bel 0.4.0.beta.13 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 36b6ae8c36eb357b5b08329a103e64e7740cb3ec
-  data.tar.gz: 26a343a329481d9d835362b1dd36805c59fdfc27
+  metadata.gz: c3c3b7bafdeffced99541f8cbefc206ad65b70f9
+  data.tar.gz: 2dc63bb3d6b163500ae5e06f2acbc5db546ca54b
 SHA512:
-  metadata.gz: 36079f41ab4111ba30d4d5fb37c6eec960287d9de59a2a4f9b6d54b32563cab2e8ee25fbddf795d2f33a5ebb986fa377dc8d16ef083d886d01b70b4392df3b4b
-  data.tar.gz: 8c4968f2338b35803d6359d0b9d6cf2ea576e48a2acad3a1bccdb25c45245d6f4d1d65c3398a21d0dd055a3787e041511c8e40fb43e0b6dbb2226c6038f13f4b
+  metadata.gz: 75ce820f1e0ea4085f6c022f7540e9f98eb04e2b4a8ca74c4c8b5a2494119e968e12b32e6516e4c5c3120980549221ee98467064ced29354d23a5a73951bf287
+  data.tar.gz: f45f37895b128b2df0c43748268d34e477c40e1b0fcdc9eb7814b312fd6c2dd12ab19fa3b8bd19d7d60ad56ffe5773e7f966d489a07c99f29bd3c2a85f9a1453

data/CHANGELOG.md

@@ -3,6 +3,26 @@ All notable changes to bel.rb will be documented in this file. The curated log b
 
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.4.0][0.4.0] - 2015-12-14
+### Fixed
+- Improved conversion of evidence to JSON Evidence format.
+- Fixed inclusion of BEL dsl (domain-specific language) extensions into all objects. The dsl methods can now be added to the BEL::Language module with BEL::Language.include_bel_dsl.
+
+### Changed
+- [Development] Removed bundler in favor or rubygems for dependency management ([Issue #82][82]).
+- Implement new plugin mechanism ([Issue #86][86]).
+- Implement translator plugins using new plugin mechanism. These were previously called Format Extensions ([Issue #86][86]).
+
+### Added
+- Added JSON read/write abstraction to support JSON streaming capabilities if the adapter supports it (see BEL::JSON).
+- Implement a translate API which allows reading evidence and translating to other formats (see BEL#evidence, BEL#translate).
+- BEL translator "write" can now yield to block or return an enumerator over translated evidence. This allows the user to control how the output is written to IO.
+- Added a new "plugins" subcommand to the bel executable that lists the plugins available to bel.rb. Run with "bel plugins --list".
+- Added RDF Repository plugin type. This allows RDF datasources to be integrated into bel.rb. The RDF Repository abstraction is provided by [RDF.rb][RDF.rb]. The initial use is with the Namespace and Annotation APIs. Plugins are provided for Apache Jena (TDB) and MongoDB RDF datasources.
+- Added Namespace and Annotation APIs to provide access to biological identifiers within an RDF Repository.
+- Added Resource Search API plugin type. This provides an API to full-text search over Namespaces and Annotations include symbols, identifiers, titles, and synonyms. A plugin named "bel.rb-search-sqlite" was created built on SQLite's full-text search.
+- Added option to RDF translator plugin to write out evidence as a VoID dataset ([Issue #66][66]).
+
 ## [0.3.3][0.3.3] - 2015-08-07
 ### Fixed
 - ResourceIndex integration test causes intermittent timeouts ([Issue #61][61]).
@@ -25,6 +45,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 - Development gem dependencies (i.e. byebug, pry, pry-byebug) for debugging.
 
+[0.4.0]:    https://github.com/OpenBEL/bel.rb/compare/0.3.3...0.4.0
 [0.3.2]:    https://github.com/OpenBEL/bel.rb/compare/0.3.1...0.3.2
 [0.3.3]:    https://github.com/OpenBEL/bel.rb/compare/0.3.2...0.3.3
 [13]:       https://github.com/OpenBEL/bel.rb/issues/13
@@ -35,5 +56,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 [59]:       https://github.com/OpenBEL/bel.rb/issues/59
 [61]:       https://github.com/OpenBEL/bel.rb/issues/61
 [64]:       https://github.com/OpenBEL/bel.rb/issues/64
+[66]:       https://github.com/OpenBEL/bel.rb/issues/66
 [68]:       https://github.com/OpenBEL/bel.rb/issues/68
+[82]:       https://github.com/OpenBEL/bel.rb/issues/82
+[86]:       https://github.com/OpenBEL/bel.rb/pull/86
 [20150611]: http://resource.belframework.org/belframework/20150611/
+[RDF.rb]:   https://github.com/ruby-rdf/rdf

data/README.md

@@ -75,7 +75,7 @@ the root of the bel.rb tree:
 ## branches
 
 - master branch
-  - Contains stable code. Releases are created from this branch using a tag (e.g. 0.3.3).
+  - Contains stable code. Releases are created from this branch using a tag (e.g. 0.4.0).
   - [![Travis CI Build](https://travis-ci.org/OpenBEL/bel.rb.svg?branch=master)](https://travis-ci.org/OpenBEL/bel.rb)
 
