Job request: 725

Organisation:
Workspace:: ethnicity-2nd-wave_master
ID:: x2fv2nhyycdufogu

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

Action:

main_eth16

Status:

Status: Failed

Job identifier:

gkbcgxewmcofqei2
Action:

main_eth5

Status:

Status: Failed

Job identifier:

ckh6xrhd7fzvrhw7

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, cr_icu]
    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, cr_icu]
    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, cr_icu]
    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: 3 years, 3 months ago 23 Jan 2021 14:29:12 UTC
Finished: 3 years, 3 months ago 23 Jan 2021 14:29:17 UTC
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: 39aeb7a
Requested actions: main_eth16

main_eth5

Code comparison

Compare the code used in this Job Request