Skip to content

Job request: 2704

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag-updated
ID:
ualegqu44zpjsr7s
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

  • Action:
    patient_count
    Status:
    Status: Succeeded
    Job identifier:
    gfdfisravbea7d3z
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    vehpo2xamb2somoe
    Error:
    No outputs found matching patterns: - output/measure_*_rate.csv
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    q35zzvulff6udj3i
    Error:
    dependency_failed: Not starting as dependency failed

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 "2018-09-01 to 2021-05-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv
        
  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
        
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.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: 00:00:15

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

Job request

Status
Failed
Backend
EMIS
Workspace
mechanical-valve-anticoag-updated
Requested by
Louis Fisher
Branch
updates
Force run dependencies
No
Git commit hash
634d21e
Requested actions
  • patient_count
  • generate_measures
  • generate_notebook

Code comparison

Compare the code used in this job request