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

Conflicts:
	.gitignore

.gitignore

@@ -7,3 +7,4 @@
 /build.properties
 /runtime.properties
 /ontology/public/catalog-v0001.xml
+

build.xml

@@ -69,6 +69,7 @@
 		<patternset id="appbase.patterns">
 			<include name="src/**/*" />
 			<include name="lib/**/*" />
+			<include name="rdf/**/*" />
 			<include name="test/**/*" />
 			<include name="themes/**/*" />
 			<include name="config/*.properties" />

doc/upgrade-1.6.html

@@ -48,6 +48,7 @@
                     	    <li><a href="#foafPersonTemplate">The foaf:Person template has been re-located.</a></li>
                     	    <li><a href="#multiple">Multiple foaf:Person Profile Pages</a></li>
                     	    <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="#BOGUS">ANYTHING ELSE?</a></li>
 	                    </ol>
 					</li>					
@@ -228,6 +229,139 @@
              	            areas of geographic focus.
              	        </p>
 
+                	    <h4 id="rdffiles">Auto-loaded RDF files move to the Home directory</h4>
+                	    <p>
+                	    	The RDF files that initialize the data model have moved, in both the distribution and 
+                	    	the runtime locations. 
+                	    	In the distribution, they have been collected in one place, and reorganized to use 
+                	    	a more consistent naming scheme. During the build process, they are copied to a
+                	    	location within the VIVO home directory, instead of residing in the webapp itself.
+                	    </p>
+                	    <p>
+                	    	If you have modified these RDF files, or added files of your own, you must adjust to
+                	    	the new locations accordingly.
+                	    	
+                	    </p>
+                	    	<h5>Old locations of RDF files</h5>
+<pre>/WEB-INF/ontologies/app/application.owl
+/WEB-INF/ontologies/app/aboutPage.n3
+/WEB-INF/ontologies/app/menu.n3
+/WEB-INF/ontologies/app/profilePageType.n3
+/WEB-INF/ontologies/app/loadedAtStartup/displayModelListViews.rdf
+/WEB-INF/ontologies/app/loadedAtStartup/homePageDataGetters.n3
+/WEB-INF/ontologies/app/loadedAtStartup/localeSelectionGUI.n3
+/WEB-INF/ontologies/app/loadedAtStartup/vivoListViewConfig.rdf
+/WEB-INF/ontologies/app/loadedAtStartup/vivoOrganizationDataGetters.n3
+/WEB-INF/ontologies/app/loadedAtStartup/vivoSearchProhibited.n3
+/WEB-INF/ontologies/app/menuload/displayTBOX.n3
+/WEB-INF/ontologies/app/menuload/displayDisplay.n3
+/WEB-INF/init-data/initialSiteConfig.rdf
+/WEB-INF/ontologies/user/abox/geopolitical.ver1.1-11-18-11-individual-labels.rdf
+/WEB-INF/ontologies/user/abox/vocabularySource-labels.n3
+/WEB-INF/ontologies/user/tbox/vitro-0.7-annotations.rdf
+/WEB-INF/ontologies/user/tbox/geopolitical-ver1.1-11-18-11-annotations.rdf
+/WEB-INF/ontologies/user/tbox/scires-1.5-annotations.rdf
+/WEB-INF/ontologies/user/tbox/vivo-core-1.5-annotations.rdf
+/WEB-INF/ontologies/user/tbox/isDefinedBy-1.5-annotations.rdf
+/WEB-INF/ontologies/user/applicationMetadata/propertygroups.rdf
+/WEB-INF/ontologies/user/applicationMetadata/classgroups.rdf
+/WEB-INF/filegraph/abox/us-states.rdf
+/WEB-INF/filegraph/abox/geopolitical.abox.ver1.1-11-18-11.owl
+/WEB-INF/filegraph/abox/academicDegree.rdf
+/WEB-INF/filegraph/abox/documentStatus.owl
+/WEB-INF/filegraph/abox/continents.n3
+/WEB-INF/filegraph/abox/vocabularySource.n3
+/WEB-INF/filegraph/abox/dateTimeValuePrecision.owl
+/WEB-INF/filegraph/tbox/vitroPublic.owl
+/WEB-INF/filegraph/tbox/vivo-dcterms-1.5.owl
+/WEB-INF/filegraph/tbox/scires-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-core-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-c4o-1.5.owl
+/WEB-INF/filegraph/tbox/geopolitical.tbox.ver1.1-11-18-11.owl
+/WEB-INF/filegraph/tbox/vivo-fabio-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-skos-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-event-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-foaf-1.5.owl
