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Job request: 6577

Organisation:
University of Leeds
Workspace:
all_cause_mortality_with_stratification
ID:
qgxrm37foihyvg7g
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: Failed
    Job identifier:
    x5tvqrb4lpuiapam
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    4wk_onboarding
    Status:
    Status: Failed
    Job identifier:
    odz7qiyfi2z3zj3y
    Error:
    dependency_failed: Not starting as dependency failed

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

    generate_study_population_cohort_check:
        run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
        outputs:
            highly_sensitive:
                cohort: output/input_*.csv
            
    check_cohort:
        run: r:latest analysis/check_cohort.R
        needs: [generate_study_population_cohort_check]
        outputs:
            moderately_sensitive:
                cohort: output/check_cohort.csv
                
    4wk_onboarding:
        run: r:latest analysis/report.R
        needs: [generate_study_population]
        outputs:
            moderately_sensitive:
                n_patients: output/count_patients.csv
                #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__Interim: output/table1_4wk_onboarding__Interim.csv
                table1_df_4wk: output/table1_4wk_onboarding.csv
                #table1_kable_4wk: output/Table1_4wk_onboarding.png
                subtable_table1_ageGroup_3mths: output/table1_ageGroup_3mths.csv
                subtable_table1_Sex_3mths: output/table1_Sex_3mths.csv
                subtable_table1_30dayMortality_3mths: output/table1_postOp_mortality_30day_3mths.csv
                table1_df_4wk_3mths: output/table1_4wk_onboarding_3mths.csv
                #table1_kable_4wk_3mths: output/Table1_4wk_onboarding_3mths.png
                subtable_table1_ageGroup_6mths: output/table1_ageGroup_6mths.csv
                subtable_table1_Sex_6mths: output/table1_Sex_6mths.csv
                subtable_table1_30dayMortality_6mths: output/table1_postOp_mortality_30day_6mths.csv
                table1_df_4wk_6mths: output/table1_4wk_onboarding_6mths.csv
                #table1_kable_4wk_6mths: output/Table1_4wk_onboarding_6mths.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:20

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
606dbbf
Requested actions
  • 4wk_onboarding

Code comparison

Compare the code used in this job request