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Job request: 626

Organisation:
Workspace:
ethnicity-master
ID:
n4rqujrpyt7y5a3i
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Rohini Mathur 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: 100000

actions:
  generate_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv


  crmain:
    run: stata-mp:latest analysis/01_eth_cr_analysis_dataset.do
    needs: [generate_cohorts]
    outputs:
      highly_sensitive:
        data: output/analysis_dataset.dta
      moderately_sensitive:
        log: logs/01_eth_cr_analysis_dataset.log

  cr_sgss:
    run: stata-mp:latest analysis/01b_eth_cr_stset_sgss.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsettested: output/analysis_dataset_STSET_tested.dta
        stsetpositiivetest: output/analysis_dataset_STSET_positivetest.dta
      moderately_sensitive:
        log: logs/01b_eth_cr_stset_sgss.log
  
  cr_hes_covid:
    run: stata-mp:latest analysis/01c_eth_cr_stset_hes.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsethes: output/analysis_dataset_STSET_hes.dta
        stseticu: output/analysis_dataset_STSET_icu.dta
        stsetonscoviddeath: output/analysis_dataset_STSET_onscoviddeath.dta
      moderately_sensitive:
        log: logs/01c_eth_cr_stset_hes_covid.log

  cr_ons:
    run: stata-mp:latest analysis/01d_eth_cr_stset_death.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsetons_noncoviddeath: output/analysis_dataset_STSET_ons_noncoviddeath.dta
        stsetonsdeath: output/analysis_dataset_STSET_onsdeath.dta 
      moderately_sensitive:
        log: logs/01d_eth_cr_stset_death.log

  cr_confirmed:
    run: stata-mp:latest analysis/01e_eth_cr_stset_confirmedcovid.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stset_onsconfirmeddeath: output/analysis_dataset_STSET_onsconfirmeddeath.dta 
      moderately_sensitive:
        log: logs/01e_eth_cr_stset_onsconfirmeddeath.log

  cr_underlying:
    run: stata-mp:latest analysis/01f_eth_cr_stset_underlyingcovid.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stset_onsconfirmeddeath: output/analysis_dataset_STSET_onsunderlyingdeath.dta 
      moderately_sensitive:
        log: logs/01e_eth_cr_stset_onsunderlyingdeath.log


  check_region:
    run: stata-mp:latest analysis/02b_eth_region_check.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/02b_region_check.log
        table: output/table0_region.txt

  check_age:
    run: stata-mp:latest analysis/05b_eth_table1_descriptives_eth5_agegroup.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/05b_eth_table1_ages_eth5.log
        table: output/table1_eth5_age.txt

  check_tested:
    run: stata-mp:latest analysis/21_eth_tested_characteristics.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        table: output/table1_tested.txt

  main_carehomes_eth5:
    run: stata-mp:latest analysis/06b_eth_an_multivariable_eth5_carehomesonly.do
    needs: [cr_hes_covid]
    outputs:
      moderately_sensitive:
        log: logs/06b_eth_an_hes_eth5_carehomesonly.log
        table: output/table2_hes_eth5_carehomesonly.txt
        estout: output/estout_table2_hes_eth5_carehomesonly.txt
        graph: output/FP_hes_eth5_carehomesonly.txt
        
  sens_nostp_eth16:
    run: stata-mp:latest analysis/07a_eth_sensanalysis_nostp_eth16.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/07a_eth_sensanalysis_nostp_eth16.log
        table: output/sens_nostp_eth16.txt
        estout: output/estout_sens_nostp_eth16.txt
        graph: output/FP_sens_nostp_eth16.txt

  sens_nostp_eth5:
    run: stata-mp:latest analysis/07b_eth_sensanalysis_nostp_eth5.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/07b_eth_sensanalysis_nostp_eth5.log
        table: output/sens_nostp_eth5.txt
        estout: output/estout_sens_nostp_eth5.txt
        graph: output/FP_sens_nostp_eth5.txt

  sens_ruralurban_eth16:
    run: stata-mp:latest analysis/07c_eth_sensanalysis_ruralurban_eth16.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/07c_eth_sensanalysis_ruralurban_eth16.log
        estout: output/estout_sens_ruralurban_eth16.txt

  sens_confirmed_eth16:
    run: stata-mp:latest analysis/06c_eth_sensanalysis_confirmedcovid_eth16.do
    needs: [cr_confirmed]
    outputs:
      moderately_sensitive:
        log: logs/06c_sens_onsconfirmeddeath_eth16.log
        estout: output/estout_onsconfirmeddeath_eth16.txt
        graph: output/FP_sens_onsconfirmeddeath_eth16.txt

  sens_confirmed_eth5:
    run: stata-mp:latest analysis/06d_eth_sensanalysis_confirmedcovid_eth5.do
    needs: [cr_confirmed]
    outputs:
      moderately_sensitive:
        log: logs/06d_sens_onsconfirmeddeath_eth5.log
        estout: output/estout_onsconfirmeddeath_eth5.txt
        graph: output/FP_sens_onsconfirmeddeath_eth5.txt

  sens_underlying_eth16:
    run: stata-mp:latest analysis/06f_eth_sensanalysis_underlyingcovid_eth16.do
    needs: [cr_underlying]
    outputs:
      moderately_sensitive:
        log: logs/06f_sens_onsunderlyingdeath_eth16.log
        estout: output/estout_onsunderlyingdeath_eth16.txt
        graph: output/FP_sens_onsunderlyingdeath_eth16.txt

  sens_underlying_eth5:
    run: stata-mp:latest analysis/06e_eth_sensanalysis_underlyingcovid_eth5.do
    needs: [cr_underlying]
    outputs:
      moderately_sensitive:
        log: logs/06e_sens_onsunderlyingdeath_eth5.log
        estout: output/estout_onsunderlyingdeath_eth5.txt
        graph: output/FP_sens_onsunderlyingdeath_eth5.txt

  main_eth16_testedpop:
    run: stata-mp:latest analysis/11a_eth_an_testedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/11a_eth_an_testedpop_eth16.log
        table: output/table3_testedpop_eth16_nocarehomes.txt
        estout: output/estout_table3_testedpop_eth16_nocarehomes.txt
        graph: output/FP_testedpop_eth16.txt

  main_eth5_testedpop:
    run: stata-mp:latest analysis/11b_eth_an_testedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/11b_eth_an_testedpop_eth5.log
        table: output/table3_testedpop_eth5_nocarehomes.txt
        estout: output/estout_table3_testedpop_eth5_nocarehomes.txt
        graph: output/FP_testedpop_eth5.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:51

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

Job information

Status
Succeeded
Backend
TPP
Workspace
ethnicity-master
Requested by
Rohini Mathur
Branch
master
Force run dependencies
No
Git commit hash
fe8bd23
Requested actions
  • main_eth16_testedpop
  • main_eth5_testedpop

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