v0.1.0

Initial release of the Neurobagel API, which interfaces with Stardog graph stores containing Neurobagel-harmonized data via SPARQL queries.

Overview

This release brings major additions to API functionality as well as automated testing setup including:

• A query endpoint for GET operations that formulate a SPARQL query to the graph based on query parameters
• Processing, validation, and tests of basic query parameters for:
  • Age
  • Sex
  • Diagnosis
  • Healthy control status
  • Assessment tool
  • Number of sessions
  • Image modality
• A pydantic data model for responses to queries from the linked graph
• Modes for returning dataset-aggregated vs subject-level query results
• Environment variable configurability in terms of the graph the API communicates with and the query result mode
• Dockerfile + docker-compose spec and usage instructions

What's new

• Setting up bagelapi + adding GET route by @alyssadai in #17
• Set up test workflow by @rmanaem in #24
• Implement query parameters for age by @alyssadai in #28
• Implemented image modality query parameter by @rmanaem in #39
• Implement query parameters for diagnosis and is_control by @alyssadai in #41
• Implemented minimum number of imaging sessions query parameter by @rmanaem in #46
• Implement query parameter for assessment by @alyssadai in #57
• Updated the API to return subject file paths and modalities and updated test workflow file by @rmanaem in #61
• Change variable storing graph DB IP address to an environment variable by @alyssadai in #71
• Implement error catching for httpx.ConnectTimeout when not connected to McGill network by @alyssadai in #77
• Add Dockerfile and instructions for deploying API using official Docker image by @alyssadai in #79
• Add docker-compose specification and instructions by @alyssadai in #90
• Make graph database name configurable as an environment variable by @alyssadai in #93
• Return (or not) subject-level attributes in query results based on env var by @alyssadai in #99
• [ENH] Updated API to return new subject level results by @rmanaem in #125
• [FIX] Return list instead of only first term for subject-level assessment by @alyssadai in #133

New Contributors

• @alyssadai made their first contribution in #17
• @rmanaem made their first contribution in #24
• @yarikoptic made their first contribution in #95
• @dependabot made their first contribution in #105
• @Remi-Gau made their first contribution in #103

Full Changelog: https://github.com/neurobagel/api/commits/v0.1.0