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 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 01fc18ed7598a19760d3aa84ce74b1c6619023b9
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data.tar.gz: 17d6501371c161b6069ad67994f218c14ef0777d
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 32a73d60c849c0a7720c0d15b36769ec7ccdc2f672348ec5b57106cee7575841b9def8ed0a738f4c67678d90092eed009459af9a376c04a8e932bcfcf94e1999
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data.tar.gz: 00c591e5792cc7c2b3a907f5238549e386931c5be3002275649c55210009c80b6ddbc1566aab5b3f523769848b88a4234a2b9e288c57f8dd8f8df1be0e650343
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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1.0.
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1.0.7
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@@ -124,6 +124,12 @@ protected
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# ...TODO
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# Everything else:
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else
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pragma.each_pair { |key, value|
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custom_uri = RDF::URI.new("#{set_uri}/custom-pragma/#{key}")
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create_triple(set_uri, @base.has_attribute, custom_uri)
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create_triple(custom_uri, RDF.type, @base.InformationContentEntity)
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create_triple(custom_uri, @base.has_value, value)
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}
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end
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elsif pragma.kind_of?(Array) then
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# VCF section:
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@@ -139,7 +139,7 @@ protected
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# The type might be a SO/SOFA term or SO/SOFA accession:
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begin
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if type.match(/^SO:\d{7}$/) then
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-
type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{
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type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{type}")
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else
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type = BioInterchange::SO.send(BioInterchange.make_safe_label(type))
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end
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@@ -188,7 +188,12 @@ protected
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def add_pragma(feature_set, line)
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line.chomp!
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name, value = line[2..-1].split(/\s/, 2)
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-
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if value then
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value.strip!
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else
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value = true
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end
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# Interpret pragmas depending on their definition (sorted alphabetically):
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if name == 'feature-ontology' then
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@@ -36,11 +36,7 @@ protected
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line.chomp!
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name, value = line[2..-1].split(/\s/, 2)
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-
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raise BioInterchange::Exceptions::InputFormatError, "Line #{@linenumber}. Pragma statement is ill-formatted. Expected name/value separation by space, but reading \"#{line}\"."
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end
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-
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value.strip!
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value.strip! if value
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# Interpret pragmas, and if not known, delegate to GFF3Reader (in alphabetical order):
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if name == 'attribute-method' or name == 'data-source' or name == 'score-method' or name == 'source-method' or name == 'technology-platform' then
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@@ -52,6 +52,8 @@ class Writer
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object_representation = object.to_s
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elsif object.kind_of?(Float) then
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object_representation = object.to_s
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elsif object.instance_of?(TrueClass) or object.instance_of?(FalseClass) then
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object_representation = object.to_s
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else
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if datatype then
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object_representation = "\"#{object.to_s}\"^^<#{datatype.to_s}>"
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: biointerchange
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version: !ruby/object:Gem::Version
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version: 1.0.
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version: 1.0.7
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platform: ruby
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authors:
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- Joachim Baran
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@@ -12,7 +12,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-12-
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date: 2014-12-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rdf
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