Job request: 2559

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 Comparative Vaccine Effectiveness 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

ID Status Action
tldubudk7xjxpheu succeeded design
ozcm2j2ofsv7kgl2 succeeded extract
lyy5qc3mrdl2y2mo succeeded data_process
5vo4jg5to3zhrdyj succeeded data_properties
nwkmkajwfampn43c succeeded data_selection
52hvmmsu2ma5hj5t succeeded descr_table1
rvqopbbpjfdlirjo succeeded descr_table1_allvax
p2iduipy7iuh5d7f succeeded model_calendar_test
fffwfwyflzpaqjp2 succeeded model_calendar_postest
qcic6fhm6pejq3xr failed report_calendar_test
237oz6t4kzyqo7ja succeeded report_calendar_postest
oyiumkipfrui2s52 succeeded model_calendar_covidadmitted
iiq3xrjkh7n66pe7 succeeded report_calendar_covidadmitted
xdcdlxiwx6jknau2 succeeded model_calendar_covidcc
lvfg32t5ujcq7xv3 succeeded report_calendar_covidcc
binz43izlohciuj6 succeeded model_calendar_coviddeath
hoiv6qlfurt2djbg succeeded report_calendar_coviddeath

Pipeline

Show Hide 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_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

  report_calendar_test:
    run: r:latest analysis/models/report_cox.R test
    needs: [design, model_calendar_postest]
    outputs:
      moderately_sensitive:
        figure: output/test/forest*.svg
        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

  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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 05:45:27

Config