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Job request: 9541

Organisation:
University of Manchester
Workspace:
hosp_rate
ID:
gpirt7mdm6mlhh4y
View repo View project.yaml

This page shows the technical details of what happened when the 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 list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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/*

  
  # study_definition_hospitalisation_rate_hxdx:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_rate_hxdx --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_hxdx:
  #   run: cohortextractor:latest generate_measures --study-definition study_definition_hospitalisation_rate_hxdx --skip-existing --output-dir=output/measures
  #   needs: [study_definition_hospitalisation_rate_hxdx]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measur_*.csv

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:19:14

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
No
Git commit hash
fb76723
Requested actions
  • generate_notebook_hospitalisation_rate

Code comparison

Compare the code used in this Job Request