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Job request: 1665

Organisation:
Bennett Institute
Workspace:
sro-pulse-oximetry-2
ID:
kyb2vfyyyp4s5bbk
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_ethnicity
    Status:
    Status: Failed
    Job identifier:
    rzebg5dnzvuda65u
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_practice_count
    Status:
    Status: Succeeded
    Job identifier:
    sqf6jbvlno2brype
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    4sbadfcqyciyunec
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    get_patient_count
    Status:
    Status: Failed
    Job identifier:
    bg5lhpojjm7yq6al
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    create_notebook
    Status:
    Status: Failed
    Job identifier:
    p3gpkvvgxcb7n3ya
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    wso3hgggmizs6acu
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    s2sqt2ybd4h5w3is
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    ruzgqqh5xerdo7sd
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measure_ethnicity
    Status:
    Status: Failed
    Job identifier:
    2zodsryp7trisley
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  # convert_codelist:
  #   run: python:latest python analysis/convert_codelist.py
  #   outputs:
  #     highly_sensitive:
  #       cohort: codelists/opensafely-pulse-oximetry-converted.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-01 to 2021-02-01 by week" --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

  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: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*.csv

  generate_measure_ethnicity:
    run: python:latest python analysis/generate_measure_ethnicity.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure: output/measure_ethnicity.csv

  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json

  create_notebook:
    run: python:latest python analysis/create_notebook.py
    needs: [get_patient_count, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: analysis/SRO_Notebook.ipynb


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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:12:44

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

Job request

Status
Failed
Backend
TPP
Workspace
sro-pulse-oximetry-2
Requested by
Louis Fisher
Branch
template
Force run dependencies
No
Git commit hash
4cf71b3
Requested actions
  • run_all

Code comparison

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