Merge branch 'maint-rel-1.6' into develop

webapp/rdf/auth/everytime/permission_config.n3

@@ -20,6 +20,7 @@ auth:ADMIN
     auth:hasPermission simplePermission:ManageUserAccounts ;
     auth:hasPermission simplePermission:RebuildVClassGroupCache ;
     auth:hasPermission simplePermission:RefreshVisualizationCache ;
+    auth:hasPermission simplePermission:SeeConfiguration ;
     auth:hasPermission simplePermission:SeeStartupStatus ;
     auth:hasPermission simplePermission:UseAdvancedDataToolsPages ;
     auth:hasPermission simplePermission:UseMiscellaneousAdminPages ;

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/SimplePermission.java

@@ -64,6 +64,8 @@ public class SimplePermission extends Permission {
 		NAMESPACE + "RebuildVClassGroupCache");
 	public static final SimplePermission REFRESH_VISUALIZATION_CACHE = new SimplePermission(
 		NAMESPACE + "RefreshVisualizationCache");
+	public static final SimplePermission SEE_CONFIGURATION = new SimplePermission(
+			NAMESPACE + "SeeConfiguration");
 	public static final SimplePermission SEE_INDVIDUAL_EDITING_PANEL = new SimplePermission(
 		NAMESPACE + "SeeIndividualEditingPanel");
 	public static final SimplePermission SEE_REVISION_INFO = new SimplePermission(

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowConfiguration.java

@@ -0,0 +1,57 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.controller.admin;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
+import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
+import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+
+/**
+ * Show the current ConfigurationProperties and the Java system properties.
+ */
+public class ShowConfiguration extends FreemarkerHttpServlet {
+	@Override
+	protected Actions requiredActions(VitroRequest vreq) {
+		return SimplePermission.SEE_CONFIGURATION.ACTIONS;
+	}
+
+	@Override
+	protected ResponseValues processRequest(VitroRequest vreq) {
+		Map<String, Object> body = new HashMap<String, Object>();
+		body.put("configurationProperties", getConfigurationProperties(vreq));
+		body.put("javaSystemProperties", getSystemProperties());
+		return new TemplateResponseValues("admin-showConfiguration.ftl", body);
+	}
+
+	private SortedMap<String, String> getConfigurationProperties(
+			VitroRequest vreq) {
+		ConfigurationProperties props = ConfigurationProperties.getBean(vreq);
+		TreeMap<String, String> map = new TreeMap<>(props.getPropertyMap());
+		for (String key : map.keySet()) {
+			if (key.toLowerCase().endsWith("password")) {
+				map.put(key, "********");
+			}
+		}
+		return map;
+	}
+
+	private SortedMap<String, String> getSystemProperties() {
+		Properties props = System.getProperties();
+		SortedMap<String, String> map = new TreeMap<>();
+		for (String key : props.stringPropertyNames()) {
+			map.put(key, props.getProperty(key));
+		}
+		return map;
+	}
+
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/DateTimeWithPrecisionVTwo.java

@@ -167,9 +167,18 @@ public class DateTimeWithPrecisionVTwo extends BaseEditElementVTwo {
                         
             DateTime value = getTimeValue(editConfig,editSub);
             /* This is the case where there is a precision so there should be a datetime */
-            if( value == null )
+            if( value == null ) {
-                log.debug("Field " + getFieldName() + " has precision " + precisionUri 
+            	//If there is no value, then this is an error condition
-                        + " but the date time is " + value);                        
+                log.error("Field " + getFieldName() + " has precision " + precisionUri 
+                        + " but the date time value is null ");  
+                map.put("year", "");
+                map.put("month", "");
+                map.put("day", "");
+                map.put("hour", "");
+                map.put("minute", "");
+                map.put("second", "") ;
+                
+            } else {
             
 	            /* only put the values in the map for ones which are significant based on the precision */
 	            if( existingPrec.ordinal() >= VitroVocabulary.Precision.SECOND.ordinal() )
@@ -202,6 +211,7 @@ public class DateTimeWithPrecisionVTwo extends BaseEditElementVTwo {
 	            else
 	                map.put("year", "");
 	            }
+        }               
         
         return map;
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DateTimeIntervalFormGenerator.java

