Job request: 6253

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
vcuunpyb7l7tsosk succeeded generate_denominator_1
xtwddukgpsm6jhip succeeded generate_denominator_2
2gt7viiygby64mga succeeded generate_measures
yb3npqvq5632hzce succeeded generate_study_population
5f24c2y37rwueiug succeeded describe_data

Pipeline

Show Hide 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 2019-01-01 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 2022-02-01 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_average.R
    needs: 
      [
        generate_study_population,
        generate_measures,
      ]
    outputs:
      moderately_sensitive:
        Fig1: output/paca_time_table.png
        Fig2: output/paca_time_table_year.png
        Fig3: output/paca_time_rates.png
        Fig4: output/paca_time_rates_year.png
        Tab1: output/monthly_count.csv
        Tab2: output/monthly_median.csv
        Tab3: output/monthly_average.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 17:13:59

Config

  • Backend:
    TPP
  • Workspace:
    pancreatic_cancer
  • Branch:
    main
  • Creator:
    lemanska
  • Force run dependencies:
    True
  • Git Commit Hash:
    55e0a72
  • Requested actions:
    • run_all