search_biomodel 1.0.3 → 2.0.0

data/.idea/.name

@@ -0,0 +1 @@
+search_biomodel

data/.idea/.rakeTasks

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Settings><!--This file was automatically generated by Ruby plugin.
+You are allowed to: 
+1. Remove rake task
+2. Add existing rake tasks
+To add existing rake tasks automatically delete this file and reload the project.
+--><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build gem into pkg/" fullCmd="build" taksId="build" /><RakeTask description="Remove rcov products for rcov" fullCmd="clobber_rcov" taksId="clobber_rcov" /><RakeTask description="Remove rdoc products" fullCmd="clobber_rdoc" taksId="clobber_rdoc" /><RakeTask description="Start IRB with all runtime dependencies loaded" fullCmd="console[script]" taksId="console[script]" /><RakeGroup description="" fullCmd="" taksId="gemcutter"><RakeTask description="Release gem to Gemcutter" fullCmd="gemcutter:release" taksId="release" /></RakeGroup><RakeTask description="Generate and validate gemspec" fullCmd="gemspec" taksId="gemspec" /><RakeGroup description="" fullCmd="" taksId="gemspec"><RakeTask description="Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)" fullCmd="gemspec:debug" taksId="debug" /><RakeTask description="Regenreate the gemspec on the filesystem" fullCmd="gemspec:generate" taksId="generate" /><RakeTask description="Regenerate and validate gemspec, and then commits and pushes to git" fullCmd="gemspec:release" taksId="release" /><RakeTask description="Validates the gemspec on the filesystem" fullCmd="gemspec:validate" taksId="validate" /></RakeGroup><RakeGroup description="" fullCmd="" taksId="git"><RakeTask description="Tag and push release to git" fullCmd="git:release" taksId="release" /></RakeGroup><RakeTask description="Build and install gem using `gem install`" fullCmd="install" taksId="install" /><RakeTask description="Analyze code coverage with tests" fullCmd="rcov" taksId="rcov" /><RakeTask description="Build the rdoc HTML Files" fullCmd="rdoc" taksId="rdoc" /><RakeTask description="Release gem" fullCmd="release" taksId="release" /><RakeTask description="Force a rebuild of the RDOC files" fullCmd="rerdoc" taksId="rerdoc" /><RakeTask description="Run tests" fullCmd="test" taksId="test" /><RakeTask description="Displays the current version" fullCmd="version" taksId="version" /><RakeGroup description="" fullCmd="" taksId="version"><RakeGroup description="" fullCmd="" taksId="bump"><RakeTask description="Bump the major version by 1" fullCmd="version:bump:major" taksId="major" /><RakeTask description="Bump the a minor version by 1" fullCmd="version:bump:minor" taksId="minor" /><RakeTask description="Bump the patch version by 1" fullCmd="version:bump:patch" taksId="patch" /></RakeGroup><RakeTask description="Writes out an explicit version" fullCmd="version:write" taksId="write" /></RakeGroup><RakeTask description="" fullCmd="clobber" taksId="clobber" /><RakeTask description="" fullCmd="console" taksId="console" /><RakeTask description="" fullCmd="default" taksId="default" /><RakeTask description="" fullCmd="gemspec_required" taksId="gemspec_required" /><RakeTask description="" fullCmd="rdoc/index.html" taksId="rdoc/index.html" /><RakeTask description="" fullCmd="version_required" taksId="version_required" /></RakeGroup></Settings>

data/.idea/dictionaries/root.xml

@@ -0,0 +1,7 @@
+<component name="ProjectDictionaryState">
+  <dictionary name="root">
+    <words>
+      <w>chebiid</w>
+    </words>
+  </dictionary>
+</component>

data/.idea/encodings.xml

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false" />
+</project>
+

data/.idea/misc.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="DependencyValidationManager">
+    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="ruby-1.8.7-p249" project-jdk-type="RUBY_SDK" />
+</project>
+

data/.idea/modules.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/search_biomodel.iml" filepath="$PROJECT_DIR$/.idea/search_biomodel.iml" />
+    </modules>
+  </component>
+</project>
+

