bel 0.4.1 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -3,6 +3,11 @@ 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/).
 
+## [0.4.2][0.4.2] - 2015-12-21
+### Fixed
+- [Regression] Failure to run BEL upgrade command; yields name error ([Issue #90][90]).
+- [Regression] Incorrect namespace concept URI when converting Term to RDF ([Issue #91][91]).
+
 ## [0.4.1][0.4.1] - 2015-12-17
 ### Added
 - Updated `find` API of `BEL::Resource::Namespaces` and `BEL::Resource::Namespace` to find by string representing a URI.
@@ -57,6 +62,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 - Development gem dependencies (i.e. byebug, pry, pry-byebug) for debugging.
 
+[0.4.2]:    https://github.com/OpenBEL/bel.rb/compare/0.4.1...0.4.2
 [0.4.1]:    https://github.com/OpenBEL/bel.rb/compare/0.4.0...0.4.1
 [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
@@ -73,5 +79,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 [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
+[90]:       https://github.com/OpenBEL/bel.rb/issues/90
+[91]:       https://github.com/OpenBEL/bel.rb/issues/91
 [20150611]: http://resource.belframework.org/belframework/20150611/
 [RDF.rb]:   https://github.com/ruby-rdf/rdf

data/bin/bel_upgrade.rb

@@ -106,7 +106,7 @@ class Main
     BEL::Script.parse(content) do |obj|
       # redefine namespace based on change log's `redefine` blocik
       # use 'namespaces' block, if available
-      if obj.is_a? NamespaceDefinition
+      if obj.is_a? BEL::Namespace::NamespaceDefinition
         if @change_log.has_key? 'redefine'
           redefine = @change_log['redefine']['namespaces']
           if not redefine
@@ -116,7 +116,7 @@ class Main
             entry = redefine[obj.prefix.to_s]
             new_keyword = entry['new_keyword'].to_sym
             new_url = entry['new_url']
-            obj = NamespaceDefinition.new(new_keyword, new_url)
+            obj = BEL::Namespace::NamespaceDefinition.new(new_keyword, new_url)
           end
         end
 
@@ -128,21 +128,21 @@ class Main
       end
 
       # update annotation definitions
-      if obj.is_a? AnnotationDefinition and obj.type.eql? :url
+      if obj.is_a? BEL::Language::AnnotationDefinition and obj.type.eql? :url
         if @redefine_annotations
           old_url = obj.value
           if @annotation_url_map.has_key? old_url.to_s
             kw = obj.prefix
             new_url = @annotation_url_map[old_url]['new_url']
             prefix = @annotation_url_map[old_url]['prefix']
-            obj = AnnotationDefinition.new(:url, kw, new_url)
+            obj = BEL::Language::AnnotationDefinition.new(:url, kw, new_url)
             @annotation_keyword_map[kw] = prefix # map bel doc annotation kw to set of changelog prefixes
           end
         end
       end
 
       # evidence always needs quoting; backwards-compatibility
-      if obj.is_a? Annotation
+      if obj.is_a? BEL::Language::Annotation
         if obj.name == 'Evidence'
           ev = obj.to_s
           ev.gsub!(EvidenceMatcher, 'SET Evidence = "\1"')
@@ -207,7 +207,7 @@ class Main
           if redefinition
             new_prefix = redefinition['new_keyword']
             new_url = redefinition['new_url']
-            obj.ns = NamespaceDefinition.new(new_prefix, new_url)
+            obj.ns = BEL::Namespace::NamespaceDefinition.new(new_prefix, new_url)
 
             # ...and replace value using new namespace prefix
             replacements = @change_log[new_prefix]

data/lib/bel/namespace.rb

@@ -42,11 +42,11 @@ module BEL
       ],
       GOBP: [
         LATEST_PREFIX + 'namespace/go-biological-process.belns',
-        'http://www.openbel.org/bel/namespace/go-biological-processes'
+        'http://www.openbel.org/bel/namespace/go-biological-process'
       ],
       GOBPID: [
         LATEST_PREFIX + 'namespace/go-biological-process-ids.belns',
-        'http://www.openbel.org/bel/namespace/go'
+        'http://www.openbel.org/bel/namespace/go-biological-process'
       ],
       GOCC: [
         LATEST_PREFIX + 'namespace/go-cellular-component.belns',
@@ -68,6 +68,14 @@ module BEL
         LATEST_PREFIX + 'namespace/mesh-cellular-structures-ids.belns',
         'http://www.openbel.org/bel/namespace/mesh-cellular-structures'
       ],
+      MECHC: [
+        LATEST_PREFIX + 'namespace/mesh-chemicals.belns',
+        'http://www.openbel.org/bel/namespace/mesh-chemicals'
+      ],
+      MECHCID: [
+        LATEST_PREFIX + 'namespace/mesh-chemicals-ids.belns',
+        'http://www.openbel.org/bel/namespace/mesh-chemicals'
+      ],
       MESHD: [
         LATEST_PREFIX + 'namespace/mesh-diseases.belns',
         'http://www.openbel.org/bel/namespace/mesh-diseases',
@@ -114,7 +122,7 @@ module BEL
       ],
       SPID: [
         LATEST_PREFIX + 'namespace/swissprot-ids.belns',
-        'http://www.openbel.org/bel/namespace/swissprot-ids'
+        'http://www.openbel.org/bel/namespace/swissprot'
       ]
     }
 

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

@@ -154,7 +154,7 @@ module BEL::Translator::Plugins
         @arguments.find_all{ |x|
           x.is_a? ::BEL::Model::Parameter and x.ns != nil
         }.each do |param|
-          concept_uri = param.ns.to_uri + param.value.to_s
+          concept_uri = "#{param.ns.to_uri}/#{param.value}"
           statements << ::RDF::Statement.new(uri, BEL::RDF::BELV.hasConcept, BEL::RDF::RDF::URI(URI.encode(concept_uri)), :graph_name => graph_name)
         end
 

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.1'
+  VERSION = '0.4.2'
 end

metadata

@@ -1,34 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.2
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-17 00:00:00.000000000 Z
+date: 2015-12-21 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
@@ -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
@@ -201,10 +201,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       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:
+has_rdoc: