Job request: 9335

Organisation:: Bennett Institute
Workspace:: covid-vaccine-preliminary-study-master
ID:: ebay66beanwjalvg

This page shows the technical details of what happened when the authorised researcher Lisa Hopcroft 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

Action:

generate_delivery_cohort

Status:

Status: Succeeded

Job identifier:

kxw5eqih5kzvo47n
Action:

generate_notebook

Status:

Status: Succeeded

Job identifier:

ejgw3zgb5qctgpwz
Action:

generate_report_third_doses

Status:

Status: Succeeded

Job identifier:

vae722jtyxinnkda
Action:

generate_report_second_doses

Status:

Status: Succeeded

Job identifier:

ktdkqdngzdmzgyli
Action:

generate_simple_report

Status:

Status: Succeeded

Job identifier:

3uqlka7owyzagdx4

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 100000
    # dummy population size must be at least 50000 to ensure the STP analysis can run successfully
    
actions:

  ### NB. THIS NEED ONLY BE RUN WHEN WE WANT TO REGENERATE COVERAGE STATISTICS
  generate_whole_cohort_to_calculate_coverage:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ALL --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ALL.csv.gz

  calculate_stp_coverage:
    run: python:latest lib/calculate_stp_coverage.py
    needs: [generate_whole_cohort_to_calculate_coverage]
    outputs:
      moderately_sensitive:
        coverage_calculation: lib/stp_tpp-coverage_total.csv


  generate_delivery_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_delivery.csv.gz


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
    needs: [calculate_stp_coverage, generate_delivery_cohort]
    outputs:
      moderately_sensitive:
        notebook: output/population_characteristics.html
        ### first, second, third/booster doses
        figures: interim-outputs/figures/*
        tables: interim-outputs/tables/*
        # stp_tables: interim-outputs/stp/tables/*.csv
        fig_csvs_1: output/machine_readable_outputs/figure_csvs/*ethnicity*.csv 
        fig_csvs_2: output/machine_readable_outputs/figure_csvs/*imd*.csv 
        fig_csvs_3: output/machine_readable_outputs/figure_csvs/*psychosis*.csv 
        fig_csvs_4: output/machine_readable_outputs/figure_csvs/*LD_*.csv 
        fig_csvs_5: output/machine_readable_outputs/figure_csvs/*eligible*.csv 
        text: interim-outputs/text/*
        
  generate_simple_report:
    run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_overall.ipynb --execute --to html --template basic --output=/workspace/output/opensafely_vaccine_report_overall_simple.html --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_delivery_cohort, generate_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/opensafely_vaccine_report_overall_simple.html
        csvs: output/machine_readable_outputs/table_csvs/*

  generate_report_second_doses:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input

    needs: [generate_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/second_doses.html
        tables: output/machine_readable_outputs/second_doses/*.csv

  generate_report_third_doses:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/booster-third-doses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/booster-third-doses.html
        tables: output/machine_readable_outputs/third_doses/*.csv

  # generate_u16_cohort:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery_u16 --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_delivery_u16.csv.gz

  # generate_u16_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics_u16.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
  #   needs: [calculate_stp_coverage, generate_u16_cohort]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/population_characteristics_u16.html 
  #       figures: interim-outputs/u16/figures/*
  #       tables: interim-outputs/u16/tables/*
  #       fig_csvs: output/machine_readable_outputs/figure_csvs/*_u16*.csv 
  #       text: interim-outputs/u16/text/*

  # generate_u16_simple_report:
  #   run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/first_dose_u16.ipynb --execute --to html --template basic --output=/workspace/output/first_dose_u16.html --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_u16_cohort, generate_u16_notebook]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/first_dose_u16.html
  #       csvs: output/machine_readable_outputs/table_csvs/*_u16*.csv
        
  # generate_u16_report_second_doses:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses_u16.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_u16_notebook]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/second_doses_u16.html
  #       tables: output/machine_readable_outputs/second_doses/*_u16*.csv

  # # generate_u16_report_third_doses:
  # #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/booster-third-doses_u16.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  # #   needs: [generate_u16_notebook]
  # #   outputs:
  # #     moderately_sensitive:
  # #       notebook: output/booster-third-doses_u16.html
  # #       tables: output/machine_readable_outputs/third_doses/*_u16*.csv


  generate_booster_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery_boosters --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_delivery_boosters.csv.gz

  generate_booster_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics_boosters.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
    needs: [calculate_stp_coverage, generate_booster_cohort]
    outputs:
      moderately_sensitive:
        # notebook: output/population_characteristics_boosters.html
        # figures_boosters: interim-outputs/spring_boosters/figures/*
        # tables_boosters: interim-outputs/spring_boosters/tables/*
        # fig_csvs_boosters: output/machine_readable_outputs/figure_csvs/*_spring_boosters*.csv 
        # text_boosters: interim-outputs/spring_boosters/text/*
        test_pickles: interim-outputs/TEST_*.pickle
        test_csvs: interim-outputs/TEST_*.csv

  debug_booster_data:
    run: python:latest analysis/debug_booster_data.py
    needs: [generate_booster_notebook]
    outputs:
      moderately_sensitive:
        coverage_calculation: interim-outputs/debug.txt

  generate_spring_booster_report:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/spring-boosters.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_booster_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/spring-boosters.html
        tables: output/machine_readable_outputs/spring_boosters/* spring booster *.csv

Timeline

Created: 2 years, 4 months ago 15 Jun 2022 14:09:29 UTC
Started: 2 years, 4 months ago 15 Jun 2022 14:08:18 UTC
Finished: 2 years, 4 months ago 16 Jun 2022 03:00:37 UTC
Runtime: 12:54:24

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

Job information

Status: Succeeded
Backend: TPP
Workspace: covid-vaccine-preliminary-study-master
Requested by: Lisa Hopcroft
Branch: master
Force run dependencies: No
Git commit hash: b2cd6d9
Requested actions: generate_delivery_cohort

generate_notebook

generate_simple_report

generate_report_second_doses

generate_report_third_doses

Code comparison

Compare the code used in this Job Request