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Job request: 24523

Organisation:
University of Bristol
Workspace:
post-covid-cvd-methods-v1
ID:
k2tnyjn6kehik6sf
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release 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: 17:58:39

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

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-cvd-methods-v1
Requested by
Venexia Walker
Branch
main
Force run dependencies
No
Git commit hash
6fe4c11
Requested actions
  • run_all

Code comparison

Compare the code used in this job request