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Job request: 1545

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag
ID:
vsmd4fisr6y32nm6
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Louis Fisher 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 15000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2021-04-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv



  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*.csv


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/measures_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population, generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/measures_notebook.html
        measures_csv: output/measures_dropped.csv
        csv: output/check.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
JobRequestError: All requested actions were already scheduled to run
Backend
TPP
Workspace
mechanical-valve-anticoag
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
4f9cca8
Requested actions
  • generate_notebook

Code comparison

Compare the code used in this Job Request