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Job request: 1106

Organisation:
Bennett Institute
Workspace:
sro-measures-initial
ID:
toyz7npupn667cf2
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:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    dmeei74fxrelmfet
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_practice_count
    Status:
    Status: Succeeded
    Job identifier:
    cb5z6plul6rrbmpp
  • Action:
    get_practice_count
    Status:
    Status: Succeeded
    Job identifier:
    dpl2yauy33frouxn
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    hcilylyh3nwz6gnv
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    do35juuzp5ycj2y5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    get_patient_count
    Status:
    Status: Failed
    Job identifier:
    v5y4e7gmli3s46rx
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000
   
    
actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-02-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count.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
  
  get_practice_count:
    run: python:latest python analysis/get_practice_count.py
    needs: [generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        text: output/practice_count.json
  
  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json
        


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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:31:46

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

Job request

Status
Failed
Backend
TPP
Workspace
sro-measures-initial
Requested by
Louis Fisher
Branch
initial-measures
Force run dependencies
No
Git commit hash
6eda7a1
Requested actions
  • generate_study_population
  • generate_study_population_practice_count
  • generate_measures
  • get_practice_count
  • get_patient_count
  • generate_notebook
  • run_all

Code comparison

Compare the code used in this job request