search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/nori-1.0.1/LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2011 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.

data/search_biomodel/ruby/1.8/gems/nori-1.0.1/README.md

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+Nori [![Build Status](http://travis-ci.org/rubiii/nori.png)](http://travis-ci.org/rubiii/nori)
+====
+
+Really simple XML parsing ripped from Crack which ripped it from Merb.  
+Nori was created to bypass the stale development of Crack, improve its XML parser  
+and fix certain issues.
+
+``` ruby
+Nori.parse("<tag>This is the contents</tag>")
+# => { 'tag' => 'This is the contents' }
+```
+
+Nori supports pluggable parsers and ships with both REXML and Nokogiri implementations.  
+It defaults to REXML, but you can change it to use Nokogiri via:
+
+``` ruby
+Nori.parser = :nokogiri
+```
+
+Make sure Nokogiri is in your LOAD_PATH when parsing XML, because Nori tries to load it  
+when it's needed.
+
+
+Typecasting
+-----------
+
+Besides regular typecasting, Nori features somewhat "advanced" typecasting:
+
+* "true" and "false" String values are converted to `TrueClass` and `FalseClass`.
+* String values matching xs:time, xs:date and xs:dateTime are converted
+  to `Time`, `Date` and `DateTime` objects.
+
+You can disable this feature via:
+
+``` ruby
+Nori.advanced_typecasting = false
+```
+
+
+Namespaces
+----------
+
+Nori can strip the namespaces from your XML tags. This feature might raise  
+problems and is therefore disabled by default. Enable it via:
+
+``` ruby
+Nori.strip_namespaces = true
+```
+
+
+XML tags -> Hash keys
+---------------------
+
+Nori lets you specify a custom formula to convert XML tags to Hash keys.  
+Let me give you an example:
+
+``` ruby
+Nori.configure do |config|
+  config.convert_tags_to { |tag| tag.snake_case.to_sym }
+end
+
+xml = '<userResponse><accountStatus>active</accountStatus></userResponse>'
+Nori.parse(xml)  # => { :user_response => { :account_status => "active" }
+```

data/search_biomodel/ruby/1.8/gems/nori-1.0.1/Rakefile

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+require "bundler"
+Bundler::GemHelper.install_tasks
+
+require "rspec/core/rake_task"
+
+desc "Benchmark Nori parsers"
+task :benchmark do
+  require "benchmark/benchmark"
+end
+
+RSpec::Core::RakeTask.new do |t|
+  t.rspec_opts = %w(-c)
+end
+
+task :default => :spec
+task :test => :spec

data/search_biomodel/ruby/1.8/gems/nori-1.0.1/benchmark/benchmark.rb

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+$:.push File.expand_path("../../lib", __FILE__)
+require "nori"
+
+require "benchmark"
+
+Benchmark.bm 30 do |x|
+
+  num = 250
+  xml = File.read File.expand_path("../soap_response.xml", __FILE__)
+
+  x.report "rexml parser" do
+    num.times { Nori.parse xml, :rexml }
+  end
+
+  x.report "nokogiri parser" do
+    num.times { Nori.parse xml, :nokogiri }
+  end
+
+end

