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Job request: 23461

Organisation:
University of Surrey
Workspace:
pancreatic_cancer
ID:
cbggjvq2dbeqpwrn
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:
    describe_data
    Status:
    Status: Failed
    Job identifier:
    e3v4eq6ti35ee5dz
    Error:
    nonzero_exit: Job exited with an error

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_denominator_1:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_denominator --index-date-range "2015-01-01 to 2019-08-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/input*.feather
  
  generate_denominator_2:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_denominator --index-date-range "2019-09-01 to 2024-05-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inpu*.feather

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_denominator --skip-existing --output-dir=output/measures
    needs: 
      [
        generate_denominator_1,
        generate_denominator_2,
      ]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_registered*_rate.csv

  describe_data:
    run: r:latest analysis/analysis_counts.R
    needs: 
      [
        generate_study_population,
        generate_measures
      ]
    outputs:
      moderately_sensitive:
        Tab1: output/monthly_count.csv
        Tab2: output/demographics.csv
        Tab3: output/measure_registered_rate_rounded.csv
        Tab4: output/month_mortality.csv
        Tab5: output/monthly_count3.csv
        Tab6: output/numberofcases.csv
        Fig1: output/weeks2.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:30

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

Job request

Status
Failed
Backend
TPP
Workspace
pancreatic_cancer
Requested by
AgzLeman
Branch
main
Force run dependencies
No
Git commit hash
78f4bb8
Requested actions
  • describe_data

Code comparison

Compare the code used in this job request