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Change Log

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.

[1.2.0][1.2.0] - 2017-01-22

Changed

  • strict=yes query param on POST /api/nanopub will result in a 422 if the BEL statement or Annotations are bad

[1.1.0][1.1.0] - 2017-01-21

Added

  • Updated BEL Statement Completion - added semantic completion

Changed

  • 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

Added

  • Docker containers for development and production use of OpenBEL

Changed

  • Converted authentication to use Keycloak Pubkey RSA256 Token authentication

1.0.1 - 2016-06-08

Added

  • 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

Added

  • Support JWT authentication via token query parameter (PR #108).

0.6.2 - 2016-03-23

Fixed

  • Missing authorization header reported when header is malformed (Issue #105).

0.6.1 - 2016-03-16

Changed

  • Bumped gems specification date. Requires new version because 0.6.0 was yanked from RubyGems.

0.6.0 - 2016-03-16

Added

  • 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).

Fixed

  • Dataset nanopub collection is missing annotation/namespace URIs (Issue 95).
  • Facets are not created for nanopub uploaded through a dataset.

Changed

  • MongoDB version 3.2.0 is now required due to use of $slice operator in Aggregation queries.

Known Issue

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.

0.5.1 - 2015-12-18

Fixed

  • Authentication error for MongoDB user when faceting on GET /api/nanopub (Issue #93).

Changed

  • MongoDB version 3.2.0 is now required due to use of $slice operator in Aggregation queries ([Issue ?][]).

0.5.0 - 2015-12-17

Added

Changed

  • 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.

Fixed

  • 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.

0.4.0 - 2015-12-14

Added

  • 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.