oba-client 1.0.1 → 1.0.2
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- data/Manifest.txt +1 -2
- data/README.md +54 -0
- data/Rakefile +5 -2
- data/lib/oba_client.rb +9 -7
- data/test/test_oba_client.rb +2 -6
- metadata +11 -13
- data/README.txt +0 -57
- data/bin/oba_client +0 -3
data/Manifest.txt
CHANGED
data/README.md
ADDED
@@ -0,0 +1,54 @@
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# oba-client
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* http://rubyforge.org/projects/oba-client
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## DESCRIPTION:
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A client for accessing the NCBO's Open Biomedical Annotator service.
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## FEATURES:
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* Many
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## REQUIREMENTS:
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* None
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## INSTALL:
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sudo gem install oba-client
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gem install --user-install oba-client
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## USAGE:
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client = OBAClient.new
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result = client.execute("some text string") # As XML.
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client2 = OBAClient.new({:parse_xml => true})
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# Returns {:statistics => {information about the annotation},
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# :annotations => [Array of annotations of text],
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# :ontologies => [Array of ontologies used]}
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client2.execute("another text string, maybe longer this time.")
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## LICENSE:
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Copyright (c) 2010 Rob Tirrell
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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data/Rakefile
CHANGED
@@ -4,8 +4,11 @@ require "hoe"
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Hoe.plugin :yard
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Hoe.spec "oba-client" do
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developer
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self.yard_options = ["--default-return", "void"
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self.developer "Rob Tirrell", "rpt@stanford.edu"
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self.yard_options = ["--default-return", "void"]
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self.yard_markup = "markdown"
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self.remote_yard_dir = ""
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self.rubyforge_name = "oba-client"
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end
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data/lib/oba_client.rb
CHANGED
@@ -5,7 +5,7 @@ require "net/http"
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require "uri"
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class OBAClient
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VERSION = "1.0.
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VERSION = "1.0.2"
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# A high HTTP read timeout, as the service sometimes takes awhile to respond.
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DEFAULT_TIMEOUT = 30
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@@ -31,10 +31,12 @@ class OBAClient
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:email
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]
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#
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#
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#
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#
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# Instantiate the class with a set of reused options. Options used by the
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# method are:
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#
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# * [String] uri: the URI of the annotator service (default: {DEFAULT_URI}).
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# * [Fixnum] timeout: the length of the read timeout (default: {DEFAULT_TIMEOUT}).
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# * [Boolean] parse_xml: whether to parse the received text (default: false).
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# @param [Hash<String, String>] options Parameters for the annotation.
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def initialize(options = {})
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@uri = URI.parse(options.delete(:uri) || DEFAULT_URI)
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doc.xpath("//ontologyUsedBean").each do |ontology|
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parsed = {}
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parsed[:localOntologyId] = ontology.xpath("localOntologyId").text
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parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text
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parsed[:localOntologyId] = ontology.xpath("localOntologyId").text.to_i
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parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text.to_i
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parsed[:name] = ontology.xpath("name").text
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ontologies << parsed
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end
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data/test/test_oba_client.rb
CHANGED
@@ -2,9 +2,7 @@ require "test/unit"
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require "oba_client"
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TEST_TEXTS = [
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-
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"zebrafish echo delta tango TURN <?xml MY VOLUME UP cancer of the thorax.",
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"zebrafish DROP TABLE !!! TURN MY VOLUME UP cancer of the thorax.",
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"Mexico,, Disease Thing \o\r\m\n\t\v\l\rzebrafish !!! cancer of the thorax.",
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%Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
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aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
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aot tt t t t t t t tae \n!!@)$@(#)%@#!)@# asoeuaohsenutahoeusaheou
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@@ -53,9 +51,7 @@ class TestOBAClient < Test::Unit::TestCase
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:parse_xml => true
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)
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parsed = ann.execute(text)
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assert parsed[:
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assert parsed[:annotations].is_a?(Array)
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assert parsed[:ontologies].is_a?(Array)
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assert (parsed[:ontologies].all? {|o| o[:localOntologyId] == 42812})
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end
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end
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metadata
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--- !ruby/object:Gem::Specification
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name: oba-client
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version: !ruby/object:Gem::Version
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hash:
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hash: 19
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prerelease: false
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segments:
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- 1
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- 0
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-
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version: 1.0.
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- 2
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version: 1.0.2
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platform: ruby
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authors:
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- Rob Tirrell
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version: 2.6.1
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type: :development
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version_requirements: *id003
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description:
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description: A client for accessing the NCBO's Open Biomedical Annotator service.
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email:
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- rpt@stanford.edu
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executables:
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-
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executables: []
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extensions: []
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extra_rdoc_files:
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- History.txt
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- Manifest.txt
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- README.txt
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files:
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- .autotest
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- History.txt
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- Manifest.txt
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- README.
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- README.md
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- Rakefile
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- bin/oba_client
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- lib/oba_client.rb
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- test/test_oba_client.rb
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has_rdoc: yard
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homepage: http://rubyforge.org/oba-client
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homepage: http://rubyforge.org/projects/oba-client
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licenses: []
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post_install_message:
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rdoc_options:
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- --default-return
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- void
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- --readme
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- README.txt
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- --title
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- ObaClient Documentation
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- --markup
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- markdown
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- --quiet
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require_paths:
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- lib
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rubygems_version: 1.3.7
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signing_key:
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specification_version: 3
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summary:
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summary: A client for accessing the NCBO's Open Biomedical Annotator service.
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test_files:
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- test/test_oba_client.rb
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data/README.txt
DELETED
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= oba_client
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* http://rubyforge.org/oba-client
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== DESCRIPTION:
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FIX (describe your package)
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== FEATURES/PROBLEMS:
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* FIX (list of features or problems)
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== SYNOPSIS:
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FIX (code sample of usage)
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== REQUIREMENTS:
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* None
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== INSTALL:
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* FIX (sudo gem install, anything else)
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== DEVELOPERS:
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After checking out the source, run:
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$ rake newb
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This task will install any missing dependencies, run the tests/specs,
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and generate the RDoc.
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== LICENSE:
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(The MIT License)
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Copyright (c) 2010 FIX
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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'Software'), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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-
distribute, sublicense, and/or sell copies of the Software, and to
|
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|
-
permit persons to whom the Software is furnished to do so, subject to
|
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|
-
the following conditions:
|
47
|
-
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The above copyright notice and this permission notice shall be
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-
included in all copies or substantial portions of the Software.
|
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-
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THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
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-
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/bin/oba_client
DELETED