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Job request: 5475

Workspace:
pancreatic_cancer
ID:
qu3ajzlcziy3jhnk

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: 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed
Completed successfully
Backend
TPP
Workspace
pancreatic_cancer
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
ca8de21
Requested actions
  • run_all