Skip to content

Job request: 6238

Organisation:
Bennett Institute
Workspace:
hypertension-sro
ID:
y4den2o2fc6t25ai
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Milan Wiedemann 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:
    join_measures
    Status:
    Status: Succeeded
    Job identifier:
    b6mjjldbh6ikat45
  • Action:
    generate_rmd
    Status:
    Status: Succeeded
    Job identifier:
    ecyjm4u7qtde3e66

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  # Extract cohort for indicator HYP001 by month 
  generate_study_population_hyp001:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp001 
      --index-date-range "2019-01-01 to 2022-01-01 by month" 
      --output-dir=output  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_hyp001_*.feather

  #  Generate measures for indicator HYP001 by month
  generate_measures_hyp001:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp001 
       --output-dir=output
     needs: [generate_study_population_hyp001]
     outputs:
       moderately_sensitive:
         measure_csv: output/measure_hyp001_*_rate.csv
  
  # Join all measure files for each indicator
  join_measures:
    run: r:latest analysis/join_measures.R
    needs: [generate_measures_hyp001]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_hyp001.csv

  # Extract cohort for indicator HYP003 by month 
  generate_study_population_hyp003:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp003 
      --index-date-range "2019-01-01 to 2022-01-01 by month" 
      --output-dir=output  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_hyp003_*.feather

  #  Generate measures for indicator HYP003 by month
  generate_measures_hyp003:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp003 
       --output-dir=output
     needs: [generate_study_population_hyp003]
     outputs:
       moderately_sensitive:
         measure_csv: output/measure_hyp003_*_rate.csv  

  # Extract cohort for indicator HYP007 by month 
  generate_study_population_hyp007:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp007 
      --index-date-range "2019-01-01 to 2022-01-01 by month" 
      --output-dir=output  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_hyp007_*.feather

  #  Generate measures for indicator HYP007 by month
  generate_measures_hyp007:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp007 
       --output-dir=output
     needs: [generate_study_population_hyp007]
     outputs:
       moderately_sensitive:
         measure_csv: output/measure_hyp007_*_rate.csv

# Generate R Markdown Report
  generate_rmd:
    run: r:latest -e 'rmarkdown::render("analysis/hypertension-sro-report.Rmd", knit_root_dir = "/workspace", output_dir = "output")'
    needs: [join_measures]
    outputs:
      moderately_sensitive:
        report: output/hypertension-sro-report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:04

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

Job request

Status
Succeeded
Backend
TPP
Workspace
hypertension-sro
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
bf7cad4
Requested actions
  • join_measures
  • generate_rmd

Code comparison

Compare the code used in this job request