search_biomodel 1.0.0 → 1.0.1

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/core_ext/string_spec.rb

@@ -1,17 +0,0 @@
-require "spec_helper"
-
-describe String do
-
-  describe "#lower_camelcase" do
-    it "converts a snakecase String to lowerCamelCase" do
-      "lower_camel_case".lower_camelcase.should == "lowerCamelCase"
-    end
-  end
-
-  describe "#camelcase" do
-    it "converts a snakecase String to CamelCase" do
-      "camel_case".camelcase.should == "CamelCase"
-    end
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/hash_spec.rb

@@ -1,160 +0,0 @@
-require "spec_helper"
-
-describe Gyoku::Hash do
-
-  describe ".to_xml" do
-    describe "returns SOAP request compatible XML" do
-      it "for a simple Hash" do
-        to_xml(:some => "user").should == "<some>user</some>"
-      end
-
-      it "for a nested Hash" do
-        to_xml(:some => { :new => "user" }).should == "<some><new>user</new></some>"
-      end
-
-      it "for a Hash with multiple keys" do
-        to_xml(:all => "users", :before => "whatever").should include(
-          "<all>users</all>",
-          "<before>whatever</before>"
-        )
-      end
-
-      it "for a Hash containing an Array" do
-        to_xml(:some => ["user", "gorilla"]).should == "<some>user</some><some>gorilla</some>"
-      end
-
-      it "for a Hash containing an Array of Hashes" do
-        to_xml(:some => [{ :new => "user" }, { :old => "gorilla" }]).
-          should == "<some><new>user</new></some><some><old>gorilla</old></some>"
-      end
-    end
-
-    it "converts Hash key Symbols to lowerCamelCase" do
-      to_xml(:find_or_create => "user").should == "<findOrCreate>user</findOrCreate>"
-    end
-
-    it "does not convert Hash key Strings" do
-      to_xml("find_or_create" => "user").should == "<find_or_create>user</find_or_create>"
-    end
-
-    it "converts DateTime objects to xs:dateTime compliant Strings" do
-      to_xml(:before => DateTime.new(2012, 03, 22, 16, 22, 33)).
-        should == "<before>2012-03-22T16:22:33+00:00</before>"
-    end
-
-    it "converts Objects responding to to_datetime to xs:dateTime compliant Strings" do
-      singleton = Object.new
-      def singleton.to_datetime
-        DateTime.new(2012, 03, 22, 16, 22, 33)
-      end
-
-      to_xml(:before => singleton).should == "<before>2012-03-22T16:22:33+00:00</before>"
-    end
-
-    it "calls to_s on Strings even if they respond to to_datetime" do
-      object = "gorilla"
-      object.expects(:to_datetime).never
-
-      to_xml(:name => object).should == "<name>gorilla</name>"
-    end
-
-    it "properly serializes nil values" do
-      to_xml(:some => nil).should == '<some xsi:nil="true"/>'
-    end
-
-    it "creates self-closing tags for Hash keys ending with a forward slash" do
-      to_xml("self-closing/" => nil).should == '<self-closing/>'
-    end
-
-    it "calls to_s on any other Object" do
-      [666, true, false].each do |object|
-        to_xml(:some => object).should == "<some>#{object}</some>"
-      end
-    end
-
-    it "defaults to escape special characters" do
-      result = to_xml(:some => { :nested => "<tag />" }, :tag => "<tag />")
-      result.should include("<tag>&lt;tag /&gt;</tag>")
-      result.should include("<some><nested>&lt;tag /&gt;</nested></some>")
-    end
-
-    it "does not escape special characters for keys marked with an exclamation mark" do
-      result = to_xml(:some => { :nested! => "<tag />" }, :tag! => "<tag />")
-      result.should include("<tag><tag /></tag>")
-      result.should include("<some><nested><tag /></nested></some>")
-    end
-
-    it "preserves the order of Hash keys and values specified through :order!" do
-      hash = { :find_user => { :name => "Lucy", :id => 666, :order! => [:id, :name] } }
-      result = "<findUser><id>666</id><name>Lucy</name></findUser>"
-      to_xml(hash).should == result
-
-      hash = { :find_user => { :mname => "in the", :lname => "Sky", :fname => "Lucy", :order! => [:fname, :mname, :lname] } }
-      result = "<findUser><fname>Lucy</fname><mname>in the</mname><lname>Sky</lname></findUser>"
-      to_xml(hash).should == result
-    end
-
-    it "raises if the :order! Array is missing Hash keys" do
-      hash = { :name => "Lucy", :id => 666, :order! => [:name] }
-      lambda { to_xml(hash) }.should raise_error(ArgumentError, "Missing elements in :order! [:id]")
-    end
-
-    it "raises if the :order! Array contains missing Hash keys" do
-      hash = { :by_name => { :first_name => "Lucy", :last_name => "Sky", :order! => [:first_name, :middle_name, :last_name] } }
-      lambda { to_xml(hash) }.should raise_error(ArgumentError, "Spurious elements in :order! [:middle_name]")
-    end
-
-    it "adds attributes to Hash keys specified through :attributes!" do
-      hash = { :find_user => { :person => "Lucy", :attributes! => { :person => { :id => 666 } } } }
-      result = '<findUser><person id="666">Lucy</person></findUser>'
-      to_xml(hash).should == result
-
-      hash = { :find_user => { :person => "Lucy", :attributes! => { :person => { :id => 666, :city => "Hamburg" } } } }
-      to_xml(hash).should include('id="666"', 'city="Hamburg"')
-    end
-
-    it "adds attributes to duplicate Hash keys specified through :attributes!" do
-      hash = { :find_user => { :person => ["Lucy", "Anna"], :attributes! => { :person => { :id => [1, 3] } } } }
-      result = '<findUser><person id="1">Lucy</person><person id="3">Anna</person></findUser>'
-      to_xml(hash).should == result
-
-      hash = { :find_user => { :person => ["Lucy", "Anna"], :attributes! => { :person => { :active => "true" } } } }
-      result = '<findUser><person active="true">Lucy</person><person active="true">Anna</person></findUser>'
-      to_xml(hash).should == result
-    end
-
-    it "adds attributes to self-closing tags" do
-      hash = {
-        "category/" => "",
-        :attributes! => { "category/" => { :id => 1 }  }
-      }
-
-      to_xml(hash).should == '<category id="1"/>'
-    end
-
-    context "with :element_form_default set to :qualified and a :namespace" do
-      it "adds the given :namespace to every element" do
-        hash = { :first => { "first_name" => "Lucy" }, ":second" => { :":first_name" => "Anna" }, "v2:third" => { "v2:firstName" => "Danie" } }
-        result = to_xml hash, :element_form_default => :qualified, :namespace => :v1
-
-        result.should include(
-          "<v1:first><v1:first_name>Lucy</v1:first_name></v1:first>",
-          "<second><firstName>Anna</firstName></second>",
-          "<v2:third><v2:firstName>Danie</v2:firstName></v2:third>"
-        )
-      end
-
-      it "adds given :namespace to every element in an array" do
-        hash = { :array => [ :first  => "Lucy", :second => "Anna" ]}
-        result = to_xml hash, :element_form_default => :qualified, :namespace => :v1
-
-        result.should include("<v1:array>", "<v1:first>Lucy</v1:first>", "<v1:second>Anna</v1:second>")
-      end
-    end
-  end
-
-  def to_xml(hash, options = {})
-    Gyoku::Hash.to_xml hash, options
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/xml_key_spec.rb

