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Job request: 5475

Organisation:
University of Surrey
Workspace:
pancreatic_cancer
ID:
qu3ajzlcziy3jhnk
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_4
    Status:
    Status: Succeeded
    Job identifier:
    ac2xdykggnq5mo43
  • Action:
    generate_study_population_1
    Status:
    Status: Failed
    Job identifier:
    m2qerffgz5wf56vy
    Error:
    Internal error
  • Action:
    generate_study_population_2
    Status:
    Status: Failed
    Job identifier:
    zrggo7dcyonpjild
    Error:
    Internal error
  • Action:
    generate_study_population_3
    Status:
    Status: Failed
    Job identifier:
    7ik5auspyrrbtwsq
    Error:
    nonzero_exit: Job exited with error code 137: likely means it ran out of memory
  • Action:
    generate_ethnicity
    Status:
    Status: Succeeded
    Job identifier:
    7e36ctl74i7nwp2f
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    dy7i5opyedgel4hc
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    albc4huql7aqpwbr
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    describe
    Status:
    Status: Failed
    Job identifier:
    bolvph67tq7ppwve
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.feather

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2015-01-01 to 2016-12-01 by month" --skip-existing --output-dir=output/measures --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/measures/inp*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2017-01-01 to 2018-12-01 by month" --skip-existing --output-dir=output/measures --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/measures/inpu*.feather

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2020-12-01 by month" --skip-existing --output-dir=output/measures --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/measures/input*.feather

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.feather

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs:
      [
      generate_study_population_1,
      generate_study_population_2,
      generate_study_population_3,
      generate_study_population_4,
      generate_ethnicity,
      ]
    outputs:
      highly_sensitive:
        cohort: output/measures/in*.feather

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: 
      [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*_rate.csv
  
  describe:
    run: r:latest analysis/report.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        Fig1: output/paca_rate.png
        Tab1: output/paca_rate.csv
        Fig2: output/paca_rate_region.png
        Tab2: output/paca_rate_region.csv
        Fig3: output/paca_rate_IMD.png
        Tab3: output/paca_rate_IMD.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 110:31:01

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
Yes
Git commit hash
ca8de21
Requested actions
  • run_all

Code comparison

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