[MNT] Replaced Cognitive Atlas with SNOMED

[rmanaem]

• Closes Replace Cognitive Atlas vocab with SNOMED #390

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• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
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Summary by Sourcery

Switch from using the Cognitive Atlas to SNOMED CT for assessments.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request replaces the Cognitive Atlas vocabulary with SNOMED for assessments. It updates the API endpoint, data fetching logic, and tests to reflect this change. A local copy of the SNOMED vocabulary is now used for lookups.

Class diagram showing updated vocabulary handling

classDiagram
    class VocabHandler {
        +create_snomed_assessment_lookup(output_path)
        +create_snomed_disorder_lookup(output_path)
        -load_json(path)
    }
    note for VocabHandler "Replaced fetch_and_save_cogatlas with SNOMED handlers"

    class Router {
        +get_vocab()
        +get_instances()
    }

    class RouteFactory {
        +create_get_vocab_handler(external_vocab, vocab_name, namespace_prefix)
    }

    Router --> RouteFactory: uses
    Router --> VocabHandler: uses

Loading

File-Level Changes

Change	Details	Files
Replaced Cognitive Atlas with SNOMED for assessments	Updated the test_stored_vocab_lookup_file_created_on_startup test to use the SNOMED vocabulary. Removed functions related to fetching the Cognitive Atlas vocabulary and added functions to create SNOMED lookup files. Updated tests to use SNOMED URIs and labels. Updated the startup event to create SNOMED lookup files instead of Cognitive Atlas. Updated the assessments router to use SNOMED. Updated the diagnoses router to use the correct SNOMED lookup. Updated the route factory to use a namespace prefix for vocabularies. Updated the default Neurobagel query file. Added a local backup copy of the SNOMED assessment vocabulary file.	tests/test_app_events.py app/api/utility.py tests/test_attribute_factory_routes.py app/main.py app/api/routers/assessments.py app/api/routers/diagnoses.py app/api/routers/route_factory.py docs/default_neurobagel_query.rq vocab/backup_external/snomed_assessment.json

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#390	Replace Cognitive Atlas vocabulary with SNOMED in the vocab endpoint and saved vocab file	✅
#390	Replace Cognitive Atlas vocabulary with SNOMED in the query template	✅
#390	Replace Cognitive Atlas vocabulary with SNOMED in the /assessments endpoint	✅

Possibly linked issues

• Replace Cognitive Atlas vocab with SNOMED #390: The PR replaces Cognitive Atlas with SNOMED as requested in the issue. The changes include updating the vocab endpoint, query template, /assessments endpoint, and tests.
• Replace Cognitive Atlas vocab with SNOMED #390: The PR closes the issue by implementing the proposed refactoring and also changes the vocabulary used for assessments.

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.94%. Comparing base (8e1c289) to head (2e1d4b3).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #397      +/-   ##
==========================================
- Coverage   97.09%   96.94%   -0.15%     
==========================================
  Files          24       24              
  Lines         861      819      -42     
==========================================
- Hits          836      794      -42     
  Misses         25       25              

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