@@ -70,8 +70,7 @@ public class DateTimeIntervalFormGenerator extends
         		"startField-value", existingStartDateQuery);
         conf.addSparqlForExistingLiteral(
         		"endField-value", existingEndDateQuery);
-        conf.addSparqlForExistingUris(
+        
-        		getNodeVar(), existingIntervalNodeQuery);
         conf.addSparqlForExistingUris("startNode", existingStartNodeQuery);
         conf.addSparqlForExistingUris("endNode", existingEndNodeQuery);
         conf.addSparqlForExistingUris(
@@ -115,7 +114,7 @@ public class DateTimeIntervalFormGenerator extends
 	
 	final  String existingStartDateQuery =
         "SELECT ?existingDateStart WHERE { \n" +     
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +     
+        "?subject <" + getToDateTimeIntervalPredicate() + "> " + getNodeN3Var() + " . \n" +     
         getNodeN3Var() + " a <" + intervalType + "> . \n" +
         getNodeN3Var() + " <" + intervalToStart + "> ?startNode . \n" +
         "?startNode a <" + dateTimeValueType + "> . \n" +
@@ -123,34 +122,30 @@ public class DateTimeIntervalFormGenerator extends
 
 	final  String existingEndDateQuery = 
         "SELECT ?existingEndDate WHERE { \n" +
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +
+        "?subject <" + getToDateTimeIntervalPredicate() + "> " + getNodeN3Var() + " . \n" +
         getNodeN3Var() + " a <" + intervalType + "> . \n" +
         getNodeN3Var() + " <" + intervalToEnd + "> ?endNode . \n" +
         "?endNode a <" + dateTimeValueType + "> . \n " +
         "?endNode <" + dateTimeValue + "> ?existingEndDate . }";
 	
-	final  String existingIntervalNodeQuery = 
-        "SELECT ?existingIntervalNode WHERE { \n" +
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +
-        "?existingIntervalNode a <" + intervalType + "> . }";
 	
 	final  String existingStartNodeQuery =
 		"SELECT ?existingStartNode WHERE { \n" +
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +
+        "?subject <" + getToDateTimeIntervalPredicate() + "> " + getNodeN3Var() + " . \n" +
         getNodeN3Var() + " a <" + intervalType + "> . \n" +
         getNodeN3Var() + " <" + intervalToStart + "> ?existingStartNode . \n" + 
         "?existingStartNode a <" + dateTimeValueType + "> .}  ";
 	
 	final  String existingEndNodeQuery = 
         "SELECT ?existingEndNode WHERE { \n" + 
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +
+        "?subject <" + getToDateTimeIntervalPredicate() + "> " + getNodeN3Var() + " . \n" +
         getNodeN3Var() + " a <" + intervalType + "> . \n" +
         getNodeN3Var() + " <" + intervalToEnd + "> ?existingEndNode . \n" + 
         "?existingEndNode a <" + dateTimeValueType + "> .} ";
 	
 	final  String existingStartPrecisionQuery = 
         "SELECT ?existingStartPrecision WHERE { \n" +    
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +      
+        "?subject <" + getToDateTimeIntervalPredicate() + "> " + getNodeN3Var() + " . \n" +      
         getNodeN3Var() + " a <" + intervalType + "> . \n" +
         getNodeN3Var() + " <" + intervalToStart + "> ?startNode . \n" +
         "?startNode a <" + dateTimeValueType + "> . \n" +          
@@ -158,7 +153,7 @@ public class DateTimeIntervalFormGenerator extends
 	
 	final  String existingEndPrecisionQuery =
 		"SELECT ?existingEndPrecision WHERE { \n" +
-        "?subject <" + getToDateTimeIntervalPredicate() + "> ?existingIntervalNode . \n" +      
+        "?subject <" + getToDateTimeIntervalPredicate() + "> " + getNodeN3Var() + " . \n" +      
         getNodeN3Var() + " a <" + intervalType + "> . \n" +
         getNodeN3Var() + " <" + intervalToEnd + "> ?endNode . \n" +
         "?endNode a <" + dateTimeValueType + "> . \n" +          

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DateTimePropertyGenerator.java