@@ -1,77 +0,0 @@
-require "spec_helper"
-
-describe Gyoku::XMLKey do
-
-  describe ".create" do
-    it "removes exclamation marks from the end of a String" do
-      create("value!").should == "value"
-    end
-
-    it "removes forward slashes from the end of a String" do
-      create("self-closing/").should == "self-closing"
-    end
-
-    it "does not convert snake_case Strings" do
-      create("lower_camel_case").should == "lower_camel_case"
-    end
-
-    it "converts snake_case Symbols to lowerCamelCase Strings" do
-      create(:lower_camel_case).should == "lowerCamelCase"
-      create(:lower_camel_case!).should == "lowerCamelCase"
-    end
-
-    context "with :element_form_default set to :qualified and a :namespace" do
-      it "adds the given namespace" do
-        key = create :qualify, :element_form_default => :qualified, :namespace => :v1
-        key.should == "v1:qualify"
-      end
-
-      it "does not add the given namespace if the key starts with a colon" do
-        key = create ":qualify", :element_form_default => :qualified, :namespace => :v1
-        key.should == "qualify"
-      end
-
-      it "adds a given :namespace after converting the key" do
-        Gyoku::XMLKey.symbol_converter = :camelcase
-
-        key = create :username, :element_form_default => :qualified, :namespace => :v1
-        key.should == "v1:Username"
-      end
-
-      after { Gyoku::XMLKey.symbol_converter = :lower_camelcase }  #reset
-    end
-  end
-
-  describe ".symbol_converter" do
-    after { Gyoku::XMLKey.symbol_converter = :lower_camelcase }  #reset
-
-    it "returns the default lower_camelcase converter" do
-      Gyoku::XMLKey.symbol_converter.call("snake_case").should == "snakeCase"
-    end
-
-    it "accepts :lower_camelcase" do
-      Gyoku::XMLKey.symbol_converter = :lower_camelcase
-      Gyoku::XMLKey.create(:snake_case).should == "snakeCase"
-    end
-
-    it "accepts :camelcase" do
-      Gyoku::XMLKey.symbol_converter = :camelcase
-      Gyoku::XMLKey.create(:snake_case).should == "SnakeCase"
-    end
-
-    it "accepts :none" do
-      Gyoku::XMLKey.symbol_converter = :none
-      Gyoku::XMLKey.create(:snake_Case).should == "snake_Case"
-    end
-
-    it "allows to set a custom converter" do
-      Gyoku::XMLKey.symbol_converter = Proc.new { |key| key.upcase }
-      Gyoku::XMLKey.create(:snake_case).should == "SNAKE_CASE"
-    end
-  end
-
-  def create(key, options = {})
-    Gyoku::XMLKey.create key, options
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/xml_value_spec.rb

