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Job request: 2647

Organisation:
Bennett Institute
Workspace:
comparative-ve-research_main
ID:
hclvwr6gm3x5mipx
View repo View project.yaml

This page shows the technical details of what happened when 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 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

  • Action:
    design
    Status:
    Status: Succeeded
    Job identifier:
    pag26yhy5z66aquw
  • Action:
    descr_table1
    Status:
    Status: Succeeded
    Job identifier:
    tgn7vsrgogey4mww

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: 00:00:46

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

Job information

Status
Succeeded
Backend
TPP
Workspace
comparative-ve-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
0510adc
Requested actions
  • design
  • descr_table1

Code comparison

Compare the code used in this Job Request