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Job request: 6542

Organisation:
University of Bristol
Workspace:
post-covid-unvaccinated
ID:
5nerr6x5yi7c2dvj
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Genevieve Cezard 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: 300000

actions:
  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

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

  preprocess_data:
    run: r:latest analysis/preprocess_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/Stage1_data_cleaning.R
    needs: [preprocess_data]
    outputs:
      moderately_sensitive:
        refactoring: output/meta_data_factors.csv
        QA_rules: output/QA_summary.csv
        IE_criteria: output/cohort_flow.csv
      highly_sensitive:
        cohort: output/input_stage1.rds

  # stage2_missing_table1:
  #   run: r:latest analysis/Stage2_missing_table1.R 
  #   needs:
  #   - stage1_data_cleaning
  #   outputs:
  #     moderately_sensitive:
  #       Missing_RangeChecks: output/Check_missing_range.csv
  #       DateChecks: output/Check_dates_range.csv
  #       Descriptive_Table: output/Table1.csv

  # stage3_diabetes_flow:
  #   run: r:latest analysis/diabetes_flowchart.R
  #   needs:
  #   - stage1_data_cleaning
  #   outputs:
  #     moderately_sensitive:
  #       flow_df: output/diabetes_flow_values.csv      
  #       flow_fig: output/diabetes_flow.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 17:31:12

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-covid-unvaccinated
Requested by
Genevieve Cezard
Branch
main
Force run dependencies
No
Git commit hash
e4f629b
Requested actions
  • run_all

Code comparison

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