Job request: 5860

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 PaCa_Enzyme_Rx 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
mrnvn23ivayd2kjf succeeded describe_ERx_rates
3j4pz4pgvqmi6sc4 succeeded generate_enzyme_replace_1
kmu3tij77hum2rev succeeded generate_enzyme_replace_2
v7psx2b4k73y42th succeeded generate_measures_enzymeRx

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_enzyme_replace_1:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-08-01 to 2021-10-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inp*.feather
  
  generate_enzyme_replace_2:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-11-01 to 2021-12-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/in*.feather

  generate_measures_enzymeRx:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: 
      [
        generate_enzyme_replace_1,
        generate_enzyme_replace_2,
      ]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_enzymeRx*_rate.csv

  describe_ERx_rates:
    run: r:latest analysis/analysis_enzymeRx.R
    needs: 
      [
        generate_measures_enzymeRx,
      ]
    outputs:
      moderately_sensitive:
        Fig1: output/ERx_number.png
        Fig2: output/ERx_rates.png

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:19:25

Config