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Job request: 4897

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag-updated
ID:
azjnf6j7xp5hvqyt
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:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-12-01 by month" --output-dir=output --skip-existing
    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

  recent_data:
    run: python:latest python analysis/recent_data.py
    needs: [generate_notebook]
    outputs:
      moderately_sensitive:
        csv: output/doac_rate_total_recent.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
        count_with_mean: released_outputs/count_with_mean.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: 00:00:23

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

Job request

Status
Succeeded
Backend
EMIS
Workspace
mechanical-valve-anticoag-updated
Requested by
Louis Fisher
Branch
updates
Force run dependencies
No
Git commit hash
8e0d0ac
Requested actions
  • generate_notebook

Code comparison

Compare the code used in this job request