data/.idea/search_biomodel.iml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="RUBY_MODULE" version="4">
+  <component name="GemRequirementsHolder" version="3">
+    <requirement>
+      <requirement>
+        <dependency name="jeweler" version="1.6.2" bound="LATEST_IN_BRANCH" git="false" path="false" doRequire="true" />
+      </requirement>
+      <source from="Gemfile" />
+    </requirement>
+    <requirement>
+      <requirement>
+        <dependency name="rcov" version="0" bound="GREATER_OR_EQUAL" git="false" path="false" doRequire="true" />
+      </requirement>
+      <source from="Gemfile" />
+    </requirement>
+    <requirement>
+      <requirement>
+        <dependency name="savon" version="0.9.2" bound="LATEST_IN_BRANCH" git="false" path="false" doRequire="true" />
+      </requirement>
+      <source from="Gemfile" />
+    </requirement>
+  </component>
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/.bundle" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] bundler (v1.0.15, /usr/lib/ruby/gems/1.8/gems/bundler-1.0.15)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] jeweler (v1.6.2, /usr/lib/ruby/gems/1.8/gems/jeweler-1.6.2)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] rcov (v0.9.9, /root/.gem/ruby/1.8/gems/rcov-0.9.9)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] savon (v0.9.2, /usr/lib/ruby/gems/1.8/gems/savon-0.9.2)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] git (v1.2.5, /usr/lib/ruby/gems/1.8/gems/git-1.2.5)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] builder (v3.0.0, /usr/lib/ruby/gems/1.8/gems/builder-3.0.0)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] gyoku (v0.4.4, /usr/lib/ruby/gems/1.8/gems/gyoku-0.4.4)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] rake (v0.8.7, /usr/lib/ruby/gems/1.8/gems/rake-0.8.7)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] pyu-ntlm-http (v0.1.3.1, /usr/lib/ruby/gems/1.8/gems/pyu-ntlm-http-0.1.3.1)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] rack (v1.3.0, /usr/lib/ruby/gems/1.8/gems/rack-1.3.0)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] nokogiri (v1.4.6, /usr/lib/ruby/gems/1.8/gems/nokogiri-1.4.6)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] httpi (v0.9.4, /usr/lib/ruby/gems/1.8/gems/httpi-0.9.4)" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="[gem] nori (v1.0.1, /usr/lib/ruby/gems/1.8/gems/nori-1.0.1)" level="application" />
+  </component>
+</module>
+

