CELE-143 CELE-129 - Update ingestion command to deal with synapses sizes and positions

[aranega]

This PR closes CELE-143 and CELE-129 adding:

• synapses size ingestion
• synapses position extraction
• synapses position conversion
• synapses position ingestion
• modification of the API to display synapses sizes and position when requested from the frontend
• binding generation for the frontend to get the size and position

[Copilot]

Pull Request Overview

This PR implements comprehensive synapse data ingestion capabilities, adding support for synapse sizes and positions to the C. elegans visualization system. The changes enable the extraction, conversion, and ingestion of synapse 3D model positions and size data, extending the API to provide this information to the frontend.

• Adds synapses size and position ingestion to the data pipeline
• Introduces 3D synapse model processing with position extraction and conversion
• Updates API schemas and database models to support synapse size and position data
• Generates frontend bindings for accessing synapse size and position information

Reviewed Changes

Copilot reviewed 22 out of 23 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
ingestion/tests/test_main.py	Updates test cases to use valid dataset IDs and include reference data directory
ingestion/tests/storage/test_filesystem.py	Adds support for synapses directory in filesystem tests
ingestion/tests/fixtures/reference-data/datasets.json	Adds dataset definitions for witvliet_2020_2 and witvliet_2020_8
ingestion/ingestion/storage/filesystem.py	Implements synapses directory discovery and 3D file processing enhancements
ingestion/ingestion/storage/blob.py	Adds blob naming function for 3D synapse files
ingestion/ingestion/schema.py	Defines SynapseInfo model and updates Data schema validation
ingestion/ingestion/ingest.py	Implements synapse position extraction and 3D file processing logic
ingestion/README.md	Documents synapse 3D file naming requirements and directory structure
data/db-raw-data/summary.txt	Updates file listing to include synapse data files
applications/visualizer/frontend/src/rest/models/SynapseEntry.ts	Adds size and position fields to frontend model
applications/visualizer/backend/visualizer/settings/production.py	Implements synapse position file downloading in production
applications/visualizer/backend/visualizer/settings/development.py	Adds development support for synapse position files
applications/visualizer/backend/requirements.txt	Adds trimesh dependency for 3D model processing
applications/visualizer/backend/openapi/openapi.json	Updates API specification with synapse size and position fields
applications/visualizer/backend/api/schemas.py	Adds size and position fields to SynapseEntry schema
applications/visualizer/backend/api/populatedb.py	Implements synapse size and position data population logic
applications/visualizer/backend/api/models.py	Adds size and position fields to Synapse model
applications/visualizer/backend/api/migrations/0004_synapse_position.py	Database migration for synapse position field
applications/visualizer/backend/api/migrations/0003_synapse_size_alter_synapse_connection.py	Database migration for synapse size field
applications/visualizer/backend/api/api.py	Updates API endpoint to return synapse size and position data
applications/visualizer/api/openapi.yaml	Updates API specification with synapse size and position fields
applications/visualizer/api/openapi.json	Updates API specification with synapse size and position fields

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[ddelpiano]

lgtm