Releases | Open Source Science

🚀 Enhancements

[MNT] Update diagnosis terms to SNOMED v20250227 and standardize vocab file format #427 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] 11 months ago

🐛 Bug Fixes

[FIX] update assessments to SNOMED v20250227 and exclude non-standard terms #421 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] 12 months ago

api - v0.6.2

:tada: This release contains work from a new contributor! :tada:

Thank you, Khushi Jitendra Rajurkar (@KhushiRajurkar), for all your work!

🐛 Bug Fixes

[FIX] Ensure defaults are correctly applied for environment variables set to empty strings #418 (@alyssadai)

🏠 Internal

[REF] Move environment variable handling to Pydantic BaseSettings class #416 (@alyssadai)
[REF] Refactor startup/shutdown events to lifespan events #407 (@KhushiRajurkar @alyssadai)

🔩 Dependency Updates

[REF] Upgrade to Pydantic>2 #413 (@alyssadai)

Authors: 2

Alyssa Dai (@alyssadai)
Khushi Jitendra Rajurkar (@KhushiRajurkar)

- Python
Published by neurobagel-bot[bot] 12 months ago

🚀 Enhancements

[MNT] Remove trailing slashes from all paths + rename NB_NAPI_ROOT_PATH #408 (@alyssadai)
[ENH] Make root_path for app configurable #400 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] about 1 year ago

💥 Breaking Changes

[MNT] Replaced Cognitive Atlas with SNOMED #397 (@rmanaem)

Authors: 1

Arman Jahanpour (@rmanaem)

- Python
Published by neurobagel-bot[bot] about 1 year ago

📝 Documentation

[DOC] Update shortcuts in README.md #391 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] about 1 year ago

🚀 Enhancements

[ENH] Implement minimum cell size #388 (@surchs)

🏠 Internal

[ENH] Add consistent badges #387 (@surchs)

Authors: 1

Sebastian Urchs (@surchs)

- Python
Published by neurobagel-bot[bot] about 1 year ago

🏠 Internal

[REF] Manually verify ID token using PyJWT instead of google_auth #386 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] about 1 year ago

🚀 Enhancements

[FIX] Filter for only ImagingSessions or PhenotypicSessions in SPARQL query #375 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

🐛 Bug Fixes

[FIX] Ensure non-agg API doesn't error out when all matches lack pipeline data #369 (@alyssadai)

🧪 Tests

[TST] Remove unneeded env file mount from test docker-compose.yml #366 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

💥 Breaking Changes

[REF] Split generic /attributes endpoints into attribute-specific routers #358 (@alyssadai)
[ENH] Implemented pipeline_version and pipeline_name query fields #345 (@rmanaem)

🚀 Enhancements

[ENH] Add /pipelines router & route for fetching available pipeline versions #350 (@alyssadai)
[REF] Update README links and simplify Docker Compose instructions #340 (@alyssadai)

🐛 Bug Fixes

[FIX] Allow only "true" or None for is_control query parameter #364 (@alyssadai)
[FIX] Fixed a typo in filtering pipeline name #351 (@rmanaem)
[FIX] Ensure pipeline variables are returned from the graph in an aggregate query #349 (@alyssadai)

🏠 Internal

[MNT] Updated default_neurobagel_query #347 (@rmanaem)
[MNT] Removed build docker nightly workflow file #342 (@rmanaem)

📝 Documentation

[MNT] Update default Neurobagel SPARQL query file and turn into PR checkbox #359 (@alyssadai)

🧪 Tests

[TST] Add integration test against local test graph #357 (@rmanaem @surchs @alyssadai)

Authors: 3

Alyssa Dai (@alyssadai)
Arman Jahanpour (@rmanaem)
Sebastian Urchs (@surchs)

- Python
Published by neurobagel-bot[bot] over 1 year ago

🐛 Bug Fixes

[FIX] Ensure subjects without imaging sessions are considered in main query #333 (@alyssadai)

🏠 Internal

[CI] Fix reference for DOCKERHUB_REPO in builddockeron_release.yml #337 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

💥 Breaking Changes

[FIX] Disable redirect slashes globally and remove trailing / from /query #328 (@alyssadai)
[ENH] Add authentication to /query route #323 (@alyssadai)

🐛 Bug Fixes

[FIX] Exclude sessions missing a queried property from matches #326 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

🐛 Bug Fixes

[FIX] Address performance issues in SPARQL query #308 (@surchs)
[FIX] Disable timeout for request to graph #305 (@alyssadai)

Authors: 2

Alyssa Dai (@alyssadai)
Sebastian Urchs (@surchs)

- Python
Published by surchs almost 2 years ago

api - v0.2.0

:tada: This release contains work from a new contributor! :tada:

Thank you, Abdul Samad Siddiqui (@samadpls), for all your work!