+/WEB-INF/filegraph/tbox/vitro-0.7.owl
+/WEB-INF/filegraph/tbox/vivo-pws-1.5.owl
+/WEB-INF/filegraph/tbox/isDefinedBy-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-dcelements-1.5.owl
+/WEB-INF/filegraph/tbox/vivo-bibo-1.5.owl</pre>
+
+                	    	<h5>New locations of RDF files</h5>
+<pre>rdf/display/firsttime/aboutPage.n3
+rdf/display/firsttime/application.owl
+rdf/display/firsttime/menu.n3
+rdf/display/firsttime/profilePageType.n3
+rdf/display/everytime/displayModelListViews.rdf
+rdf/display/everytime/homePageDataGetters.n3
+rdf/display/everytime/localeSelectionGUI.n3
+rdf/display/everytime/vivoListViewConfig.rdf
+rdf/display/everytime/vivoOrganizationDataGetters.n3
+rdf/display/everytime/vivoSearchProhibited.n3
+rdf/displayTbox/everytime/displayTBOX.n3
+rdf/displayDisplay/everytime/displayDisplay.n3
+rdf/applicationMetadata/firsttime/classgroups.rdf
+rdf/applicationMetadata/firsttime/initialSiteConfig.rdf
+rdf/applicationMetadata/firsttime/propertygroups.rdf
+rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf
+rdf/abox/firsttime/vocabularySource-labels.n3
+rdf/abox/filegraph/abox/academicDegree.rdf
+rdf/abox/filegraph/abox/continents.n3
+rdf/abox/filegraph/abox/dateTimeValuePrecision.owl
+rdf/abox/filegraph/abox/documentStatus.owl
+rdf/abox/filegraph/abox/geopolitical.abox.ver1.1-11-18-11.owl
+rdf/abox/filegraph/abox/us-states.rdf
+rdf/abox/filegraph/abox/vocabularySource.n3
+rdf/tbox/firsttime/geopolitical-ver1.1-11-18-11-annotations.rdf
+rdf/tbox/firsttime/isDefinedBy-1.5-annotations.rdf
+rdf/tbox/firsttime/scires-1.5-annotations.rdf
+rdf/tbox/firsttime/vitro-0.7-annotations.rdf
+rdf/tbox/firsttime/vivo-core-1.5-annotations.rdf
+rdf/tbox/filegraph/tbox/geopolitical.tbox.ver1.1-11-18-11.owl
+rdf/tbox/filegraph/tbox/isDefinedBy-1.5.owl
+rdf/tbox/filegraph/tbox/scires-1.5.owl
+rdf/tbox/filegraph/tbox/vitro-0.7.owl
+rdf/tbox/filegraph/tbox/vitroPublic.owl
+rdf/tbox/filegraph/tbox/vivo-bibo-1.5.owl
+rdf/tbox/filegraph/tbox/vivo-c4o-1.5.owl
+rdf/tbox/filegraph/tbox/vivo-core-1.5.owl
+rdf/tbox/filegraph/tbox/vivo-dcelements-1.5.owl
+rdf/tbox/filegraph/tbox/vivo-dcterms-1.5.owl
+rdf/tbox/filegraph/tbox/vivo-event-1.5.owl
+rdf/tbox/filegraph/tbox/vivo-fabio-1.5.owl
+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
+                	    	to the build script so the RDF files will be merged properly across the tiers. So this:
+<pre>&lt;patternset id="appbase.patterns"&gt;
+&lt;include name="src/**/*" /&gt;
+&lt;include name="lib/**/*" /&gt;
+&lt;include name="test/**/*" /&gt;
+&lt;include name="themes/**/*" /&gt;
+&lt;include name="config/*.properties" /&gt;
+&lt;include name="config/*.txt" /&gt;
+&lt;include name="config/jarlist/*.txt" /&gt;
+&lt;include name="config/solr/*" /&gt;
+&lt;include name="context.xml" /&gt;
+&lt;/patternset&gt;</pre>
+ becomes this: 
+ <pre>&lt;patternset id="appbase.patterns"&gt;
+&lt;include name="src/**/*" /&gt;
+&lt;include name="lib/**/*" /&gt;
+&lt;include name="rdf/**/*" /&gt;
+&lt;include name="test/**/*" /&gt;
+&lt;include name="themes/**/*" /&gt;
+&lt;include name="config/*.properties" /&gt;
+&lt;include name="config/*.txt" /&gt;
+&lt;include name="config/jarlist/*.txt" /&gt;
+&lt;include name="config/solr/*" /&gt;
+&lt;include name="context.xml" /&gt;
+&lt;/patternset&gt;</pre>
+                	    </p>
+
                 	    <h4 id="BOGUS">ANYTHING ELSE?</h4>
              	        <p>
              	        </p>
@@ -514,6 +648,11 @@
                         </li>
                     </ul>
                 </blockquote>
+                <p>
+                    4. Apply any previous changes you have made to the RDF initialization files. 
+                    See the section on the <a href="#rdffiles">Auto-loaded RDF files</a>
+                    above for more details. 
+                </p>
                 <p>
                     5. Stop Apache Tomcat and from your VIVO source directory, run 
                     ant  

