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Job request: 24575

Organisation:
University of Bristol
Workspace:
post-covid-cvd-methods-v1
ID:
crwcg4qchvndo4jg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Venexia Walker requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 5000

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 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Define study dates 

  study_dates:
    run: r:latest analysis/study_dates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json

  ## Generate dates for all cohorts 

  generate_dates:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_dates.py
      --output output/dataset_definition/index_dates.csv.gz
    needs:
    - study_dates
    outputs:
      highly_sensitive:
        dataset: output/dataset_definition/index_dates.csv.gz

  ## Generate input_prevax 

  generate_input_prevax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_prevax.py
      --output output/dataset_definition/input_prevax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_prevax.csv.gz

  ## Generate input_prevax_clean, with describe = TRUE 

  generate_input_prevax_clean:
    run: r:latest analysis/dataset_clean/dataset_clean.R prevax TRUE
    needs:
    - study_dates
    - generate_input_prevax
    outputs:
      moderately_sensitive:
        describe_raw: output/describe/prevax_raw.txt
        describe_venn: output/describe/prevax_venn.txt
        describe_preprocessed: output/describe/prevax_preprocessed.txt
        flow: output/dataset_clean/flow-cohort_prevax.csv
        flow_midpoint6: output/dataset_clean/flow-cohort_prevax-midpoint6.csv
      highly_sensitive:
        venn: output/dataset_clean/venn-cohort_prevax.rds
        cohort_clean: output/dataset_clean/input_prevax_clean.rds

  ## Run models 

  make_model_input-cohort_prevax-main-ami:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-ami
    needs:
    - generate_input_prevax_clean
    outputs:
      highly_sensitive:
        model_input: output/model/model_input-cohort_prevax-main-ami.rds

  cox_ipw-cohort_prevax-main-ami:
    run: cox-ipw:v0.0.37 --df_input=model/model_input-cohort_prevax-main-ami.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=strat_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_imd;cov_num_consrate2019;cov_bin_hcworker;cov_cat_smoking;cov_bin_carehome;cov_bin_obesity;cov_bin_ami;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_depression;cov_bin_copd;cov_bin_stroke_all;cov_bin_other_ae;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_lipidmed;cov_bin_antiplatelet;cov_bin_anticoagulant;cov_bin_cocp;cov_bin_hrt
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2024-04-30 --cut_points=1;7;14;28;56;84;183;365;730;1065;1582 --controls_per_case=20
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --save_analysis_ready=FALSE --run_analysis=TRUE --df_output=model/model_output-cohort_prevax-main-ami.csv
    needs:
    - make_model_input-cohort_prevax-main-ami
    outputs:
      moderately_sensitive:
        model_output: output/model/model_output-cohort_prevax-main-ami.csv

  make_model_input-cohort_prevax-main-stroke_sahhs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-stroke_sahhs
    needs:
    - generate_input_prevax_clean
    outputs:
      highly_sensitive:
        model_input: output/model/model_input-cohort_prevax-main-stroke_sahhs.rds

  cox_ipw-cohort_prevax-main-stroke_sahhs:
    run: cox-ipw:v0.0.37 --df_input=model/model_input-cohort_prevax-main-stroke_sahhs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=strat_cat_region
      --covariate_sex=cov_cat_sex --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_imd;cov_num_consrate2019;cov_bin_hcworker;cov_cat_smoking;cov_bin_carehome;cov_bin_obesity;cov_bin_ami;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_depression;cov_bin_copd;cov_bin_stroke_all;cov_bin_other_ae;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_lipidmed;cov_bin_antiplatelet;cov_bin_anticoagulant;cov_bin_cocp;cov_bin_hrt
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2024-04-30 --cut_points=1;7;14;28;56;84;183;365;730;1065;1582 --controls_per_case=20
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --save_analysis_ready=FALSE --run_analysis=TRUE --df_output=model/model_output-cohort_prevax-main-stroke_sahhs.csv
    needs:
    - make_model_input-cohort_prevax-main-stroke_sahhs
    outputs:
      moderately_sensitive:
        model_output: output/model/model_output-cohort_prevax-main-stroke_sahhs.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:46:01

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Failed
Backend
TPP
Workspace
post-covid-cvd-methods-v1
Requested by
Venexia Walker
Branch
main
Force run dependencies
No
Git commit hash
bdd1978
Requested actions
  • make_model_input-cohort_prevax-main-ami
  • cox_ipw-cohort_prevax-main-ami
  • make_model_input-cohort_prevax-main-stroke_sahhs
  • cox_ipw-cohort_prevax-main-stroke_sahhs

Code comparison

Compare the code used in this Job Request