Release Notes

[MNT] Release new data model (#300)

We have updated the Neurobagel data model to allow users to specify phenotypic information at the session level (https://github.com/neurobagel/planning/issues/83). This release updates the node API so it can understand the new graph data.

💥 Breaking Changes

[REF] Make session count names clearer in query response #282 (@alyssadai)
[ENH] Support queries of session-level phenotypic attributes #264 (@alyssadai)

🚀 Enhancements

[ENH] Added root endpoint with welcome message and API docs link #286 (@samadpls)
[MNT] Release new data model #300 (@surchs)
Delete .github/workflows/add_pr2project.yml #244 (@surchs)

📝 Documentation

[DOC] Added warning about quoting in .env file for Docker commands #284 (@samadpls)
[DOC] Add sample default SPARQL query to repo #277 (@alyssadai)

🧪 Tests

[TST] Refactor tests #269 (@alyssadai)

🔩 Dependency Updates

Bumped fastapi, starlette, and typing_extensions #295 (@rmanaem)

Authors: 4

Abdul Samad Siddiqui (@samadpls)
Alyssa Dai (@alyssadai)
Arman Jahanpour (@rmanaem)
Sebastian Urchs (@surchs)

- Python
Published by surchs almost 2 years ago

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

Data model-related updates :gear:

[MNT] Add NCIT namespace and update healthy control term by @alyssadai in https://github.com/neurobagel/api/pull/181
[FIX] Make session optional in SPARQL query template by @alyssadai in https://github.com/neurobagel/api/pull/229

Documentation updates 📜

[REF] Remove environment variable table from README by @alyssadai in https://github.com/neurobagel/api/pull/168
[DOC] Generalized environment variables' table by @rmanaem in https://github.com/neurobagel/api/pull/198
[DOC] Add link to official docs by @surchs in https://github.com/neurobagel/api/pull/219

Bug fixes 🛠️

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

Other changes 🧹

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

New Contributors

@surchs made their first contribution in https://github.com/neurobagel/api/pull/144

Full Changelog: https://github.com/neurobagel/api/compare/v0.1.0...v0.1.1

- Python
Published by alyssadai about 2 years ago

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

New Contributors

@alyssadai made their first contribution in https://github.com/neurobagel/api/pull/17
@rmanaem made their first contribution in https://github.com/neurobagel/api/pull/24
@yarikoptic made their first contribution in https://github.com/neurobagel/api/pull/95
@dependabot made their first contribution in https://github.com/neurobagel/api/pull/105
@Remi-Gau made their first contribution in https://github.com/neurobagel/api/pull/103

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

- Python
Published by alyssadai over 2 years ago

Recent Releases of api

api - v0.6.4

🚀 Enhancements

Authors: 1

api - v0.6.3

🐛 Bug Fixes

Authors: 1

api - v0.6.2

🐛 Bug Fixes

🏠 Internal

🔩 Dependency Updates

Authors: 2

api - v0.6.1

🚀 Enhancements

Authors: 1

api - v0.6.0

💥 Breaking Changes

Authors: 1

api - v0.5.1

📝 Documentation

Authors: 1

api - v0.5.0

🚀 Enhancements

🏠 Internal

Authors: 1

api - v0.4.3

🏠 Internal

Authors: 1

api - v0.4.2

🚀 Enhancements

Authors: 1

api - v0.4.1

🐛 Bug Fixes

🧪 Tests

Authors: 1

api - v0.4.0

💥 Breaking Changes

🚀 Enhancements

🐛 Bug Fixes

🏠 Internal

📝 Documentation

🧪 Tests

Authors: 3

api - v0.3.1

🐛 Bug Fixes

🏠 Internal

Authors: 1

api - v0.3.0

💥 Breaking Changes

🐛 Bug Fixes

Authors: 1

api - v0.2.1

🐛 Bug Fixes

Authors: 2

api - v0.2.0

Release Notes

[MNT] Release new data model (#300)

💥 Breaking Changes

🚀 Enhancements

📝 Documentation

🧪 Tests

🔩 Dependency Updates

Authors: 4

api - v0.1.1

Summary

What's Changed

New or improved features ✨

Data model-related updates :gear:

Documentation updates 📜

Bug fixes 🛠️

Other changes 🧹

New Contributors

api - v0.1.0

Overview

What's new

New Contributors