Merge branch 'rel-1.12.0-RC' into main

.github/workflows/build.yml

@@ -28,4 +28,4 @@ jobs:
           java-version: 11
 
       - name: Maven Build
-        run: mvn clean install
+        run: mvn clean package -s installer/example-settings.xml

.github/workflows/deploy.yml

@@ -35,7 +35,7 @@ jobs:
           server-password: MAVEN_PASSWORD
 
       - name: Maven Deploy
-        run: mvn --batch-mode deploy
+        run: mvn --batch-mode deploy -Pskip
         env:
           MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }}
           MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}

.github/workflows/docker.yml

@@ -32,7 +32,7 @@ jobs:
           java-version: 11
 
       - name: Maven Build
-        run: mvn clean install
+        run: mvn clean package -s installer/example-settings.xml
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v1

Dockerfile

@@ -1,20 +1,18 @@
 FROM tomcat:9-jdk11-openjdk
 
 ARG SOLR_URL=http://localhost:8983/solr/vivocore
-ARG VIVO_DIR=/opt/vivo/home
+ARG VIVO_DIR=/usr/local/vivo/home
 ARG TDB_FILE_MODE=direct
 
 ENV SOLR_URL=${SOLR_URL}
-ENV JAVA_OPTS="${JAVA_OPTS} -Dvivo-dir=$VIVO_DIR -Dtdb:fileMode=$TDB_FILE_MODE"
+ENV JAVA_OPTS="${JAVA_OPTS} -Dtdb:fileMode=$TDB_FILE_MODE"
 
-RUN mkdir /opt/vivo
+RUN mkdir /usr/local/vivo
-RUN mkdir /opt/vivo/home
+RUN mkdir /usr/local/vivo/home
 
+COPY ./installer/home/target/vivo /vivo-home
 COPY ./installer/webapp/target/vivo.war /usr/local/tomcat/webapps/ROOT.war
 
-COPY ./home/src/main/resources/config/default.applicationSetup.n3 /applicationSetup.n3
-COPY ./home/src/main/resources/config/default.runtime.properties /runtime.properties
-
 COPY start.sh /start.sh
 
 EXPOSE 8080

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2018, Cornell University
+Copyright (c) 2021, Cornell University
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -19,7 +19,7 @@ https://wiki.duraspace.org/display/VIVO/
 ### Installation Instructions
 
 Installation instructions for the latest release can be found at this location on the wiki:  
-https://wiki.duraspace.org/display/VIVODOC110x/Installing+VIVO
+https://wiki.duraspace.org/display/VIVODOC112x/Installing+VIVO
 
 ### Docker
 
@@ -27,7 +27,7 @@ VIVO docker container is available at [vivoweb/vivo](https://hub.docker.com/repo
 
 ### Docker Compose
 
-Docker Compose environment variables.
+Docker Compose environment variables:
 
 .env defaults
 ```
@@ -36,14 +36,27 @@ RESET_HOME=false
 RESET_CORE=false
 ```
 
-- `LOCAL_VIVO_HOME`: VIVO home directory on your host machine which will mount to volume in docker container.
+- `LOCAL_VIVO_HOME`: VIVO home directory on your host machine which will mount to volume in docker container. Set this environment variable to persist your VIVO data on your host machine.
-- `RESET_HOME`: Convinience to reset VIVO home when starting container. **Caution** will delete local configuration, content, and configuration model.
+- `RESET_HOME`: Convenience to reset VIVO home when starting container. **Caution**, will delete local configuration, content, and configuration model.
-- `RESET_CORE`: Convinience to reset VIVO Solr core when starting container. **Caution** will require complete reindex.
+- `RESET_CORE`: Convenience to reset VIVO Solr core when starting container. **Caution**, will require complete reindex.
+
+Before building VIVO, you will also need to clone (and switch to the same branch, if other than main) of [Vitro](https://github.com/vivo-project/Vitro). The Vitro project must be cloned to a sibling directory next to VIVO so that it can be found during the build. You will also need to clone (and switch to the appropriate branch) of [Vitro-languages](https://github.com/vivo-project/Vitro-languages) and [VIVO-languages](https://github.com/vivo-project/VIVO-languages).
 
 Build and start VIVO.
 
+1. In Vitro-languages, run:
 ```
-mvn clean install
+mvn install
+```
+
+2. In VIVO-languages, run:
+```
+mvn install
+```
+
+3. In VIVO (with Vitro cloned alongside it), run:
+```
+mvn clean package -s installer/example-settings.xml
 docker-compose up
 ```
 

api/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-api</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-project</artifactId>
-        <version>1.11.2-SNAPSHOT</version>
+        <version>1.12.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

api/src/main/java/edu/cornell/mannlib/semservices/service/impl/UMLSService.java

@@ -4,12 +4,18 @@ package edu.cornell.mannlib.semservices.service.impl;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Properties;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.apache.http.HttpVersion;
+import org.apache.http.client.fluent.Form;
+import org.apache.http.client.fluent.Request;
+import org.apache.http.client.utils.URIBuilder;
+import org.springframework.util.StringUtils;
 
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
@@ -18,11 +24,6 @@ import edu.cornell.mannlib.semservices.bo.Concept;
 import edu.cornell.mannlib.semservices.exceptions.ConceptsNotFoundException;
 import edu.cornell.mannlib.semservices.service.ExternalConceptService;
 import edu.cornell.mannlib.vitro.webapp.utils.json.JacksonUtils;
-import org.apache.http.HttpVersion;
-import org.apache.http.client.fluent.Form;
-import org.apache.http.client.fluent.Request;
-import org.apache.http.client.utils.URIBuilder;
-import org.springframework.util.StringUtils;
 
 /**
  * @author jaf30
@@ -54,11 +55,13 @@ public class UMLSService implements ExternalConceptService {
     private static String UMLS_AUTH_USER_URL = "https://utslogin.nlm.nih.gov/cas/v1/tickets";
     private static String UMLS_AUTH_KEY_URL = "https://utslogin.nlm.nih.gov/cas/v1/api-key";
     private static String UTS_SERVICE_URL   = "http://umlsks.nlm.nih.gov";
+    private static final String UMLS_PROPERTIES =  "/umls.properties";
+    private static final Log log = LogFactory.getLog(UMLSService.class);
 