data/.idea/vcs.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
+

data/.idea/workspace.xml

@@ -0,0 +1,443 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="c5060248-6b34-4e75-b0c1-8bf3e1f0b7e1" name="Default" comment="">
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/lib/search_biomodel.rb" afterPath="$PROJECT_DIR$/lib/search_biomodel.rb" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/test/test_search_biomodel.rb" afterPath="$PROJECT_DIR$/test/test_search_biomodel.rb" />
+    </list>
+    <ignored path="search_biomodel.iws" />
+    <ignored path=".idea/workspace.xml" />
+    <option name="TRACKING_ENABLED" value="true" />
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
+  <component name="CoverageDataManager" choice="3" />
+  <component name="CreatePatchCommitExecutor">
+    <option name="PATCH_PATH" value="" />
+    <option name="REVERSE_PATCH" value="false" />
+  </component>
+  <component name="DaemonCodeAnalyzer">
+    <disable_hints />
+  </component>
+  <component name="FavoritesManager">
+    <favorites_list name="search_biomodel" />
+  </component>
+  <component name="FileEditorManager">
+    <leaf>
+      <file leaf-file-name="test_search_biomodel.rb" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/test/test_search_biomodel.rb">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="28" column="77" selection-start="811" selection-end="811" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="search_biomodel.rb" pinned="false" current="true" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/lib/search_biomodel.rb">
+          <provider selected="true" editor-type-id="text-editor">
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+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="search_biomodel.gemspec" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/search_biomodel.gemspec">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="59" column="99" selection-start="1896" selection-end="1896" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="helper.rb" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/test/helper.rb">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="7" column="25" selection-start="224" selection-end="224" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+    </leaf>
+  </component>
+  <component name="FindManager">
+    <FindUsagesManager>
+      <setting name="OPEN_NEW_TAB" value="false" />
+    </FindUsagesManager>
+  </component>
+  <component name="Git.Settings">
+    <option name="CHECKOUT_INCLUDE_TAGS" value="false" />
+    <option name="UPDATE_CHANGES_POLICY" value="STASH" />
+  </component>
+  <component name="IdeDocumentHistory">
+    <option name="changedFiles">
+      <list>
+        <option value="$PROJECT_DIR$/test/helper.rb" />
+        <option value="$PROJECT_DIR$/LICENSE.txt" />
+        <option value="$PROJECT_DIR$/README.rdoc" />
+        <option value="$PROJECT_DIR$/search_biomodel.gemspec" />
+        <option value="$PROJECT_DIR$/test/test_search_biomodel.rb" />
+        <option value="$PROJECT_DIR$/lib/search_biomodel.rb" />
+      </list>
+    </option>
+  </component>
+  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
+    <OptionsSetting value="true" id="Add" />
+    <OptionsSetting value="true" id="Remove" />
+    <OptionsSetting value="true" id="Checkout" />
+    <OptionsSetting value="true" id="Update" />
+    <OptionsSetting value="true" id="Status" />
+    <OptionsSetting value="true" id="Edit" />
+    <ConfirmationsSetting value="0" id="Add" />
+    <ConfirmationsSetting value="0" id="Remove" />
+  </component>
+  <component name="ProjectReloadState">
+    <option name="STATE" value="0" />
+  </component>
+  <component name="ProjectView">
+    <navigator currentView="ProjectPane" proportions="" version="1" splitterProportion="0.5">
+      <flattenPackages />
+      <showMembers />
+      <showModules />
+      <showLibraryContents />
+      <hideEmptyPackages />
+      <abbreviatePackageNames />
+      <autoscrollToSource />
+      <autoscrollFromSource />
+      <sortByType />
+    </navigator>
+    <panes>
+      <pane id="ProjectPane">
+        <subPane>
+          <PATH>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
+            </PATH_ELEMENT>
+          </PATH>
+          <PATH>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+          </PATH>
+          <PATH>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="test" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+          </PATH>
+          <PATH>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="search_biomodel" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="lib" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
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+          </PATH>
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+      </pane>
+      <pane id="Favorites" />
+      <pane id="Scope" />
+    </panes>
+  </component>
+  <component name="PropertiesComponent">
+    <property name="recentsLimit" value="5" />
+  </component>
+  <component name="RunManager" selected="Test::Unit/Shoulda.TestSearchBiomodel">
+    <configuration default="false" name="test_find_all_models" type="TestUnitRunConfigurationType" factoryName="Test::Unit/Shoulda" temporary="true">
+      <predefined_log_file id="RUBY_TESTUNIT" enabled="true" />
+      <module name="search_biomodel" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="WORK DIR" VALUE="$PROJECT_DIR$/test" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="SHOULD_USE_SDK" VALUE="false" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="ALTERN_SDK_NAME" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="myPassParentEnvs" VALUE="true" />
+      <envs />
+      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="true" />
+      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" track_test_folders="true" runner="rcov">
+        <COVERAGE_PATTERN ENABLED="true">
+          <PATTERN REGEXPS="/.rvm/" INCLUDED="false" />
+        </COVERAGE_PATTERN>
+      </EXTENSION>
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TESTS_FOLDER_PATH" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_SCRIPT_PATH" VALUE="$PROJECT_DIR$/test/test_search_biomodel.rb" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_CLASS_NAME" VALUE="TestSearchBiomodel" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_FILE_MASK" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_METHOD_NAME" VALUE="test_find_all_models" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_TEST_TYPE" VALUE="TEST_METHOD" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="INHERITANCE_CHECK_DISABLED" VALUE="false" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="DRB" VALUE="false" />
+      <RunnerSettings RunnerId="RubyRunner" />
+      <ConfigurationWrapper RunnerId="RubyRunner" />
+      <method />
+    </configuration>
+    <configuration default="false" name="TestSearchBiomodel" type="TestUnitRunConfigurationType" factoryName="Test::Unit/Shoulda" temporary="true">
+      <predefined_log_file id="RUBY_TESTUNIT" enabled="true" />
+      <module name="search_biomodel" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="WORK DIR" VALUE="$PROJECT_DIR$/test" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="SHOULD_USE_SDK" VALUE="false" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="ALTERN_SDK_NAME" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="myPassParentEnvs" VALUE="true" />
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+      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="true" />
+      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" track_test_folders="true" runner="rcov">
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+        </COVERAGE_PATTERN>
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+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_CLASS_NAME" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_FILE_MASK" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_METHOD_NAME" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_TEST_TYPE" VALUE="TEST_SCRIPT" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="INHERITANCE_CHECK_DISABLED" VALUE="false" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="DRB" VALUE="false" />
+      <RunnerSettings RunnerId="RubyRunner" />
+      <ConfigurationWrapper RunnerId="RubyRunner" />
+      <method />
+    </configuration>
+    <configuration default="false" name="test_search_by_ChEBIID" type="TestUnitRunConfigurationType" factoryName="Test::Unit/Shoulda" temporary="true">
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+      <module name="search_biomodel" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="WORK DIR" VALUE="$PROJECT_DIR$/test" />
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+      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" track_test_folders="true" runner="rcov">
+        <COVERAGE_PATTERN ENABLED="true">
+          <PATTERN REGEXPS="/.rvm/" INCLUDED="false" />
+        </COVERAGE_PATTERN>
+      </EXTENSION>
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TESTS_FOLDER_PATH" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_SCRIPT_PATH" VALUE="$PROJECT_DIR$/test/test_search_biomodel.rb" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_CLASS_NAME" VALUE="TestSearchBiomodel" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_FILE_MASK" VALUE="" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_METHOD_NAME" VALUE="test_search_by_ChEBIID" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="TEST_TEST_TYPE" VALUE="TEST_METHOD" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="INHERITANCE_CHECK_DISABLED" VALUE="false" />
+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="DRB" VALUE="false" />
+      <RunnerSettings RunnerId="RubyRunner" />
+      <ConfigurationWrapper RunnerId="RubyRunner" />
+      <method />
+    </configuration>
+    <configuration default="true" type="RubyRunConfigurationType" factoryName="Ruby">
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+      <RUBY_RUN_CONFIG NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
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+      <RUBY_RUN_CONFIG NAME="SHOULD_USE_SDK" VALUE="false" />
+      <RUBY_RUN_CONFIG NAME="ALTERN_SDK_NAME" VALUE="" />
+      <RUBY_RUN_CONFIG NAME="myPassParentEnvs" VALUE="true" />
+      <envs />
+      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="false" />
+      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" track_test_folders="true" runner="rcov">
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+      <RUBY_RUN_CONFIG NAME="SCRIPT_PATH" VALUE="" />
+      <RUBY_RUN_CONFIG NAME="SCRIPT_ARGS" VALUE="" />
+      <method />
+    </configuration>
+    <configuration default="true" type="TestUnitRunConfigurationType" factoryName="Test::Unit/Shoulda">
+      <predefined_log_file id="RUBY_TESTUNIT" enabled="true" />
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+      <RTEST_RUN_CONFIG_SETTINGS_ID NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
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+          <folding />
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+  </component>
+</project>
+

