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Job request: 2714

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag-updated
ID:
hhwsfsvj3sqpeyrs
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 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: 15000

actions:

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv
      
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-09-01 to 2019-04-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv
  
  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-05-01 to 2019-11-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input*.csv
  
  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-12-01 to 2020-06-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv
  
  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-01 to 2021-05-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv
        
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/in*.csv
        
  patient_count:
    run: python:latest python analysis/get_patient_count.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        csv: output/patient_count.csv

  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*_rate.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: [join_ethnicity, generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/notebook.html
        figures: output/measure_*.jpeg
        total_csv: output/doac_rate_total.csv
        csvs: output/current_doac_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 13:00:15

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

Job information

Status
Failed
Backend
EMIS
Workspace
mechanical-valve-anticoag-updated
Requested by
Louis Fisher
Branch
updates
Force run dependencies
No
Git commit hash
b0551d1
Requested actions
  • generate_study_population_ethnicity
  • generate_study_population_1

Code comparison

Compare the code used in this Job Request