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Job request: 15162

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
healthcare_needs_chronic_kidney_disease
ID:
i5nc65xmp4s4bo7f
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Viyaasan Mahalingasivam 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: 50000

actions:

  2017:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2017
    outputs:
      highly_sensitive:
        cohort: output/input_2017.csv

  2017_ckd:
    run: stata-mp:latest analysis/ckd.do 2017
    needs: [2017]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2017_ckd.csv
      moderately_sensitive:
        log: logs/2017_ckd.log
  
  2017_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2017_ckd_complete
    needs: [2017, 2017_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2017_ckd_complete.csv

  2017_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2017_ckd_complete.dta
      moderately_sensitive:
        log: logs/2017_ckd_complete.log

  2017_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2017
    needs: [2017, 2017_ckd, 2017_ckd_complete, 2017_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2017_healthcare_use.log
        output: output/2017_healthcare_use.csv

  2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2018
    outputs:
      highly_sensitive:
        cohort: output/input_2018.csv

  2018_ckd:
    run: stata-mp:latest analysis/ckd.do 2018
    needs: [2018]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2018_ckd.csv
      moderately_sensitive:
        log: logs/2018_ckd.log
  
  2018_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2018_ckd_complete
    needs: [2018, 2018_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2018_ckd_complete.csv

  2018_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2018_ckd_complete.dta
      moderately_sensitive:
        log: logs/2018_ckd_complete.log

  2018_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2018
    needs: [2018, 2018_ckd, 2018_ckd_complete, 2018_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2018_healthcare_use.log
        output: output/2018_healthcare_use.csv

  2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
    outputs:
      highly_sensitive:
        cohort: output/input_2019.csv

  2019_ckd:
    run: stata-mp:latest analysis/ckd.do 2019
    needs: [2019]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2019_ckd.csv
      moderately_sensitive:
        log: logs/2019_ckd.log
  
  2019_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019_ckd_complete
    needs: [2019, 2019_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2019_ckd_complete.csv

  2019_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2019_ckd_complete.dta
      moderately_sensitive:
        log: logs/2019_ckd_complete.log

  2019_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2019
    needs: [2019, 2019_ckd, 2019_ckd_complete, 2019_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2019_healthcare_use.log
        output: output/2019_healthcare_use.csv

  2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2020
    outputs:
      highly_sensitive:
        cohort: output/input_2020.csv

  2020_ckd:
    run: stata-mp:latest analysis/ckd.do 2020
    needs: [2020]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2020_ckd.csv
      moderately_sensitive:
        log: logs/2020_ckd.log
  
  2020_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2020_ckd_complete
    needs: [2020, 2020_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2020_ckd_complete.csv

  2020_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2020_ckd_complete.dta
      moderately_sensitive:
        log: logs/2020_ckd_complete.log

  2020_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2020
    needs: [2020, 2020_ckd, 2020_ckd_complete, 2020_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2020_healthcare_use.log
        output: output/2020_healthcare_use.csv

  2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2021
    outputs:
      highly_sensitive:
        cohort: output/input_2021.csv

  2021_ckd:
    run: stata-mp:latest analysis/ckd.do 2021
    needs: [2021]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2021_ckd.csv
      moderately_sensitive:
        log: logs/2021_ckd.log
  
  2021_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2021_ckd_complete
    needs: [2021, 2021_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2021_ckd_complete.csv

  2021_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2021_ckd_complete.dta
      moderately_sensitive:
        log: logs/2021_ckd_complete.log

  2021_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2021
    needs: [2021, 2021_ckd, 2021_ckd_complete, 2021_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2021_healthcare_use.log
        output: output/2021_healthcare_use.csv

  2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2022
    outputs:
      highly_sensitive:
        cohort: output/input_2022.csv

  2022_ckd:
    run: stata-mp:latest analysis/ckd.do 2022
    needs: [2022]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2022_ckd.csv
      moderately_sensitive:
        log: logs/2022_ckd.log
  
  2022_ckd_complete:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2022_ckd_complete
    needs: [2022, 2022_ckd]
    outputs:
      highly_sensitive:
        cohort: output/input_2022_ckd_complete.csv

  2022_clean_ckd_complete:
    run: stata-mp:latest analysis/ckd_complete.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete]
    outputs:
      highly_sensitive:
        analysis_dataset: output/2022_ckd_complete.dta
      moderately_sensitive:
        log: logs/2022_ckd_complete.log

  2022_healthcare_use:
    run: stata-mp:latest analysis/healthcare_use.do 2022
    needs: [2022, 2022_ckd, 2022_ckd_complete, 2022_clean_ckd_complete]
    outputs:
      moderately_sensitive:
        log: logs/2022_healthcare_use.log
        output: output/2022_healthcare_use.csv        

  ckd_progression:
    run: stata-mp:latest analysis/ckd_progression.do
    needs: [2017_clean_ckd_complete, 2018_clean_ckd_complete, 2019_clean_ckd_complete, 2020_clean_ckd_complete, 2021_clean_ckd_complete, 2022_clean_ckd_complete, 2017_healthcare_use, 2018_healthcare_use, 2019_healthcare_use, 2020_healthcare_use, 2021_healthcare_use, 2022_healthcare_use]
    outputs:
      moderately_sensitive:
        log: logs/ckd_progression.log
        output: output/ckd_progression.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 18:38:58

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

Job information

Status
Succeeded
Backend
TPP
Workspace
healthcare_needs_chronic_kidney_disease
Requested by
Viyaasan Mahalingasivam
Branch
main
Force run dependencies
No
Git commit hash
25cbe37
Requested actions
  • 2017_ckd_complete
  • 2017_clean_ckd_complete
  • 2017_healthcare_use
  • 2018_ckd_complete
  • 2018_clean_ckd_complete
  • 2018_healthcare_use
  • 2019_ckd_complete
  • 2019_clean_ckd_complete
  • 2019_healthcare_use
  • 2020_ckd_complete
  • 2020_clean_ckd_complete
  • 2020_healthcare_use
  • 2021_ckd_complete
  • 2021_clean_ckd_complete
  • 2021_healthcare_use
  • 2022_ckd_complete
  • 2022_clean_ckd_complete
  • 2022_healthcare_use
  • ckd_progression

Code comparison

Compare the code used in this Job Request