data/LICENSE.txt

@@ -1,20 +1,29 @@
-Copyright (c) 2011 Niall Beard
+Copyright (c) 2011, The University of Manchester, UK.
 
-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:
+All rights reserved.
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-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.
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+ * Neither the names of The University of Manchester nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission. 
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

data/README.rdoc

@@ -1,45 +1,74 @@
 = search_biomodel
 
-search biomodel is a small gem ready to be used for running queries through the biomodel web service API. 
+search biomodel is a small ruby gem ready to be used for running queries through the biomodel web service API. 
 
-There are (currently) 3 methods to communicate with the biomodels website (found at http://www.ebi.ac.uk/biomodels-main/). 
+There are (currently) 5 methods implemented here to communicate with the biomodels website (found at http://www.ebi.ac.uk/biomodels-main/).
+
+These methods are "search_by_chebiid", "search_by_name", "get_all_models", "search_by_person" and "get_model_name_by_id".
 
-These methods are "search_by_chebiid", "search_by_name" and "get_all_models". The former two return an array and the latter a hash map of :key and :value
 
 == Installation 
 
   gem install seach_biomodel
 
+
 == Usage
-example:
-  
+The first four methods return an array of model IDs (or an empty array if nothing is found) and the 5th returns the name of the model of an ID you search for. The ChEBIID can take quite some time to run on the biomodel servers side.
+
+The "get_all_models" method returns a hash map of :key's and :value's which can be retrieved as such:
+
+
+
   require 'rubygems'
-  require 'seach_biomodel'
+  require 'search_biomodel'
 
