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Job request: 1740

Organisation:
Bennett Institute
Workspace:
covid_vaccine_decline_variation
ID:
ynh7qmtepn4frzgn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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: 10000

actions:

  
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-12-01 to 2021-04-01 by month" --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count.csv.gz

  
  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*.csv

  generate_measure_ethnicity:
    run: python:latest python analysis/generate_measure_ethnicity.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure: output/measure_ethnicity.csv

  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json

  create_notebook:
    run: python:latest python analysis/create_notebook.py
    needs: [get_patient_count, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: analysis/SRO_Notebook.ipynb


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/SRO_Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [create_notebook, generate_measures, generate_measure_ethnicity, generate_study_population_practice_count, generate_study_population, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/SRO_Notebook.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:54:09

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid_vaccine_decline_variation
Requested by
Helen Curtis
Branch
master
Force run dependencies
No
Git commit hash
27ebda7
Requested actions
  • generate_study_population
  • join_ethnicity
  • generate_measures
  • generate_measure_ethnicity
  • get_patient_count
  • create_notebook
  • generate_notebook

Code comparison

Compare the code used in this job request