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Job request: 12020

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study-master
ID:
rnp6wak4bfwgg4ze
View repo View project.yaml

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

  extract_date_fields:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery_impossibledates --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_delivery_impossibledates.csv.gz

  count_impossible_dates:
    run: python:latest lib/count_impossible_dates.py
    needs: [extract_date_fields]
    outputs:
      moderately_sensitive:
        date_report_summary: interim-outputs/date-report_summary.txt

  ### 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:
      highly_sensitive:
        pickle: interim-outputs/u16/objects/*.pkl
      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/*

  investigate_impossible_dates_time2seconddose:
    run: python:latest lib/investigate_impossible_dates_time2seconddose.py
    needs: [generate_u16_notebook]
    outputs:
      moderately_sensitive:
        date_report: interim-outputs/date-report_time2seconddose.txt


  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_publication_objects:
    run: r:latest analysis/generate_u16_publication_objects.R
    needs: [generate_u16_notebook]
    outputs:
      moderately_sensitive:
        table: interim-outputs/u16/tables/u16_publication_table.csv
        figure_option1: interim-outputs/u16/figures/u16_publication_figure.png
        figure_option2: interim-outputs/u16/figures/u16_publication_figure_facetted.png
        figure_option3: interim-outputs/u16/figures/u16_publication_figure_combined.png
        figure_option4: interim-outputs/u16/figures/u16_publication_figure_combined_free.png

  # 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/*

  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:

  • Started:

  • Finished:

  • Runtime: 00:00:31

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-preliminary-study-master
Requested by
Lisa Hopcroft
Branch
master
Force run dependencies
No
Git commit hash
d2830ea
Requested actions
  • generate_u16_publication_objects

Code comparison

Compare the code used in this job request