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Job request: 704

Organisation:
Workspace:
ethnicity-2nd-wave_master
ID:
pnr4stfbkzjgb2xc
View repo View project.yaml

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_tested
    Status:
    Status: Failed
    Job identifier:
    qztutdvebvf373rn

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
        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_icu:
    run: stata-mp:latest analysis/01e_eth_cr_stset_icu.do
    needs: [crmain]
    outputs:
      highly_sensitive:
        stsetons_icu: output/analysis_dataset_STSET_icu.dta
      moderately_sensitive:
        log: logs/01e_eth_cr_stset_icu.log

  check_eth16:
    run: stata-mp:latest analysis/02a_eth_outcomes_checks_eth16.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/02a_outcomes_checks_eth16.log
        table: output/table0_outcomes_eth16.txt

  check_eth5:
    run: stata-mp:latest analysis/02b_eth_outcomes_checks_eth5.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/02b_outcomes_checks_eth5.log
        table: output/table0_outcomes_eth5.txt

  check_tested:
    run: stata-mp:latest analysis/06_eth_tested_characteristics.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        table: output/table1_tested.txt
        
  table1_eth16:
    run: stata-mp:latest analysis/03a_eth_table1_descriptives_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/03a_eth_table1_eth16_nocarehomes.log
        table: output/table1_eth16.txt

  table1_eth5:
    run: stata-mp:latest analysis/03b_eth_table1_descriptives_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/03b_eth_table1_eth5.log
        table: output/table1_eth5.txt

  table1_eth5_carehomes:
    run: stata-mp:latest analysis/03d_eth_table1_descriptives_eth5_carehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/03d_eth_table1_eth5_carehomes.log
        table: output/table1_eth5_carehomes.txt

  main_eth16:
    run: stata-mp:latest analysis/04a_eth_an_multivariable_eth16_nocarehomes.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/04a_eth_an_multivariable_eth16.log
        table: output/table2_eth16.txt
        estout: output/estout_table2_eth16.txt
        graph: output/FP_multivariable_eth16.txt

  icu_eth16:
    run: stata-mp:latest analysis/04a_eth_an_icu_eth16_nocarehomes.do
    needs: [cr_icu]
    outputs:
      moderately_sensitive:
        log: logs/04a_eth_an_icu_eth16.log
        table: output/table2_icu_eth16.txt
        estout: output/estout_icu_eth16.txt
        graph: output/FP_icu_eth16.txt


  main_eth5:
    run: stata-mp:latest analysis/04b_eth_an_multivariable_eth5_nocarehomes.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/04b_eth_an_multivariable_eth5.log
        table: output/table2_eth5.txt
        estout: output/estout_table2_eth5.txt
        graph: output/FP_multivariable_eth5.txt

  icu_eth5:
    run: stata-mp:latest analysis/04b_eth_an_icu_eth5_nocarehomes.do
    needs: [cr_icu]
    outputs:
      moderately_sensitive:
        log: logs/04b_eth_an_icu_eth5.log
        table: output/table2_icu_eth5.txt
        estout: output/estout_icu_eth5.txt
        graph: output/FP_icu_eth5.txt

  main_eth5_carehomes:
    run: stata-mp:latest analysis/04d_eth_an_multivariable_eth5_carehomes.do
    needs: [cr_sgss, cr_hes_covid, cr_ons]
    outputs:
      moderately_sensitive:
        log: logs/04d_eth_an_multivariable_eth5_carehomes.log
        table: output/table2_eth5_carehomes.txt
        estout: output/estout_table2_eth5_carehomes.txt
        graph: output/FP_multivariable_eth5_carehomes.txt

  main_eth16_testedpop:
    run: stata-mp:latest analysis/07a_eth_an_testedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/07a_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/07b_eth_an_testedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/07b_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/08a_eth_an_infectedpop_eth16_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/08a_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/08b_eth_an_infectedpop_eth5_nocarehomes.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/08b_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

  icu_eth5_carehomes:
    run: stata-mp:latest analysis/04d_eth_an_icu_eth5_carehomes.do
    needs: [cr_icu]
    outputs:
      moderately_sensitive:
        log: logs/04d_eth_an_icu_eth5_carehomes.log
        table: output/table2_icu_eth5_carehomes.txt
        estout: output/estout_icu_eth5_carehomes.txt
        graph: output/FP_icu_eth5_carehomes.txt

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job information

Status
Failed
Backend
TPP
Workspace
ethnicity-2nd-wave_master
Requested by
Rohini Mathur
Branch
master
Force run dependencies
No
Git commit hash
35aefa8
Requested actions
  • check_tested

Code comparison

Compare the code used in this Job Request