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Job request: 583

Organisation:
Workspace:
eth-2nd-wave-branch
ID:
nfjn2buxy37djaso
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

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

  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_region:
    run: stata-mp:latest analysis/05a_eth_region_check.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: logs/05_region_check.log
        table: output/table3_region.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_carehomes.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

  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

  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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:06

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

Job request

Status
Failed
Backend
TPP
Workspace
eth-2nd-wave-branch
Requested by
Rohini Mathur
Branch
remove-ICU-outcome
Force run dependencies
No
Git commit hash
e093acc
Requested actions
  • table1_eth5_carehomes
  • main_eth5_carehomes

Code comparison

Compare the code used in this job request