     {
         if (username == null || apikey == null) {
             final Properties properties = new Properties();
-            try (InputStream stream = getClass().getResourceAsStream("/umls.properties")) {
+            try (InputStream stream = getClass().getResourceAsStream(UMLS_PROPERTIES)) {
                 properties.load(stream);
                 username = properties.getProperty("username");
                 password = properties.getProperty("password");
@@ -73,11 +76,18 @@ public class UMLSService implements ExternalConceptService {
                         }
                     }
                 } catch (Exception e) {
+                    log.error(e, e);
                 }
             } catch (IOException e) {
+                log.error(e, e);
             }
         }
     }
+    
+    public static boolean configurationFileExists() {
+        URL config = UMLSService.class.getResource(UMLS_PROPERTIES);
+        return (config != null);        
+    }
 
     public boolean isConfigured() {
         return !(StringUtils.isEmpty(username) && StringUtils.isEmpty(apikey));

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java

@@ -69,7 +69,7 @@ public class ManagePublicationsForIndividualController extends FreemarkerHttpSer
         + "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
-        + "SELECT DISTINCT ?subclass ?authorship (str(?label) as ?title) ?pub ?hideThis WHERE { \n"
+        + "SELECT DISTINCT ?subclass ?authorship (?label as ?title) ?pub ?hideThis WHERE { \n"
         + "    ?subject core:relatedBy ?authorship . \n"
         + "    ?authorship a core:Authorship  . \n"
         + "    OPTIONAL { \n "

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForPersonGenerator.java

@@ -15,6 +15,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Set;
 
 import javax.servlet.http.HttpSession;
 
@@ -41,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.FoafNameToRdfsLabelPreprocessor;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.ManageLabelsForPersonPreprocessor;
 import edu.cornell.mannlib.vitro.webapp.i18n.selection.SelectedLocale;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.filter.LanguageFilteringUtils;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.DataPropertyStatementTemplateModel;
 
 /**
@@ -246,12 +248,12 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 
 	private void addFormSpecificData(EditConfigurationVTwo config,
 			VitroRequest vreq) {
-		//Get all language codes/labels in the system, and this list is sorted by language name
+	    ArrayList<Literal> existingLabels = this.getExistingLabels(config.getSubjectUri(), vreq);
-        List<HashMap<String, String>> locales = this.getLocales(vreq);
+		//Get language codes/labels for existing labels, and this list is sorted by language name
+        List<HashMap<String, String>> locales = this.getLocales(vreq, existingLabels);
         //Get code to label hashmap - we use this to get the language name for the language code returned in the rdf literal
         HashMap<String, String> localeCodeToNameMap = this.getFullCodeToLanguageNameMap(locales);
 		//the labels already added by the user
-		ArrayList<Literal> existingLabels = this.getExistingLabels(config.getSubjectUri(), vreq);
 		int numberExistingLabels = existingLabels.size();
 		//existing labels keyed by language name and each of the list of labels is sorted by language name
 		HashMap<String, List<LabelInformation>> existingLabelsByLanguageName = this.getLabelsSortedByLanguageName(existingLabels, localeCodeToNameMap, config, vreq);
@@ -432,28 +434,27 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 	        + "    ?subject rdfs:label ?label \n"
 	        + "} ORDER BY ?label";
 
-
+	
     private ArrayList<Literal>  getExistingLabels(String subjectUri, VitroRequest vreq) {
         String queryStr = QueryUtils.subUriForQueryVar(LABEL_QUERY, "subject", subjectUri);
         log.debug("queryStr = " + queryStr);
 
         ArrayList<Literal>  labels = new ArrayList<Literal>();
         try {
-        	//We want to get the labels for all the languages, not just the display language
+            // No longer retrieving language-neutral results here, so that
-            ResultSet results = QueryUtils.getLanguageNeutralQueryResults(queryStr, vreq);
+            // language editing is consistent with other editing forms.
+            // Editable values depend on the interface's locale selector.
+            ResultSet results = QueryUtils.getQueryResults(queryStr, vreq);
             while (results.hasNext()) {
                 QuerySolution soln = results.nextSolution();
                 Literal nodeLiteral = soln.get("label").asLiteral();
                 labels.add(nodeLiteral);
-
-
             }
         } catch (Exception e) {
             log.error(e, e);
         }
        return labels;
-}
+    }
-
 
 
     //Putting this into a method allows overriding it in subclasses
@@ -467,30 +468,32 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
     	return template;
     }
 
+    //get locales present in list of literals
+    public List<HashMap<String, String>> getLocales(VitroRequest vreq, 
+            List<Literal> existingLiterals) {
+        Set<Locale> locales = new HashSet<Locale>();
+        for(Literal literal : existingLiterals) {
+            String language = literal.getLanguage();
+            if(!StringUtils.isEmpty(language)) {
+                locales.add(LanguageFilteringUtils.languageToLocale(language));
+            }
+        }
+        if (locales.isEmpty()) {
+            return Collections.emptyList();
+        }
+        List<HashMap<String, String>> list = new ArrayList<HashMap<String, String>>();
+        Locale currentLocale = SelectedLocale.getCurrentLocale(vreq);
+        for (Locale locale : locales) {
+            try {
+                list.add(buildLocaleMap(locale, currentLocale));
+            } catch (FileNotFoundException e) {
+                log.warn("Can't show locale '" + locale + "': " + e);
+            }
+        }
 
-
+        return list;
-    //get locales
-    public List<HashMap<String, String>> getLocales(VitroRequest vreq) {
-    	List<Locale> selectables = SelectedLocale.getSelectableLocales(vreq);
-		if (selectables.isEmpty()) {
-			return Collections.emptyList();
-		}
-		List<HashMap<String, String>> list = new ArrayList<HashMap<String, String>>();
-		Locale currentLocale = SelectedLocale.getCurrentLocale(vreq);
-		for (Locale locale : selectables) {
-			try {
-				list.add(buildLocaleMap(locale, currentLocale));
-			} catch (FileNotFoundException e) {
-				log.warn("Can't show the Locale selector for '" + locale
-						+ "': " + e);
-			}
-		}
-
-		return list;
     }
 
-
-
     public HashMap<String, String> getFullCodeToLanguageNameMap(List<HashMap<String, String>> localesList) {
     	HashMap<String, String> codeToLanguageMap = new HashMap<String, String>();
     	for(Map<String, String> locale: localesList) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/ConceptSearchService/ConceptSearchServiceUtils.java

