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Job request: 5576

Organisation:
University of Surrey
Workspace:
pancreatic_cancer
ID:
jgsvpe4cnstx7d5b
View repo View project.yaml

This page shows the technical details of what happened when 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 10000

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 2019-01-01 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 "2019-02-01 to today 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*_rate.csv
  
  describe:
    run: r:latest analysis/analysis1.R
    needs: 
      [
        generate_study_population,
        # generate_measures,
      ]
    outputs:
      moderately_sensitive:
        Fig1: output/paca_time210222.png
        Tab1: output/paca_counts.csv
        Fig2: output/paca_time_table.png
        Fig3: output/paca_time_table_year.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:14:23

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pancreatic_cancer
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
3b0e1be
Requested actions
  • run_all