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Job request: 6115

Organisation:
University of Leeds
Workspace:
all_cause_mortality_with_stratification
ID:
upj67pazixjm6z5w
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ciarán D. McInerney 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:
    buyeasv57dfodvna
  • Action:
    describe
    Status:
    Status: Failed
    Job identifier:
    rkbgjwd6a3lczzwt
    Error:
    nonzero_exit: Job exited with error code 1

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

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

  describe:
    run: r:latest analysis/report.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
       #cohort1: output/plot_postOp_mortality_30day.png
       subtable_table1_ageGroup: output/table1_ageGroup.csv
       subtable_table1_Sex: output/table1_Sex.csv
       subtable_table1_30dayMortality: output/table1_postOp_mortality_30day.csv
       table1_df_4wk: output/table1_4wk_onboarding.csv
       #table1_kable_4wk: output/Table1_4wk_onboarding.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:15:43

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

Job request

Status
Failed
Backend
TPP
Workspace
all_cause_mortality_with_stratification
Requested by
Ciarán D. McInerney
Branch
main
Force run dependencies
Yes
Git commit hash
694170f
Requested actions
  • run_all

Code comparison

Compare the code used in this job request