Job request: 9100

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Jose Ignacio Cuitun Coronado 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
243ds6a6omwl6r3c succeeded Analysis_cox_addiction
3heehtzxbnf4ny2h failed Analysis_cox_anxiety_general
wajmepn6xhl7i5bj succeeded Analysis_cox_anxiety_ocd
ehbiysnjifrzmti4 succeeded Analysis_cox_anxiety_ptsd
cqhrya4u2wggukme failed Analysis_cox_depression
hyglh434xno23kk4 succeeded Analysis_cox_eating_disorders
a42xgdwhxd4vr7pz succeeded Analysis_cox_self_harm_10plus
ravmjvcz2aklgrti succeeded Analysis_cox_self_harm_15plus
2xnpxns4s5k4q32e succeeded Analysis_cox_serious_mental_illness
q2bz7v2rbtfnzyge succeeded Analysis_cox_suicide
tu44nhkhf7hwbufg succeeded preprocess_data
bmop5fgoejwoq2h3 succeeded stage1_data_cleaning
evwp4sjdya4wgvex succeeded stage1_end_date_table
tmrpl2c3yrckefjp succeeded stage2_missing_table1
uioj6xfy6eplsquz succeeded stage3_diabetes_flow
n5strdop75nlndlb succeeded stage4_table_2
xamtrqqdsgc7oskk 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/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 depression 

  Analysis_cox_depression:
    run: r:latest analysis/model/01_cox_pipeline.R depression
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_depression.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_depression.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_depression_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_depression.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_depression.csv
        compiled_event_counts: output/review/model/compiled_event_counts_depression.csv

  ## Apply cox model for anxiety_general 

  Analysis_cox_anxiety_general:
    run: r:latest analysis/model/01_cox_pipeline.R anxiety_general
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_anxiety_general.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_general.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_general_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_general.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_general.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_general.csv

  ## Apply cox model for anxiety_ocd 

  Analysis_cox_anxiety_ocd:
    run: r:latest analysis/model/01_cox_pipeline.R anxiety_ocd
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_anxiety_ocd.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_ocd.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_ocd.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_ocd.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_ocd.csv

  ## Apply cox model for anxiety_ptsd 

  Analysis_cox_anxiety_ptsd:
    run: r:latest analysis/model/01_cox_pipeline.R anxiety_ptsd
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_anxiety_ptsd.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_ptsd.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_ptsd.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_ptsd.csv

  ## Apply cox model for eating_disorders 

  Analysis_cox_eating_disorders:
    run: r:latest analysis/model/01_cox_pipeline.R eating_disorders
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_eating_disorders.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_eating_disorders.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_eating_disorders_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_eating_disorders.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_eating_disorders.csv
        compiled_event_counts: output/review/model/compiled_event_counts_eating_disorders.csv

  ## Apply cox model for serious_mental_illness 

  Analysis_cox_serious_mental_illness:
    run: r:latest analysis/model/01_cox_pipeline.R serious_mental_illness
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_serious_mental_illness.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_serious_mental_illness.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_serious_mental_illness.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_serious_mental_illness.csv
        compiled_event_counts: output/review/model/compiled_event_counts_serious_mental_illness.csv

  ## Apply cox model for self_harm_10plus 

  Analysis_cox_self_harm_10plus:
    run: r:latest analysis/model/01_cox_pipeline.R self_harm_10plus
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_self_harm_10plus.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_self_harm_10plus.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_self_harm_10plus.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_self_harm_10plus.csv
        compiled_event_counts: output/review/model/compiled_event_counts_self_harm_10plus.csv

  ## Apply cox model for self_harm_15plus 

  Analysis_cox_self_harm_15plus:
    run: r:latest analysis/model/01_cox_pipeline.R self_harm_15plus
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_self_harm_15plus.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_self_harm_15plus.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_self_harm_15plus.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_self_harm_15plus.csv
        compiled_event_counts: output/review/model/compiled_event_counts_self_harm_15plus.csv

  ## Apply cox model for suicide 

  Analysis_cox_suicide:
    run: r:latest analysis/model/01_cox_pipeline.R suicide
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_suicide.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_suicide.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_suicide_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_suicide.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_suicide.csv
        compiled_event_counts: output/review/model/compiled_event_counts_suicide.csv

  ## Apply cox model for addiction 

  Analysis_cox_addiction:
    run: r:latest analysis/model/01_cox_pipeline.R addiction
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_addiction.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_addiction.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_addiction_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_addiction.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_addiction.csv
        compiled_event_counts: output/review/model/compiled_event_counts_addiction.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 125:53:33

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-unvaccinated
  • Branch:
    main
  • Creator:
    josephignace
  • Force run dependencies:
    False
  • Git Commit Hash:
    1b44255
  • Requested actions:
    • preprocess_data
    • stage1_data_cleaning
    • stage1_end_date_table
    • stage2_missing_table1
    • stage3_diabetes_flow
    • stage4_table_2
    • stage4_venn_diagram
    • Analysis_cox_depression
    • Analysis_cox_anxiety_general
    • Analysis_cox_anxiety_ocd
    • Analysis_cox_anxiety_ptsd
    • Analysis_cox_eating_disorders
    • Analysis_cox_serious_mental_illness
    • Analysis_cox_self_harm_10plus
    • Analysis_cox_self_harm_15plus
    • Analysis_cox_suicide
    • Analysis_cox_addiction