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Job request: 415

Organisation:
Bennett Institute
Workspace:
restoration-observatory-emis-tpp-test
ID:
tpa6fwz3d5kx4cm2
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Helen Curtis 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:
# for testing in command line use:
# cohortextractor generate_cohort --index-date-range "2020-01-01 to 2020-12-01 by month" --output-dir output/measures/tpp --expectations-population 2000 --study-definition study_definition_tpp
# followed by:
#  cohortextractor generate_measures --output-dir output/measures/tpp --study-definition study_definition_tpp


  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tpp --index-date-range "2020-01-01 to 2020-11-01 by month" --output-dir=output/measures/tpp
    outputs:
      highly_sensitive:
        cohort: output/measures/tpp/input_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_tpp --skip-existing --output-dir=output/measures/tpp
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/tpp/measure_*.csv
        
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/event_incidence.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/event_incidence.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:02

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

Job information

Status
Succeeded
Backend
TPP
Workspace
restoration-observatory-emis-tpp-test
Requested by
Helen Curtis
Branch
notebooks
Force run dependencies
No
Git commit hash
597f8f2
Requested actions
  • generate_notebook

Code comparison

Compare the code used in this Job Request