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Job request: 1255

Organisation:
Bennett Institute
Workspace:
immunosuppressant-meds-research_v2
ID:
57oqd27dcbgjiwrl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Anna Rowan 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:
    generate_study_population
    Status:
    Status: Succeeded
    Job identifier:
    w3zlmvvvtyxrfdrs
  • Action:
    run_model
    Status:
    Status: Failed
    Job identifier:
    pyl6gdjjyommuqyx
    Error:
    nonzero_exit: Job exited with an error code

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  run_model:
    run: stata-mp:latest analysis/STATA_code.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log1: logs/cr_create_analysis_dataset.smcl 
        data1: output/data/tables.csv
        data2: output/data/primaryobjective1unadj.ster
        data3: output/data/primaryobjective1TVCtest.ster
        data4: output/data/primaryobjective1limitedadjusted.ster
        data5: output/data/primaryobjective1adjusted_completecaseethnicity.ster
        data6: output/data/primaryobjective1adjusted.ster
        data7: output/data/primaryobjective1adjusted_noethnicity.ster
        data8: output/data/primaryobjective1adjusted_completecaseethnicityTVC.ster
        data9: output/data/primaryobjective1adjustedTVC.ster
        data10: output/data/primaryobjective1adjusted_noethnicityTVC.ster
        data11: output/data/primaryobjective1sensitivity1.ster
        data12: output/data/primaryobjective1sensitivity2.ster
        data13: output/data/primaryobjective1limitedadjitudeath.ster
        data14: output/data/primaryobjective1adjusteditudeath.ster
        data15: output/data/primaryobjective1adjusteditudeath_ethnicity.ster
        data16: output/data/primaryobjective1adjusteditudeath_ethnicity_nomiss.ster
        data17: output/data/primaryobjective2aunadj.ster
        data18: output/data/primaryobjective2aTVCtest.ster
        data19: output/data/primaryobjective2alimitedadj.ster
        data20: output/data/primaryobjective2aadjusted.ster
        data21: output/data/primaryobjective2aadjustedTVC.ster
        data22: output/data/primaryobjective2aunadj_inc_icu.ster
        data23: output/data/primaryobjective2limitedadj_inc_icu.ster
        data24: output/data/primaryobjective2aadjusted_inc_icu.ster
        data25: output/data/primaryobjective2asensitivity1.ster
        data26: output/data/primaryobjective2asensitivity2.ster
        data27: output/data/primaryobjective2asensitivity3.ster
        data28: output/data/primaryobjective2asensitivity4.ster
        data29: output/data/primaryobjective2asensitivity5.ster
        data30: output/data/primaryobjective2asensitivity6.ster
        data31: output/data/primaryobjective2bunadj.ster
        data32: output/data/primaryobjective2bTVCtest.ster
        data33: output/data/primaryobjective2badjusted.ster
        data34: output/data/primaryobjective2badjustedTVC.ster
        data35: output/data/primaryobjective2bsensitivity1.ster
        data36: output/data/primaryobjective2bsensitivity2.ster
        data37: output/data/primaryobjective2bsensitivity3.ster
        data38: output/data/primaryobjective2bsensitivity4.ster
        data39: output/data/primaryobjective2cunadj.ster
        data40: output/data/primaryobjective2cTVCtest.ster
        data41: output/data/primaryobjective2cadjusted.ster
        data42: output/data/primaryobjective2cadjustedTVC.ster
        data43: output/data/primaryobjective2csensitivity1.ster
        data44: output/data/primaryobjective2csensitivity2.ster
        data45: output/data/primaryobjective2csensitivity3.ster
        data46: output/data/primaryobjective2csensitivity4.ster
        data47: output/data/primaryobjective2dunadj.ster
        data48: output/data/primaryobjective2dTVCtest.ster
        data49: output/data/primaryobjective2dadjusted.ster
        data50: output/data/primaryobjective2dadjustedTVC.ster
        data51: output/data/primaryobjective2dsensitivity1.ster
        data52: output/data/primaryobjective2dsensitivity2.ster
        data53: output/data/primaryobjective2dsensitivity3.ster
        data54: output/data/primaryobjective2dsensitivity4.ster
        figure1: output/figures/primeob2d_NA.pdf
        figure2: output/figures/primeob2d.pdf
        figure3: output/figures/primeob2b_NA.pdf
        figure4: output/figures/primeob2b.pdf
        figure5: output/figures/primeob2a_inc_icu_NA.pdf
        figure6: output/figures/primeob2a_inc_icu.pdf
        figure7: output/figures/primeob2a_NA.pdf
        figure8: output/figures/primeob2a.pdf
        figure9: output/figures/primeob1_nonadjitudeath.pdf
        figure10: output/figures/primeob1sens1_NA.pdf
        figure11: output/figures/primeob1sens1.pdf
        figure12: output/figures/primeob1_NA.pdf
        figure13: output/figures/primeob1_nonadj.pdf
        figure14: output/figures/out_death_freq.pdf
        figure15: output/figures/primeob1_nonadjitudeath_NA.pdf
        figure16: output/figures/primeob2c.pdf
        figure17: output/figures/primeob2c_NA.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 49:01:11

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

Job request

Status
Failed
Backend
TPP
Workspace
immunosuppressant-meds-research_v2
Requested by
Anna Rowan
Branch
Update_StudyDef
Force run dependencies
Yes
Git commit hash
3e38418
Requested actions
  • run_all

Code comparison

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