-  include SysMODB::SearchBiomodel
 
+  @connection = SysMODB::SearchBiomodel.instance
 
-  puts "\n\n ------------------ List All -----------------------------\n\n"
 
-  all_models = get_all_models
+  puts "\n\n ------------------ List All -----------------------------\n"
+  all_models = @connection.get_all_models
   all_models.each { |item| puts "ID = #{item[:key]}    |    NAME = #{item[:value]}\n" }
+  puts " ----------------------------------------------------------\n\n\n"
 
+  puts "\n\n ------------------ By Chebiid --------------------------\n" 
+  i=0
+  models_by_chebiid = @connection.search_by_ChEBIID("CHEBI:15422")
+  models_by_chebiid.each { |item| puts "#{i+=1} #{item.to_s}\n"}
+  puts " ----------------------------------------------------------\n\n\n"
 
-  puts "\n\n ------------------ By Chebiid --------------------------\n\n"  i=0
+  puts "\n\n ------------------ By Name -----------------------------\n"  
+  i=0
+  models_by_name = @connection.search_by_name("Kolomeisky2003")
+  models_by_name.each { |item| puts "#{i+=1} #{item.to_s}\n"}
+  puts " ----------------------------------------------------------\n\n\n"
 
-  models_by_chebiid = search_by_ChEBIID("CHEBI:15422")
-  models_by_chebiid.each { |item| puts "#{i+=1} #{item.to_s}\n"}
+
+  puts "\n\n ------------------ By Person----------------------------\n"  
+  i=0
+  models_by_person = @connection.search_by_person("Jim")
+  models_by_person.each { |item| puts "#{i+=1} #{item.to_s}\n"}
+  puts " ----------------------------------------------------------\n\n\n"
+
+  puts "\n\n ------------------ Model ID by Name---------------------------\n"   
+  i=0
+  models_by_person = @connection.get_model_name_by_id("BIOMD0000000190")
+  models_by_person.each { |item| puts "#{i+=1} #{item.to_s}\n"}
+  puts " ----------------------------------------------------------\n\n\n"
+
+
+== Fun Fact
+
+You can append the Model ID to the URL http://www.ebi.ac.uk/biomodels-main/ to load the link
+eg (continuing from above).
 
 
-  puts "\n\n ------------------ By Name -----------------------------\n\n"  i=0
 
-  models_by_name = search_by_name("Kolomeisky2003")
-  models_by_name.each { |item| puts "#{i+=1} #{item.to_s}\n"}
 
+  models_by_person.each { |item| puts "http://www.ebi.ac.uk/biomodels-main/#{item.to_s}\n" } 
 
-  puts "\n ----------------------------------------------------------\n\n\n"
-  
-  
+  #=> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000190
+  #=> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000191
 
 == Contributing to search_biomodel
  

data/VERSION

@@ -1 +1 @@
-1.0.3
+2.0.0

data/lib/search_biomodel.rb

@@ -1,74 +1,145 @@
-
-
-require 'rubygems'
 require 'savon'
-
+require 'singleton'
 
 module SysMODB
 
   class SearchBiomodelException < Exception
   end
 
-  module SearchBiomodel
+  class SearchBiomodel
+    include Singleton
 
-    def search_by_ChEBIID(search_string)
-      client = create_connection
-      response = client.request(:biom, "get_models_id_by_ch_ebi_id") do
-        soap.body = { :ChEBBId => search_string, :attributes! => { :ChEBBId => { "xsi:type" => "xsd:string" } } }  
+    def initialize
+      @connection = Savon.configure do |config|
+        config.log = false
+        HTTPI.log = false
+        config.raise_errors = true
+        Savon::Client.new do
+          wsdl.document = "http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl"
+          wsdl.namespace = "http://biomodels.ebi.ac.uk"
+        end
       end
-      return response.to_hash[:get_models_id_by_ch_ebi_id_response][:get_models_id_by_ch_ebi_id_return][:get_models_id_by_ch_ebi_id_return]
+
     end
-    
 
