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Job request: 7677

Organisation:
University of Surrey
Workspace:
pancreaticcancer_enzyme_rx
ID:
4jggcx45hbs4ehwo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher AgzLeman 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:
    cax3vors45x2nzbv
    Error:
    nonzero_exit: Job exited with error code 4
  • Action:
    generate_enzyme_replace_1
    Status:
    Status: Failed
    Job identifier:
    yodnd2tzkeojiy6u
    Error:
    nonzero_exit: Job exited with error code 4
  • Action:
    generate_enzyme_replace_2
    Status:
    Status: Failed
    Job identifier:
    tjrkzvx5j4ewsv4f
    Error:
    nonzero_exit: Job exited with error code 4
  • Action:
    generate_measures_enzymeRx
    Status:
    Status: Failed
    Job identifier:
    25fxhjv2uzzf4kso
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    describe_ERx_rates
    Status:
    Status: Failed
    Job identifier:
    5v3uuiwxnccfgwbc
    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 --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_enzyme_replace_1:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2015-01-01 to 2018-08-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inp*.feather
  
  generate_enzyme_replace_2:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-09-01 to 2022-03-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/in*.feather

  generate_measures_enzymeRx:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: 
      [
        generate_enzyme_replace_1,
        generate_enzyme_replace_2,
      ]
    outputs:
      moderately_sensitive:
        measure_csv1: output/measures/measure_enzymeRx*_rate.csv
        measure_csv2: output/measures/measure_ExByRegion*_rate.csv

  describe_ERx_rates:
    run: r:latest analysis/analysis_enzymeRx.R
    needs: 
      [
        generate_measures_enzymeRx,
      ]
    outputs:
      moderately_sensitive:
        Fig1: output/ERx_number.png
        Fig2: output/ERx_rates.png
        Fig3: output/model_rates.png
        Fig4: output/Region.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:25

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

Job request

Status
Failed
Backend
TPP
Workspace
pancreaticcancer_enzyme_rx
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
99abec0
Requested actions
  • run_all

Code comparison

Compare the code used in this job request