data/search_biomodel/ruby/1.8/gems/nori-1.0.1/benchmark/soap_response.xml

@@ -0,0 +1,266 @@
+<?xml version="1.0" encoding="utf-8"?>
+<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+  <soap:Body>
+    <GetICB_9_2_4_DestInfoWithDestIdResponse xmlns="http://airline.com/">
+      <GetICB_9_2_4_DestInfoWithDestIdResult>
+        <xs:schema id="NewDataSet" xmlns="" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:msdata="urn:schemas-microsoft-com:xml-msdata">
+          <xs:element name="NewDataSet" msdata:IsDataSet="true" msdata:MainDataTable="CL_9_2_4_DestInfo" msdata:UseCurrentLocale="true">
+            <xs:complexType>
+              <xs:choice minOccurs="0" maxOccurs="unbounded">
+                <xs:element name="CL_9_2_4_DestInfo">
+                  <xs:complexType>
+                    <xs:sequence>
+                      <xs:element name="DESTINATION" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="64" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="COUNTRY" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="50" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="AIRPORTNAME" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="70" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="DISTANCE_APT_CTY" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="50" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="TRANSPORT_APT_CTY" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="50" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="REVCABIN" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="50" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="REVCOCKPIT" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="50" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="GROUPTEXT" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="50" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="SORT" type="xs:decimal" minOccurs="0" />
+                      <xs:element name="HEADING" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="30" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="VISIBLE" type="xs:decimal" minOccurs="0" />
+                      <xs:element name="SORT1" type="xs:decimal" minOccurs="0" />
+                      <xs:element name="ITEMSORT" type="xs:decimal" minOccurs="0" />
+                      <xs:element name="AUSWAHLTEXT" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="255" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                      <xs:element name="REVDATE" type="xs:dateTime" minOccurs="0" />
+                      <xs:element name="CABIN" type="xs:decimal" minOccurs="0" />
+                      <xs:element name="COCKPIT" type="xs:decimal" minOccurs="0" />
+                      <xs:element name="APIATA" minOccurs="0">
+                        <xs:simpleType>
+                          <xs:restriction base="xs:string">
+                            <xs:maxLength value="3" />
+                          </xs:restriction>
+                        </xs:simpleType>
+                      </xs:element>
+                    </xs:sequence>
+                  </xs:complexType>
+                </xs:element>
+              </xs:choice>
+            </xs:complexType>
+          </xs:element>
+        </xs:schema>
+        <diffgr:diffgram xmlns:msdata="urn:schemas-microsoft-com:xml-msdata" xmlns:diffgr="urn:schemas-microsoft-com:xml-diffgram-v1">
+          <DocumentElement xmlns="">
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo1" msdata:rowOrder="0">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>Passengers</GROUPTEXT>
+              <SORT>1</SORT>
+              <HEADING>Disembarking:</HEADING>
+              <VISIBLE>-1</VISIBLE>
+              <SORT1>2</SORT1>
+              <ITEMSORT>0</ITEMSORT>
+              <AUSWAHLTEXT>Baby buggies are delivered at aircraft door or stairs.</AUSWAHLTEXT>
+              <REVDATE>2008-09-01T00:00:00+02:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>0</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo2" msdata:rowOrder="1">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>Aircraft</GROUPTEXT>
+              <SORT>2</SORT>
+              <HEADING>Turnaround:</HEADING>
+              <VISIBLE>-1</VISIBLE>
+              <SORT1>5.30</SORT1>
+              <ITEMSORT>0</ITEMSORT>
+              <AUSWAHLTEXT>Station applies EST process.</AUSWAHLTEXT>
+              <REVDATE>2009-05-05T00:00:00+02:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>-1</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo3" msdata:rowOrder="2">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>General</GROUPTEXT>
+              <SORT>4</SORT>
+              <HEADING>Addresses:</HEADING>
+              <VISIBLE>-1</VISIBLE>
+              <SORT1>8.50</SORT1>
+              <ITEMSORT>1</ITEMSORT>
+              <AUSWAHLTEXT>
+                Station Manager:
+                YYYYYYYY XXXXXXX
+                PMIKXXX
+                Tel.:+34 971 xxx xxx
+                Mobile:+ 34 600 46 xx xx
+              </AUSWAHLTEXT>
+              <REVDATE>2010-02-08T00:00:00+01:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>-1</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo4" msdata:rowOrder="3">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>General</GROUPTEXT>
+              <SORT>4</SORT>
+              <HEADING>Addresses:</HEADING>
+              <VISIBLE>-1</VISIBLE>
+              <SORT1>8.50</SORT1>
+              <ITEMSORT>2</ITEMSORT>
+              <AUSWAHLTEXT>
+                Handling Agent:
+                xxxxxxx Airport Services
+                Operations
+                PMIIxxx
+                Tel   +34 971 xxx xxx
+                Passenger Services
+                PMIPXXX
+                Tel : +34 971 xxx xxx
+              </AUSWAHLTEXT>
+              <REVDATE>2010-02-08T00:00:00+01:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>-1</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo5" msdata:rowOrder="4">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>General</GROUPTEXT>
+              <SORT>4</SORT>
+              <HEADING>Announcements:</HEADING>
+              <VISIBLE>-1</VISIBLE>
+              <SORT1>11</SORT1>
+              <ITEMSORT>1</ITEMSORT>
+              <AUSWAHLTEXT>Prerecorded Spanish announcements available.</AUSWAHLTEXT>
+              <REVDATE>2009-12-30T00:00:00+01:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>0</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo6" msdata:rowOrder="5">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>General</GROUPTEXT>
+              <SORT>4</SORT>
+              <HEADING>Life jackets / DEMO:</HEADING>
+              <VISIBLE>-1</VISIBLE>
+              <SORT1>12</SORT1>
+              <ITEMSORT>0</ITEMSORT>
+              <AUSWAHLTEXT>
+                Infant life jackets to be distributed.
+                DEMO with life jackets.
+              </AUSWAHLTEXT>
+              <REVDATE>2002-07-24T00:00:00+02:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>0</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+            <CL_9_2_4_DestInfo diffgr:id="CL_9_2_4_DestInfo7" msdata:rowOrder="6">
+              <DESTINATION>PALMA DE MALLORCA</DESTINATION>
+              <COUNTRY>Spain Schengen</COUNTRY>
+              <AIRPORTNAME>Son San Juan</AIRPORTNAME>
+              <DISTANCE_APT_CTY>11 km</DISTANCE_APT_CTY>
+              <REVCABIN>08.02.10</REVCABIN>
+              <REVCOCKPIT>08.02.10</REVCOCKPIT>
+              <GROUPTEXT>Catering</GROUPTEXT>
+              <SORT>5</SORT>
+              <HEADING>General:</HEADING>
+              <VISIBLE>0</VISIBLE>
+              <SORT1>1</SORT1>
+              <ITEMSORT>1</ITEMSORT>
+              <AUSWAHLTEXT>
+                LSG XXX XXXX
+                Tel.: +34 971 xxx xxx or xxx xxx
+                Sita: PMIAXXX
+              </AUSWAHLTEXT>
+              <REVDATE>2005-06-01T00:00:00+02:00</REVDATE>
+              <CABIN>-1</CABIN>
+              <COCKPIT>0</COCKPIT>
+              <APIATA>PMI</APIATA>
+            </CL_9_2_4_DestInfo>
+          </DocumentElement>
+        </diffgr:diffgram>
+      </GetICB_9_2_4_DestInfoWithDestIdResult>
+    </GetICB_9_2_4_DestInfoWithDestIdResponse>
+  </soap:Body>
+</soap:Envelope>

