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Job request: 960

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_doses
ID:
eijjoiykatw364sp
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 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

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_cohorts:
    run: r:latest analysis/R/data_define_cohorts.R
    needs: [data_process_all]
    outputs:
      highly_sensitive:
        data: output/modeldata/data_cohorts.rds
      moderately_sensitive:
        metadata: output/modeldata/metadata_cohorts.rds

  data_stset_over80s:
    run: r:latest analysis/R/data_stset.R over80s
    needs: [data_cohorts, data_process_all]
    outputs:
      highly_sensitive:
        data: output/modeldata/data_*over80s.rds

  data_properties_over80s:
    run: r:latest analysis/R/data_properties.R output/modeldata/data_wide_over80s.rds output/data_properties
    needs: [data_stset_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_wide_over80s*.txt

  models_msm_over80s:
    run: r:latest analysis/R/models_msms.R over80s
    needs: [data_cohorts, data_stset_over80s]
    outputs:
      moderately_sensitive:
        weights: output/models/msm/over80s/weights.txt
        forest: output/models/msm/over80s/forest*.svg
        trend: output/models/msm/over80s/secular_trends*.svg
        tables: output/models/msm/over80s/*.csv


  data_stset_under65s:
    run: r:latest analysis/R/data_stset.R under65s
    needs: [data_cohorts, data_process_all]
    outputs:
      highly_sensitive:
        data: output/modeldata/data_*under65s.rds

  data_properties_under65s:
    run: r:latest analysis/R/data_properties.R output/modeldata/data_wide_under65s.rds output/data_properties
    needs: [data_stset_under65s]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_wide_under65s*.txt

  models_msm_under65s:
    run: r:latest analysis/R/models_msms.R under65s
    needs: [data_cohorts, data_stset_under65s]
    outputs:
      moderately_sensitive:
        weights: output/models/msm/under65s/weights.txt
        forest: output/models/msm/under65s/forest*.svg
        trend: output/models/msm/under65s/secular_trends*.svg
        tables: output/models/msm/under65s/*.csv


  # models_cox_over80s:
  #   run: r:latest analysis/R/models_cox_over80s.R
  #   needs: [data_stset_over80s]
  #   outputs:
  #     moderately_sensitive:
  #       zph: output/models/cox/over80s/zph*.png
  #       forest: output/models/cox/over80s/forest*.svg
  #       tables: output/models/cox/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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:47:47

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_doses
Requested by
Will Hulme
Branch
doses
Force run dependencies
No
Git commit hash
eb70f92
Requested actions
  • data_cohorts
  • data_stset_over80s
  • data_properties_over80s
  • models_msm_over80s

Code comparison

Compare the code used in this Job Request