Job request: 7442

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
2f5rihpauftzyqdd succeeded Analysis_cox_gestationaldm
hftrp2vjswjdw5v2 succeeded Analysis_cox_otherdm
56f3tdlroe5aoalh succeeded Analysis_cox_t1dm
dhp6bspbkhxa722k succeeded Analysis_cox_t2dm
w4dwv4iwjkz75tdt succeeded stage2_missing_table1
6nnbz6g6qzf7jrdx succeeded stage3_diabetes_flow
g267krocktvi7jl2 succeeded stage4_venn_diagram

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_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

  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

  ## Apply cox model for t1dm 

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

  ## Apply cox model for t2dm 

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

  ## Apply cox model for otherdm 

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

  ## Apply cox model for gestationaldm 

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

  ## Apply cox model for depression 

  Analysis_cox_depression:
    run: r:latest analysis/01_pipe.R depression
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_depression.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_depression.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_depression_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_depression.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_depression.csv
        compiled_event_counts: output/compiled_event_counts_depression.csv

  ## Apply cox model for anxiety_general 

  Analysis_cox_anxiety_general:
    run: r:latest analysis/01_pipe.R anxiety_general
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_anxiety_general.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_general.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_anxiety_general_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_general.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_anxiety_general.csv
        compiled_event_counts: output/compiled_event_counts_anxiety_general.csv

  ## Apply cox model for anxiety_ocd 

  Analysis_cox_anxiety_ocd:
    run: r:latest analysis/01_pipe.R anxiety_ocd
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_anxiety_ocd.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ocd.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_anxiety_ocd_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_ocd.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_anxiety_ocd.csv
        compiled_event_counts: output/compiled_event_counts_anxiety_ocd.csv

  ## Apply cox model for anxiety_ptsd 

  Analysis_cox_anxiety_ptsd:
    run: r:latest analysis/01_pipe.R anxiety_ptsd
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_anxiety_ptsd.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ptsd.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_anxiety_ptsd_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_ptsd.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_anxiety_ptsd.csv
        compiled_event_counts: output/compiled_event_counts_anxiety_ptsd.csv

  ## Apply cox model for eating_disorders 

  Analysis_cox_eating_disorders:
    run: r:latest analysis/01_pipe.R eating_disorders
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_eating_disorders.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_eating_disorders.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_eating_disorders_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_eating_disorders.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_eating_disorders.csv
        compiled_event_counts: output/compiled_event_counts_eating_disorders.csv

  ## Apply cox model for serious_mental_illness 

  Analysis_cox_serious_mental_illness:
    run: r:latest analysis/01_pipe.R serious_mental_illness
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_serious_mental_illness.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_serious_mental_illness.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_serious_mental_illness_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_serious_mental_illness.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_serious_mental_illness.csv
        compiled_event_counts: output/compiled_event_counts_serious_mental_illness.csv

  ## Apply cox model for self_harm_10plus 

  Analysis_cox_self_harm_10plus:
    run: r:latest analysis/01_pipe.R self_harm_10plus
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_self_harm_10plus.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_10plus.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_self_harm_10plus_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_self_harm_10plus.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_self_harm_10plus.csv
        compiled_event_counts: output/compiled_event_counts_self_harm_10plus.csv

  ## Apply cox model for self_harm_15plus 

  Analysis_cox_self_harm_15plus:
    run: r:latest analysis/01_pipe.R self_harm_15plus
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_self_harm_15plus.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_15plus.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_self_harm_15plus_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_self_harm_15plus.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_self_harm_15plus.csv
        compiled_event_counts: output/compiled_event_counts_self_harm_15plus.csv

  ## Apply cox model for suicide 

  Analysis_cox_suicide:
    run: r:latest analysis/01_pipe.R suicide
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_suicide.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_suicide.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_suicide_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_suicide.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_suicide.csv
        compiled_event_counts: output/compiled_event_counts_suicide.csv

  ## Apply cox model for addiction 

  Analysis_cox_addiction:
    run: r:latest analysis/01_pipe.R addiction
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        analyses_not_run: output/analyses_not_run_addiction.csv
        compiled_hrs_csv: output/suppressed_compiled_HR_results_addiction.csv
        compiled_hrs_csv_to_release: output/suppressed_compiled_HR_results_addiction_to_release.csv
        compiled_event_counts_csv: output/suppressed_compiled_event_counts_addiction.csv
      highly_sensitive:
        compiled_hrs: output/compiled_HR_results_addiction.csv
        compiled_event_counts: output/compiled_event_counts_addiction.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 66:31:30

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-unvaccinated
  • Branch:
    main
  • Creator:
    kurttaylor
  • Force run dependencies:
    False
  • Git Commit Hash:
    d161b64
  • Requested actions:
    • stage2_missing_table1
    • stage3_diabetes_flow
    • stage4_venn_diagram
    • Analysis_cox_t1dm
    • Analysis_cox_t2dm
    • Analysis_cox_otherdm
    • Analysis_cox_gestationaldm