csv

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity, generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/notebook.html
        figures: output/measure_*.jpeg
        total_csv: output/doac_rate_total.csv
        csvs: output/current_doac_*.csv
  
  # to be run locally
  # combine:
  #     run: python:latest python analysis/combined_analysis.py
  #     outputs:
  #       moderately_sensitive:
  #         measure_csv: released_outputs/combined_rate.csv
  #         count: released_outputs/count.jpeg
  #         rate: released_outputs/rate.jpeg

  # to be run locally
  # generate_report_notebook:
  #     run: jupyter:latest jupyter nbconvert /workspace/analysis/report_notebook.ipynb --execute --to html --output-dir=/workspace/released_outputs --ExecutePreprocessor.timeout=86400 --no-input
  #     needs: [combine]
  #     outputs:
  #       moderately_sensitive:
  #         notebook: released_outputs/report_notebook.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:54

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mechanical-valve-anticoag
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
a54ab64
Requested actions
  • aortic_valve_count

Code comparison

Compare the code used in this job request