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Job request: 889

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-admissions-admissions-kb
ID:
nvkwzoesc2fw4lqn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Krishnan Bhaskaran 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: 1000

actions:

  generate_study_pop_covdischarged:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covdischarged
    outputs:
      highly_sensitive:
        cohort: output/input_covdischarged.csv
        
  generate_pool02:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool02
    outputs:
      highly_sensitive:
        cohort: output/input_pool02.csv        

  generate_pool03:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool03
    outputs:
      highly_sensitive:
        cohort: output/input_pool03.csv        

  generate_pool04:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool04
    outputs:
      highly_sensitive:
        cohort: output/input_pool04.csv        

  generate_pool05:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool05
    outputs:
      highly_sensitive:
        cohort: output/input_pool05.csv        

  generate_pool06:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool06
    outputs:
      highly_sensitive:
        cohort: output/input_pool06.csv        

  generate_pool07:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool07
    outputs:
      highly_sensitive:
        cohort: output/input_pool07.csv        

  generate_pool08:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool08
    outputs:
      highly_sensitive:
        cohort: output/input_pool08.csv        
           
  generate_pool09:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool09
    outputs:
      highly_sensitive:
        cohort: output/input_pool09.csv        

  generate_pool10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool10
    outputs:
      highly_sensitive:
        cohort: output/input_pool10.csv        
      
  generate_pool11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pool11
    outputs:
      highly_sensitive:
        cohort: output/input_pool11.csv        
                   
  create_dataset:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do 
    needs: [generate_study_pop_covdischarged]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset.log

  create_pool02:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 02
    needs: [generate_pool02]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_02.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_02.log

  create_pool03:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 03
    needs: [generate_pool03]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_03.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_03.log

  create_pool04:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 04
    needs: [generate_pool04]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_04.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_04.log

  create_pool05:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 05
    needs: [generate_pool05]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_05.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_05.log

  create_pool06:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 06
    needs: [generate_pool06]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_06.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_06.log

  create_pool07:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 07
    needs: [generate_pool07]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_07.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_07.log

  create_pool08:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 08
    needs: [generate_pool08]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_08.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_08.log

  create_pool09:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 09
    needs: [generate_pool09]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_09.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_09.log

  create_pool10:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 10
    needs: [generate_pool10]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_10.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_10.log

  create_pool11:
    run: stata-mp:latest analysis/cr_create_pool_basicdata.do 11
    needs: [generate_pool11]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_pool_basicdata_11.dta
      moderately_sensitive:
        log: analysis/output/cr_create_pool_basicdata_11.log


  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_study_pop_covdischarged]
    outputs:
      moderately_sensitive:
        log: logs/model.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:02:46

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-admissions-admissions-kb
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
c6685b8
Requested actions
  • generate_study_pop_covdischarged
  • generate_pool02
  • generate_pool03
  • create_dataset
  • create_pool02
  • create_pool03

Code comparison

Compare the code used in this Job Request