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Job request: 4909

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag-updated
ID:
6b3it3d7cialaavp
View repo View project.yaml

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

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 "2021-08-01 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

  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: 01:18:15

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

Job information

Status
Succeeded
Backend
EMIS
Workspace
mechanical-valve-anticoag-updated
Requested by
Louis Fisher
Branch
updates
Force run dependencies
No
Git commit hash
8a1db91
Requested actions
  • generate_study_population_monitoring
  • generate_measures_monitoring

Code comparison

Compare the code used in this Job Request