Job request: 8376

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 post-covid-unvaccinated 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
eljp6xzy7pachgxv succeeded generate_study_population
atq57idbajbm324y succeeded preprocess_data
hn4iu4hirf447ydf succeeded stage1_data_cleaning
nx6tfalh3equyube succeeded stage2_missing_table1
osespxua4f2bjexf succeeded stage3_diabetes_flow
5fpphfwcdv3o57on succeeded vax_eligibility_inputs

Pipeline

Show Hide 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:
      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
      highly_sensitive:
        cohort: output/input_stage1*.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

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

  ## Apply cox model for t1dm 

  Analysis_cox_t1dm:
    run: r:latest analysis/model/01_pipe.R t1dm
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_t1dm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_t1dm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_t1dm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_t1dm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_t1dm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_t1dm.csv

  ## Apply cox model for t2dm 

  Analysis_cox_t2dm:
    run: r:latest analysis/model/01_pipe.R t2dm
    needs:
    - stage1_data_cleaning
    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

  ## Apply cox model for otherdm 

  Analysis_cox_otherdm:
    run: r:latest analysis/model/01_pipe.R otherdm
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_otherdm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_otherdm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_otherdm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_otherdm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_otherdm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_otherdm.csv

  ## Apply cox model for gestationaldm 

  Analysis_cox_gestationaldm:
    run: r:latest analysis/model/01_pipe.R gestationaldm
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_gestationaldm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_gestationaldm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_gestationaldm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_gestationaldm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_gestationaldm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_gestationaldm.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 33:01:34

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-unvaccinated
  • Branch:
    main
  • Creator:
    kurttaylor
  • Force run dependencies:
    False
  • Git Commit Hash:
    bf67cc4
  • Requested actions:
    • vax_eligibility_inputs
    • generate_study_population
    • preprocess_data
    • stage1_data_cleaning
    • stage2_missing_table1
    • stage3_diabetes_flow