@@ -12,6 +12,7 @@ import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.semservices.bo.Concept;
 import edu.cornell.mannlib.semservices.service.ExternalConceptService;
+import edu.cornell.mannlib.semservices.service.impl.UMLSService;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 /**
  * Utilities for search
@@ -38,7 +39,9 @@ public class ConceptSearchServiceUtils {
 	//URL to label
 	public static HashMap<String, VocabSourceDescription> getVocabSources() {
 		HashMap<String, VocabSourceDescription> map = new HashMap<String, VocabSourceDescription>();
-    	map.put(UMLSVocabSource, new VocabSourceDescription("UMLS", UMLSVocabSource, "http://www.nlm.nih.gov/research/umls/", "Unified Medical Language System"));
+        if(UMLSService.configurationFileExists()) {
+    	    map.put(UMLSVocabSource, new VocabSourceDescription("UMLS", UMLSVocabSource, "http://www.nlm.nih.gov/research/umls/", "Unified Medical Language System"));
+        }
     	//Commenting out agrovoc for now until implementation is updated
     	map.put(AgrovocVocabSource, new VocabSourceDescription("AGROVOC", AgrovocVocabSource, "http://www.fao.org/agrovoc/", "Agricultural Vocabulary"));
     	map.put(GemetVocabSource, new VocabSourceDescription("GEMET", GemetVocabSource, "http://www.eionet.europa.eu/gemet", "GEneral Multilingual Environmental Thesaurus"));
@@ -53,6 +56,7 @@ public class ConceptSearchServiceUtils {
     //Get the hashmap mapping service name to Service class
     private static HashMap<String, String> getMapping() {
     	HashMap<String, String> map = new HashMap<String, String>();
+
     	map.put(UMLSVocabSource, "edu.cornell.mannlib.semservices.service.impl.UMLSService");
     	map.put(AgrovocVocabSource, "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
     	map.put(GemetVocabSource, "edu.cornell.mannlib.semservices.service.impl.GemetService");

api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java

@@ -2,29 +2,40 @@
 
 package org.vivoweb.webapp.sitemap;
 
-import org.apache.commons.lang3.StringUtils;
+import java.io.FileInputStream;
-import org.apache.jena.query.QuerySolution;
+import java.io.IOException;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
+import java.io.InputStream;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import java.util.ArrayList;
-import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
+import java.util.List;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
-import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
-import org.apache.commons.io.IOUtils;
 
 import javax.servlet.ServletException;
 import javax.servlet.ServletOutputStream;
 import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-import java.io.FileInputStream;
+
-import java.io.IOException;
+import org.apache.commons.io.IOUtils;
-import java.io.InputStream;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.jena.query.QuerySolution;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
+import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
 
 @WebServlet(name = "SiteMapServlet", urlPatterns = {"/robots.txt","/sitemap.xml"})
 public class SiteMapServlet extends VitroHttpServlet {
+    
+    private static final int MAX_URLS = 50000; // max URLs per sitemap
+    private static final Log log = LogFactory.getLog(SiteMapServlet.class);
+    
     @Override
-    protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+    protected void doGet(HttpServletRequest request, HttpServletResponse response) 
+            throws ServletException, IOException {
         String requestURI  = request.getRequestURI();
 
         if (requestURI != null) {
@@ -60,7 +71,7 @@ public class SiteMapServlet extends VitroHttpServlet {
                         "WHERE\n" +
                         "{\n" +
                         "  ?person a foaf:Person .\n" +
-                        "}\n";
+                        "} LIMIT " + MAX_URLS + "\n";
 
                 final VitroRequest vreq = new VitroRequest(request);
                 final ServletOutputStream out = response.getOutputStream();
@@ -68,28 +79,33 @@ public class SiteMapServlet extends VitroHttpServlet {
                 out.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
                 out.println("<urlset xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\">");
 
+                List<String> personURIs = new ArrayList<String>();
+                
                 try {
                     vreq.getRDFService().sparqlSelectQuery(query, new ResultSetConsumer() {
                         @Override
                         protected void processQuerySolution(QuerySolution qs) {
-                            String person = qs.getResource("person").getURI();
+                            personURIs.add(qs.getResource("person").getURI());                            
-
-                            String profileUrl = UrlBuilder.getIndividualProfileUrl(person, vreq);
-
-                            if (!StringUtils.isEmpty(profileUrl)) {
-                                try {
-                                    out.println("  <url>");
-                                    out.println("    <loc>" + schemeAndServer + profileUrl + "</loc>");
-                                    out.println("    <changefreq>weekly</changefreq>");
-                                    out.println("  </url>");
-                                } catch (Exception e) {
-                                }
-                            }
                         }
                     });
                 } catch (RDFServiceException rse) {
+                    log.error(rse, rse);
                 }
 
+                for(String person : personURIs) {
+                    String profileUrl = UrlBuilder.getIndividualProfileUrl(person, vreq);    
+                    if (!StringUtils.isEmpty(profileUrl)) {
+                        try {
+                            out.println("  <url>");
+                            out.println("    <loc>" + schemeAndServer + profileUrl + "</loc>");
+                            out.println("    <changefreq>weekly</changefreq>");
+                            out.println("  </url>");
+                        } catch (Exception e) {
+                            log.error(e, e);
+                        }
+                    }
+                }
+                
                 out.println("</urlset>");
             }
         }
@@ -104,7 +120,8 @@ public class SiteMapServlet extends VitroHttpServlet {
         if ("http".equalsIgnoreCase(scheme) || "https".equalsIgnoreCase(scheme)) {
             StringBuilder builder = new StringBuilder();
             builder.append(scheme).append("://").append(serverName);
-            if (("http".equalsIgnoreCase(scheme) && serverPort != 80) || ("https".equalsIgnoreCase(scheme) && serverPort != 443) ) {
+            if (("http".equalsIgnoreCase(scheme) && serverPort != 80) 
+                    || ("https".equalsIgnoreCase(scheme) && serverPort != 443) ) {
                 builder.append(":").append(serverPort);
             }
 

docker-compose.yml

@@ -19,7 +19,7 @@ services:
       context: ./
       dockerfile: Dockerfile
       args:
-        - VIVO_DIR=/opt/vivo/home
+        - VIVO_DIR=/usr/local/vivo/home
         - TDB_FILE_MODE=direct
         - SOLR_URL=http://solr:8983/solr/vivocore
     environment:
@@ -28,7 +28,7 @@ services:
     ports:
       - 8080:8080
     volumes:
-      - ${LOCAL_VIVO_HOME}:/opt/vivo/home
+      - ${LOCAL_VIVO_HOME}:/usr/local/vivo/home
     networks:
       - vivo
 

home/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-home</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-project</artifactId>
-        <version>1.11.2-SNAPSHOT</version>
+        <version>1.12.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

