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Job request: 4940

Organisation:
Bennett Institute
Workspace:
booster-effectiveness_main
ID:
pqynkbdi2m2clb4b
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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create-project.R 
  ## Edit and run create-project.R to update the project.yaml 
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  ## Pre-server scripts 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and tidy 
  ## # # # # # # # # # # # # # # # # # # # 

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

  data_process:
    run: r:latest analysis/data_process.R
    needs:
    - extract
    outputs:
      highly_sensitive:
        processed: output/data/data_processed.rds
        vaxlong: output/data/data_vaxlong.rds

  data_process_long:
    run: r:latest analysis/data_process_long.R
    needs:
    - data_process
    outputs:
      highly_sensitive:
        processed: output/data/data_long*.rds

  data_selection:
    run: r:latest analysis/data_selection.R
    needs:
    - data_process
    outputs:
      highly_sensitive:
        data: output/data/data_cohort.rds
      moderately_sensitive:
        flow: output/data/flowchart.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Descriptive stats 
  ## # # # # # # # # # # # # # # # # # # # 
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  ## Models 
  ## # # # # # # # # # # # # # # # # # # # 
  ## ###  Positive SARS-CoV-2 Test 

  model_seqtrialcox_pfizer_postest:
    run: r:latest analysis/model_seqtrialcox.R pfizer postest
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/pfizer/postest/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/pfizer/postest/model_*.txt
        csv: output/models/seqtrialcox/pfizer/postest/model_*.csv

  report_seqtrialcox_pfizer_postest:
    run: r:latest analysis/report_seqtrialcox.R pfizer postest
    needs:
    - model_seqtrialcox_pfizer_postest
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/pfizer/postest/report_*.csv
        svg: output/models/seqtrialcox/pfizer/postest/report_*.svg
        png: output/models/seqtrialcox/pfizer/postest/report_*.png

  model_seqtrialcox_az_postest:
    run: r:latest analysis/model_seqtrialcox.R az postest
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/az/postest/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/az/postest/model_*.txt
        csv: output/models/seqtrialcox/az/postest/model_*.csv

  report_seqtrialcox_az_postest:
    run: r:latest analysis/report_seqtrialcox.R az postest
    needs:
    - model_seqtrialcox_az_postest
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/az/postest/report_*.csv
        svg: output/models/seqtrialcox/az/postest/report_*.svg
        png: output/models/seqtrialcox/az/postest/report_*.png

  model_seqtrialcox_moderna_postest:
    run: r:latest analysis/model_seqtrialcox.R moderna postest
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/moderna/postest/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/moderna/postest/model_*.txt
        csv: output/models/seqtrialcox/moderna/postest/model_*.csv

  report_seqtrialcox_moderna_postest:
    run: r:latest analysis/report_seqtrialcox.R moderna postest
    needs:
    - model_seqtrialcox_moderna_postest
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/moderna/postest/report_*.csv
        svg: output/models/seqtrialcox/moderna/postest/report_*.svg
        png: output/models/seqtrialcox/moderna/postest/report_*.png

  ## ###  COVID-19 unplanned admission 

  model_seqtrialcox_pfizer_covidadmitted:
    run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/pfizer/covidadmitted/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/pfizer/covidadmitted/model_*.txt
        csv: output/models/seqtrialcox/pfizer/covidadmitted/model_*.csv

  report_seqtrialcox_pfizer_covidadmitted:
    run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted
    needs:
    - model_seqtrialcox_pfizer_covidadmitted
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/pfizer/covidadmitted/report_*.csv
        svg: output/models/seqtrialcox/pfizer/covidadmitted/report_*.svg
        png: output/models/seqtrialcox/pfizer/covidadmitted/report_*.png

  model_seqtrialcox_az_covidadmitted:
    run: r:latest analysis/model_seqtrialcox.R az covidadmitted
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/az/covidadmitted/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/az/covidadmitted/model_*.txt
        csv: output/models/seqtrialcox/az/covidadmitted/model_*.csv

  report_seqtrialcox_az_covidadmitted:
    run: r:latest analysis/report_seqtrialcox.R az covidadmitted
    needs:
    - model_seqtrialcox_az_covidadmitted
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/az/covidadmitted/report_*.csv
        svg: output/models/seqtrialcox/az/covidadmitted/report_*.svg
        png: output/models/seqtrialcox/az/covidadmitted/report_*.png

  model_seqtrialcox_moderna_covidadmitted:
    run: r:latest analysis/model_seqtrialcox.R moderna covidadmitted
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/moderna/covidadmitted/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/moderna/covidadmitted/model_*.txt
        csv: output/models/seqtrialcox/moderna/covidadmitted/model_*.csv

  report_seqtrialcox_moderna_covidadmitted:
    run: r:latest analysis/report_seqtrialcox.R moderna covidadmitted
    needs:
    - model_seqtrialcox_moderna_covidadmitted
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/moderna/covidadmitted/report_*.csv
        svg: output/models/seqtrialcox/moderna/covidadmitted/report_*.svg
        png: output/models/seqtrialcox/moderna/covidadmitted/report_*.png

  ## ###  COVID-19 death 

  model_seqtrialcox_pfizer_coviddeath:
    run: r:latest analysis/model_seqtrialcox.R pfizer coviddeath
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/pfizer/coviddeath/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/pfizer/coviddeath/model_*.txt
        csv: output/models/seqtrialcox/pfizer/coviddeath/model_*.csv

  report_seqtrialcox_pfizer_coviddeath:
    run: r:latest analysis/report_seqtrialcox.R pfizer coviddeath
    needs:
    - model_seqtrialcox_pfizer_coviddeath
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/pfizer/coviddeath/report_*.csv
        svg: output/models/seqtrialcox/pfizer/coviddeath/report_*.svg
        png: output/models/seqtrialcox/pfizer/coviddeath/report_*.png

  model_seqtrialcox_az_coviddeath:
    run: r:latest analysis/model_seqtrialcox.R az coviddeath
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/az/coviddeath/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/az/coviddeath/model_*.txt
        csv: output/models/seqtrialcox/az/coviddeath/model_*.csv

  report_seqtrialcox_az_coviddeath:
    run: r:latest analysis/report_seqtrialcox.R az coviddeath
    needs:
    - model_seqtrialcox_az_coviddeath
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/az/coviddeath/report_*.csv
        svg: output/models/seqtrialcox/az/coviddeath/report_*.svg
        png: output/models/seqtrialcox/az/coviddeath/report_*.png

  model_seqtrialcox_moderna_coviddeath:
    run: r:latest analysis/model_seqtrialcox.R moderna coviddeath
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/moderna/coviddeath/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/moderna/coviddeath/model_*.txt
        csv: output/models/seqtrialcox/moderna/coviddeath/model_*.csv

  report_seqtrialcox_moderna_coviddeath:
    run: r:latest analysis/report_seqtrialcox.R moderna coviddeath
    needs:
    - model_seqtrialcox_moderna_coviddeath
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/moderna/coviddeath/report_*.csv
        svg: output/models/seqtrialcox/moderna/coviddeath/report_*.svg
        png: output/models/seqtrialcox/moderna/coviddeath/report_*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Reports 
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Timeline

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  • Finished:

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

Job request

Status
Failed 
JobRequestError: extract failed on a previous run and must be re-run
Backend
TPP
Workspace
booster-effectiveness_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
fc5a48c
Requested actions
  • run_all

Code comparison

Compare the code used in this job request