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Job request: 2636

Organisation:
Bennett Institute
Workspace:
comparative-ve-research_main
ID:
5vxyzreksdducb6i
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:
    design
    Status:
    Status: Succeeded
    Job identifier:
    2t6ugddnphs4lldk
  • Action:
    extract
    Status:
    Status: Succeeded
    Job identifier:
    yt6pry2rbuo2pbr6
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    a5v7gyvzywxq62sa
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    tbgr2ux2bex3igia
  • Action:
    data_selection
    Status:
    Status: Succeeded
    Job identifier:
    ogjcvrye6pe6t3o5
  • Action:
    model_calendar_postest
    Status:
    Status: Failed
    Job identifier:
    rg3oxx2uswo3joex
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    descr_table1_allvax
    Status:
    Status: Succeeded
    Job identifier:
    vvz7eyaunsrbxt4v
  • Action:
    model_calendar_noncoviddeath
    Status:
    Status: Failed
    Job identifier:
    gway32fzhdmpngjy
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    model_calendar_test
    Status:
    Status: Failed
    Job identifier:
    7yr6iojpmt6j7m3n
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    model_calendar_coviddeath
    Status:
    Status: Failed
    Job identifier:
    ptbd7htjpxl6yixi
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    descr_km
    Status:
    Status: Succeeded
    Job identifier:
    s4jlxpqhpmutsvh6
  • Action:
    model_calendar_covidadmitted
    Status:
    Status: Failed
    Job identifier:
    7dheuibp4zawkaio
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    descr_irr
    Status:
    Status: Succeeded
    Job identifier:
    ikvjxagfbjy4ok24
  • Action:
    model_calendar_covidcc
    Status:
    Status: Failed
    Job identifier:
    kzr2pghdyfctzf4e
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    model_calendar_emergency
    Status:
    Status: Failed
    Job identifier:
    oyaqw4kwlbey2nl5
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    descr_table1
    Status:
    Status: Succeeded
    Job identifier:
    27s7vtisnojqrwxj
  • Action:
    report_calendar_coviddeath
    Status:
    Status: Failed
    Job identifier:
    b5ndtkw252i2dtqw
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_test
    Status:
    Status: Failed
    Job identifier:
    23hj27fipn4edpsd
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_postest
    Status:
    Status: Failed
    Job identifier:
    2shtlkyioo4wuyq2
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_emergency
    Status:
    Status: Failed
    Job identifier:
    z6d6v7zhm5if6zzh
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_covidadmitted
    Status:
    Status: Failed
    Job identifier:
    mm7n5dorkdb37gdg
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_covidcc
    Status:
    Status: Failed
    Job identifier:
    eiyyl2zz7pyapbmj
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_noncoviddeath
    Status:
    Status: Failed
    Job identifier:
    l3r2h2lkqmf5wiqy
    Error:
    dependency_failed: Not starting as dependency failed

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:
        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: 05:48:54

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

Job request

Status
Failed
Backend
TPP
Workspace
comparative-ve-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
Yes
Git commit hash
1001f4f
Requested actions
  • data_process
  • data_properties
  • data_selection
  • descr_table1
  • descr_table1_allvax
  • descr_irr
  • descr_km
  • model_calendar_test
  • report_calendar_test
  • model_calendar_postest
  • report_calendar_postest
  • model_calendar_emergency
  • report_calendar_emergency
  • model_calendar_covidadmitted
  • report_calendar_covidadmitted
  • model_calendar_covidcc
  • report_calendar_covidcc
  • model_calendar_coviddeath
  • report_calendar_coviddeath
  • model_calendar_noncoviddeath
  • report_calendar_noncoviddeath

Code comparison

Compare the code used in this job request