Skip to content

Job request: 2151

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag
ID:
khrzjgcnhxgyc3vn
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.

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

  get_patient_count:
    run: python:latest python analysis/get_patient_count.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        patient_count: output/patient_count.json
        valve_code_counts: output/patient_valve_codes.json
        doac_valve_code_counts: output/patient_doac_valve_codes.json
        recent_doac_valve_code_counts: output/recent_patient_doac_valve_codes.json

  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, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/notebook.html
        figures: output/measure_*.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:07

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

Job information

Status
Failed
Backend
EMIS
Workspace
mechanical-valve-anticoag
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
d7c1109
Requested actions
  • generate_study_population

Code comparison

Compare the code used in this Job Request