home/src/main/resources/config/example.runtime.properties

@@ -19,6 +19,26 @@
 # BASIC PROPERTIES
 # -----------------------------------------------------------------------------
 
+  #
+  # This namespace will be used when generating URIs for objects created in the
+  # editor. In order to serve linked data, the default namespace must be composed
+  # as follows (optional elements in parentheses):
+  #
+  # scheme + server_name (+ port) (+ servlet_context) + "/individual/"
+  #
+  # For example, Cornell's default namespace is:
+  #
+  # http://vivo.cornell.edu/individual/
+  #
+Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
+
+  #
+  # The email address of the root user for the VIVO application. The password
+  # for this user is initially set to "rootPassword", but you will be asked to
+  # change the password the first time you log in.
+  #
+rootUser.emailAddress = vivo_root@mydomain.edu
+
 #
 # Argon2 password hashing parameters for time, memory and parallelism required to
 # compute a hash.
@@ -51,8 +71,12 @@ argon2.time = 1000
   # Email parameters which VIVO can use to send mail. If these are left empty,
   # the "Contact Us" form will be disabled and users will not be notified of
   # changes to their accounts.
-# email.smtpHost = smtp.mydomain.edu
+  #   Example:
-# email.replyTo = vivoAdmin@mydomain.edu
+  #     email.smtpHost = smtp.mydomain.edu
+  #     email.replyTo = vivoAdmin@mydomain.edu
+  #
+# email.smtpHost =
+# email.replyTo =
 
   #
   # URL of Solr context used in local VIVO search. This will usually consist of:
@@ -90,6 +114,22 @@ selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
   #
 #externalAuth.netIdHeaderName = remote_userID
 
+# -----------------------------------------------------------------------------
+# OPTIMIZING LIST VIEW QUERIES
+# -----------------------------------------------------------------------------
+
+  #
+  # Include sections between <precise-subquery></precise-subquery>
+  # tags when executing 'list view' queries that retrieve data
+  # for property lists on profile pages.
+  #
+  # Including these optional sections does not change the query
+  # semantics, but may improve performance.
+  #
+  # Default is true if not set.
+  # (Prior to v1.12, default was true for SDB and false for TDB.)
+  #
+# listview.usePreciseSubquery = true
 
 # -----------------------------------------------------------------------------
 # TUNING THE DATABASE CONNECTION POOL
@@ -108,7 +148,6 @@ selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
   #
 # VitroConnection.DataSource.pool.maxIdle = 10
 
-
 # -----------------------------------------------------------------------------
 # USING A DIFFERENT DATABASE
 # -----------------------------------------------------------------------------
@@ -387,7 +426,15 @@ Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Ro
   # If you do not wish to use the claiming interface, set this property to nothing (empty)
 createAndLink.providers = doi, pmid
 
-  # Triple pattern fragments is a very fast, very simple means for querying a triple store.
+  # Triple Pattern Fragments is a very fast, very simple means for querying a
-  # The triple pattern fragments API in VIVO puts little load on the server, providing a simple means for getting data from the triple store. The API has a web interface for manual use, can be used from the command line via curl, and can be used by programs.
+  # triple store.  The Triple Pattern Fragments API in VIVO puts little load on
+  # the server, providing a simple means for getting data from the triple store.
+  # The API has a web interface for manual use, can be used from the command
+  # line via curl, and can be used by programs.
+  #
+  # VIVO's Triple Pattern Fragments API does not require authentication and
+  # makes the full RDF graph available regardless of display or publish levels
+  # set on particular properties.  Enable Triple Pattern Fragments only if your
+  # VIVO does not contain restricted data that should not be shared with others.
   #
 # tpf.activeFlag = true

home/src/main/resources/rdf/display/everytime/searchIndexerConfigurationVivo.n3

@@ -117,6 +117,22 @@
         }
         """ .
 
+# URI finder that will find the relevant person to update when the 
+# property linking to the email or preferred title resource is removed
+:vivoUriFinder_VCard_2
+    a   searchIndex:indexing.IndexingUriFinder ,
+        searchIndex:indexing.SelectQueryUriFinder ;
+    rdfs:label "Preferred title / email person URI finder #2" ;
+    :hasPredicateRestriction "http://www.w3.org/2006/vcard/ns#hasTitle" ;
+    :hasPredicateRestriction "http://www.w3.org/2006/vcard/ns#hasEmail" ;
+    :hasSelectQuery """
+        PREFIX obo: <http://purl.obolibrary.org/obo/>
+        SELECT ?uri
+        WHERE {
+            ?uri obo:ARG_2000028 ?subject .
+        }
+        """ .
+
 :vivodocumentModifier_PreferredTitle
     a   searchIndex:documentBuilding.SelectQueryDocumentModifier ,
         searchIndex:documentBuilding.DocumentModifier ;

home/src/main/resources/rdf/tbox/firsttime/README.md

@@ -1,6 +1,20 @@
-This directory contains ontology "TBox" files with class and property definitions. 
+This directory contains ontology "TBox" files with class and property 
-These are loaded by the VIVO application when it starts for the first time, after 
+definitions or annotations that are intended to be editable in the VIVO GUI.
-the initial installation or after an upgrade installation that involves changes 
+
-to these files.
+These files are loaded by the VIVO application when it starts for the first time
+and during later restarts if the contents have changed.  A triple is updated
+if there is no conflicting value for the same subject and predicate that was
+added to the triple store via the GUI or data ingest (e.g. SPARQL UPDATE).
+
+The file vitroAnnotations.n3 contains triples with predicates in the vitro
+namespace and objects that are not literals with language tags.
+
+The VIVO-languages project contains additional language-specific 
+vitroAnnotations.n3 files where all of the triples contain language-tagged
+literals.
+
+VIVO-languages also provides additional annotation files 
+(e.g. initialTBoxAnnotations_en_US.n3) containing triples with predicates
+in ontologies/voabularies outside the vitro namespace (e.g. rdfs:label).
 
 See ../filegraph/README.md for more information about "TBox" files.

installer/example-settings.xml

@@ -0,0 +1,22 @@
+<settings xmlns="http://maven.apache.org/SETTINGS/1.1.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.1.0 http://maven.apache.org/xsd/settings-1.1.0.xsd">
+
+    <profiles>
+        <profile>
+            <id>defaults</id>
+            <properties>
+                <app-name>vivo</app-name>
+
+                <vivo-dir>/usr/local/vivo/home</vivo-dir>
+                <tomcat-dir>/usr/local/tomcat</tomcat-dir>
+
+                <default-theme>wilma</default-theme>
+            </properties>
+        </profile>
+    </profiles>
+
+    <activeProfiles>
+        <activeProfile>defaults</activeProfile>
+    </activeProfiles>
+</settings>

installer/home/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-installer-home</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-installer</artifactId>
-        <version>1.11.2-SNAPSHOT</version>
+        <version>1.12.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -23,24 +23,108 @@
         <default-theme>wilma</default-theme>
     </properties>
 
