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Job request: 6646

Organisation:
University of Bristol
Workspace:
post-covid-unvaccinated
ID:
rgvon6nmxz6ngzca
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Kurt Taylor 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.

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:

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

Job request

Status
Failed 
JobRequestError: generate_study_population failed on a previous run and must be re-run
Backend
TPP
Workspace
post-covid-unvaccinated
Requested by
Kurt Taylor
Branch
main
Force run dependencies
No
Git commit hash
6051ed4
Requested actions
  • run_all

Code comparison

Compare the code used in this job request