@@ -1,49 +0,0 @@
-require "spec_helper"
-
-describe Gyoku::XMLValue do
-
-  let(:datetime) { DateTime.new 2012, 03, 22, 16, 22, 33 }
-  let(:datetime_string) { "2012-03-22T16:22:33+00:00" }
-
-  describe ".create" do
-    context "for DateTime objects" do
-      it "returns an xs:dateTime compliant String" do
-        create(datetime).should == datetime_string
-      end
-    end
-
-    it "returns the String value and escapes special characters" do
-      create("string").should == "string"
-      create("<tag>").should == "&lt;tag&gt;"
-      create("at&t").should == "at&amp;t"
-      create('"quotes"').should == "&quot;quotes&quot;"
-    end
-
-    it "returns the String value without escaping special characters" do
-      create("<tag>", false).should == "<tag>"
-    end
-
-    it "returns an xs:dateTime compliant String for Objects responding to #to_datetime" do
-      singleton = Object.new
-      def singleton.to_datetime
-        DateTime.new 2012, 03, 22, 16, 22, 33
-      end
-
-      create(singleton).should == "2012-03-22T16:22:33+00:00"
-    end
-
-    it "calls Proc objects and converts their return value" do
-      object = lambda { DateTime.new 2012, 03, 22, 16, 22, 33 }
-      create(object).should == "2012-03-22T16:22:33+00:00"
-    end
-
-    it "calls #to_s unless the Object responds to #to_datetime" do
-      create("value").should == "value"
-    end
-  end
-
-  def create(object, escape_xml = true)
-    Gyoku::XMLValue.create object, escape_xml
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku_spec.rb

@@ -1,46 +0,0 @@
-require "spec_helper"
-
-describe Gyoku do
-
-  describe ".xml" do
-    it "translates a given Hash to XML" do
-      Gyoku.xml({ :id => 1 }, :element_form_default => :qualified).should == "<id>1</id>"
-    end
-
-    it "does not modify the original Hash" do
-      hash = {
-        :person => {
-          :first_name => "Lucy",
-          :last_name => "Sky",
-          :order! => [:first_name, :last_name]
-        },
-        :attributes! => { :person => { :id => "666" } }
-      }
-      original_hash = hash.dup
-
-      Gyoku.xml(hash)
-      original_hash.should == hash
-    end
-  end
-
-  describe ".configure" do
-    it "yields the Gyoku module" do
-      Gyoku.configure { |config| config.should respond_to(:convert_symbols_to) }
-    end
-  end
-
-  describe ".convert_symbols_to" do
-    after { Gyoku.convert_symbols_to(:lower_camelcase) }  # reset
-
-    it "accepts a predefined formula" do
-      Gyoku.convert_symbols_to(:camelcase)
-      Gyoku::XMLKey.create(:snake_case).should == "SnakeCase"
-    end
-
-    it "accepts a block" do
-      Gyoku.convert_symbols_to { |key| key.upcase }
-      Gyoku::XMLKey.create(:snake_case).should == "SNAKE_CASE"
-    end
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/spec_helper.rb

