biointerchange 1.0.6 → 1.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ff53013843083d635a15a381413355e0beef65bb
-  data.tar.gz: 134d9f46b28c3e6d249f2be3260d7297f65ff6ab
+  metadata.gz: 01fc18ed7598a19760d3aa84ce74b1c6619023b9
+  data.tar.gz: 17d6501371c161b6069ad67994f218c14ef0777d
 SHA512:
-  metadata.gz: b44d56b1e5e14671c2dcb7580d20167557fdf0a66ca68a1f3ab994fd2cde69f80e24fd99828f8dfc1825e1155d609232a71cd20d5ad8896c29451b433dfabf91
-  data.tar.gz: ecec5b7c9c55a4050af658c3e95d1401a8b848f28bb283c8ad05970428fee1f1f8b756e8e8e14cdc139760acfd798dd980c4265219c4aa2e854f2af656ea406f
+  metadata.gz: 32a73d60c849c0a7720c0d15b36769ec7ccdc2f672348ec5b57106cee7575841b9def8ed0a738f4c67678d90092eed009459af9a376c04a8e932bcfcf94e1999
+  data.tar.gz: 00c591e5792cc7c2b3a907f5238549e386931c5be3002275649c55210009c80b6ddbc1566aab5b3f523769848b88a4234a2b9e288c57f8dd8f8df1be0e650343

data/VERSION

@@ -1 +1 @@
-1.0.6
+1.0.7

data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb

@@ -124,6 +124,12 @@ protected
       # ...TODO
       # Everything else:
       else
+        pragma.each_pair { |key, value|
+          custom_uri = RDF::URI.new("#{set_uri}/custom-pragma/#{key}")
+          create_triple(set_uri, @base.has_attribute, custom_uri)
+          create_triple(custom_uri, RDF.type, @base.InformationContentEntity)
+          create_triple(custom_uri, @base.has_value, value)
+        }
       end
     elsif pragma.kind_of?(Array) then
       # VCF section:

data/lib/biointerchange/genomics/gff3_reader.rb

@@ -139,7 +139,7 @@ protected
     # The type might be a SO/SOFA term or SO/SOFA accession:
     begin
       if type.match(/^SO:\d{7}$/) then
-        type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{feature.type}")
+        type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{type}")
       else
         type = BioInterchange::SO.send(BioInterchange.make_safe_label(type))
       end
@@ -188,7 +188,12 @@ protected
   def add_pragma(feature_set, line)
     line.chomp!
     name, value = line[2..-1].split(/\s/, 2)
-    value.strip!
+
+    if value then
+      value.strip!
+    else
+      value = true
+    end
     
     # Interpret pragmas depending on their definition (sorted alphabetically):
     if name == 'feature-ontology' then

data/lib/biointerchange/genomics/gvf_reader.rb

@@ -36,11 +36,7 @@ protected
     line.chomp!
     name, value = line[2..-1].split(/\s/, 2)
 
-    unless value then
-      raise BioInterchange::Exceptions::InputFormatError, "Line #{@linenumber}. Pragma statement is ill-formatted. Expected name/value separation by space, but reading \"#{line}\"."
-    end
-
-    value.strip!
+    value.strip! if value
 
     # Interpret pragmas, and if not known, delegate to GFF3Reader (in alphabetical order):
     if name == 'attribute-method' or name == 'data-source' or name == 'score-method' or name == 'source-method' or name == 'technology-platform' then

data/lib/biointerchange/writer.rb

@@ -52,6 +52,8 @@ class Writer
       object_representation = object.to_s
     elsif object.kind_of?(Float) then
       object_representation = object.to_s
+    elsif object.instance_of?(TrueClass) or object.instance_of?(FalseClass) then
+      object_representation = object.to_s
     else
       if datatype then
         object_representation = "\"#{object.to_s}\"^^<#{datatype.to_s}>"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biointerchange
 version: !ruby/object:Gem::Version
-  version: 1.0.6
+  version: 1.0.7
 platform: ruby
 authors:
 - Joachim Baran
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-15 00:00:00.000000000 Z
+date: 2014-12-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf