Job request: 700

Organisation:
Workspace:: ethnicity-master
ID:: 5c5ktrupssdiiqvn

This page shows the technical details of what happened when the 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 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

Action:

check_ph

Status:

Status: Succeeded

Job identifier:

wli3hspphqa3qicd

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_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_underying_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

  main_eth16_infectedpop:
    run: stata-mp:latest analysis/12a_eth_an_infectedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/12a_eth_an_infectedpop_eth16.log
        table: output/table4_infectedpop_eth16_nocarehomes.txt
        estout: output/estout_table4_infectedpop_eth16_nocarehomes.txt
        graph: output/FP_infectedpop_eth16.txt

  main_eth5_infectedpop:
    run: stata-mp:latest analysis/12b_eth_an_infectedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/12b_eth_an_infectedpop_eth5.log
        table: output/table4_infectedpop_eth5_nocarehomes.txt
        estout: output/estout_table4_infectedpop_eth5_nocarehomes.txt
        graph: output/FP_infectedpop_eth5.txt

  check_ph:
    run: stata-mp:latest analysis/20_eth_an_model_checks.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        table: output/Table_phtest_eth5.txt
        graph1: output/kmplots_combined.svg
        graph2: output/stphplots_combined.svg

Timeline

Created: 3 years, 11 months ago 21 Jan 2021 15:32:43 UTC
Started: 3 years, 11 months ago 21 Jan 2021 15:53:36 UTC
Finished: 3 years, 10 months ago 23 Jan 2021 00:52:33 UTC
Runtime: 32:58:57

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: 35a6007
Requested actions: check_ph

Code comparison

Compare the code used in this Job Request