@@ -0,0 +1,54 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators;
+
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+
+import javax.servlet.http.HttpSession;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.vocabulary.XSD;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.DateTimeWithPrecisionVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
+import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils.EditMode;
+import edu.cornell.mannlib.vitro.webapp.utils.generators.EditModeUtils;
+
+/**
+ * 
+ * @author hjk54
+ *
+ * There are multiple date time properties in VIVO, all of which have a DateTimeValue individual as an object.
+ * I am extending DateTimeValueFormGenerator to enable the predicate to be utilized as the "toDateTimeValue" property, i.e. 
+ * the property associating the subject with the date time value individual.  The dateTimeValueForm template has been
+ * used as the basis for the general form for this generator that can be applied to multiple properties. 
+ */
+
+public class DateTimePropertyGenerator extends DateTimeValueFormGenerator {
+	
+	String predicate = null;
+	@Override
+	public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq,
+			HttpSession session) {
+		predicate = EditConfigurationUtils.getPredicateUri(vreq);  
+        EditConfigurationVTwo conf = super.getEditConfiguration(vreq, session);
+        return conf; 
+	} 	
+
+	//isolating the predicate in this fashion allows this class to be subclassed for other date time value
+	//properties
+	@Override
+	protected String getToDateTimeValuePredicate() {
+		return predicate;
+	}
+	
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DateTimeValueFormGenerator.java

@@ -46,7 +46,7 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
         conf.setVarNameForSubject("subject");
         conf.setVarNameForPredicate("toDateTimeValue");
         conf.setVarNameForObject("valueNode");
-        
+        //Value node value will be in scope if we have an object uri that exists for editing
         conf.setN3Optional(Arrays.asList(getN3ForValue()));
         
         conf.addNewResource("valueNode", DEFAULT_NS_FOR_NEW_RESOURCE);
@@ -55,7 +55,6 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
         		"dateTimeField-value", getExistingDateTimeValueQuery());
         conf.addSparqlForExistingUris(
         		"dateTimeField-precision", getExistingPrecisionQuery());
-        conf.addSparqlForExistingUris("valueNode", getExistingNodeQuery());
         
         FieldVTwo dateTimeField = new FieldVTwo().setName(this.getDateTimeFieldName());
         		dateTimeField.setEditElement(new DateTimeWithPrecisionVTwo(dateTimeField, 
@@ -84,23 +83,18 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
 	
 	protected String getExistingDateTimeValueQuery () {
         return "SELECT ?existingDateTimeValue WHERE { \n" +
-        "?subject <" + this.getToDateTimeValuePredicate() + "> ?existingValueNode . \n" +
+        "?subject <" + this.getToDateTimeValuePredicate() + "> ?valueNode . \n" +
-        "?existingValueNode a <" + valueType + "> . \n" +
+        "?valueNode a <" + valueType + "> . \n" +
-        "?existingValueNode <" + dateTimeValue + "> ?existingDateTimeValue }";
+        "?valueNode <" + dateTimeValue + "> ?existingDateTimeValue }";
 	}
 	
 	protected String getExistingPrecisionQuery() {
         return "SELECT ?existingPrecision WHERE { \n" +
-        "?subject <" + this.getToDateTimeValuePredicate() + "> ?existingValueNode . \n" +
+        "?subject <" + this.getToDateTimeValuePredicate() + "> ?valueNode . \n" +
-        "?existingValueNode a <" + valueType + "> . \n" +
+        "?valueNode a <" + valueType + "> . \n" +
-        "?existingValueNode <"  + dateTimePrecision + "> ?existingPrecision }";
+        "?valueNode <"  + dateTimePrecision + "> ?existingPrecision }";
 	}
-	protected String getExistingNodeQuery() {
-        return "SELECT ?existingNode WHERE { \n" +
-        "?subject <" + this.getToDateTimeValuePredicate() + "> ?existingNode . \n" +
-        "?existingNode a <" + valueType + "> }";
 	
-	}
 	public static String getNodeVar() {
 		return "valueNode";
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/freemarker/loader/FreemarkerTemplateLoader.java