+    <profiles>
+        <profile>
+            <id>package</id>
+            <activation>
+                <property><name>vivo-dir</name></property>
+            </activation>
+            <build>
+                <finalName>${app-name}</finalName>
+                <plugins>
+                    <plugin>
+                        <artifactId>maven-assembly-plugin</artifactId>
+                        <configuration>
+                            <descriptors>
+                                <descriptor>src/main/assembly/home.xml</descriptor>
+                            </descriptors>
+                            <appendAssemblyId>false</appendAssemblyId>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <phase>package</phase>
+                                <goals>
+                                    <goal>single</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <id>install</id>
+            <activation>
+                <property><name>vivo-dir</name></property>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <artifactId>maven-assembly-plugin</artifactId>
+                        <configuration>
+                            <descriptors>
+                                <descriptor>src/main/assembly/home.xml</descriptor>
+                            </descriptors>
+                            <appendAssemblyId>false</appendAssemblyId>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <phase>package</phase>
+                                <goals>
+                                    <goal>single</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                    <plugin>
+                        <artifactId>maven-antrun-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>remove-webapp</id>
+                                <phase>verify</phase>
+                                <goals>
+                                    <goal>run</goal>
+                                </goals>
+                                <configuration>
+                                    <target>
+                                        <delete dir="${vivo-dir}/rdf" />
+                                    </target>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                    <plugin>
+                        <artifactId>maven-resources-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>install</id>
+                                <phase>install</phase>
+                                <goals>
+                                    <goal>copy-resources</goal>
+                                </goals>
+                                <configuration>
+                                    <outputDirectory>${vivo-dir}</outputDirectory>
+                                    <resources>
+                                        <resource>
+                                            <directory>${project.build.directory}/${project.build.finalName}</directory>
+                                        </resource>
+                                    </resources>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
     <build>
         <plugins>
             <plugin>
-                <artifactId>maven-assembly-plugin</artifactId>
+                <artifactId>maven-install-plugin</artifactId>
                 <configuration>
-                    <descriptors>
+                    <skip>true</skip>
-                        <descriptor>src/main/assembly/home.xml</descriptor>
-                    </descriptors>
-                    <appendAssemblyId>false</appendAssemblyId>
                 </configuration>
-                <executions>
-                    <execution>
-                        <phase>package</phase>
-                        <goals>
-                            <goal>single</goal>
-                        </goals>
-                    </execution>
-                </executions>
             </plugin>
         </plugins>
     </build>

installer/home/src/main/assembly/home.xml

@@ -4,7 +4,6 @@
     <id>home</id>
     <formats>
         <format>dir</format>
-        <format>tar</format>
     </formats>
     <includeBaseDirectory>false</includeBaseDirectory>
     <dependencySets>

installer/pom.xml

@@ -7,7 +7,7 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-installer</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>VIVO Installer</name>
@@ -29,6 +29,12 @@
                     <encoding>UTF-8</encoding>
                 </configuration>
             </plugin>
+            <plugin>
+                <artifactId>maven-install-plugin</artifactId>
+                <configuration>
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-gpg-plugin</artifactId>
@@ -142,6 +148,12 @@
                             </execution>
                         </executions>
                     </plugin>
+                    <plugin>
+                        <artifactId>maven-dependency-plugin</artifactId>
+                        <configuration>
+                            <skip>true</skip>
+                        </configuration>
+                    </plugin>
                     <plugin>
                         <artifactId>maven-resources-plugin</artifactId>
                         <version>2.6</version>
@@ -165,6 +177,60 @@
                             </execution>
                         </executions>
                     </plugin>
+                    <plugin>
+                        <artifactId>maven-war-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>default-war</id>
+                                <phase/>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <id>install</id>
+            <activation>
+                <property><name>vivo-dir</name></property>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <artifactId>maven-enforcer-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>enforce-properties</id>
+                                <phase>validate</phase>
+                                <goals>
+                                    <goal>enforce</goal>
+                                </goals>
+                                <configuration>
+                                    <rules>
+                                        <requireProperty>
+                                            <property>app-name</property>
+                                            <message>You must provide an application name (app-name)</message>
+                                        </requireProperty>
+                                    </rules>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <id>skip</id>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-deploy-plugin</artifactId>
+                        <version>2.8.2</version>
+                        <configuration>
+                          <skip>true</skip>
+                        </configuration>
+                      </plugin>
                 </plugins>
             </build>
         </profile>

installer/webapp/pom.xml

@@ -7,21 +7,129 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-installer-vivo</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>war</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-installer</artifactId>
-        <version>1.11.2-SNAPSHOT</version>
+        <version>1.12.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
     <name>VIVO Install Web App</name>
 
