Merge branch 'develop' of https://github.com/vivo-project/VIVO into develop

doc/upgrade-1.6.html

@@ -50,6 +50,7 @@
                     	    <li><a href="#homePage">Home Page Re-design</a></li>
                     	    <li><a href="#rdffiles">Auto-loaded RDF files move to the Home directory</a></li>
                     	    <li><a href="#language">Support for additional languages</a></li>
+                    	    <li><a href="#extended_lod">More compact responses to Linked data requests</a></li>
 	                        <li><a href="#BOGUS">ANYTHING ELSE?</a></li>
 	                    </ol>
 					</li>					
@@ -335,8 +336,9 @@ rdf/tbox/filegraph/tbox/vivo-foaf-1.5.owl
 rdf/tbox/filegraph/tbox/vivo-pws-1.5.owl
 rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
                 	    <p>
-                	    	If you are using a three-tier build process, you will need to add a single line
+                	    	If you are using a three-tier build process, you will need to add two lines
-                	    	to the build script so the RDF files will be merged properly across the tiers. So this:
+                	    	to the build script to accomodate the RDF files, and the language support (see below)
+                	    	So this:
 <pre>&lt;patternset id="appbase.patterns"&gt;
 &lt;include name="src/**/*" /&gt;
 &lt;include name="lib/**/*" /&gt;
@@ -353,6 +355,7 @@ rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
 &lt;include name="src/**/*" /&gt;
 &lt;include name="lib/**/*" /&gt;
 &lt;include name="rdf/**/*" /&gt;
+&lt;include name="languages/**/*" /&gt;
 &lt;include name="test/**/*" /&gt;
 &lt;include name="themes/**/*" /&gt;
 &lt;include name="config/*.properties" /&gt;
@@ -387,6 +390,47 @@ rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
              	        	Add a new language to VIVO</a>.
              	        </p>
 
+                	    <h4 id="extended_lod">More compact responses to Linked data requests</h4>
+             	        <p>
+             	        	In VIVO 1.6, the response to requests for linked data is changed, to be smaller and faster.
+             	        </p>
+             	        <p>
+	             	        When responding to a request for linked data about an individual, VIVO 1.6 returns:
+	             	        <ul>
+	             	        <li>Data properties of the individual</li>
+	             	        <li>Object relationships to and from the individual</li>
+	             	        <li>The RDF types and RDFS labels for any object that directly relates to the individual</li>
+	             	        </ul>
+	             	        This data is filtered by the usual VIVO privacy policies, 
+	             	        so properties such as salary or employee ID number may not be revealed 
+	             	        unless the requester has been properly authenticated.
+             	        </p>
+             	        <p>
+	             	        VIVO releases prior to VIVO 1.6 returned a more complex set of statements, 
+	             	        referred to as "extended linked data":
+	             	        <ul>
+	             	        <li>Data properties of the individual</li>
+	             	        <li>Object relationships from the individual</li>
+	             	        <li>All properties of the context nodes (positions, roles, etc.) that are associated with the individual.</li>
+	             	        <li>Labels of objects that are joined to the individual through context nodes.</li>
+	             	        <li>Full details of time intervals that are attached to context nodes: start, end, precision.</li>
+	             	        </ul>
+	             	        As above, this data was filtered by the VIVO privacy policies.
+	                        Although these additional items were included, 
+	                        extended linked data was based only on relationships from the individual. 
+	                        Relationships to the individual were not included.	
+	             	        </p>
+             	        <p>
+             	        	Extended linked data was costly to produce, in terms of resources, 
+             	        	because it required a recursive search of the data model. 
+             	        	Extended linked data typically contained 50% more information than its non-extended equivalent, 
+             	        	and took more than 10 times as long to produce.
+             	        </p>
+             	        <p>
+             	        	VIVO release 1.6 can be configured to produce extended linked data like previous releases.
+             	        	However, extended linked data will not be supported in future releases.
+             	        </p>
+
                 	    <h4 id="BOGUS">ANYTHING ELSE?</h4>
              	        <p>
              	        </p>
@@ -614,7 +658,7 @@ rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
                     </tr>
                     <tr class="odd_row blue">
                         <td>
-                          developer.defeatI18nCache = true
+                          developer.defeatI18nCache
                         </td>
                         <td>
                           false
@@ -632,7 +676,7 @@ rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
                     </tr>
                     <tr class="odd_row blue">
                         <td>
-                          developer.insertFreemarkerDelimiters = true
+                          developer.insertFreemarkerDelimiters
                         </td>
                         <td>
                           false
@@ -647,7 +691,7 @@ rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
                     </tr>
                     <tr class="odd_row blue">
                         <td>
-                          homePage.geoFocusMaps = enabled
+                          homePage.geoFocusMaps
                         </td>
                         <td>
                           enabled
@@ -667,13 +711,35 @@ rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
                     </tr>
                     <tr class="odd_row blue">
                         <td>
-                          MultiViews.profilePageTypes=disabled
+                          MultiViews.profilePageTypes
                         </td>
                         <td>
                           disabled
                         </td>
                     </tr>
                     
+                    <tr>
+                        <td colspan="2">
+                          Setting this property causes VIVO 1.6 to produce extended responses to requests
+                          for linked data. This provides compatibility with earlier releases.
+                          The default is <code>false</code>.
+                          <br/>
+                          Extended linked data is costly, in terms of server resource. Typically, extended 
+                          linke data contains 50% more information than its non-extended equivalent, and
+                          takes 10 times as long to produce.
+                          <br/>
+                          <b>Extended linked data will not be supported in future releases of VIVO.</b>
+                        </td>
+                    </tr>
+                    <tr class="odd_row blue">
+                        <td>
+                          serveExtendedLinkedData
+                        </td>
+                        <td>
+                          true
+                        </td>
+                    </tr>
+                    
                 </tbody>
             </table>
 

src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/IndividualSearchResult.java

