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Job request: 4896

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag
ID:
w6zsx36xh6bfpdw6

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: 15000

actions:
  generate_study_population_monitoring:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monitoring --index-date-range "2019-01-01 to 2021-12-01 by month" --output-dir=output --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/input_monitoring_*.csv

  generate_measures_monitoring:
    run: cohortextractor:latest generate_measures --study-definition study_definition_monitoring --output-dir=output
    needs: [generate_study_population_monitoring]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_monitoring_*_rate.csv
        measures_csv_inr: output/measure_inr_result*.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

  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: 00:00:50

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
cd9b39f
Requested actions
  • generate_measures_monitoring

Code comparison

Compare the code used in this Job Request