+    <profiles>
+        <profile>
+            <id>package</id>
+            <activation>
+                <property><name>app-name</name></property>
+            </activation>
+            <build>
+                <finalName>${app-name}</finalName>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-war-plugin</artifactId>
+                        <configuration>
+                            <archive>
+                                <manifest>
+                                    <addClasspath>true</addClasspath>
+                                </manifest>
+                            </archive>
+                            <archiveClasses>false</archiveClasses>
+                            <overlays>
+                                <overlay>
+                                    <groupId>org.vivoweb</groupId>
+                                    <artifactId>vivo-webapp</artifactId>
+                                    <type>war</type>
+                                </overlay>
+                                <!-- Overlays for multilingual support -->
+                                <!-- overlay>
+                                    <groupId>org.vivoweb</groupId>
+                                    <artifactId>vitro-languages-webapp</artifactId>
+                                    <type>war</type>
+                                </overlay>
+                                <overlay>
+                                    <groupId>org.vivoweb</groupId>
+                                    <artifactId>vivo-languages-webapp</artifactId>
+                                    <type>war</type>
+                                </overlay -->
+                            </overlays>
+                            <webResources>
+                                <resource>
+                                    <directory>src/main/webResources</directory>
+                                    <filtering>true</filtering>
+                                </resource>
+                            </webResources>
+                        </configuration>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <id>install</id>
+            <activation>
+                <property><name>tomcat-dir</name></property>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <artifactId>maven-antrun-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>remove-webapp</id>
+                                <phase>verify</phase>
+                                <goals>
+                                    <goal>run</goal>
+                                </goals>
+                                <configuration>
+                                    <target>
+                                        <delete dir="${tomcat-dir}/webapps/${project.build.finalName}" />
+                                    </target>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-dependency-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>install</id>
+                                <phase>install</phase>
+                                <goals>
+                                    <goal>unpack</goal>
+                                </goals>
+                                <configuration>
+                                    <artifactItems>
+                                        <artifactItem>
+                                            <groupId>${project.groupId}</groupId>
+                                            <artifactId>${project.artifactId}</artifactId>
+                                            <version>${project.version}</version>
+                                            <type>war</type>
+                                            <overWrite>true</overWrite>
+                                            <outputDirectory>${tomcat-dir}/webapps/${project.build.finalName}</outputDirectory>
+                                        </artifactItem>
+                                    </artifactItems>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
     <build>
         <finalName>${app-name}</finalName>
         <plugins>
+            <plugin>
+                <artifactId>maven-install-plugin</artifactId>
+                <configuration>
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
             <plugin>
                 <artifactId>maven-clean-plugin</artifactId>
                 <configuration>
@@ -32,75 +140,6 @@
                     </filesets>
                 </configuration>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-dependency-plugin</artifactId>
-
-                <configuration>
-                    <skip>false</skip>
-                </configuration>
-                <executions>
-                    <execution>
-                        <id>include-home</id>
-                        <phase>process-resources</phase>
-                        <goals>
-                            <goal>copy</goal>
-                        </goals>
-                        <configuration>
-                            <artifactItems>
-                                <artifactItem>
-                                    <groupId>org.vivoweb</groupId>
-                                    <artifactId>vivo-installer-home</artifactId>
-                                    <version>${project.version}</version>
-                                    <type>tar</type>
-                                    <destFileName>vivo-home.tar</destFileName>
-                                    <outputDirectory>${project.build.directory}/home-files</outputDirectory>
-                                </artifactItem>
-                            </artifactItems>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-war-plugin</artifactId>
-                <configuration>
-                    <archive>
-                        <manifest>
-                            <addClasspath>true</addClasspath>
-                        </manifest>
-                    </archive>
-                    <archiveClasses>false</archiveClasses>
-                    <overlays>
-                        <overlay>
-                            <groupId>org.vivoweb</groupId>
-                            <artifactId>vivo-webapp</artifactId>
-                            <type>war</type>
-                        </overlay>
-                        <!-- Overlays for multilingual support -->
-                        <overlay>
-                            <groupId>org.vivoweb</groupId>
-                            <artifactId>vitro-languages-webapp-core</artifactId>
-                            <type>war</type>
-                        </overlay>
-                        <overlay>
-                            <groupId>org.vivoweb</groupId>
-                            <artifactId>vivo-languages-webapp-core</artifactId>
-                            <type>war</type>
-                        </overlay>
-                    </overlays>
-                    <webResources>
-                        <resource>
-                            <directory>src/main/webResources</directory>
-                            <filtering>true</filtering>
-                        </resource>
-                        <resource>
-                            <directory>${project.build.directory}/home-files/</directory>
-                            <targetPath>WEB-INF/resources/home-files/</targetPath>
-                        </resource>
-                    </webResources>
-                </configuration>
-            </plugin>
         </plugins>
     </build>
 

installer/webapp/src/main/webResources/META-INF/context.xml

@@ -1,52 +1,9 @@
 <Context> <!-- useHttpOnly="false" -->
-
-   <!--
-     # The 'home' property specifies the location of VIVO HOME.
-     # The system user used to run the VIVO web application must have write access
-     # to the parent directory of the directory defined in this property, if VIVO HOME
-     # does not already exist.
-     # If this directory already exists, the system user used to run the VIVO web application
-     # must have write access to this directory.
-   -->
    <Environment
         type="java.lang.String" 
         name="vitro/home"
         value="${vivo-dir}" override="true"/>
 
-   <!--
-     # The name of the application (possibly not used).
-   -->
-   <Environment
-           type="java.lang.String"
-           name="vitro/appName"
-           value="${app-name}" override="true"/>
-
-   <!--
-     # The email address of the root user for the VIVO application. The password
-     # for this user is initially set to "rootPassword", but you will be asked to
-     # change the password the first time you log in.
-   -->
-   <Environment
-           type="java.lang.String"
-           name="vitro/rootUserAddress"
-           value="vivo_root@mydomain.edu" override="true"/>
-
-   <!--
-     # This namespace will be used when generating URIs for objects created in the
-     # editor. In order to serve linked data, the default namespace must be composed
-     # as follows (optional elements in parentheses):
-     #
-     # scheme + server_name (+ port) (+ servlet_context) + "/individual/"
-     #
-     # For example, Cornell's default namespace is:
-     #
-     # http://vivo.cornell.edu/individual/
-   -->
-   <Environment
-           type="java.lang.String"
-           name="vitro/defaultNamespace"
-           value="http://vivo.mydomain.edu/individual/" override="true"/>
-
    <!-- Disable persist sessions on shut down.-->
    <Manager pathname="" />
 </Context>

installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties

@@ -24,7 +24,7 @@
 # debug.log4j.properties exists will be used instead, if it exists, but is not stored in Subversion.
 
 log4j.appender.AllAppender=org.apache.log4j.RollingFileAppender
-log4j.appender.AllAppender.File= ${catalina.base}/logs/vivo.all.log
+log4j.appender.AllAppender.File=${catalina.base}/logs/${app-name}.all.log
 log4j.appender.AllAppender.MaxFileSize=10MB
 log4j.appender.AllAppender.MaxBackupIndex=10
 log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout

pom.xml

@@ -1,13 +1,11 @@
-<project
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xmlns="http://maven.apache.org/POM/4.0.0"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-project</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>VIVO</name>
@@ -43,11 +41,9 @@
         </developer>
     </developers>
 
-    <!--
+    <!-- The SCM repository location is used by Continuum to update against 
-       The SCM repository location is used by Continuum to update against
+        when changes have occurred. This spawns a new build cycle and releases snapshots 
-       when changes have occurred.  This spawns a new build cycle and releases
+        into the snapshot repository below. -->
-       snapshots into the snapshot repository below.
-    -->
     <scm>
         <connection>scm:git:git@github.com:vivo-project/VIVO.git</connection>
         <developerConnection>scm:git:git@github.com:vivo-project/VIVO.git</developerConnection>
@@ -56,7 +52,6 @@
     </scm>
 
     <properties>
-        <app-name>vivo</app-name>
         <vitro-version>${project.version}</vitro-version>
         <vivo-dir>${basedir}</vivo-dir>
         <maven.build.timestamp.format>yyyy-MM-dd HH:mm:ss</maven.build.timestamp.format>
@@ -73,7 +68,29 @@
     </modules>
 
     <profiles>
-        <profile>
+       <profile>
+            <id>Vitro-languages</id>
+            <activation>
+                <file>
+                    <exists>../Vitro-languages/pom.xml</exists>
+                </file>
+            </activation>
+            <modules>
+                <module>../Vitro-languages</module>
+            </modules>
+       </profile>
+       <profile>
+            <id>VIVO-languages</id>
+            <activation>
+                <file>
+                    <exists>../VIVO-languages/pom.xml</exists>
+                </file>
+            </activation>
+            <modules>
+                <module>../VIVO-languages</module>
+            </modules>
+       </profile>
+       <profile>
             <id>vitro</id>
             <activation>
                 <file>
@@ -336,7 +353,8 @@
                 </configuration>
             </plugin>
 