@@ -285,7 +285,7 @@ public class FreemarkerTemplateLoader implements TemplateLoader {
 		}
 
 		public boolean fileQualifies(Path path) {
-			return Files.isReadable(path) && !Files.isDirectory(path);
+			return !Files.isDirectory(path);
 		}
 
 		public SortedSet<PathPieces> getMatches() {

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JvmSmokeTests.java

@@ -22,9 +22,26 @@ public class JvmSmokeTests implements ServletContextListener {
 		ServletContext ctx = sce.getServletContext();
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
+		checkJvmLevel(ss);
 		checkTempDirectory(ss);
 	}
 
+	/**
+	 * We need to run at 1.7 or later.
+	 */
+	private void checkJvmLevel(StartupStatus ss) {
+		String specLevel = System.getProperty("java.specification.version", "");
+		if (specLevel.isEmpty()) {
+			ss.warning(this, "Can't determine the current level of Java. "
+					+ "VIVO requires at least Java 1.7.");
+		} else if (specLevel.compareTo("1.7") < 0) {
+			ss.warning(this, "VIVO requires at least Java 1.7 - "
+					+ "currently running on Java " + specLevel);
+		} else {
+			ss.info(this, "Java version is " + specLevel);
+		}
+	}
+
 	/**
 	 * Check the Java temp directory. Make sure that it exists, it is a
 	 * directory, we can read it, we can write to it.

webapp/web/WEB-INF/web.xml

@@ -660,6 +660,15 @@
     <url-pattern>/admin/showAuth</url-pattern>
   </servlet-mapping>
 
+  <servlet>
+    <servlet-name>ShowConfiguration</servlet-name>
+    <servlet-class>edu.cornell.mannlib.vitro.webapp.controller.admin.ShowConfiguration</servlet-class>
+  </servlet>
+  <servlet-mapping>
+    <servlet-name>ShowConfiguration</servlet-name>
+    <url-pattern>/admin/showConfiguration</url-pattern>
+  </servlet-mapping>
+
   <servlet>
     <servlet-name>StartupStatus</servlet-name>
     <servlet-class>edu.cornell.mannlib.vitro.webapp.controller.admin.StartupStatusController</servlet-class>

webapp/web/templates/freemarker/body/admin/admin-showConfiguration.ftl

@@ -0,0 +1,28 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<#-- Template viewing the authorization mechanisms: current identifiers, factories, policies, etc. -->
+
+${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/showAuth.css" />')}
+
+<h2>Configuration settings</h2>
+
+<section id="show-auth" role="region">
+    <h4>Build and runtime properties:</h4>
+    <table summary="Build and Runtime Properties">
+    	<#list configurationProperties?keys as key>
+            <tr>
+                <td>${key}</td>
+                <td>${configurationProperties[key]}</td>
+            </tr>
+        </#list>
+    </table>
+    <h4>Java system properties:</h4>
+    <table summary="Java System Properties">
+    	<#list javaSystemProperties?keys as key>
+            <tr>
+                <td>${key}</td>
+                <td>${javaSystemProperties[key]}</td>
+            </tr>
+        </#list>
+    </table>
+</section>

webapp/web/templates/freemarker/edit/forms/dateTimeValueForm.ftl

@@ -33,8 +33,7 @@
         <a class="cancel" href="${editConfiguration.cancelUrl}" title="${i18n().cancel_title}">${i18n().cancel_link}</a>
     </p>
 </form>
-${stylesheets.add('<link rel="stylesheet" href="${urls.base}/edit/forms/css/customForm.css" />',
+${stylesheets.add('<link rel="stylesheet" href="${urls.base}/templates/freemarker/edit/forms/css/customForm.css" />')}
-                  '<link rel="stylesheet" href="${urls.base}/edit/forms/css/personHasEducationalTraining.css" />')}
 
 ${scripts.add('<script type="text/javascript" src="${urls.base}/js/utils.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/customFormUtils.js"></script>')}

webapp/web/templates/freemarker/page/partials/developerPanel.ftl

@@ -56,6 +56,8 @@
 					Links
 					<br/>
 					<a href="${urls.base}/admin/log4j.jsp">Set log levels</a>
+					<a href="${urls.base}/admin/showConfiguration">Show Configuration</a>
+					<br/>
 					<a href="${urls.base}/admin/showAuth">Show authorization info</a>
 					<a href="${urls.base}/admin/showThreads">Show background threads</a>
 				</div>