rdf/display/everytime/aboutPage_es.n3

@@ -7,7 +7,7 @@ about:ABOUTDG
         """<h2>Acerca VIVO</h2>
         <div class=\"pageGroupBody\" id=\"aboutText\"><p>La aplicación VIVO permite el descubrimiento de los investigadores a través de las instituciones. Los participantes en la red se encuentran instituciones con instalaciones locales de VIVO o con la investigación y el descubrimiento de aplicaciones de perfiles que pueden proporcionar datos web compatibles semánticas. Por tanto, la información accesible a través de la búsqueda de VIVO y capacidad de exploración se residir y ser controlado a nivel local, dentro de vivos institucionales o de otras aplicaciones web compatibles con semánticos.</p>
 
-        <p>VIVO es una aplicación web semántica código abierto originalmente desarrollado e implementado en Cornell. Cuando se instala y se rellena con el contenido en una institución, que permite el descubrimiento de la investigación y de becas en todas las disciplinas de esta institución. VIVO compatible con la navegación y una función de búsqueda que devuelve resultados facetas para una rápida recuperación de la información deseada. Contenido en cualquier instalación VIVO local puede mantenerse manualmente o puesto en la base de datos de forma automática de los sistemas locales de registro, tales como recursos humanos, carreras impulsadas, becas, cursos, y bases de datos de la actividad docente.</p>
+        <p>VIVO es una aplicación web semántica código abierto originalmente desarrollado e implementado en Cornell. Cuando se instala y se rellena con el contenido en una institución, que permite el descubrimiento de la investigación y de becas en todas las disciplinas de esta institución. VIVO compatible con la navegación y una función de búsqueda que devuelve resultados facetas para una rápida recuperación de la información deseada. Contenido en cualquier instalación VIVO local puede mantenerse manualmente o puesto en la base de datos de forma automática de los sistemas locales de registro, tales como recursos humanos, becas, cursos, y bases de datos de la actividad docente.</p>
 
         <p>Ver más información sobre el <a href=\"http://vivoweb.org\">Proyecto VIVO</a>.</p></div>
         """@es .

rdf/display/firsttime/aboutPage.n3

@@ -8,7 +8,7 @@ about:ABOUTDG
         """<h2>About VIVO</h2>
         <div class=\"pageGroupBody\" id=\"aboutText\"><p>The VIVO application enables the discovery of researchers across institutions. Participants in the network include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through VIVO's search and browse capability will therefore reside and be controlled locally, within institutional VIVOs or other semantic web-compliant applications.</p>
 
-        <p>VIVO is an open source semantic web application originally developed and implemented at Cornell. When installed and populated with content at an institution, it enables the discovery of research and scholarship across disciplines at that institution. VIVO supports browsing and a search function which returns faceted results for rapid retrieval of desired information. Content in any local VIVO installation may be maintained manually or brought into the database in automated ways from local systems of record, such as grants, course, and faculty activity databases.</p>
+        <p>VIVO is an open source semantic web application originally developed and implemented at Cornell. When installed and populated with content at an institution, it enables the discovery of research and scholarship across disciplines at that institution. VIVO supports browsing and a search function which returns faceted results for rapid retrieval of desired information. Content in any local VIVO installation may be maintained manually or brought into the database in automated ways from local systems of record, such as human resources, scholarships, grants, course, and faculty activity databases.</p>
 
         <p>See more information on the <a href=\"http://vivoweb.org\">VIVO Project</a>.</p></div>
         """@en ;