-            <!-- Used to validate all code style rules in source code using Checkstyle -->
+            <!-- Used to validate all code style rules in source code using 
+                Checkstyle -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-checkstyle-plugin</artifactId>
@@ -344,7 +362,8 @@
                 <executions>
                     <execution>
                         <id>verify-style</id>
-                        <!-- Bind to verify so it runs after package & unit tests, but before install -->
+                        <!-- Bind to verify so it runs after package & unit 
+                            tests, but before install -->
                         <phase>verify</phase>
                         <goals>
                             <goal>check</goal>
@@ -353,10 +372,10 @@
                 </executions>
                 <configuration>
                     <configLocation>
-                      duraspace-checkstyle/checkstyle.xml
+                        duraspace-checkstyle/checkstyle.xml
                     </configLocation>
                     <suppressionsLocation>
-                      vitro-checkstyle/checkstyle-suppressions.xml
+                        vitro-checkstyle/checkstyle-suppressions.xml
                     </suppressionsLocation>
                     <encoding>UTF-8</encoding>
                     <consoleOutput>true</consoleOutput>
@@ -476,9 +495,11 @@
                             <report>test-javadoc</report>
                         </reports>
                     </reportSet>
-                    <reportSet><!-- aggregate reportSet, to define in poms having modules -->
+                    <reportSet><!-- aggregate reportSet, to define in poms 
+                            having modules -->
                         <id>aggregate</id>
-                        <inherited>false</inherited><!-- don't run aggregate in child modules -->
+                        <inherited>false</inherited><!-- don't run aggregate 
+                            in child modules -->
                         <reports>
                             <report>aggregate</report>
                         </reports>
@@ -502,10 +523,9 @@
         </plugins>
     </reporting>
 
-    <!--
+    <!-- Add a custom repository, which is actually just a simple GitHub 
-        Add a custom repository, which is actually just a simple GitHub project
+        project in order to distribute some dependencies that aren't part of Maven 
-        in order to distribute some dependencies that aren't part of Maven central
+        central -->
-    -->
     <repositories>
         <repository>
             <id>vivo-dependencies</id>

start.sh

@@ -9,43 +9,51 @@ fi
 
 # allow easier reset home with `docker run -e RESET_HOME=true`
 if [[ "$RESET_HOME" = "true" ]]; then
-  echo 'Clearing VIVO HOME /opt/vivo/home'
+  echo 'Clearing VIVO HOME /usr/local/vivo/home'
-  rm -rf /opt/vivo/home/*
+  rm -rf /usr/local/vivo/home/*
 fi
 
-# ensure home config directory exists
+# copy home bin if not exists
-mkdir -p /opt/vivo/home/config
+if [ ! -d /usr/local/vivo/home/bin ]; then
-
+  echo "Copying home bin directory to /usr/local/vivo/home/bin"
-# generate digest.md5 for existing VIVO home if not already exist
+  cp -r /vivo-home/bin /usr/local/vivo/home/bin
-if [ ! -f /opt/vivo/home/digest.md5 ]; then
-  find /opt/vivo/home -type f | grep -E '^/opt/vivo/home/bin/|^/opt/vivo/home/config/|^/opt/vivo/home/rdf/' | xargs md5sum > /opt/vivo/home/digest.md5
-  echo "Generated digest.md5 for VIVO home"
-  cat /opt/vivo/home/digest.md5
 fi
 
-# only move runtime.properties first time and if it does not already exist in target home directory
+# copy home config if not exists
-if [ -f /runtime.properties ]; then
+if [ ! -d /usr/local/vivo/home/config ]; then
-  # template runtime.properties vitro.local.solr.url value to $SOLR_URL value
+  echo "Copying home config directory to /usr/local/vivo/home/config"
-  echo "Templating runtime.properties vitro.local.solr.url = $SOLR_URL"
+  cp -r /vivo-home/config /usr/local/vivo/home/config
-  sed -i "s,http://localhost:8983/solr/vivocore,$SOLR_URL,g" /runtime.properties
+fi
 
-  if [ ! -f /opt/vivo/home/config/runtime.properties ]
+# copy home rdf if not exists
+if [ ! -d /usr/local/vivo/home/rdf ]; then
+  echo "Copying home rdf directory to /usr/local/vivo/home/rdf"
+  cp -r /vivo-home/rdf /usr/local/vivo/home/rdf
+fi
+
+# copy runtime.properties if it does not already exist in target home directory
+if [ -f /usr/local/vivo/home/config/example.runtime.properties ]; then
+  if [ ! -f /usr/local/vivo/home/config/runtime.properties ]
   then
-    echo "First time: moving /runtime.properties to /opt/vivo/home/config/runtime.properties"
+    echo "Copying example.runtime.properties to /usr/local/vivo/home/config/runtime.properties"
-    mv -n /runtime.properties /opt/vivo/home/config/runtime.properties
+    cp /usr/local/vivo/home/config/example.runtime.properties /usr/local/vivo/home/config/runtime.properties
+
+    # template runtime.properties vitro.local.solr.url value to $SOLR_URL value
+    echo "Templating runtime.properties vitro.local.solr.url = $SOLR_URL"
+    sed -i "s,http://localhost:8983/solr/vivocore,$SOLR_URL,g" /usr/local/vivo/home/config/runtime.properties
   else
-    echo "Using existing /opt/vivo/home/config/runtime.properties"
+    echo "Using existing /usr/local/vivo/home/config/runtime.properties"
   fi
 fi
 
