bel 0.4.0.beta.11 → 0.4.0.beta.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 548d6b84e170ccb7e8e575cea4008c7167ce0d33
-  data.tar.gz: 3fb0d2f6b1097b95805a6f0012da005ac5b7fc60
+  metadata.gz: 1de2e3597f5e9e16484beb22668582c728a31296
+  data.tar.gz: f43c19636c538cf6efc1d69420e1d76183e0608c
 SHA512:
-  metadata.gz: 19a1cd0adad981782608a06500ce8884f44c915fa5413b2940a88feb532dd183bd1a43a26a0604ff9022258a710160c66b6400524fa5c859f8774af0701389ce
-  data.tar.gz: 1347303f1c419ae1942cfda04efc71f9eca778de6edb931e57eac8de9f42a66ab1298151b12cf86a28ba9e96a0c8c2219ee746e00392984b7d4a1c88e7a0886a
+  metadata.gz: 75d4efe4137aba17e5ab685282fa998b9e6013a3e7e67ba253651d51b0eb97a81d5ff82a7ef7fa5cd926a3cfd87787fdd0ec8c54d3a67b87789583e92798cb1f
+  data.tar.gz: 3d76283d55261eb0460b1828ba894fafeb344d48d8231d71252b1bcc5502b790e9415a125e00b8ee9b4fe8cfaf3cceb3a92a6aa57e0b055fa42a8af7f4e4e071

data/lib/bel/evidence_model/citation.rb

@@ -52,6 +52,9 @@ module BEL
         if args.length == 1
           enumerable = args.first
           if enumerable.respond_to? :each_pair
+            enumerable.keys.each do |key|
+              enumerable[key.to_s.to_sym] = enumerable.delete(key)
+            end
             (MEMBER_ORDER & enumerable.keys).each do |member|
               self.send(:"#{member}=", enumerable[member])
             end

data/lib/bel/evidence_model/experiment_context.rb

@@ -10,7 +10,14 @@ module BEL
       include Enumerable
 
       def initialize(values = [])
-        @values = values
+        @values = values.map { |item|
+          name  = item[:name]  || item['name']
+          value = item[:value] || item['value']
+          {
+            :name  => name.to_sym,
+            :value => value
+          }
+        }
       end
 
       def_delegators :@values, :<<,    :[],    :"[]=",

data/lib/bel/evidence_model/metadata.rb

@@ -15,7 +15,9 @@ module BEL
         if values.is_a? Array
           @values = Hash[
             values.map { |item|
-              [item[:name].to_sym, item[:value]]
+              name  = item[:name]  || item['name']
+              value = item[:value] || item['value']
+              [name.to_sym, value]
             }
           ]
         else

data/lib/bel/translator/plugins/bel_script/bel_yielder.rb

@@ -82,7 +82,6 @@ module BEL::Translator::Plugins
       def namespaces(namespaces)
         return "" unless namespaces
 
-        binding.pry
         namespaces.reduce("") { |bel, namespace|
           keyword = namespace[:keyword]
           uri     = namespace[:uri]

data/lib/bel/translator/plugins/bel_script/translator.rb

@@ -14,10 +14,21 @@ module BEL::Translator::Plugins
       end
 
       def write(objects, writer = StringIO.new, options = {})
-        BelYielder.new(objects).each { |bel_part|
-          writer << "#{bel_part}"
-          writer.flush
-        }
+        if block_given?
+          BelYielder.new(objects).each { |bel_part|
+            yield bel_part
+          }
+        else
+          if writer
+            BelYielder.new(objects).each { |bel_part|
+              writer << "#{bel_part}"
+              writer.flush
+            }
+            writer
+          else
+            BelYielder.new(objects)
+          end
+        end
       end
     end
   end

data/lib/bel/translator/plugins/json_evidence/translator.rb

@@ -18,26 +18,42 @@ module BEL::Translator::Plugins
       end
 
       def write(objects, writer = StringIO.new, options = {})
-        write_array_start(writer)
-        begin
-          evidence_enum = objects.each
+        json_strings = Enumerator.new { |yielder|
+          yielder << '['
+          begin
+            evidence_enum = objects.each
 
-          # write first evidence object
-          evidence = evidence_enum.next
-          ::BEL::JSON.write(wrap(evidence), writer)
-
-          # each successive evidence starts with a comma
-          while true
+            # write first evidence object
             evidence = evidence_enum.next
-            writer  << ","
-            ::BEL::JSON.write(wrap(evidence), writer)
+            yielder << ::BEL::JSON.write(wrap(evidence), nil)
+
+            # each successive evidence starts with a comma
+            while true
+              evidence = evidence_enum.next
+              yielder << ','
+              yielder << ::BEL::JSON.write(wrap(evidence), nil)
+            end
+          rescue StopIteration
+            # end of evidence hashes
           end
-        rescue StopIteration
-          # end of evidence hashes
-        end
-        write_array_end(writer)
+          yielder << ']'
+        }
 
-        writer
+        if block_given?
+          json_strings.each do |string|
+            yield string
+          end
+        else
+          if writer
+            json_strings.each do |string|
+              writer << string
+              writer.flush
+            end
+            writer
+          else
+            json_strings
+          end
+        end
       end
 
       private

data/lib/bel/translator/plugins/xbel/translator.rb

@@ -24,6 +24,7 @@ module BEL::Translator::Plugins
               writer << xml_data
               writer.flush
             }
+            writer
           else
             XBELYielder.new(objects)
           end

data/lib/bel/translator/plugins/xbel/xbel_yielder.rb

@@ -77,12 +77,21 @@ module BEL::Translator::Plugins
       end
 
       def self.statement(statement, el_statement)
+        if statement.is_a?(String)
+          statement = BEL::Script.parse(statement.to_s).find { |x|
+            x.is_a? BEL::Model::Statement
+          }
+          return el_statement if statement == nil
+        end
+
         if statement.relationship
           el_statement.add_attribute 'bel:relationship', statement.relationship
         end
 
-        el_subject = self.subject(statement.subject)
-        el_statement.add_element(el_subject)
+        if statement.subject
+          el_subject = self.subject(statement.subject)
+          el_statement.add_element(el_subject)
+        end
 
         if statement.object
           el_object = self.object(statement.object)

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0.beta.11'
+  VERSION = '0.4.0.beta.12'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta.11
+  version: 0.4.0.beta.12
 platform: ruby
 authors:
 - Anthony Bargnesi