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Job request: 11041

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study-master
ID:
j5nvtumag6vzrtbe
View repo View project.yaml

This page shows the technical details of what happened when 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 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_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: 00:47:54

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
a423929
Requested actions
  • extract_date_fields
  • count_impossible_dates
  • investigate_impossible_dates_time2seconddose

Code comparison

Compare the code used in this Job Request