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Job request: 5838

Organisation:
The UK Renal Registry
Workspace:
ckd-coverage-ve
ID:
vx3w2ua7m5hzfbnq
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 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

  • Action:
    data_selection_VE
    Status:
    Status: Succeeded
    Job identifier:
    3h627ltoddlvq66c
  • Action:
    table_1_VE
    Status:
    Status: Succeeded
    Job identifier:
    xrmntb4gylmr7ke5

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

  # 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: 00:04:16

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

Job request

Status
Succeeded
Backend
TPP
Workspace
ckd-coverage-ve
Requested by
Ed Parker
Branch
main
Force run dependencies
No
Git commit hash
8b196e7
Requested actions
  • data_selection_VE
  • table_1_VE

Code comparison

Compare the code used in this job request