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Job request: 1272

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-admissions-admissions-kb
ID:
qrhkrafbddc4lqui
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 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.

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_study_pop_pneum2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneum2019
    outputs:
      highly_sensitive:
        cohort: output/input_pneum2019.csv

  generate_study_pop_flu2017_19:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flu2017_19
    outputs:
      highly_sensitive:
        cohort: output/input_flu2017_19.csv
        
  generate_2019pool02:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool02
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool02.csv        

  generate_2019pool03:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool03
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool03.csv        

  generate_2019pool04:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool04
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool04.csv        

  generate_2019pool05:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool05
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool05.csv        

  generate_2019pool06:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool06
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool06.csv        

  generate_2019pool07:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool07
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool07.csv        

  generate_2019pool08:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool08
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool08.csv        
           
  generate_2019pool09:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool09
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool09.csv        

  generate_2019pool10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool10
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool10.csv        
      
  generate_2019pool11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool11
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool11.csv        
                   
  create_covid:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do COVID
    needs: [generate_study_pop_covdischarged]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_COVID.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_COVID.log

  create_pneum2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do PNEUM 
    needs: [generate_study_pop_pneum2019]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_PNEUM.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_PNEUM.log
 
  create_flu2017_19:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do FLU 
    needs: [generate_study_pop_flu2017_19]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_FLU.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_FLU.log



  create_2019pool02:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 02
    needs: [generate_2019pool02]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_02.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_02.log

  create_2019pool03:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 03
    needs: [generate_2019pool03]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_03.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_03.log

  create_2019pool04:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 04
    needs: [generate_2019pool04]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_04.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_04.log

  create_2019pool05:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 05
    needs: [generate_2019pool05]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_05.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_05.log

  create_2019pool06:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 06
    needs: [generate_2019pool06]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_06.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_06.log

  create_2019pool07:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 07
    needs: [generate_2019pool07]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_07.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_07.log

  create_2019pool08:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 08
    needs: [generate_2019pool08]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_08.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_08.log

  create_2019pool09:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 09
    needs: [generate_2019pool09]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_09.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_09.log

  create_2019pool10:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 10
    needs: [generate_2019pool10]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_10.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_10.log

  create_2019pool11:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 11
    needs: [generate_2019pool11]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_11.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_11.log


  getmatches2019:
    run: stata-mp:latest analysis/cr_getmatches2019.do
    needs:
      - create_covid
      - create_2019pool02
      - create_2019pool03
      - create_2019pool04
      - create_2019pool05
      - create_2019pool06
      - create_2019pool07
      - create_2019pool08
      - create_2019pool09
      - create_2019pool10
      - create_2019pool11
    outputs:
      highly_sensitive:
        cohort: analysis/cr_getmatches2019.dta
      moderately_sensitive:
        log: analysis/output/cr_getmatches2019.log

  appenddata:
    run: stata-mp:latest analysis/cr_append_process_data.do
    needs:
      - create_covid
      - create_pneum2019
      - create_flu2017_19
      - getmatches2019
    outputs:
      highly_sensitive:
        cohort: analysis/cr_append_process_data.dta
      moderately_sensitive:
        log: analysis/output/cr_append_process_data.log

  andescriptives_composites:
    run: stata-mp:latest analysis/model_descriptives_composites.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/cr_append_process_data.log
        logs: analysis/output/an_cox.log
        tables: analysis/output/an_desctable.txt
        figures: analysis/output/an_cumulativeincidence*.svg
        models: analysis/output/models/an_cox*.ster

  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:

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

Job request

Status
Failed 
ProjectYAMLError: DuplicateKeyError while constructing a mapping
  in "project.yaml", line 244, column 9:
            logs: analysis/output/cr_append_ ... 
            ^ (line: 244)
found duplicate key "logs" with value "analysis/output/an_cox.log" (original value: "analysis/output/cr_append_process_data.log")
  in "project.yaml", line 245, column 9:
            logs: analysis/output/an_cox.log
            ^ (line: 245)
Backend
TPP
Workspace
post-admissions-admissions-kb
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
a3bc586
Requested actions
  • andescriptives_composites

Code comparison

Compare the code used in this job request