v0.1.1

Summary

This release introduces new API endpoints which return:

• queryable Neurobagel variables/attributes
• available instances of a specific Neurobagel attribute in the linked graph
• all term IDs and associated human-readable labels of concepts from the vocabulary used for a given Neurobagel attribute

The release also introduces:

• greater configurability of API and graph server parameters via environment variables
• a helper shell script for automatically uploading graph-ready data (JSONLD/TTL) to an existing graph database
• returning sizes of matching datasets in the API response for a subject query

What's Changed

New or improved features ✨

• [ENH] Increase configurability of API/graph server parameters by @alyssadai in #146
• [ENH] Add environment variable for allowed origins for CORS by @alyssadai in #151
• [ENH] Add query tool to docker compose by @surchs in #154
• [FEAT] Add script to upload data to graph by @alyssadai in #156
• [ENH] Implemented endpoint for returning available termURLs by @rmanaem in #183
• [ENH] Add Neurobagel vocab graph file by @alyssadai in #184
• [ENH] Update aggregate response body by @alyssadai in #193
• [ENH] Add endpoint returning queryable attributes + refine existing endpoint for attribute instances by @alyssadai in #194
• [ENH] Update add_data_to_graph.sh to also upload TTL files by @alyssadai in #196
• [ENH] Add endpoint that returns term ID-label mappings for vocab of a given attribute (nb:Assessment) by @alyssadai in #201
• [ENH] Make data upload script backend responsive by @alyssadai in #205
• [ENH] Return human-readable labels (if available) as well as term IDs from /attributes/{data_element_URI} by @alyssadai in #218
• [ENH] Changed the favicon to neurobagel logo by @rmanaem in #222
• [ENH] Return dataset sizes in query response by @alyssadai in #223
• [ENH] Add support for endpoint that will return nb:Diagnosis options from SNOMED by @alyssadai in #228

Data model-related updates ⚙️

• [MNT] Add NCIT namespace and update healthy control term by @alyssadai in #181
• [FIX] Make session optional in SPARQL query template by @alyssadai in #229

Documentation updates 📜

• [REF] Remove environment variable table from README by @alyssadai in #168
• [DOC] Generalized environment variables' table by @rmanaem in #198
• [DOC] Add link to official docs by @surchs in #219

Bug fixes 🛠️

• [FIX] Fix typo in .template-env by @alyssadai in #149
• [FIX] Remove yaml list key for API_QUERY_URL by @surchs in #164
• [FIX] Properly expose NB_GRAPH_PORT_HOST to API container by @alyssadai in #167
• [FIX] Removed the nested variable for API_QUERY_URL env var by @rmanaem in #177
• [FIX] Properly expose NB_GRAPH_PORT to API container by @rmanaem in #191
• [FIX] Remove --no-progress-meter by @surchs in #227
• [FIX] Copy vocab/ directory into container filesystem in Dockerfile by @alyssadai in #231
• [FIX] Filtered out null imaging modalities by @rmanaem in #233
• [FIX] Remove query tool config by @surchs in #238

Other changes 🧹

• [MNT] Added docker-pre-commit pre-commit hook by @rmanaem in #178
• [REF] Refactor httpx.post call to Stardog and context creation by @alyssadai in #195
• [MNT] Removed session_file_path from aggregate results by @rmanaem in #214
• [REF] Organize related tests into modules and refactor setting of toy credentials by @alyssadai in #220
• [REF] Refactor dataset size request into separate function by @alyssadai in #235
• [CI] Renamed ci workflow to build_docker and image tag from latest to nightly by @rmanaem in #242
• [CI] Add workflow for building image on release by @alyssadai in #243

New Contributors

• @surchs made their first contribution in #144

Full Changelog: v0.1.0...v0.1.1