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Job request: 2644

Organisation:
Bennett Institute
Workspace:
comparative-ve-research_main
ID:
r3poq32nxbmy5x6g
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

  • Action:
    hcw_extract
    Status:
    Status: Succeeded
    Job identifier:
    gckjszwxpecutbvr
  • Action:
    hcw_process
    Status:
    Status: Succeeded
    Job identifier:
    4c243delcoclbsmn
  • Action:
    hcw_descr
    Status:
    Status: Succeeded
    Job identifier:
    nfq2tvwzrync5fua

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

## check H&SC worker flag

  hcw_extract:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hcw --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_hcw.feather

  hcw_process:
    run: r:latest analysis/hcw/process.R
    needs: [hcw_extract]
    outputs:
      highly_sensitive:
        data: output/data/hcw_data_processed.rds
        datavax: output/data/hcw_data_vax.rds

  hcw_descr:
    run: r:latest analysis/hcw/descr.R
    needs: [hcw_process]
    outputs:
      moderately_sensitive:
        png: output/hcw/*.png
        svg: output/hcw/*.svg
        html: output/hcw/*.html
        csv: output/hcw/*.csv

## analysis proper

  design:
    run: r:latest analysis/process/design.R
    outputs:
      moderately_sensitive:
        metadata: output/data/metadata*

  extract:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  data_process:
    run: r:latest analysis/process/data_process.R
    needs: [extract]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds

  data_properties:
    run: r:latest analysis/process/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data*.txt

  data_selection:
    run: r:latest analysis/process/data_selection.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data_allvax: output/data/data_cohort_allvax.rds
        data: output/data/data_cohort.rds
      moderately_sensitive:
        flow: output/data/flowchart.csv

  descr_table1:
    run: r:latest analysis/descriptive/table1.R
    needs: [design, data_selection]
    outputs:
      moderately_sensitive:
        html: output/descriptive/tables/table1.html
        csv: output/descriptive/tables/table1.csv

  descr_table1_allvax:
    run: r:latest analysis/descriptive/table1_allvax.R
    needs: [design, data_selection]
    outputs:
      moderately_sensitive:
        html: output/descriptive/tables/table1_allvax.html
        csv: output/descriptive/tables/table1_allvax.csv

  descr_irr:
    run: r:latest analysis/descriptive/table_irr.R
    needs: [design, data_selection]
    outputs:
      moderately_sensitive:
        html: output/descriptive/tables/table_irr.html
        csv: output/descriptive/tables/table_irr.csv

  descr_km:
    run: r:latest analysis/descriptive/km.R
    needs: [design, data_selection]
    outputs:
      moderately_sensitive:
        png: output/descriptive/km/plot_survival*.png
        svg: output/descriptive/km/plot_survival*.svg

#######################################
 ## MATCHING
#######################################

  # data_selection:
  #   run: r:latest analysis/process/data_selection.R
  #   needs: [data_process]
  #   outputs:
  #     highly_sensitive:
  #       data_az: output/data/data_vax_az_withoutdate.csv
  #       data_pfizer: output/data/data_vax_pfizer_withoutdate.csv
  #       data_az_date: output/data/data_vax_az_withdate.csv
  #       data_pfizer_date: output/data/data_vax_pfizer_withdate.csv
  #
  # matchwithoutdate_recipients:
  #   run: python:latest python analysis/matching/matchwithoutdate.py
  #   needs: [data_selection]
  #   outputs:
  #     highly_sensitive:
  #       cases: output/data/matched_cases_withoutdate.csv
  #       matches: output/data/matched_matches_withoutdate.csv
  #       combined: output/data/matched_combined_withoutdate.csv
  #     moderately_sensitive:
  #       report: output/data/matching_report_withoutdate.txt
  #
  # matchwithoutdate_process:
  #   run: r:latest analysis/matching/match_process.R withoutdate
  #   needs: [design, matchwithoutdate_recipients, data_selection]
  #   outputs:
  #     highly_sensitive:
  #       data: output/data/data_matches_withoutdate.rds
  #     moderately_sensitive:
  #       report: output/matching/matching_balance_withoutdate.html
  #
  #
  # matchwithdate_recipients:
  #   run: python:latest python analysis/matching/matchwithdate.py
  #   needs: [data_selection]
  #   outputs:
  #     highly_sensitive:
  #       cases: output/data/matched_cases_withdate.csv
  #       matches: output/data/matched_matches_withdate.csv
  #       combined: output/data/matched_combined_withdate.csv
  #     moderately_sensitive:
  #       report: output/data/matching_report_withdate.txt
  #
  #
  # matchwithdate_process:
  #   run: r:latest analysis/matching/match_process.R withdate
  #   needs: [design, matchwithdate_recipients, data_selection]
  #   outputs:
  #     highly_sensitive:
  #       data: output/data/data_matches_withdate.rds
  #     moderately_sensitive:
  #       report: output/matching/matching_balance_withdate.html



