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Job request: 2439

Organisation:
Bennett Institute
Workspace:
comparative-ve-research_main
ID:
owr6fbuaza6b2xi7
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:

  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:
        data1: output/data/data_processed.rds
        data2: output/data/data_long_vax_dates.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: output/data/data_cohort.rds
        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
      moderately_sensitive:
        flow: output/data/flowchart.csv

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


  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
#######################################

  model1_postest:
    run: r:latest analysis/models/model_cox.R postest
    needs: [design, matchwithoutdate_process]
    outputs:
      highly_sensitive:
        data: output/postest/data_cox_split.rds
        models: output/postest/model*.rds
      moderately_sensitive:
        logs:  output/postest/log*.txt

  report1_postest:
    run: r:latest analysis/models/report_cox.R postest
    needs: [design, model1_postest]
    outputs:
      moderately_sensitive:
        figure: output/postest/forest*.svg
        table: output/postest/estimates*.csv

  model1_covidadmitted:
    run: r:latest analysis/models/model_cox.R covidadmitted
    needs: [design, matchwithoutdate_process]
    outputs:
      highly_sensitive:
        data: output/covidadmitted/data_cox_split.rds
        models: output/covidadmitted/model*.rds
      moderately_sensitive:
        logs:  output/covidadmitted/log*.txt

  report1_covidadmitted:
    run: r:latest analysis/models/report_cox.R covidadmitted
    needs: [design, model1_covidadmitted]
    outputs:
      moderately_sensitive:
        figure: output/covidadmitted/forest*.svg
        table: output/covidadmitted/estimates*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:20:00

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
235c52d
Requested actions
  • model1_postest
  • report1_postest
  • model1_covidadmitted
  • report1_covidadmitted

Code comparison

Compare the code used in this Job Request