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Job request: 8531

Organisation:
University of Manchester
Workspace:
hosp_rate
ID:
nmwm5nkoltnqmc3g

This page shows the technical details of what happened when authorised researcher ali 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:

  study_definition_hospitalisation_rate:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_rate --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_hospitalisation_rate --skip-existing --output-dir=output/measures
    needs: [study_definition_hospitalisation_rate]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  generate_notebook_hospitalisation_rate:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_rate.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_rate --ExecutePreprocessor.timeout=86400
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_rate/hospitalisation_rate.html 
        figures: output/hospitalisation_rate/*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:02:41

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

Job information

Status
Succeeded
Backend
TPP
Workspace
hosp_rate
Requested by
ali
Branch
hospitalisation_rate
Force run dependencies
Yes
Git commit hash
2ea25e4
Requested actions
  • run_all