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Job request: 2541

Organisation:
Bennett Institute
Workspace:
comparative-ve-research_main
ID:
fywpdsufomjy2vl3
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

  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    lbtqkzahx7ofh3jm
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    data_selection
    Status:
    Status: Failed
    Job identifier:
    5t4h45yzpamon2dx
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    descr_table1
    Status:
    Status: Failed
    Job identifier:
    pp76jhspr5wgol74
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    descr_table1_allvax
    Status:
    Status: Failed
    Job identifier:
    q7o7jvdr2ctpitn5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    model_calendar_postest
    Status:
    Status: Failed
    Job identifier:
    au2ggkngsibx6xws
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    model_calendar_covidadmitted
    Status:
    Status: Failed
    Job identifier:
    mr5helazbws7prpe
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    model_calendar_covidcc
    Status:
    Status: Failed
    Job identifier:
    uduyyxryohjteftb
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_covidcc
    Status:
    Status: Failed
    Job identifier:
    ckfrpt52hekd2me7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_coviddeath
    Status:
    Status: Failed
    Job identifier:
    ixbojqa6bm6cjgwo
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    zewvtoigbparm4no
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_postest
    Status:
    Status: Failed
    Job identifier:
    awvxil22rkdv45pb
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_calendar_covidadmitted
    Status:
    Status: Failed
    Job identifier:
    xds3fvci7w77c6pg
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    model_calendar_coviddeath
    Status:
    Status: Failed
    Job identifier:
    2w2xu76dw7jxqu27
    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

#######################################
 ## 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_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

  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
        table: output/postest/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

  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
        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

  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
        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

  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
        table: output/coviddeath/estimates*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:24

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

Job information

Status
Failed
Backend
TPP
Workspace
comparative-ve-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
c2fb191
Requested actions
  • data_process
  • data_properties
  • data_selection
  • descr_table1
  • descr_table1_allvax
  • model_calendar_postest
  • report_calendar_postest
  • model_calendar_covidadmitted
  • report_calendar_covidadmitted
  • model_calendar_covidcc
  • report_calendar_covidcc
  • model_calendar_coviddeath
  • report_calendar_coviddeath

Code comparison

Compare the code used in this Job Request