Job request: 9323

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
hlkoo74wsswjnbn3 failed Analysis_cox_gestationaldm
452ljhw3exh3zphl failed Analysis_cox_otherdm
3ucm4hns63afgfbh failed Analysis_cox_t1dm
3b352xxn4fugrwxd failed Analysis_cox_t2dm
oaa53ehhixnfipte succeeded generate_study_population
lqa36pgaxegskdog succeeded preprocess_data
ze5ms36riwhs6lsu succeeded stage1_data_cleaning
kr7xvbjyne3wx3tc succeeded stage1_end_date_table
26gr2w3bualdqekj succeeded stage2_missing_table1
vktsinszrpb32nsr succeeded stage3_diabetes_flow
kd4bwljifisiyobb succeeded stage4_table_2
o4idjvomrpb5mctm succeeded stage4_venn_diagram
vcdxowueqcslwxlb 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:
      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_*.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_cox_pipeline.R t1dm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    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_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

  ## Apply cox model for otherdm 

  Analysis_cox_otherdm:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    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_cox_pipeline.R gestationaldm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    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: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 44:40:25

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-unvaccinated
  • Branch:
    main
  • Creator:
    kurttaylor
  • Force run dependencies:
    True
  • Git Commit Hash:
    04b2cbb
  • Requested actions:
    • vax_eligibility_inputs
    • generate_study_population
    • preprocess_data
    • stage1_data_cleaning
    • stage1_end_date_table
    • stage2_missing_table1
    • stage3_diabetes_flow
    • stage4_table_2
    • stage4_venn_diagram
    • Analysis_cox_t1dm
    • Analysis_cox_t2dm
    • Analysis_cox_otherdm
    • Analysis_cox_gestationaldm