-# only move applicationSetup.n3 first time and if it does not already exist in target home directory
+# copy applicationSetup.n3 if it does not already exist in target home directory
-if [ -f /applicationSetup.n3 ]; then
+if [ -f /usr/local/vivo/home/config/example.applicationSetup.n3 ]; then
-  if [ ! -f /opt/vivo/home/config/applicationSetup.n3 ]
+  if [ ! -f /usr/local/vivo/home/config/applicationSetup.n3 ]
   then
-    echo "First time: moving /applicationSetup.n3 to /opt/vivo/home/config/applicationSetup.n3"
+    echo "Copying example.applicationSetup.n3 to /usr/local/vivo/home/config/applicationSetup.n3"
-    mv -n /applicationSetup.n3 /opt/vivo/home/config/applicationSetup.n3
+    cp /usr/local/vivo/home/config/example.applicationSetup.n3 /usr/local/vivo/home/config/applicationSetup.n3
   else
-    echo "Using existing /opt/vivo/home/config/applicationSetup.n3"
+    echo "Using existing /usr/local/vivo/home/config/applicationSetup.n3"
   fi
 fi
 

webapp/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-webapp</artifactId>
-    <version>1.11.2-SNAPSHOT</version>
+    <version>1.12.1-SNAPSHOT</version>
     <packaging>war</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-project</artifactId>
-        <version>1.11.2-SNAPSHOT</version>
+        <version>1.12.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -69,7 +69,7 @@
         <dependency>
             <groupId>org.vivoweb</groupId>
             <artifactId>vivo-api</artifactId>
-            <version>1.11.2-SNAPSHOT</version>
+            <version>1.12.1-SNAPSHOT</version>
         </dependency>
     </dependencies>
 </project>

webapp/src/main/webapp/js/visualization/entitycomparison/util.js

@@ -1069,7 +1069,7 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
 
 //	console.log(processJSONData.currentEntityLevel);
 
-	if (processJSONData.currentEntityLevel.toUpperCase() === "ORGANIZATIONS AND PEOPLE") {
+	if (processJSONData.currentEntityLevel === i18nStringsGuiEvents.organizationsAndPeople) {
 		$.fn.dataTableExt.afnFiltering.push(DatatableCustomFilters.peopleOrOrganizations);
 	}
 
@@ -1193,7 +1193,7 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
  */
 function reloadDataTablePagination(preselectedEntityURIs, jsonData){
 
-	if (processJSONData.currentEntityLevel.toUpperCase() === "ORGANIZATIONS AND PEOPLE") {
+	if (processJSONData.currentEntityLevel === i18nStringsGuiEvents.organizationsAndPeople) {
 
 		/*
 		 * This will make sure that duplicate filters are not added.

webapp/src/main/webapp/templates/freemarker/body/individual/individual--foaf-person-2column.ftl

@@ -51,7 +51,7 @@
             <#else>
                 <h1 itemprop="name" class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>>
                     <#-- Label -->
-                    <@p.label individual editable labelCount localesCount/>
+                    <@p.label individual editable labelCount localesCount languageCount />
                 </h1>
                 <#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->
                 <#assign title = propertyGroups.pullProperty("http://purl.obolibrary.org/obo/ARG_2000028","http://www.w3.org/2006/vcard/ns#Title")!>

webapp/src/main/webapp/templates/freemarker/body/individual/individual--foaf-person-quickview.ftl

@@ -62,7 +62,7 @@
                 <div id="photo-wrapper">${individualImage}</div>
                 <h1 itemprop="name" class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>>
                     <#-- Label -->
-                    <@p.label individual editable labelCount localesCount/>
+                    <@p.label individual editable labelCount localesCount languageCount />
                 </h1>
                 <#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->
                 <#assign title = propertyGroups.pullProperty("http://purl.obolibrary.org/obo/ARG_2000028","http://www.w3.org/2006/vcard/ns#Title")!>

webapp/src/main/webapp/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl

@@ -34,7 +34,7 @@
 
 <#assign temporalGraphDownloadCSVCommonURL = '${urls.base}${dataVisualizationURLRoot}?uri=${organizationURI}&labelField=label'>
 
-<#assign publicationParameter = {   "name": "${i18n().publication?js_string}",
+<#assign publicationParameter = {   "name": "publication",
                                     "pluralName": "${i18n().publications?js_string}",
                                     "verbName": "${i18n().published?js_string}",
                                     "dropDownText": "${i18n().by_publications?js_string}",
@@ -44,7 +44,7 @@
                                     "csvLink": "${temporalGraphDownloadCSVCommonURL}&vis=entity_comparison",
                                     "value": "${i18n().publications?js_string}" }>
 
-<#assign grantParameter = {   "name": "${i18n().grant?js_string}",
+<#assign grantParameter = {   "name": "grant",
                               "pluralName": "${i18n().grants?js_string}",
                               "verbName": "${i18n().granted?js_string}",
                               "dropDownText": "${i18n().by_grants?js_string}",
@@ -74,7 +74,7 @@ var activitiesLabel = {
     plural: '${i18n().activities?js_string}'
 };
 var i18nStringsGuiEvents = {
-    temporalGraphCapped: '${i18n().temporal_graph_capitalized?js_string?js_string},
+    temporalGraphCapped: '${i18n().temporal_graph_capitalized?js_string?js_string}',
     temporalGraphLower: '${i18n().temporal_graph?js_string?js_string}',
     viewString: '${i18n().view?js_string}',
     entityMaxNote: '${i18n().max_entity_note?js_string}',

webapp/src/main/webapp/themes/tenderfoot/templates/body/individual/individual--foaf-person.ftl

@@ -65,7 +65,7 @@
 					<section class="vcard person">
 						<h1 class="foaf-person">
 							<#-- Label -->
-								<span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount/></span>
+								<span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount languageCount /></span>
 						</h1>
 						<section id="preferredTitle">
 							<#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->

webapp/src/main/webapp/themes/tenderfoot/templates/page/page-home.ftl

@@ -15,7 +15,7 @@
 <#import "lib-home-page.ftl" as lh>
 
 <!DOCTYPE html>
-<html lang="en">
+<html lang="${country}">
     <head>
         <#include "head.ftl">
         <#if geoFocusMapsEnabled >

webapp/src/main/webapp/themes/tenderfoot/templates/page/page.ftl

@@ -3,7 +3,7 @@
 <#import "lib-list.ftl" as l>
 
 <!DOCTYPE html>
-<html lang="en">
+<html lang="${country}">
     <head>
         <#include "head.ftl">
     </head>

webapp/src/main/webapp/themes/wilma/templates/individual--foaf-person.ftl

@@ -89,7 +89,7 @@
             <#else>
                 <h1 class="foaf-person">
                     <#-- Label -->
-                    <span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount/></span>
+                    <span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount languageCount /></span>
                 </h1>
                 <section id="preferredTitle">
                     <#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->

webapp/src/main/webapp/themes/wilma/templates/page-home.ftl

@@ -15,7 +15,7 @@
 <#import "lib-home-page.ftl" as lh>
 
 <!DOCTYPE html>
-<html lang="en">
+<html lang="${country}">
     <head>
         <#include "head.ftl">
         <#if geoFocusMapsEnabled >

webapp/src/main/webapp/themes/wilma/templates/page.ftl

@@ -3,7 +3,7 @@
 <#import "lib-list.ftl" as l>
 
 <!DOCTYPE html>
-<html lang="en">
+<html lang="${country}">
     <head>
         <#include "head.ftl">
     </head>