Job request: 7259

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
fkvczhbxtdtfxrtx succeeded generate_study_population
ugli2c5dly2f7shq succeeded preprocess_data
ovszn23edsfdbimz succeeded stage1_data_cleaning
efxw3i6ghsjpgmpy succeeded stage3_diabetes_flow
yftf6acxnmeo33hy succeeded stage4_venn_diagram
iqskj5vifdrmsrs7 succeeded vax_eligibility_inputs
l3awfwaxifpusycs failed stage2_missing_table1
xctmz2s5aliqs6i4 failed Analysis_cox_t1dm
3nwg46fhtxsk36ym failed Analysis_cox_t2dm
xai52h2opwuhzrts succeeded Analysis_cox_otherdm
fp36rbz7gyt7lzvd failed Analysis_cox_gestationaldm
ospw44lctmqfrzwx succeeded Analysis_cox_depression
6sldufepqyartcis succeeded Analysis_cox_anxiety_general
vhpkncl6vl2dwnpt succeeded Analysis_cox_anxiety_ocd
lurwuolnip3spclp succeeded Analysis_cox_anxiety_ptsd
hmplifvgod6xh7b6 succeeded Analysis_cox_eating_disorders
tqy5qgzmkscetbq6 succeeded Analysis_cox_serious_mental_illness
24ffgs5repsd6r32 succeeded Analysis_cox_self_harm_10plus
qawco64u27c4erfu succeeded Analysis_cox_self_harm_15plus
qrkg6e46kzfs2uob succeeded Analysis_cox_suicide
7fyebvth2xva7rlb succeeded Analysis_cox_addiction

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: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 605:29:38

Config