#######################################
 ## COMPARATIVE EFFECTIVENESS MODELS
 ## positive test outcome
#######################################


  model_calendar_test:
    run: r:latest analysis/models/model_cox_calendar.R test
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/test/data_cox_split.rds
        models: output/test/model*.rds
      moderately_sensitive:
        logs:  output/test/log*.txt
        glance: output/test/glance*.csv

  report_calendar_test:
    run: r:latest analysis/models/report_cox.R test
    needs: [design, model_calendar_test]
    outputs:
      moderately_sensitive:
        figure: output/test/forest*.svg
        figure2: output/test/forest*.png
        table: output/test/estimates*.csv

  model_calendar_postest:
    run: r:latest analysis/models/model_cox_calendar.R postest
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/postest/data_cox_split.rds
        models: output/postest/model*.rds
      moderately_sensitive:
        logs:  output/postest/log*.txt
        glance: output/postest/glance*.csv

  report_calendar_postest:
    run: r:latest analysis/models/report_cox.R postest
    needs: [design, model_calendar_postest]
    outputs:
      moderately_sensitive:
        figure: output/postest/forest*.svg
        figure2: output/postest/forest*.png
        table: output/postest/estimates*.csv


  model_calendar_emergency:
    run: r:latest analysis/models/model_cox_calendar.R emergency
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/emergency/data_cox_split.rds
        models: output/emergency/model*.rds
      moderately_sensitive:
        logs:  output/emergency/log*.txt
        glance: output/emergency/glance*.csv

  report_calendar_emergency:
    run: r:latest analysis/models/report_cox.R emergency
    needs: [design, model_calendar_emergency]
    outputs:
      moderately_sensitive:
        figure: output/emergency/forest*.svg
        figure2: output/emergency/forest*.png
        table: output/emergency/estimates*.csv

  model_calendar_covidadmitted:
    run: r:latest analysis/models/model_cox_calendar.R covidadmitted
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/covidadmitted/data_cox_split.rds
        models: output/covidadmitted/model*.rds
      moderately_sensitive:
        logs:  output/covidadmitted/log*.txt
        glance: output/covidadmitted/glance*.csv

  report_calendar_covidadmitted:
    run: r:latest analysis/models/report_cox.R covidadmitted
    needs: [design, model_calendar_covidadmitted]
    outputs:
      moderately_sensitive:
        figure: output/covidadmitted/forest*.svg
        figure2: output/covidadmitted/forest*.png
        table: output/covidadmitted/estimates*.csv

  model_calendar_covidcc:
    run: r:latest analysis/models/model_cox_calendar.R covidcc
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/covidcc/data_cox_split.rds
        models: output/covidcc/model*.rds
      moderately_sensitive:
        logs:  output/covidcc/log*.txt
        glance: output/covidcc/glance*.csv

  report_calendar_covidcc:
    run: r:latest analysis/models/report_cox.R covidcc
    needs: [design, model_calendar_covidcc]
    outputs:
      moderately_sensitive:
        figure: output/covidcc/forest*.svg
        figure2: output/covidcc/forest*.png
        table: output/covidcc/estimates*.csv

  model_calendar_coviddeath:
    run: r:latest analysis/models/model_cox_calendar.R coviddeath
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/coviddeath/data_cox_split.rds
        models: output/coviddeath/model*.rds
      moderately_sensitive:
        logs:  output/coviddeath/log*.txt
        glance: output/coviddeath/glance*.csv

  report_calendar_coviddeath:
    run: r:latest analysis/models/report_cox.R coviddeath
    needs: [design, model_calendar_coviddeath]
    outputs:
      moderately_sensitive:
        figure: output/coviddeath/forest*.svg
        figure2: output/coviddeath/forest*.png
        table: output/coviddeath/estimates*.csv

  model_calendar_noncoviddeath:
    run: r:latest analysis/models/model_cox_calendar.R noncoviddeath
    needs: [design, data_selection]
    outputs:
      highly_sensitive:
        data: output/noncoviddeath/data_cox_split.rds
        models: output/noncoviddeath/model*.rds
      moderately_sensitive:
        logs:  output/noncoviddeath/log*.txt
        glance: output/noncoviddeath/glance*.csv

  report_calendar_noncoviddeath:
    run: r:latest analysis/models/report_cox.R noncoviddeath
    needs: [design, model_calendar_noncoviddeath]
    outputs:
      moderately_sensitive:
        figure: output/noncoviddeath/forest*.svg
        figure2: output/noncoviddeath/forest*.png
        table: output/noncoviddeath/estimates*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:09:05

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

Job request

Status
Succeeded
Backend
TPP
Workspace
comparative-ve-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
be0693c
Requested actions
  • hcw_extract
  • hcw_process
  • hcw_descr

Code comparison

Compare the code used in this job request