-    def get_all_models
-      client = create_connection  
-      response = client.request(:biom, "get_all_models" ) do
-        soap.body = { :modelName => "?", :attributes! => { :modelName => { "xsi:type" => "xsd:string" } } }
+
+    def models(search_string)
+      #collect results from sub-methods
+      results = Array.new
+      results << @connection.search_by_name(search_string)
+      results << @connection.search_by_chebiid(search_string)
+      results << @connection.search_by_person(search_string)
+
+      #turn into one big array, remove duplicates and select first X
+      results = results.flatten
+      results = results.uniq
+      results = results.first(3)
+
+      sbml_results = Array.new
+      results.each{ |a| sbml_results << "#{@connection.getModel(a)}" }
+      sbml_results
+    end
+
+
+
+    def getModel(model_id)
+      client = connection
+      response = client.request(:biom, "get_model_by_id") do
+        soap.body = {:id => model_id, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
+      end
+
+      search_results = response.to_hash[:get_model_by_id_response][:get_model_by_id_return]
+      if search_results.nil?
+        []
+      else
+        search_results
+      end
+    end
+
+
+    #search_by_chebiid
+    #search_by_name
+    #search_by_person
+
+    def search_by_chebiid(search_string)
+      client = connection
+      response = client.request(:biom, "get_models_id_by_ch_ebi_id") do
+        soap.body = {:ChEBBId => search_string, :attributes! => {:ChEBBId => {"xsi:type" => "xsd:string"}}}
+      end
+
+      search_results = response.to_hash[:get_models_id_by_ch_ebi_id_response][:get_models_id_by_ch_ebi_id_return][:get_models_id_by_ch_ebi_id_return]
+      if search_results.nil?
+        []
+      else
+        search_results
       end
-      return response.to_hash[:multi_ref][:item]
     end
-  
+
 
     def search_by_name (search_string)
-      client = create_connection
+      client = connection
       response = client.request(:biom, "get_models_id_by_name") do
-        soap.body = { :modelName => search_string, :attributes! => { :modelName => { "xsi:type" => "xsd:string" } } }  
+        soap.body = {:modelName => search_string, :attributes! => {:modelName => {"xsi:type" => "xsd:string"}}}
+      end
+      search_results = response.to_hash[:get_models_id_by_name_response][:get_models_id_by_name_return][:get_models_id_by_name_return]
+      if search_results.nil?
+        []
+      else
+        search_results
       end
-      return response.to_hash[:get_models_id_by_name_response][:get_models_id_by_name_return][:get_models_id_by_name_return]
     end
 
-   def get_models_id_by_person (search_string)
-      client = create_connection
+    def search_by_person (search_string)
+      client = connection
       response = client.request(:biom, "get_models_id_by_person") do
-        soap.body = { :personName => search_string, :attributes! => { :personName => { "xsi:type" => "xsd:string" } } }  
+        soap.body = {:personName => search_string, :attributes! => {:personName => {"xsi:type" => "xsd:string"}}}
+      end
+      search_results = response.to_hash[:get_models_id_by_person_response][:get_models_id_by_person_return][:get_models_id_by_person_return]
+      if search_results.nil?
+        []
+      else
+        search_results
       end
-      return response.to_hash[:get_models_id_by_person_response][:get_models_id_by_person_return][:get_models_id_by_person_return]
-   end
+    end
 
-   def get_model_name_by_id (search_string)
-      client = create_connection
+
+    #more used for testing
+
+    def get_model_name_by_id (search_string)
+      client = connection
       response = client.request(:biom, "get_model_name_by_id") do
-        soap.body = { :id => search_string, :attributes! => { :id => { "xsi:type" => "xsd:string" } } }  
+        soap.body = {:id => search_string, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
       end
-      return response.to_hash[:get_model_name_by_id_response][:get_model_name_by_id_return]
-   end
-  
-
+      search_results = response.to_hash[:get_model_name_by_id_response][:get_model_name_by_id_return]
+      if search_results.nil? || search_results.include?('is an invalid Model ID.')
+        []
+      else
+        search_results
+      end
+    end
 
-    private
-   
-    def create_connection
-      Savon.configure do |config|
-        config.log = false
-        HTTPI.log = false
-        client = Savon::Client.new do
-          wsdl.document = "http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl"
-          wsdl.namespace = "http://biomodels.ebi.ac.uk"
-        end
+    def get_all_models
+      client = connection
+      response = client.request(:biom, "get_all_models") do
+        soap.body = {:modelName => "?", :attributes! => {:modelName => {"xsi:type" => "xsd:string"}}}
+      end
+      search_results = response.to_hash[:multi_ref][:item]
+      if search_results.nil?
+        []
+      else
+        search_results
       end
-    end 
+    end
+
+
 
