ncbo_annotator 1.0.7 → 1.0.8
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- data/lib/ncbo_annotator.rb +14 -0
- metadata +4 -4
data/lib/ncbo_annotator.rb
CHANGED
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@@ -30,6 +30,9 @@ module NCBO
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30
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@options.merge!(args)
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31
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@ontologies = nil
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33
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+
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34
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+
# Check to make sure mappingTypes are capitalized
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35
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+
fix_params
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raise ArgumentError, ":apikey is required, you can obtain one at http://bioportal.bioontology.org/accounts/new" if @options[:apikey].nil?
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end
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@@ -42,6 +45,7 @@ module NCBO
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def annotate(text = nil, options = {})
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@options[:textToAnnotate] = text unless text.nil?
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@options.merge!(options) unless options.empty?
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+
fix_params
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raise ArgumentError, ":textToAnnotate must be included" if @options[:textToAnnotate].nil?
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@@ -81,6 +85,16 @@ module NCBO
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private
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+
def fix_params
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@options[:mappingTypes] = @options[:mappingTypes].split(",") unless @options[:mappingTypes].kind_of?(Array)
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@options[:ontologiesToExpand] = @options[:ontologiesToExpand].split(",") unless @options[:ontologiesToExpand].kind_of?(Array)
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@options[:ontologiesToKeepInResult] = @options[:ontologiesToKeepInResult].split(",") unless @options[:ontologiesToKeepInResult].kind_of?(Array)
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@options[:semanticTypes] = @options[:semanticTypes].split(",") unless @options[:semanticTypes].kind_of?(Array)
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@options[:stopWords] = @options[:stopWords].split(",") unless @options[:stopWords].kind_of?(Array)
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+
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@options[:mappingTypes].collect! {|e| e.capitalize}
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end
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+
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def annotate_post
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url = @options[:annotator_location] + "/annotator"
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options = @options.clone
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metadata
CHANGED
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@@ -1,13 +1,13 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: ncbo_annotator
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version: !ruby/object:Gem::Version
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4
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-
hash:
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4
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+
hash: 7
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prerelease:
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segments:
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7
7
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- 1
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8
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- 0
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9
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-
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-
version: 1.0.
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9
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+
- 8
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version: 1.0.8
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platform: ruby
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authors:
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- Paul R Alexander
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@@ -15,7 +15,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2011-
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date: 2011-12-01 00:00:00 -08:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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