biointerchange 1.0.6 → 1.0.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: ff53013843083d635a15a381413355e0beef65bb
4
- data.tar.gz: 134d9f46b28c3e6d249f2be3260d7297f65ff6ab
3
+ metadata.gz: 01fc18ed7598a19760d3aa84ce74b1c6619023b9
4
+ data.tar.gz: 17d6501371c161b6069ad67994f218c14ef0777d
5
5
  SHA512:
6
- metadata.gz: b44d56b1e5e14671c2dcb7580d20167557fdf0a66ca68a1f3ab994fd2cde69f80e24fd99828f8dfc1825e1155d609232a71cd20d5ad8896c29451b433dfabf91
7
- data.tar.gz: ecec5b7c9c55a4050af658c3e95d1401a8b848f28bb283c8ad05970428fee1f1f8b756e8e8e14cdc139760acfd798dd980c4265219c4aa2e854f2af656ea406f
6
+ metadata.gz: 32a73d60c849c0a7720c0d15b36769ec7ccdc2f672348ec5b57106cee7575841b9def8ed0a738f4c67678d90092eed009459af9a376c04a8e932bcfcf94e1999
7
+ data.tar.gz: 00c591e5792cc7c2b3a907f5238549e386931c5be3002275649c55210009c80b6ddbc1566aab5b3f523769848b88a4234a2b9e288c57f8dd8f8df1be0e650343
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.0.6
1
+ 1.0.7
@@ -124,6 +124,12 @@ protected
124
124
  # ...TODO
125
125
  # Everything else:
126
126
  else
127
+ pragma.each_pair { |key, value|
128
+ custom_uri = RDF::URI.new("#{set_uri}/custom-pragma/#{key}")
129
+ create_triple(set_uri, @base.has_attribute, custom_uri)
130
+ create_triple(custom_uri, RDF.type, @base.InformationContentEntity)
131
+ create_triple(custom_uri, @base.has_value, value)
132
+ }
127
133
  end
128
134
  elsif pragma.kind_of?(Array) then
129
135
  # VCF section:
@@ -139,7 +139,7 @@ protected
139
139
  # The type might be a SO/SOFA term or SO/SOFA accession:
140
140
  begin
141
141
  if type.match(/^SO:\d{7}$/) then
142
- type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{feature.type}")
142
+ type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{type}")
143
143
  else
144
144
  type = BioInterchange::SO.send(BioInterchange.make_safe_label(type))
145
145
  end
@@ -188,7 +188,12 @@ protected
188
188
  def add_pragma(feature_set, line)
189
189
  line.chomp!
190
190
  name, value = line[2..-1].split(/\s/, 2)
191
- value.strip!
191
+
192
+ if value then
193
+ value.strip!
194
+ else
195
+ value = true
196
+ end
192
197
 
193
198
  # Interpret pragmas depending on their definition (sorted alphabetically):
194
199
  if name == 'feature-ontology' then
@@ -36,11 +36,7 @@ protected
36
36
  line.chomp!
37
37
  name, value = line[2..-1].split(/\s/, 2)
38
38
 
39
- unless value then
40
- raise BioInterchange::Exceptions::InputFormatError, "Line #{@linenumber}. Pragma statement is ill-formatted. Expected name/value separation by space, but reading \"#{line}\"."
41
- end
42
-
43
- value.strip!
39
+ value.strip! if value
44
40
 
45
41
  # Interpret pragmas, and if not known, delegate to GFF3Reader (in alphabetical order):
46
42
  if name == 'attribute-method' or name == 'data-source' or name == 'score-method' or name == 'source-method' or name == 'technology-platform' then
@@ -52,6 +52,8 @@ class Writer
52
52
  object_representation = object.to_s
53
53
  elsif object.kind_of?(Float) then
54
54
  object_representation = object.to_s
55
+ elsif object.instance_of?(TrueClass) or object.instance_of?(FalseClass) then
56
+ object_representation = object.to_s
55
57
  else
56
58
  if datatype then
57
59
  object_representation = "\"#{object.to_s}\"^^<#{datatype.to_s}>"
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: biointerchange
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.6
4
+ version: 1.0.7
5
5
  platform: ruby
6
6
  authors:
7
7
  - Joachim Baran
@@ -12,7 +12,7 @@ authors:
12
12
  autorequire:
13
13
  bindir: bin
14
14
  cert_chain: []
15
- date: 2014-12-15 00:00:00.000000000 Z
15
+ date: 2014-12-17 00:00:00.000000000 Z
16
16
  dependencies:
17
17
  - !ruby/object:Gem::Dependency
18
18
  name: rdf