@@ -16,18 +16,18 @@ public class IndividualSearchResult extends BaseIndividualSearchResult {
        
     public IndividualSearchResult(Individual individual, VitroRequest vreq) {
     	super(individual, vreq);
-    	log.info("Called Individual Search Result");
+    	log.debug("Called Individual Search Result");
     }
     
     /* Access methods for templates */
     
     public String getPreferredTitle() {
-    	log.info("Called get Title");
+    	log.debug("Called get Title");
         return individual.getDataValue(CORE + "preferredTitle");
     }
     
     public String getEmail() {
-    	log.info("Called get Email");
+    	log.debug("Called get Email");
     	return individual.getDataValue(CORE + "email");
     }
 

utilities/acceptance-tests/suites/AdminSecurity/NewAdminCheckPrivileges.html

@@ -128,7 +128,7 @@
 </tr>
 <tr>
 	<td>verifyElementPresent</td>
-	<td>link=Restrict Logins</td>
+	<td>link=Restrict logins</td>
 	<td></td>
 </tr>
 <tr>
@@ -329,7 +329,7 @@
 </tr>
 <tr>
 	<td>verifyTextPresent</td>
-	<td>Page Management</td>
+	<td>Page management</td>
 	<td></td>
 </tr>
 <tr>
@@ -504,7 +504,7 @@
 </tr>
 <tr>
 	<td>verifyTextPresent</td>
-	<td>Email Address</td>
+	<td>Email address</td>
 	<td></td>
 </tr>
 <tr>

utilities/acceptance-tests/suites/AdminSecurity/NewAdminDelete.html

@@ -124,7 +124,7 @@
 </tr>
 <tr>
 	<td>verifyTextPresent</td>
-	<td>Deleted 1 accounts.</td>
+	<td>Deleted 1 account.</td>
 	<td></td>
 </tr>
 <tr>

utilities/acceptance-tests/suites/AdminSecurity/NewAdminFirstLogin.html

@@ -223,7 +223,7 @@
 </tr>
 <tr>
 	<td>verifyTextPresent</td>
-	<td>Please enter a password between 6 and 12 characters in length.</td>
+	<td>Password must be between 6 and 12 characters.</td>
 	<td></td>
 </tr>
 <!--Try using the original password as the new password-->

utilities/releaseScripts/4_extract_files.rb

@@ -21,7 +21,23 @@ require '_common'
 #
 # Get the VIVO files and the Vitro files, and remove the .git directories.
 #
-def export_files(vivo_path, vitro_path, tag, export_dir)
+def export_files(vivo_path, vitro_path, tag, branch, export_dir)
+	Dir.chdir(vivo_path) do |path|
+		cmds = ["git checkout #{branch}", 
+				"git pull",
+				]
+		cmds.delete_at(1) unless is_remote_branch?(branch)
+		approve_and_execute(cmds, "in #{path}")
+	end
+	
+	Dir.chdir(vitro_path) do |path|
+		cmds = ["git checkout #{branch}", 
+				"git pull",
+				]
+		cmds.delete_at(1) unless is_remote_branch?(branch)
+		approve_and_execute(cmds, "in #{path}")
+	end
+	
 	approve_and_execute([
 			"rm -Rf #{File.expand_path("..", export_dir)}",
 			"mkdir -pv #{export_dir}",
@@ -31,6 +47,10 @@ def export_files(vivo_path, vitro_path, tag, export_dir)
 			])
 end
 
+def is_remote_branch?(branch)
+	! `git branch --list -a origin/#{branch}`.strip.empty?
+end
+
 #
 # ------------------------------------------------------------------------------------
 # Main method
@@ -39,6 +59,7 @@ end
 
 begin
 	tag = Settings.tag_name
+	branch = Settings.branch_name
 	vivo_path = Settings.vivo_path
 	vitro_path = Settings.vitro_path
 	export_dir = Settings.export_dir
@@ -54,7 +75,7 @@ begin
 	
 	get_permission_and_go(p) do
 		puts "Building export area"
-		export_files(vivo_path, vitro_path, tag, export_dir)
+		export_files(vivo_path, vitro_path, tag, branch, export_dir)
 	end
 rescue BadState
 	puts "#{$!.message} - Aborting."

utilities/releaseScripts/8_push_changes.rb

@@ -0,0 +1,39 @@
+=begin
+--------------------------------------------------------------------------------
+
+Push any branches, tags, or merges back to GitHub.
+
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+=end
+
+$: << File.dirname(File.expand_path(__FILE__))
+require '_common'
+
+#
+# Merge the maintenance branch to the master branch and create the tag.
+#
+def push_to_origin(repo_path)
+	Dir.chdir(repo_path) do |path|
+		approve_and_execute(["git push --all", "git push --tags"], "in #{path}")
+	end
+end
+
+#
+# ------------------------------------------------------------------------------------
+# Main method
+# ------------------------------------------------------------------------------------
+#
+
+begin
+	vivo_path = Settings.vivo_path
+	vitro_path = Settings.vitro_path
+	
+	get_permission_and_go("OK to push changes to the origin?") do
+		puts "Merging tags"
+		push_to_origin(vivo_path)
+		push_to_origin(vitro_path)
+	end
+rescue BadState
+	puts "#{$!.message} - Aborting."
+end