 
+    protected
+
+    def connection
+      @connection
+    end
+
   end #SearchBiomodel
 end #SysMODB
 

data/search_biomodel.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{search_biomodel}
-  s.version = "1.0.3"
+  s.version = "2.0.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Niall Beard"]
-  s.date = %q{2011-07-05}
+  s.date = %q{2012-02-17}
   s.description = %q{Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine }
   s.email = %q{beardn9@cs.man.ac.uk}
   s.extra_rdoc_files = [
@@ -18,6 +18,15 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".idea/.name",
+    ".idea/.rakeTasks",
+    ".idea/dictionaries/root.xml",
+    ".idea/encodings.xml",
+    ".idea/misc.xml",
+    ".idea/modules.xml",
+    ".idea/search_biomodel.iml",
+    ".idea/vcs.xml",
+    ".idea/workspace.xml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -25,6 +34,8 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "lib/search_biomodel.rb",
+    "search_biomodel-1.1.1.gem",
+    "search_biomodel-1.1.2.gem",
     "search_biomodel.gemspec",
     "test/helper.rb",
     "test/test_search_biomodel.rb"

data/test/helper.rb

@@ -8,7 +8,7 @@ rescue Bundler::BundlerError => e
   exit e.status_code
 end
 require 'test/unit'
-require 'shoulda'
+
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))

data/test/test_search_biomodel.rb

@@ -1,60 +1,97 @@
 require 'test/unit'
-require '/home/cspc018/Work/Repos/gems/search_biomodel/lib/search_biomodel.rb'
+require 'helper'
+class TestSearchBiomodel < Test::Unit::TestCase
 
+  def setup
+    @instance = SysMODB::SearchBiomodel.instance
+  end
 
-class TestSearchBiomodel < Test::Unit::TestCase
+  def test_find_all_models
+    puts "\n\n ---------------------find all models---------------------\n\n"
+    response = []
+    i=0
+    response = @instance.get_all_models
+    response.each { |x| puts "Response #{i+=1}:   #{x[:key].to_s} " }
+    response.each { |x| assert_not_nil x[:key] }
+    assert_not_nil response
+  end
+
+
+  def test_search_by_chebiid
+    puts "\n\n ---------------------search by chebiid---------------------\n\n"
+    response = []
+    i = 0
+    response = @instance.search_by_chebiid("CHEBI:15422")
+    response.each { |x| puts "Response #{i+=1}:   #{x} " }
+    response.each { |x| assert_not_nil x }
+    assert_not_nil response
+  end
+
+  def test_search_by_incorrect_chebiid
+    puts "\n\n ---------------------search by incorrect chebiid---------------------\n\n"
+    response = []
+    i = 0
+    response = @instance.search_by_chebiid("THIS IS NOT A VALID CHEBIID!!!!!<P></P>")
+    response.each { |x| puts "Response #{i+=1}:   #{x} " }
+    response.each { |x| assert_not_nil x }
+    assert_not_nil response
+  end
+
+
+  def test_search_by_name
+    puts "\n\n ---------------------model ID by name---------------------\n\n"
+    response = []
+    i = 0
+    response = @instance.search_by_name("Kolomeisky2003") #_MyosinV_Processivity")
+    response.each { |x| puts "Response #{i+=1}:   #{x} " }
+    response.each { |x| assert_not_nil x }
+    assert_not_nil response
+  end
+
+  def test_search_by_incorrect_name
+    puts "\n\n ---------------------model ID by incorrect name---------------------\n\n"
+    response = []
+    i = 0
+    response = @instance.search_by_name("THIS IS NOT A VALID NAME!!!!!<P></P>") #_MyosinV_Processivity")
+    response.each { |x| puts "Response #{i+=1}:   #{x} " }
+    response.each { |x| assert_not_nil x }
+    assert_not_nil response
+  end
 