data/search_biomodel/ruby/1.8/gems/nori-1.0.1/lib/nori.rb

@@ -0,0 +1,59 @@
+require "nori/version"
+require "nori/core_ext"
+require "nori/parser"
+require "nori/xml_utility_node"
+
+module Nori
+  extend self
+
+  # Translates the given +xml+ to a Hash. Accepts an optional +parser+ to use.
+  def parse(xml, parser = nil)
+    return {} if xml.blank?
+    Parser.parse xml, parser
+  end
+
+  # Sets the +parser+ to use.
+  def parser=(parser)
+    Parser.use = parser
+  end
+
+  # Yields +self+ for configuration.
+  def configure
+    yield self
+  end
+
+  # Sets whether to use advanced typecasting.
+  attr_writer :advanced_typecasting
+
+  # Returns whether to use advanced typecasting.
+  # Defaults to +true+.
+  def advanced_typecasting?
+    @advanced_typecasting != false
+  end
+
+  # Sets whether to strip namespaces.
+  attr_writer :strip_namespaces
+
+  # Returns whether to strip namespaces.
+  # Defaults to +false+.
+  def strip_namespaces?
+    @strip_namespaces
+  end
+
+  # Expects a +block+ which receives a tag to convert.
+  # Accepts +nil+ for a reset to the default behavior of not converting tags.
+  def convert_tags_to(reset = nil, &block)
+    @convert_tag = reset || block
+  end
+
+  # Transforms a given +tag+ using the specified conversion formula.
+  def convert_tag(tag)
+    @convert_tag.call(tag)
+  end
+
+  # Returns whether to convert tags.
+  def convert_tags?
+    @convert_tag
+  end
+
+end