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Job request: 1767

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag
ID:
f53lqsoyipw5pia5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

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_study_population_demographics:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_demographics
    outputs:
      highly_sensitive:
        cohort: output/input_demographics.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


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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:37

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mechanical-valve-anticoag
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
86d76b3
Requested actions
  • generate_notebook

Code comparison

Compare the code used in this job request