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Job request: 9312

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study-master
ID:
vo3eg4264yatmrcw
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.

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:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
GitRepoNotReachableError: Could not read from https://github.com/opensafely/covid-vaccine-preliminary-study
Backend
TPP
Workspace
covid-vaccine-preliminary-study-master
Requested by
Lisa Hopcroft
Branch
master
Force run dependencies
No
Git commit hash
dccc854
Requested actions
  • generate_booster_notebook
  • debug_booster_data

Code comparison

Compare the code used in this job request