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Job request: 5841

Organisation:
The UK Renal Registry
Workspace:
ckd-coverage-ve
ID:
y2ab4zcdwq5b6wib
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ed Parker 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

  • Action:
    data_selection_VE
    Status:
    Status: Succeeded
    Job identifier:
    5eiorltymvb2vbzm
  • Action:
    table_1_VE
    Status:
    Status: Succeeded
    Job identifier:
    tgruiw57uehhlslp
  • Action:
    table_irr
    Status:
    Status: Succeeded
    Job identifier:
    syyk64uf2v5r4elg

Pipeline

Show project.yaml 
######################################
# Script defines project pipeline via series of actions
######################################

version: '3.0'

expectations:
  population_size: 30000

actions:

  # Extract data ----
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv
  
# Process data ----
  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
        csv: output/data/data_processed.csv
        
# Select cohort ----
  data_selection_coverage:
    run: r:latest analysis/data_selection_coverage.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_coverage.rds
        csv: output/data/data_cohort_coverage.csv
      moderately_sensitive:
        csv: output/tables/flowchart_coverage.csv

 # Data properties ----      
  data_properties:
    run: r:latest analysis/data_properties.R output/data/data_cohort_coverage.rds output/data_properties
    needs: [data_selection_coverage]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_cohort*.txt
        
  # Table 1 ----
  table_1_coverage:
    run: r:latest analysis/table_1_coverage.R
    needs: [data_selection_coverage]
    outputs:
      highly_sensitive:
        data: output/tables/table1_coverage_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_coverage_redacted.html
        
  # Cox models - dose-2 coverage ----
  cox_model:
    run: r:latest analysis/cox_model.R
    needs: [data_selection_coverage]
    outputs:
      highly_sensitive:
        data1: output/data/data_cox.rds
        data2: output/model/mod_strat_coxph_redacted.rds
        csv: output/data/data_cox.csv
      moderately_sensitive:
        csv: output/model/mod_strat_coxph_redacted.csv
        
  # Logistic models - dose-2 coverage ----
  logistic_model:
    run: r:latest analysis/logistic_model.R
    needs: [cox_model]
    outputs:
      highly_sensitive:
        data: output/model/mod_strat_logistic_redacted.rds
      moderately_sensitive:
        csv: output/model/mod_strat_logistic_redacted.csv

  # Coverage summaries ----
  vaccine_coverage:
    run: r:latest -e 'rmarkdown::render("analysis/vaccine_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [data_selection_coverage, table_1_coverage, cox_model, logistic_model]
    outputs:
      moderately_sensitive:
        html: output/markdown/vaccine_coverage.html
        csv: output/tables/coverage_over_time_rounded.csv

  # Coverage summaries ----
  cox_model_check:
    run: r:latest -e 'rmarkdown::render("analysis/cox_model_check.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [data_selection_coverage, cox_model]
    outputs:
      moderately_sensitive:
        html: output/markdown/cox_model_check.html

# Select cohort (VE) ----
  data_selection_VE:
    run: r:latest analysis/data_selection_VE.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_VE.rds
        csv: output/data/data_cohort_VE.csv
      moderately_sensitive:
        csv: output/tables/flowchart_VE.csv

  # Table 1 (VE) ----
  table_1_VE:
    run: r:latest analysis/table_1_VE.R
    needs: [data_selection_VE]
    outputs:
      highly_sensitive:
        data: output/tables/table1_VE_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_VE_redacted.html

  # Table IRR
  table_irr:
    run: r:latest analysis/table_irr.R
    needs: [data_selection_VE]
    outputs:
      moderately_sensitive:
        html: output/tables/table_irr_simple.html
        csv: output/tables/table_irr.csv
        
  # Check session info for set of packages ----
  #session:
  #  run: r:latest -e 'rmarkdown::render("analysis/session.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
  #  needs: [data_selection]
  #  outputs:
  #    moderately_sensitive:
  #      html: output/markdown/session.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:15:32

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

Job information

Status
Succeeded
Backend
TPP
Workspace
ckd-coverage-ve
Requested by
Ed Parker
Branch
main
Force run dependencies
No
Git commit hash
09fe3bc
Requested actions
  • data_selection_VE
  • table_1_VE
  • table_irr

Code comparison

Compare the code used in this Job Request