Skip to content

Job request: 2845

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag
ID:
uavenlqiph66iury

This page shows the technical details of what happened when 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 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

  • Action:
    generate_notebook
    Status:
    Status: Succeeded
    Job identifier:
    c6ieqfxpaoqqt2nb
  • Action:
    mean_age
    Status:
    Status: Succeeded
    Job identifier:
    sib4ppsijdu5smvz

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:
      moderately_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

  mean_age:
    run: python:latest python analysis/mean_age.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        cohort: output/mean_age.json
        
  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: 00:12:44

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
95c6b2d
Requested actions
  • mean_age
  • generate_notebook

Code comparison

Compare the code used in this Job Request