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Job request: 1378

Workspace:
post-admissions-admissions-testarea
ID:
so5io63i6efspqrk

This page shows the technical details of what happened when 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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_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_2019pool02_ALT:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019 --index-date-range "2019-02-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2019_2019-02-01.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        

  generate_2019pool12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool12
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool12.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

  create_2019pool12:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 12
    needs: [generate_2019pool12]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_12.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_12.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
      - create_2019pool12
    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/*.log 
        tables: analysis/output/an_desc*.txt
        figures: analysis/output/an_cumulativeincidence*.svg
        models: analysis/output/models/an_cox*.ster

  ancrreg_flu1:
    run: stata-mp:latest analysis/an_crreg_outcome.do 1 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome1_cflu.log
        models: analysis/output/models/an_crreg_outcome1_cflu*.ster

  ancrreg_flu2:
    run: stata-mp:latest analysis/an_crreg_outcome.do 2 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome2_cflu.log
        models: analysis/output/models/an_crreg_outcome2_cflu*.ster

  ancrreg_flu3:
    run: stata-mp:latest analysis/an_crreg_outcome.do 3 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome3_cflu.log
        models: analysis/output/models/an_crreg_outcome3_cflu*.ster

  ancrreg_flu4:
    run: stata-mp:latest analysis/an_crreg_outcome.do 4 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome4_cflu.log
        models: analysis/output/models/an_crreg_outcome4_cflu*.ster

  ancrreg_flu5:
    run: stata-mp:latest analysis/an_crreg_outcome.do 5 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome5_cflu.log
        models: analysis/output/models/an_crreg_outcome5_cflu*.ster

  ancrreg_flu6:
    run: stata-mp:latest analysis/an_crreg_outcome.do 6 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome6_cflu.log
        models: analysis/output/models/an_crreg_outcome6_cflu*.ster

  ancrreg_flu7:
    run: stata-mp:latest analysis/an_crreg_outcome.do 7 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome7_cflu.log
        models: analysis/output/models/an_crreg_outcome7_cflu*.ster

  ancrreg_flu8:
    run: stata-mp:latest analysis/an_crreg_outcome.do 8 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome8_cflu.log
        models: analysis/output/models/an_crreg_outcome8_cflu*.ster

  ancrreg_flu9:
    run: stata-mp:latest analysis/an_crreg_outcome.do 9 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome9_cflu.log
        models: analysis/output/models/an_crreg_outcome9_cflu*.ster

  ancrreg_flu11:
    run: stata-mp:latest analysis/an_crreg_outcome.do 11 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome11_cflu.log
        models: analysis/output/models/an_crreg_outcome11_cflu*.ster

  ancrreg_flu12:
    run: stata-mp:latest analysis/an_crreg_outcome.do 12 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome12_cflu.log
        models: analysis/output/models/an_crreg_outcome12_cflu*.ster

  ancrreg_flu13:
    run: stata-mp:latest analysis/an_crreg_outcome.do 13 flu
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome13_cflu.log
        models: analysis/output/models/an_crreg_outcome13_cflu*.ster

  ancrreg_2019gp1:
    run: stata-mp:latest analysis/an_crreg_outcome.do 1 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome1_c2019gp.log
        models: analysis/output/models/an_crreg_outcome1_c2019gp*.ster

  ancrreg_2019gp2:
    run: stata-mp:latest analysis/an_crreg_outcome.do 2 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome2_c2019gp.log
        models: analysis/output/models/an_crreg_outcome2_c2019gp*.ster

  ancrreg_2019gp3:
    run: stata-mp:latest analysis/an_crreg_outcome.do 3 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome3_c2019gp.log
        models: analysis/output/models/an_crreg_outcome3_c2019gp*.ster

  ancrreg_2019gp4:
    run: stata-mp:latest analysis/an_crreg_outcome.do 4 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome4_c2019gp.log
        models: analysis/output/models/an_crreg_outcome4_c2019gp*.ster

  ancrreg_2019gp5:
    run: stata-mp:latest analysis/an_crreg_outcome.do 5 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome5_c2019gp.log
        models: analysis/output/models/an_crreg_outcome5_c2019gp*.ster

  ancrreg_2019gp6:
    run: stata-mp:latest analysis/an_crreg_outcome.do 6 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome6_c2019gp.log
        models: analysis/output/models/an_crreg_outcome6_c2019gp*.ster

  ancrreg_2019gp7:
    run: stata-mp:latest analysis/an_crreg_outcome.do 7 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome7_c2019gp.log
        models: analysis/output/models/an_crreg_outcome7_c2019gp*.ster

  ancrreg_2019gp8:
    run: stata-mp:latest analysis/an_crreg_outcome.do 8 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome8_c2019gp.log
        models: analysis/output/models/an_crreg_outcome8_c2019gp*.ster

  ancrreg_2019gp9:
    run: stata-mp:latest analysis/an_crreg_outcome.do 9 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome9_c2019gp.log
        models: analysis/output/models/an_crreg_outcome9_c2019gp*.ster

  ancrreg_2019gp11:
    run: stata-mp:latest analysis/an_crreg_outcome.do 11 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome11_c2019gp.log
        models: analysis/output/models/an_crreg_outcome11_c2019gp*.ster

  ancrreg_2019gp12:
    run: stata-mp:latest analysis/an_crreg_outcome.do 12 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome12_c2019gp.log
        models: analysis/output/models/an_crreg_outcome12_c2019gp*.ster

  ancrreg_2019gp13:
    run: stata-mp:latest analysis/an_crreg_outcome.do 13 2019gp
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        logs: analysis/output/an_crreg_outcome13_c2019gp.log
        models: analysis/output/models/an_crreg_outcome13_c2019gp*.ster

  ancrforests:
    run: stata-mp:latest analysis/an_processout_regressionmodels_FOREST.do
    needs:
      - andescriptives_composites
      - ancrreg_flu1
      - ancrreg_flu2
      - ancrreg_flu3
      - ancrreg_flu4
      - ancrreg_flu5
      - ancrreg_flu6
      - ancrreg_flu7
      - ancrreg_flu8
      - ancrreg_flu9
      - ancrreg_flu11
      - ancrreg_flu12
      - ancrreg_flu13
      - ancrreg_2019gp1
      - ancrreg_2019gp2
      - ancrreg_2019gp3
      - ancrreg_2019gp4
      - ancrreg_2019gp5
      - ancrreg_2019gp6
      - ancrreg_2019gp7
      - ancrreg_2019gp8
      - ancrreg_2019gp9
      - ancrreg_2019gp11
      - ancrreg_2019gp12
      - ancrreg_2019gp13
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_regressionmodels_FOREST*.svg       
      
  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 backend.

Job information

Status
Succeeded
Backend
TPP
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
2edd3af
Requested actions
  • generate_2019pool02_ALT