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Job request: 1123

Organisation:
Bennett Institute
Workspace:
covid-vaccine-effectiveness-research_main
ID:
hhxvyzsxrrcotlqp
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: 1000000

actions:

  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

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

  ## VE models in over 80s

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

  data_properties_over80s_fixed:
    run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_fixed.rds output/over80s/data_properties
    needs: [data_stset_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/over80s/data_properties/data_wide_fixed*.txt

  data_properties_over80s_tte:
    run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_tte.rds output/over80s/data_properties
    needs: [data_stset_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/over80s/data_properties/data_wide_tte*.txt

  descr_eventsperday_over80s:
    run: r:latest analysis/R/plot_outcomes_per_day.R over80s postest
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/over80s/postest/descr/events*.svg

  descr_table1_over80s:
    run: r:latest analysis/R/table1.R over80s
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      moderately_sensitive:
        table1: output/over80s/descr/table*


 # vax1 only (ignores second dose)

  models_msm_over80s_any_dose1:
    run: r:latest analysis/R/models_msms_dose1.R over80s postest any
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/any/dose1/model*.rds
        data: output/over80s/postest/any/dose1/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/any/dose1/weights.txt
        weightsplot: output/over80s/postest/any/dose1/histogram_weights.svg

  reportmodels_msm_over80s_any_dose1:
    run: r:latest analysis/R/reportmodels_msms_dose1.R over80s postest any
    needs: [data_define_cohorts, models_msm_over80s_any_dose1]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/any/dose1/forest*.svg
        trend: output/over80s/postest/any/dose1/secular_trends*.svg
        tables: output/over80s/postest/any/dose1/*.csv

  models_msm_over80s_pfizer_dose1:
    run: r:latest analysis/R/models_msms_dose1.R over80s postest pfizer
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/pfizer/dose1/model*.rds
        data: output/over80s/postest/pfizer/dose1/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/pfizer/dose1/weights.txt
        weightsplot: output/over80s/postest/pfizer/dose1/histogram_weights.svg

  reportmodels_msm_over80s_pfizer_dose1:
    run: r:latest analysis/R/reportmodels_msms_dose1.R over80s postest pfizer
    needs: [data_define_cohorts, models_msm_over80s_pfizer_dose1]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/pfizer/dose1/forest*.svg
        trend: output/over80s/postest/pfizer/dose1/secular_trends*.svg
        tables: output/over80s/postest/pfizer/dose1/*.csv

  models_msm_over80s_az_dose1:
    run: r:latest analysis/R/models_msms_dose1.R over80s postest az
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/az/dose1/model*.rds
        data: output/over80s/postest/az/dose1/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/az/dose1/weights.txt
        weightsplot: output/over80s/postest/az/dose1/histogram_weights.svg

  reportmodels_msm_over80s_az_dose1:
    run: r:latest analysis/R/reportmodels_msms_dose1.R over80s postest az
    needs: [data_define_cohorts, models_msm_over80s_az_dose1]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/az/dose1/forest*.svg
        trend: output/over80s/postest/az/dose1/secular_trends*.svg
        tables: output/over80s/postest/az/dose1/*.csv


 # vax1 and vax2

  models_msm_over80s_any_dose12:
    run: r:latest analysis/R/models_msms_dose12.R over80s postest any
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/any/dose12/model*.rds
        data: output/over80s/postest/any/dose12/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/any/dose12/weights.txt
        weightsplot: output/over80s/postest/any/dose12/histogram_weights.svg

  reportmodels_msm_over80s_any_dose12:
    run: r:latest analysis/R/reportmodels_msms_dose12.R over80s postest any
    needs: [data_define_cohorts, models_msm_over80s_any_dose12]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/any/dose12/forest*.svg
        trend: output/over80s/postest/any/dose12/secular_trends*.svg
        tables: output/over80s/postest/any/dose12/*.csv


  models_msm_over80s_pfizer_dose12:
    run: r:latest analysis/R/models_msms_dose12.R over80s postest pfizer
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/pfizer/dose12/model*.rds
        data: output/over80s/postest/pfizer/dose12/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/pfizer/dose12/weights.txt
        weightsplot: output/over80s/postest/pfizer/dose12/histogram_weights.svg

  reportmodels_msm_over80s_pfizer_dose12:
    run: r:latest analysis/R/reportmodels_msms_dose12.R over80s postest pfizer
    needs: [data_define_cohorts, models_msm_over80s_pfizer_dose12]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/pfizer/dose12/forest*.svg
        trend: output/over80s/postest/pfizer/dose12/secular_trends*.svg
        tables: output/over80s/postest/pfizer/dose12/*.csv


  models_msm_over80s_az_dose12:
    run: r:latest analysis/R/models_msms_dose12.R over80s postest az
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/az/dose12/model*.rds
        data: output/over80s/postest/az/dose12/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/az/dose12/weights.txt
        weightsplot: output/over80s/postest/az/dose12/histogram_weights.svg

  reportmodels_msm_over80s_az_dose12:
    run: r:latest analysis/R/reportmodels_msms_dose12.R over80s postest az
    needs: [data_define_cohorts, models_msm_over80s_az_dose12]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/az/dose12/forest*.svg
        trend: output/over80s/postest/az/dose12/secular_trends*.svg
        tables: output/over80s/postest/az/dose12/*.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: 08:57:41

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-effectiveness-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
803cda8
Requested actions
  • data_define_cohorts
  • data_stset_over80s
  • data_properties_over80s_fixed
  • data_properties_over80s_tte
  • descr_eventsperday_over80s
  • descr_table1_over80s
  • models_msm_over80s_any_dose1
  • reportmodels_msm_over80s_any_dose1
  • models_msm_over80s_pfizer_dose1
  • reportmodels_msm_over80s_pfizer_dose1
  • models_msm_over80s_az_dose1
  • reportmodels_msm_over80s_az_dose1

Code comparison

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