 - next branch
@@ -107,9 +107,10 @@ the root of the bel.rb tree:
       summarize
       translate
       upgrade
+      plugins
 
 
-    bel 0.3.3
+    bel 0.4.0
     Copyright (C) 2015 OpenBEL
     Apache License, Version 2.0, January 2004
     http://www.apache.org/licenses/
@@ -297,6 +298,12 @@ the root of the bel.rb tree:
 ```ruby
 
     require 'bel'
+
+    # opt-in to DSL methods
+    BEL::Language.include_bel_dsl
+
+    # include DSL methods in scoped module
+    include BEL::Language
     
     # create BEL statements
     p(HGNC['SKIL']).directlyDecreases tscript(p(HGNC['SMAD3']))

data/ext/mri/libbel.h

@@ -0,0 +1,15 @@
+#ifndef _LIBBEL_H
+#define _LIBBEL_H
+
+/*
+ * Value size: The maximum number of characters to hold in an
+ * accumulated value.
+ */
+#define BEL_VALUE_CHAR_LEN 512
+
+/*
+ * Stack size of the ARG, TERM, and STATEMENT stack.
+ */
+#define STACK_SIZE 32
+
+#endif /* not defined _LIBBEL_H */

data/lib/bel/translator/plugins/rdf/reader.rb

@@ -103,8 +103,8 @@ module BEL::Translator::Plugins
 
       def each
         if block_given?
-          graph = RUBYRDF::Graph.new
-          RUBYRDF::Reader.for(@format).new(@data) do |reader|
+          graph = RDF::Graph.new
+          RDF::Reader.for(@format).new(@data) do |reader|
             reader.each_statement do |statement|
               graph << statement
             end
@@ -129,13 +129,13 @@ module BEL::Translator::Plugins
 
       def each
         if block_given?
-          graph             = RUBYRDF::Graph.new
+          graph             = RDF::Graph.new
           evidence_resource = nil
-          RUBYRDF::Reader.for(@format).new(@data) do |reader|
+          RDF::Reader.for(@format).new(@data) do |reader|
             reader.each_statement do |statement|
               case
               when statement.object == BELV.Evidence &&
-                   statement.predicate == RUBYRDF.type
+                   statement.predicate == RDF.type
                 evidence_resource = statement.subject
               when evidence_resource &&
                    statement.predicate != BELV.hasEvidence &&

data/lib/bel/translator/plugins/rdf/writer.rb

@@ -39,7 +39,10 @@ module BEL::Translator::Plugins
         statements.each do |statement|
           @writer.write_statement(statement)
         end
-        @writer.write_statement(RDF::Statement.new(@void_dataset_uri, RDF::DC.hasPart, evidence_uri))
+
+        if @void_dataset_uri
+          @writer.write_statement(RDF::Statement.new(@void_dataset_uri, RDF::DC.hasPart, evidence_uri))
+        end
       end
 
       def done

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0.beta.13'
+  VERSION = '0.4.0'
 end

metadata

@@ -1,34 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta.13
+  version: 0.4.0
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-13 00:00:00.000000000 Z
+date: 2015-12-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
+  name: ffi
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-  name: ffi
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-description: " The BEL gem allows the reading, writing, and processing of BEL (Biological\
-  \ Expression Language) with a natural DSL. "
+description: " The BEL gem allows the reading, writing, and processing of BEL (Biological
+  Expression Language) with a natural DSL. "
 email:
 - abargnesi@selventa.com
 - ncatlett@selventa.com
@@ -73,9 +73,9 @@ files:
 - ext/mri/extconf.rb
 - ext/mri/libbel.c
 - ext/mri/libbel.def
+- ext/mri/libbel.h
 - lib/bel.rb
 - lib/bel/completion.rb
-- lib/bel/completion/value_match_rule.rb
 - lib/bel/completion_rule.rb
 - lib/bel/evidence_model.rb
 - lib/bel/evidence_model/bel_parameter.rb
@@ -167,7 +167,7 @@ homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options:
 - "--title"
 - BEL Ruby Documentation
@@ -197,13 +197,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: 2.0.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
-rubyforge_project:
-rubygems_version: 2.4.8
-signing_key:
+rubyforge_project: 
+rubygems_version: 2.4.5.1
+signing_key: 
 specification_version: 4
 summary: Process BEL with ruby.
 test_files: []
+has_rdoc: 

data/lib/bel/completion/value_match_rule.rb

@@ -1,10 +0,0 @@
-module BEL
-  module Completion
-
-    class ValueMatch
-
-      def call(ast)
-      end
-    end
-  end
-end