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Job request: 8435

Organisation:
University of Bristol
Workspace:
long-covid-risk-factors
ID:
6ujnpqa5347dsent
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Yinghui Wei 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: 10000

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 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Generate dummy data for study_definition for all eligible population 

  generate_study_population_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_all.feather

  ## Generate dummy data for study_definition - vaccinated 

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

  ## Stage 0 - Data cleaning 

  stage0_data_cleaning:
    run: r:latest analysis/stage0_data_cleaning.R both
    needs:
    - generate_study_population_all
    - generate_study_population_vaccinated
    outputs:
      highly_sensitive:
        cohort: output/input_stage0_*.rds
      moderately_sensitive:
        variable_check_table_CSV: output/table_0_*.csv
        variable_check_table_HTML: output/table_0_*.html

  ## Stage 1 - Define eligible population 

  stage1_define_eligible_population:
    run: r:latest analysis/stage1_define_eligible_population.R both
    needs:
    - stage0_data_cleaning
    outputs:
      highly_sensitive:
        cohort: output/input_stage1_*.rds
      moderately_sensitive:
        flow_chart_csv: output/flow_chart_*.csv
        flow_chart_html: output/flow_chart_*.html

  ## table_1 - Patient characteristics 

  table_1:
    run: r:latest analysis/table_1.R both
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        descriptive_table_CSV: output/table_1_*.csv
        descriptive_table_HTML: output/table_1_*.html

  ## table_2 - event count and incidence rate 

  table_2:
    run: r:latest analysis/table_2.R both
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        incidence_rate_table_CSV: output/table_2_*.csv
        incidence_rate_talbe_HTML: output/table_2_*.html

  ## table_3 - sequence count 

  table_3:
    run: r:latest analysis/table_3.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        sequence_count_table_CSV: output/table_3.csv
        sequence_count_table_HTML: output/table_3.html

  ## Figure_1 - long covid count 

  figure_1:
    run: r:latest analysis/figure_1.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        figure_long_covid_count_all: output/figure_1_*.svg
        table_csv_long_covid_count_all: output/long_covid_count_*_all.csv
        table_html_long_covid_count_all: output/long_covid_count_*_all.html

  ## Figure_2 - days from covid to long covid 

  figure_2:
    run: r:latest analysis/figure_2.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        figure_days_c_to_lc: output/figure_hist.svg
        table_csv_summary: output/summary_days_c_to_long.csv

  ## Suppl_table_1 - frequencies of snomed code for long covid diagnosis 

  suppl_table_1:
    run: r:latest analysis/suppl_table_1.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        pie_chart_long_covid_code: output/suppl_figure_pie.svg
        table_csv_long_covid_code: output/suppl_table_1.csv
        table_html_long_covid_code: output/suppl_table_1.html

  ## Suppl_figure_1 - long covid count by region 

  suppl_figure_1:
    run: r:latest analysis/suppl_figure_1.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        figure_long_covid_count_region: output/suppl_figure_1_*.svg
        table_csv_long_covid_count_region: output/long_covid_count_*.csv
        table_html_long_covid_region: output/long_covid_count_*.html

  ## Summarise survival data 

  summarise_survival_data:
    run: r:latest analysis/stage2_summarise_survival_data.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        summary_survival_data_CSV: output/summarise_survival_data.csv
        summary_survival_data_HTML: output/summarise_survival_data.html

  ## Development Cox model 
  ## Development Cox Model - all 

  development_cox_model_all:
    run: r:latest analysis/stage3_model_development.R all
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        ph_test_CSV: output/PH_test_*_all.csv
        hazard_ratios_CSV: output/hazard_ratio_estimates_*_all.csv
        hazard_ratios_HTML: output/hazard_ratio_estimates_*_all.html

  ## Development Cox Model - vax_c 

  development_cox_model_vax_c:
    run: r:latest analysis/stage3_model_development.R vax_c
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        ph_test_CSV: output/PH_test_*_vax_c.csv
        hazard_ratios_CSV: output/hazard_ratio_estimates_*_vax_c.csv
        hazard_ratios_HTML: output/hazard_ratio_estimates_*_vax_c.html

