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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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

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 information

Status
Failed
Backend
TPP
Workspace
pancreatic_cancer
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
ca8de21
Requested actions
  • run_all

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