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Job request: 932

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_doses
ID:
3kmaeuiehfck6kcu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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

actions:

  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #
  #   needs: [generate_delivery_cohort]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/population_characteristics.html

  get_packages:
    run: r:latest analysis/R/export_package_names.R
    outputs:
      moderately_sensitive:
        cohort: output/available_packages.csv



## Descriptive info on vaccinated patients

  extract_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.csv

  data_process_vaccinated:
    run: r:latest analysis/R/data_process_vaccinated.R
    needs: [extract_vaccinated]
    outputs:
      highly_sensitive:
        cohort: output/data/data_vaccinated.rds
        vaxdates: output/data/data_vaccinated_vax_dates.rds

  data_properties_vaccinated:
    run: r:latest analysis/R/data_properties.R output/data/data_vaccinated.rds output/data_properties
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        summary: output/data_properties/data_vaccinated*.txt

  data_summarise_vaccinated:
    run: r:latest analysis/R/data_summarise.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        summary1: output/variable_summary/categorical.txt
        summary2: output/variable_summary/numeric.txt
        summary3: output/variable_summary/date.txt
        summarytables: output/variable_summary/tables/categorical_*.csv
        summarystats: output/summary_stats.json

  vaccine_tables:
    run: r:latest analysis/R/vaccine_type.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        tables: output/vaccine_type/tables/vaccine_type_*.csv

  tte_tables:
    run: r:latest analysis/R/tte_tables.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        tables: output/tte/tables/event_rates_*.csv

  tte_plots:
    run: r:latest analysis/R/tte_plots.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        plots: output/tte/figures/plot_*.svg



  # data for whole cohort

  extract_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all
    outputs:
      highly_sensitive:
        cohort: output/input_all.csv


  data_process_all:
    run: r:latest analysis/R/data_process_all.R
    needs: [extract_all]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_long_vax_dates.rds
        data3: output/data/data_long_admission_dates.rds

  data_properties_all:
    run: r:latest analysis/R/data_properties.R output/data/data_all.rds output/data_properties
    needs: [data_process_all]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt


  ## VE models in over 80s

  data_tte_over80s:
    run: r:latest analysis/R/data_tte_over80s.R
    needs: [data_process_all]
    outputs:
      highly_sensitive:
        data: output/modeldata/data_tte_*.rds

  models_cox_over80s:
    run: r:latest analysis/R/models_cox_over80s.R
    needs: [data_tte_over80s]
    outputs:
      moderately_sensitive:
        zph: output/models/cox/over80s/zph*.png
        forest: output/models/cox/over80s/forest*.svg
        tables: output/models/cox/over80s/*.csv

  models_msm_over80s:
    run: r:latest analysis/R/models_msm_over80s.R
    needs: [data_tte_over80s]
    outputs:
      moderately_sensitive:
        weights: output/models/msm/over80s/weights.txt
        forest: output/models/msm/over80s/forest*.svg
        tables: output/models/msm/over80s/*.csv


  # run_ve:
  #   run: cohortextractor:latest --version
  #   needs: [extract_all, data_process_all, data_properties_all, data_tte_over80s, models_cox_over80s]
  #   outputs:
  #     moderately_sensitive:
  #       whatever: output/.gitignore

  # models_under65s:
  #   run: r:latest analysis/R/models_under65s.R
  #   needs: [data_process_all]
  #   outputs:
  #     moderately_sensitive:
  #       #datasummary: output/data_properties/data_tte_over80s*.txt
  #       zph: output/models/under65s/zph*.png
  #       forest: output/models/under65s/forest*.svg
  #       tables: output/models/under65s/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:29:57

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_doses
Requested by
Will Hulme
Branch
doses
Force run dependencies
No
Git commit hash
3f8108f
Requested actions
  • data_process_all
  • data_properties_all
  • data_tte_over80s
  • models_msm_over80s

Code comparison

Compare the code used in this job request