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Job request: 5320

Organisation:
Bennett Institute
Workspace:
vaccine-effectiveness-hospital-admissions-validation
ID:
tav2w3jljswve6ro
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 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: 10000

actions:
  generate_study_population_ae:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ae
    outputs:
      highly_sensitive:
        cohort: output/input_ae.csv

  generate_ae_count:
    run: python:latest python analysis/ae_count.py
    needs: [generate_study_population_ae]
    outputs:
      moderately_sensitive:
        count: output/ae_count.json
        hospital_count: output/hospital_admission_count.json
        hist: output/hist.jpeg
        same_count: output/same_count.json

  generate_study_population_descriptives:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_descriptives
    outputs:
      highly_sensitive:
        cohort: output/input_descriptives.csv

  generate_study_population_alternative:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_alternative
    outputs:
      highly_sensitive:
        cohort: output/input_alternative.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_results:
    run: python:latest python analysis/generate_results.py
    needs: [generate_study_population, generate_study_population_descriptives]
    outputs:
      moderately_sensitive:
        num_patients: output/num_patients.json
        ae_attendance_count_dict: output/num_ae_attendances.json
        hosp_dict: output/emergency_hospitalisation.json
        ae_dict: output/ae.json
        any_ae_dict: output/ae_any.json
        all_ae_dict: output/ae_all.json
        discharge_csv: output/discharge_destination.csv
        performance_dict: output/model_performance_updated.json
        sensitivity_dict: output/sensitivity.json
        model_csvs: output/model_*.csv
        venn: output/venn.jpeg

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/results.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population, generate_study_population_descriptives]
    outputs:
      moderately_sensitive:
        notebook: output/results.html

  generate_notebook_alternative:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/analysis.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population_alternative]
    outputs:
      moderately_sensitive:
        notebook: output/analysis.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:12:03

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vaccine-effectiveness-hospital-admissions-validation
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
9f19431
Requested actions
  • generate_study_population_ae
  • generate_ae_count

Code comparison

Compare the code used in this Job Request