Skip to content

Job request: 6803

Organisation:
University of Bristol
Workspace:
post-covid-unvaccinated
ID:
lk7r7vozgrxfcdix
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Kurt Taylor requested one or more actions to be run against real patient data in the 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

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:
        QA_rules: output/QA_summary.csv
        refactoring: output/meta_data_factors.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

  # stage4_table2:
  #   run: r:latest analysis/table_2.R
  #   needs:
  #   - stage1_data_cleaning
  #   outputs:
  #     moderately_sensitive:
  #       table2: output/table2.csv

  stage4_venn_diagram:
    run: r:latest analysis/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        venn_diagram: output/venn_diagram_*.svg
        venn_diagram_number_check: output/venn_diagram_number_check_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:35:06

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
Kurt Taylor
Branch
main
Force run dependencies
No
Git commit hash
f881521
Requested actions
  • preprocess_data
  • stage1_data_cleaning
  • stage3_diabetes_flow
  • stage4_venn_diagram

Code comparison

Compare the code used in this Job Request