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Job request: 10373

Organisation:
University of Bristol
Workspace:
post-covid-unvaccinated
ID:
5spgtumv5bvxwgk6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Yinghui Wei 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: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  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/preprocess_data.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_stage0.txt
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/review/descriptives/QA_summary.csv
        refactoring: output/not-for-review/meta_data_factors.csv
        IE_criteria: output/review/descriptives/cohort_flow*.csv
        histograms: output/not-for-review/numeric_histograms_*.svg
      highly_sensitive:
        cohort: output/input_stage1*.rds

  stage1_end_date_table:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates*.rds

  stage2_missing_table1:
    run: r:latest analysis/descriptives/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range*.csv
        DateChecks: output/not-for-review/Check_dates_range*.csv
        Descriptive_Table: output/review/descriptives/Table1*.csv

  stage3_diabetes_flow:
    run: r:latest analysis/descriptives/diabetes_flowchart.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values*.csv

  ## Stage 4 - Table 2 

  stage4_table_2:
    run: 'r:latest analysis/descriptives/table_2.R '
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2*.csv

  stage4_venn_diagram:
    run: r:latest analysis/descriptives/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  ## Apply cox model for t2dm 

  Analysis_cox_t2dm:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_t2dm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_t2dm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_t2dm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_t2dm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_t2dm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_t2dm.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:09:14

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
Yinghui Wei
Branch
main
Force run dependencies
No
Git commit hash
824f1c3
Requested actions
  • stage4_venn_diagram

Code comparison

Compare the code used in this Job Request