bel 0.4.0.beta.5 → 0.4.0.beta.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6bb79ce88a768f48ee7ed3200ec80552c541165b
-  data.tar.gz: df0d4949c261213198cfdab4d3140dc4040782b7
+  metadata.gz: d0b4945512529e67124a858ba03f03b18c617ee5
+  data.tar.gz: a57e2e8142d0ed1ef080e4ff206aaf76e69243b4
 SHA512:
-  metadata.gz: e80a9b4954a24f8e16b816972f67a1ae854d8742d86b3ced5cbb18b481ad29d024377a947b9228bdcdedab20a17cebb22fe81a5541e2acbe3a1300c43f499db9
-  data.tar.gz: 247e7bfba0b685001a3ac4548fdf121eca9761fd5c4de05444c7231e559dc827129931d7b409be144321a936a4f62b063f84b044dda901d0f35bc0c61988f3a6
+  metadata.gz: 860f4fa04e20ae6614701eb4714e6cf525781e23cffe1da36307894d62fa26916b5b8d78795b1d90d973c8aa57cd80c792c943d3305e14e9c29b23f8fc2db29c
+  data.tar.gz: 7c68969a47cb4d4a21642c6cc3bfbe825373cf7dab2cf087d410972fb07e5c569a13b88b574e62ffb5d0c921ab6ea2783494bde813cd58c01b04aa4cbaf025d1

data/bin/bel_summarize.rb

@@ -38,7 +38,7 @@ CSV do |csv_out|
     report['fx_' + v[:long_form].to_s] = 0
   end
 
-  RELATIONSHIPS.each do |r|
+  RELATIONSHIPS.values.each do |r|
     report['rel_' + r.to_s] = 0
   end
 

data/lib/bel/json/adapter/multi_json.rb

@@ -13,8 +13,13 @@ module BEL::JSON
     def read(data, options = {})
       if block_given?
         options = { :symbolize_keys => true }.merge!(options)
-        MultiJson.load(data, options).each do |obj|
-          yield obj
+        parsed  = MultiJson.load(data, options)
+        if parsed.respond_to?(:each_pair)
+          yield parsed
+        else
+          parsed.each do |obj|
+            yield obj
+          end
         end
       else
         to_enum(:read, data, options)

data/lib/bel/json/adapter/ruby_json.rb

@@ -13,8 +13,13 @@ module BEL::JSON
     def read(data, options = {})
       if block_given?
         options = { :symbolize_names => true }.merge!(options)
-        JSON.load(data, nil, options).each do |obj|
-          yield obj
+        parsed  = JSON.load(data, nil, options)
+        if parsed.respond_to?(:each_pair)
+          yield parsed
+        else
+          parsed.each do |obj|
+            yield obj
+          end
         end
       else
         to_enum(:read, data, options)

data/lib/bel/language.rb

@@ -567,40 +567,49 @@ module BEL
       r: [:r, :a]
     }
 
-    RELATIONSHIPS = [
-      :actsIn,
-      :analogous,
-      :association,
-      :biomarkerFor,
-      :causesNoChange,
-      :decreases,
-      :directlyDecreases,
-      :directlyIncreases,
-      :hasComponent, :hasComponents,
-      :hasMember, :hasMembers,
-      :hasModification,
-      :hasProduct,
-      :hasVariant,
-      :includes,
-      :increases,
-      :isA,
-      :negativeCorrelation,
-      :orthologous,
-      :positiveCorrelation,
-      :prognosticBiomarkerFor,
-      :rateLimitingStepOf,
-      :reactantIn,
-      :subProcessOf,
-      :transcribedTo,
-      :translatedTo,
-      :translocates
-    ]
+    RELATIONSHIPS = {
+      :actsIn                 => :actsIn,
+      :analogous              => :analogous,
+      :'--'                   => :association,
+      :association            => :association,
+      :biomarkerFor           => :biomarkerFor,
+      :causesNoChange         => :causesNoChange,
+      :'-|'                   => :decreases,
+      :decreases              => :decreases,
+      :'=|'                   => :directlyDecreases,
+      :directlyDecreases      => :directlyDecreases,
+      :'=>'                   => :directlyIncreases,
+      :directlyIncreases      => :directlyIncreases,
+      :'->'                   => :increases,
+      :increases              => :increases,
+      :hasComponent           => :hasComponent,
+      :hasComponents          => :hasComponents,
+      :hasMember              => :hasMember,
+      :hasMembers             => :hasMembers,
+      :hasModification        => :hasModification,
+      :hasProduct             => :hasProduct,
+      :hasVariant             => :hasVariant,
+      :includes               => :includes,
+      :isA                    => :isA,
+      :negativeCorrelation    => :negativeCorrelation,
+      :orthologous            => :orthologous,
+      :positiveCorrelation    => :positiveCorrelation,
+      :prognosticBiomarkerFor => :prognosticBiomarkerFor,
+      :rateLimitingStepOf     => :rateLimitingStepOf,
+      :reactantIn             => :reactantIn,
+      :subProcessOf           => :subProcessOf,
+      :':>'                   => :transcribedTo,
+      :transcribedTo          => :transcribedTo,
+      :'>>'                   => :translatedTo,
+      :translatedTo           => :translatedTo,
+      :translocates           => :translocates,
+    }
 
     def self.include_bel_dsl
-      RELATIONSHIPS.each do |rel|
+      RELATIONSHIPS.each do |rel, long_form|
         BEL::Model::Term.send(:define_method, rel) do |another|
           s = BEL::Model::Statement.new self
-          s.relationship = rel
+          s.relationship = long_form
           s.object = another
           s
         end

data/lib/bel/script.rb

@@ -21048,7 +21048,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end
@@ -42200,7 +42200,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end
@@ -63352,7 +63352,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end
@@ -84504,7 +84504,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end
@@ -105656,7 +105656,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end
@@ -126880,7 +126880,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end
@@ -148071,7 +148071,7 @@ cmtbuffer << data[p].ord		end
 
       ns =
 			  if pfx
-				  @namespaces[pfx.to_sym] ||= NamespaceDefinition.new(pfx, nil, nil)
+				  @namespaces[pfx.to_sym] ||= BEL::Namespace::NamespaceDefinition.new(pfx, nil, nil)
 			  else
 				  nil
 			  end

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0.beta.5'
+  VERSION = '0.4.0.beta.7'
 end

metadata

@@ -1,34 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta.5
+  version: 0.4.0.beta.7
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-02 00:00:00.000000000 Z
+date: 2015-12-03 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
@@ -166,7 +166,7 @@ homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options:
 - "--title"
 - BEL Ruby Documentation
@@ -200,9 +200,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 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: