Job request: 5576

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 Pancreatic cancer 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

ID Status Action
atkjgg2gybojbybu succeeded describe
bh74w3s32vsue4ir succeeded generate_study_population

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:14:23

Config

  • Backend:
    TPP
  • Workspace:
    pancreatic_cancer
  • Branch:
    main
  • Creator:
    lemanska
  • Force run dependencies:
    True
  • Git Commit Hash:
    3b0e1be
  • Requested actions:
    • run_all