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Job request: 21463

Organisation:
University of Bristol
Workspace:
lockdown-and-vulnerable-groups
ID:
6qqwya2amp4xxnbj
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Scott Walter 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

  • Action:
    model_alcmisuse
    Status:
    Status: Failed
    Job identifier:
    fs7evt67qx7recxa
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_drugmisuse
    Status:
    Status: Failed
    Job identifier:
    asaxyfqn453hjkoa
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_dvafemale
    Status:
    Status: Failed
    Job identifier:
    sth3nafos7aflkfa
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_dvamale
    Status:
    Status: Failed
    Job identifier:
    m43mhdyhuhfkicvm
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_intdisover14
    Status:
    Status: Failed
    Job identifier:
    jyw6uxcbab7hyqtl
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_intdissub14
    Status:
    Status: Failed
    Job identifier:
    g75ajme3vjvil437
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_opioid
    Status:
    Status: Failed
    Job identifier:
    g54ver3kh3pfreb4
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    model_rcgpsafeguard
    Status:
    Status: Failed
    Job identifier:
    xq4swzde6lgvhw4c
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    combine_results
    Status:
    Status: Failed
    Job identifier:
    mtmzvte35zgxefoq
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-02 to 2020-01-13 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-20 to 2020-06-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-08 to 2020-10-19 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-10-26 to 2021-03-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-08 to 2021-06-14 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/in*.csv.gz

  generate_study_population_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-06-21 to 2021-09-27 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/i*.csv.gz


  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv


  subgroup_setup:
    run: stata-mp:latest analysis/subgroup_data_setup.do
    needs: 
    - generate_measures
    outputs:
      highly_sensitive:
        subgroup1: output/measure_dvafemale_rate.dta
        subgroup2: output/measure_dvamale_rate.dta
        subgroup3: output/measure_intdissub14_rate.dta
        subgroup4: output/measure_intdisover14_rate.dta
        subgroup5: output/measure_rcgpsafeguard_rate.dta
        subgroup6: output/measure_alcmisuse_rate.dta
        subgroup7: output/measure_drugmisuse_rate.dta
        subgroup8: output/measure_opioid_rate.dta

  model_alcmisuse:
    run: stata-mp:latest analysis/model.do alcmisuse
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/alcmisuse_RR_LD1.dta
        results2: output/alcmisuse_RD_LD1.dta
        results3: output/alcmisuse_RR_LD2.dta
        results4: output/alcmisuse_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/alcmisuse_diagnostics1.svg
        diagnostics2: output/diagnostics/alcmisuse_diagnostics2.svg
        plot1: output/alcmisuse_plot1.svg
        plot2: output/alcmisuse_plot2.svg

  model_drugmisuse:
    run: stata-mp:latest analysis/model.do drugmisuse
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/drugmisuse_RR_LD1.dta
        results2: output/drugmisuse_RD_LD1.dta
        results3: output/drugmisuse_RR_LD2.dta
        results4: output/drugmisuse_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/drugmisuse_diagnostics1.svg
        diagnostics2: output/diagnostics/drugmisuse_diagnostics2.svg
        plot1: output/drugmisuse_plot1.svg
        plot2: output/drugmisuse_plot2.svg

  model_opioid:
    run: stata-mp:latest analysis/model.do opioid
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/opioid_RR_LD1.dta
        results2: output/opioid_RD_LD1.dta
        results3: output/opioid_RR_LD2.dta
        results4: output/opioid_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/opioid_diagnostics1.svg
        diagnostics2: output/diagnostics/opioid_diagnostics2.svg
        plot1: output/opioid_plot1.svg
        plot2: output/opioid_plot2.svg

  model_dvafemale:
    run: stata-mp:latest analysis/model.do dvafemale
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/dvafemale_RR_LD1.dta
        results2: output/dvafemale_RD_LD1.dta
        results3: output/dvafemale_RR_LD2.dta
        results4: output/dvafemale_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/dvafemale_diagnostics1.svg
        diagnostics2: output/diagnostics/dvafemale_diagnostics2.svg
        plot1: output/dvafemale_plot1.svg
        plot2: output/dvafemale_plot2.svg

  model_dvamale:
    run: stata-mp:latest analysis/model.do dvamale
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/dvamale_RR_LD1.dta
        results2: output/dvamale_RD_LD1.dta
        results3: output/dvamale_RR_LD2.dta
        results4: output/dvamale_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/dvamale_diagnostics1.svg
        diagnostics2: output/diagnostics/dvamale_diagnostics2.svg
        plot1: output/dvamale_plot1.svg
        plot2: output/dvamale_plot2.svg

  model_intdissub14:
    run: stata-mp:latest analysis/model.do intdissub14
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/intdissub14_RR_LD1.dta
        results2: output/intdissub14_RD_LD1.dta
        results3: output/intdissub14_RR_LD2.dta
        results4: output/intdissub14_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/intdissub14_diagnostics1.svg
        diagnostics2: output/diagnostics/intdissub14_diagnostics2.svg
        plot1: output/intdissub14_plot1.svg
        plot2: output/intdissub14_plot2.svg

  model_intdisover14:
    run: stata-mp:latest analysis/model.do intdisover14
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/intdisover14_RR_LD1.dta
        results2: output/intdisover14_RD_LD1.dta
        results3: output/intdisover14_RR_LD2.dta
        results4: output/intdisover14_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/intdisover14_diagnostics1.svg
        diagnostics2: output/diagnostics/intdisover14_diagnostics2.svg
        plot1: output/intdisover14_plot1.svg
        plot2: output/intdisover14_plot2.svg


  model_rcgpsafeguard:
    run: stata-mp:latest analysis/model.do rcgpsafeguard
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/rcgpsafeguard_RR_LD1.dta
        results2: output/rcgpsafeguard_RD_LD1.dta
        results3: output/rcgpsafeguard_RR_LD2.dta
        results4: output/rcgpsafeguard_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/rcgpsafeguard_diagnostics1.svg
        diagnostics2: output/diagnostics/rcgpsafeguard_diagnostics2.svg
        plot1: output/rcgpsafeguard_plot1.svg
        plot2: output/rcgpsafeguard_plot2.svg

  combine_results:
    run: stata-mp:latest analysis/combine_results.do
    needs:
    - model_alcmisuse
    - model_drugmisuse
    - model_opioid
    - model_dvafemale
    - model_dvamale
    - model_intdissub14
    - model_intdisover14
    - model_rcgpsafeguard
    outputs:
      moderately_sensitive:
        results: output/CITS_results.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:10:21

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

Job request

Status
Failed
Backend
TPP
Workspace
lockdown-and-vulnerable-groups
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
095e227
Requested actions
  • model_alcmisuse
  • model_drugmisuse
  • model_opioid
  • model_dvafemale
  • model_dvamale
  • model_intdissub14
  • model_intdisover14
  • model_rcgpsafeguard
  • combine_results

Code comparison

Compare the code used in this job request