@@ -1,2 +0,0 @@
-require "bundler"
-Bundler.require :default, :development

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.autotest

@@ -1,5 +0,0 @@
-Autotest.add_hook(:initialize) do |at|
-  at.clear_mappings
-  at.add_mapping(%r%^spec/httpi/.*_spec.rb$%) { |filename, _| filename }
-  at.add_mapping(%r%^lib/(.*)\.rb$%) { |_, m| ["spec/#{m[1]}_spec.rb"] }
-end

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.gitignore

@@ -1,9 +0,0 @@
-.DS_Store
-.yardoc
-doc
-coverage
-tmp
-*~
-*.gem
-.bundle
-Gemfile.lock

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.rspec

@@ -1 +0,0 @@
---color

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.travis.yml

@@ -1,7 +0,0 @@
-script: "rake"
-rvm:
-  - 1.8.7
-  - 1.9.2
-  - ree
-  - rbx
-  - jruby

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/CHANGELOG.md

@@ -1,60 +0,0 @@
-## 0.9.4 (2011-05-15)
-
-* Fix: issues [34](https://github.com/rubiii/httpi/issues/34) and
-  [29](https://github.com/rubiii/httpi/issues/29) - replaced the dependency
-  on `ntlm-http` with a dependency on `pyu-ntlm-http` which comes with quite
-  a few bugfixes.
-
-* Fix: Setting the default adapter did not always load the adapter's client library.
-
-* Improvement: Added a shortcut method to set the default adapter to use.
-
-      HTTPI.adapter = :net_http
-
-## 0.9.3 (2011-04-28)
-
-* Fix: [issue 31](https://github.com/rubiii/httpi/issues/31) missing headers when using httpclient.
-
-* Fix: [issue 30](https://github.com/rubiii/httpi/issues/30) fix for using SSL with Net::HTTP.
-
-## 0.9.2 (2011-04-05)
-
-* Fix: issues [161](https://github.com/rubiii/savon/issues/161) and [165](https://github.com/rubiii/savon/issues/165)
-  reported at [rubiii/savon](https://github.com/rubiii/savon).
-
-## 0.9.1 (2011-04-04)
-
-* Fix: [issue 25](https://github.com/rubiii/httpi/issues/22) problem with HTTPI using the Net::HTTP adapter [hakanensari].
-
-## 0.9.0 (2011-03-08)
-
-* Feature: improved the adapter loading process ([d4a091](https://github.com/rubiii/httpi/commit/d4a091)) [rubiii].
-
-  Instead of using HTTPClient as the default and falling back to NetHTTP, the loading process now does the following:
-
-  1. Check if either HTTPClient, Curb or NetHTTP are already defined.
-     If any one of those is defined, use it.
-
-  2. Try to require HTTPClient, Curb and NetHTTP at last.
-     If any one of those can be required, use it.
-
-  Of course you can still manually specify the adapter to use.
-
-* Fix: [issue 22](https://github.com/rubiii/httpi/issues/22) argument error on logging adapter warning [rubiii].
-
-* Fix: [issue 23](https://github.com/rubiii/httpi/issues/23) the HTTPI.log method now works as expected [rubiii].
-
-## 0.8.0 (2011-03-07)
-
-* Feature: added support for NTLM authentication ([96ceb1](https://github.com/rubiii/httpi/commit/96ceb1)) [MattHall].
-
-  You should now be able to use NTLM authentication by specifying your credentials via `HTTPI::Auth::Config#ntlm`:
-
-      request = HTTPI::Request.new
-      request.auth.ntlm "username", "password"
-
-* Improvement: changed the default log level to :warn ([d01591](https://github.com/rubiii/httpi/commit/d01591))
-  and log at appropriate levels ([21ee1b](https://github.com/rubiii/httpi/commit/21ee1b)) [ichverstehe].
-
-* Fix: [issue 18](https://github.com/rubiii/httpi/issues/18) don't mask exceptions in decoded_gzip_body
-  ([f3811b](https://github.com/rubiii/httpi/commit/f3811b)) [fj].

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/Gemfile

@@ -1,8 +0,0 @@
-source :rubygems
-gemspec
-
-gem "jruby-openssl", :platforms => :jruby
-
-# http clients
-gem "httpclient", "~> 2.1.7"
-gem "curb", "~> 0.7.8", :platforms => :ruby

data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/LICENSE

@@ -1,20 +0,0 @@
-Copyright (c) 2010 Daniel Harrington
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.