  ## Development Cox Model - vaccinated 

  development_cox_model_vaccinated:
    run: r:latest analysis/stage3_model_development.R vaccinated
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        ph_test_CSV: output/PH_test_*_vaccinated.csv
        hazard_ratios_CSV: output/hazard_ratio_estimates_*_vaccinated.csv
        hazard_ratios_HTML: output/hazard_ratio_estimates_*_vaccinated.html

  ## Development Cox Model - all_vax_td 

  development_cox_model_all_vax_td:
    run: r:latest analysis/stage3_model_development.R all_vax_td
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        ph_test_CSV: output/PH_test_*_all_vax_td.csv
        hazard_ratios_CSV: output/hazard_ratio_estimates_*_all_vax_td.csv
        hazard_ratios_HTML: output/hazard_ratio_estimates_*_all_vax_td.html

  ## Evaluation Cox model 
  ## Evaluation Cox Model - all 

  evaluation_cox_model_all:
    run: r:latest analysis/stage4_model_evaluation.R all
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        performance_measure_CSV: output/performance_measures_*_all.csv
        performance_measure_HTML: output/performance_measures_*_all.html
        survival_plot: output/survival_plot_*_all.svg

  ## Evaluation Cox Model - vax_c 

  evaluation_cox_model_vax_c:
    run: r:latest analysis/stage4_model_evaluation.R vax_c
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        performance_measure_CSV: output/performance_measures_*_vax_c.csv
        performance_measure_HTML: output/performance_measures_*_vax_c.html
        survival_plot: output/survival_plot_*_vax_c.svg

  ## Evaluation Cox Model - vaccinated 

  evaluation_cox_model_vaccinated:
    run: r:latest analysis/stage4_model_evaluation.R vaccinated
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        performance_measure_CSV: output/performance_measures_*_vaccinated.csv
        performance_measure_HTML: output/performance_measures_*_vaccinated.html
        survival_plot: output/survival_plot_*_vaccinated.svg

  ## Evaluation Cox Model - all_vax_td 

  evaluation_cox_model_all_vax_td:
    run: r:latest analysis/stage4_model_evaluation.R all_vax_td
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        performance_measure_CSV: output/performance_measures_*_all_vax_td.csv
        performance_measure_HTML: output/performance_measures_*_all_vax_td.html
        survival_plot: output/survival_plot_*_all_vax_td.svg

  ## Validation Cox Model - all 

  validation_cox_model_all:
    run: r:latest analysis/stage5_model_validation.R all
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        val_performance_measure_CSV: output/val_performance_measures_all.csv
        val_cal_plot: output/val_cal_plot_*_all.svg
        val_re_cal_plot: output/val_re_cal_plot_*_all.svg

  ## Validation Cox Model - vax_c 

  validation_cox_model_vax_c:
    run: r:latest analysis/stage5_model_validation.R vax_c
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        val_performance_measure_CSV: output/val_performance_measures_vax_c.csv
        val_cal_plot: output/val_cal_plot_*_vax_c.svg
        val_re_cal_plot: output/val_re_cal_plot_*_vax_c.svg

  ## Validation Cox Model - vaccinated 

  validation_cox_model_vaccinated:
    run: r:latest analysis/stage5_model_validation.R vaccinated
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        val_performance_measure_CSV: output/val_performance_measures_vaccinated.csv
        val_cal_plot: output/val_cal_plot_*_vaccinated.svg
        val_re_cal_plot: output/val_re_cal_plot_*_vaccinated.svg

  ## Validation Cox Model - all_vax_td 

  validation_cox_model_all_vax_td:
    run: r:latest analysis/stage5_model_validation.R all_vax_td
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        val_performance_measure_CSV: output/val_performance_measures_all_vax_td.csv
        val_cal_plot: output/val_cal_plot_*_all_vax_td.svg
        val_re_cal_plot: output/val_re_cal_plot_*_all_vax_td.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:58:53

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

Job information

Status
Succeeded
Backend
TPP
Workspace
long-covid-risk-factors
Requested by
Yinghui Wei
Branch
main
Force run dependencies
No
Git commit hash
36e537f
Requested actions
  • evaluation_cox_model_all
  • evaluation_cox_model_vaccinated

Code comparison

Compare the code used in this Job Request