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Job request: 7006

Organisation:
University of Bristol
Workspace:
long-covid-risk-factors
ID:
curxz7zoaz2v476r
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 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: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather
  stage0_data_cleaning:
    run: r:latest analysis/stage0_data_cleaning.R
    needs:
    - generate_study_population
    outputs:
      highly_sensitive:
        cohort: output/input_stage0.rds
      moderately_sensitive:
        table_0_CSV: output/table_0.csv
        table_0_HTML: output/table_0.html
  stage1_define_eligible_population:
    run: r:latest analysis/stage1_define_eligible_population.R
    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:
    run: r:latest analysis/table_1.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        descriptive_table_CSV: output/table_1.csv
        descriptive_table_HTML: output/table_1.html
  table_2:
    run: r:latest analysis/table_2.R
    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:
    run: r:latest analysis/table_3.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        incidence_rate_table_CSV: output/table_3.csv
        incidence_rate_talbe_HTML: output/table_3.html
  figure_1:
    run: r:latest analysis/figure_1.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        Figure_long_covid_cases: output/figure_1.svg
  suppl_figure_1:
    run: r:latest analysis/suppl_figure_1.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        pie_chart_long_covid_code: output/suppl_figure_1.svg 
        table_csv_long_covid_code: output/suppl_figure_1_data.csv
        table_html_long_covid_code: output/suppl_figure_1_data.html
  suppl_figure_2:
    run: r:latest analysis/suppl_figure_2.R
    needs:
    - stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        figure_monthly_long_covid: output/suppl_figure_2.svg     
        table_csv_monthly_long_covid: output/suppl_figure_2_data.csv  
        table_html_monthly_long_covid: output/suppl_figure_2_data.html
  development_cox_model:
    run: r:latest analysis/stage3_model_development.R
    needs:
    -  stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        hazard_ratios_CSV: output/hazard_ratio_estimates_*.csv
        hazard_ratios_HTML: output/hazard_ratio_estimates_*.html
        #calibration: output/calibration_development_*.svg
  evaluation_cox_model:
    run: r:latest analysis/stage4_model_evaluation.R
    needs:
    -  stage1_define_eligible_population
    outputs:
      moderately_sensitive:
        performance_measure_CSV: output/performance_measures_*.csv
        performance_measure_HTML: output/performance_measures_*.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:59:00

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

Job request

Status
Succeeded
Backend
TPP
Workspace
long-covid-risk-factors
Requested by
Yinghui Wei
Branch
main
Force run dependencies
No
Git commit hash
3725560
Requested actions
  • development_cox_model

Code comparison

Compare the code used in this job request