Job request: 5475

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
7e36ctl74i7nwp2f succeeded generate_ethnicity
m2qerffgz5wf56vy failed generate_study_population_1
zrggo7dcyonpjild failed generate_study_population_2
7ik5auspyrrbtwsq failed generate_study_population_3
ac2xdykggnq5mo43 succeeded generate_study_population_4
albc4huql7aqpwbr failed join_ethnicity
dy7i5opyedgel4hc failed generate_measures
bolvph67tq7ppwve failed describe

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 110:31:01

Config

  • Backend:
    TPP
  • Workspace:
    pancreatic_cancer
  • Branch:
    main
  • Creator:
    lemanska
  • Force run dependencies:
    True
  • Git Commit Hash:
    ca8de21
  • Requested actions:
    • run_all