-  include SysMODB::SearchBiomodel
-
-   def test_find_all_models
-      puts "\n\n ---------------------find all models---------------------\n\n"
-      response = []
-      i=0
-      response = get_all_models
-      response.each {|x| puts "Response #{i+=1}:   #{x[:key].to_s} "}
-      response.each {|x| assert_not_nil x[:key] }
-      assert_not_nil response
-   end
-
-
-   def test_search_by_ChEBIID
-      puts "\n\n ---------------------search by chebiid---------------------\n\n"
-      response = []
-      i = 0 
-      response = search_by_ChEBIID("CHEBI:15422")
-      response.each {|x| puts "Response #{i+=1}:   #{x} "}
-      response.each {|x| assert_not_nil x }
-      assert_not_nil response
-   end
-
-   def test_search_by_name
-      puts "\n\n ---------------------model ID by name---------------------\n\n"
-      response = []
-      i = 0 
-      response = search_by_name("Kolomeisky2003")    #_MyosinV_Processivity")
-      response.each {|x| puts "Response #{i+=1}:   #{x} "}
-      response.each {|x| assert_not_nil x }
-      assert_not_nil response
-   end
- 
 
   def test_get_model_name_by_id
-      puts "\n\n ---------------------model name by ID---------------------\n\n"
-      response = get_model_name_by_id("BIOMD0000000190")
-      puts response
-      assert_not_nil response
+    puts "\n\n ---------------------model name by ID---------------------\n\n"
+    response = @instance.get_model_name_by_id("BIOMD0000000190")
+    puts response
+    assert_not_nil response
+  end
+
+  def test_get_model_name_by_incorrect_id
+    puts "\n\n ---------------------model name by incorrect ID---------------------\n\n"
+    response = @instance.get_model_name_by_id("THIS IS NOT A VALID ID!!!!!<P></P>")
+    puts response
+    assert_not_nil response
   end
 
 
+  def test_search_id_by_person
+    puts "\n\n ---------------------model ID by person---------------------\n\n"
+    response = []
+    i=0
+    response = @instance.search_by_person("Jim")
+    response.each { |x| puts "Response #{i+=1}:    #{x} " }
+    response.each { |x| assert_not_nil x }
+    assert_not_nil response
+  end
 
-   def test_get_models_id_by_person
-      puts "\n\n ---------------------model ID by person---------------------\n\n"
-      response = []
-      i=0
-      response = get_models_id_by_person("Jim")
-      response.each {|x| puts "Response #{i+=1}:    #{x} "} 
-      response.each {|x| assert_not_nil x }
-      assert_not_nil response
+  def test_search_by_incorrect_person
+    puts "\n\n ---------------------model ID by incorrect person---------------------\n\n"
+    response = []
+    i=0
+    response = @instance.search_by_person("THIS IS NOT A VALID PERSONS NAME!!!!!<P></P>")
+    response.each { |x| puts "Response #{i+=1}:    #{x} " }
+    response.each { |x| assert_not_nil x }
+    assert_not_nil response
   end
 
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: search_biomodel
 version: !ruby/object:Gem::Version 
-  hash: 17
+  hash: 15
   prerelease: false
   segments: 
-  - 1
+  - 2
   - 0
-  - 3
-  version: 1.0.3
+  - 0
+  version: 2.0.0
 platform: ruby
 authors: 
 - Niall Beard
@@ -15,13 +15,13 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-05 00:00:00 +01:00
+date: 2012-02-17 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  prerelease: false
   name: jeweler
-  version_requirements: &id001 !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -32,12 +32,12 @@ dependencies:
         - 6
         - 2
         version: 1.6.2
-  requirement: *id001
   type: :development
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  prerelease: false
   name: rcov
-  version_requirements: &id002 !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -46,12 +46,12 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  requirement: *id002
   type: :development
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  prerelease: false
   name: savon
-  version_requirements: &id003 !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -62,8 +62,8 @@ dependencies:
         - 9
         - 2
         version: 0.9.2
-  requirement: *id003
   type: :development
+  version_requirements: *id003
 description: "Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine "
 email: beardn9@cs.man.ac.uk
 executables: []
@@ -75,6 +75,15 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .document
+- .idea/.name
+- .idea/.rakeTasks
+- .idea/dictionaries/root.xml
+- .idea/encodings.xml
+- .idea/misc.xml
+- .idea/modules.xml
+- .idea/search_biomodel.iml
+- .idea/vcs.xml
+- .idea/workspace.xml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -82,6 +91,8 @@ files:
 - Rakefile
 - VERSION
 - lib/search_biomodel.rb
+- search_biomodel-1.1.1.gem
+- search_biomodel-1.1.2.gem
 - search_biomodel.gemspec
 - test/helper.rb
 - test/test_search_biomodel.rb