All notable changes to openbel-api will be documented in this file. The curated log begins at changes to version 0.4.0.
This project adheres to Semantic Versioning.
- strict=yes query param on POST /api/nanopub will result in a 422 if the BEL statement or Annotations are bad
- Updated BEL Statement Completion - added semantic completion
-
Enhanced deployment tooling using make and bumpversion
-
Altered validation to return 422 when BEL Statement is invalid
-
Annotation and Namespace API endpoints with prefixes will uppercase prefix as prefixes are now stored in Uppercase format
-
POST/PUT /api/nanopubs uses default namespaces/annotations if references object is not part of nanopub
-
Now /completions and /validation both return the same resource type for the "validation" JSON object
-
Added location to POST /api/nanopub to response body
1.0.4 - 2016-12-28
- Docker containers for development and production use of OpenBEL
- Converted authentication to use Keycloak Pubkey RSA256 Token authentication
1.0.1 - 2016-06-08
-
Renaming APIs and code on new terminology.
-
BEL specification version can be set in configuration file which controls the BEL version used as input/output. Affected APIs:
- /api/datasets
- /api/expressions
- /api/nanopubs
-
Support storage of BEL 2.0 nanopubs.
-
Added /api/expressions/validation API that returns syntax and signature validations for a BEL expression.
1.0.0 - TBD
- Support JWT authentication via token query parameter (PR #108).
0.6.2 - 2016-03-23
- Missing authorization header reported when header is malformed (Issue #105).
0.6.1 - 2016-03-16
- Bumped gems specification date. Requires new version because 0.6.0 was yanked from RubyGems.
0.6.0 - 2016-03-16
- Retrieve nanopub in a format supported by BEL translator plugins (Issue 44).
- Retrieve dataset nanopub in a format supported by BEL translator plugins (Issue 99).
- Dataset nanopub collection is missing annotation/namespace URIs (Issue 95).
- Facets are not created for nanopub uploaded through a dataset.
- MongoDB version 3.2.0 is now required due to use of
$slice
operator in Aggregation queries.
Datasets are stored with a URI computed from the scheme and host that is serving the OpenBEL API. For example if OpenBEL API is served from http://web.site.com
then dataset URIs will be of the form http://web.site.com/api/datasets/{UUID}
. If you change the scheme and host these URIs will be inconsistent and you will not be able to retrieve your datasets. You will have to re-import your documents.
- See Issue #102.
0.5.1 - 2015-12-18
- Authentication error for MongoDB user when faceting on
GET /api/nanopub
(Issue #93).
- MongoDB version 3.2.0 is now required due to use of
$slice
operator in Aggregation queries ([Issue ?][]).
0.5.0 - 2015-12-17
- Report API version from executables (
openbel-api
,openbel-config
) and REST API (GET /api/version
) (Issue #91). - Support for MongoDB user authentication (Issue #92).
- Namespace value autocompletion will not return identifier-based namespace (e.g. Entrez Gene) suggestions unless the namespace prefix is used. For example "p(AKT" will not suggest "EGID:207" although "p(EG:AKT" will.
- Namespace value autocompletion will return the namespace prefix if the BEL term requires it. For example "p(AKT" will now suggest "HGNC:AKT1".
- Namespace value autocompletion now queries against the Resource RDF to lookup namespaces by prefix. Previously this resolves namespaces from hardcoded values in bel.rb.
- Nanopub Store
- Storage of nanopub including creation, retrieval, modification, and deletion actions.
- Flexible filtering of stored, nanopub based on user's custom data requirements.
- Upload a document (e.g. BEL script, XBEL, or Nanopub JSON), to the Nanopub Store, as a dataset. These can later be retrieved or deleted from the Nanopub Store.
- Flexible filtering of nanopub contained within a dataset.
- Download a document (e.g. BEL script, XBEL, or Nanopub JSON) from a dataset.
- BEL Expressions
- Autocomplete a BEL term expression.
- Retrieve the structural components of a BEL expression.
- Annotations and Namespaces
- Retrieve annotation (e.g. Disease Ontology) and namespace (e.g. GO) data.
- Retrieve equivalent namespace values from the individual.
- Retrieve orthologous namespace values from the individual.