External vocabulary service and integration of Agrovoc with work beginning for applying concept semantic type to UMLS concepts.

olddeploy.properties

@@ -0,0 +1,162 @@
+# -----------------------------------------------------------------------------
+#
+# VIVO deployment properties
+#
+# This file is provided as example.deploy.properties.
+#
+# Save a copy of this file as deploy.properties, and edit the properties as 
+# needed for your deployment.
+#
+# -----------------------------------------------------------------------------
+
+# 
+# This namespace will be used when generating URIs for objects created in the 
+# editor. Change it to reflect your own domain. For example, Cornell's 
+# namespace is http://vivo.cornell.edu/individual/
+#
+# Note: it is essential that this namespace end with a trailing slash.
+#
+Vitro.defaultNamespace = http://vivo.mannlib.cornell.edu/individual/
+
+#
+# Where is the Vitro core directory?
+# In most deployments, this is set to ./vitro-core (It is not uncommon for this 
+# setting to point elsewhere in development environments).
+#   Examples:
+#      vitro.core.dir = ./vitro-core
+#      vitro.core.dir = ../vitro
+#      vitro.core.dir = /usr/local/vitro/trunk
+vitro.core.dir = ../vivovitro
+
+#
+# The base install directory for your Tomcat server. The VIVO application 
+# will be deployed in the /webapps directory below this base. 
+#
+tomcat.home = C:/apache/apache-tomcat-7.0.40
+
+#
+# The name of the VIVO application. This will be used as the name of the
+# subdirectory within your Tomcat server's /webapps directory. It also appears
+# in the URL for the application. For example, http://my.vivo.server/vivo
+#
+webapp.name = vivo
+
+#
+# The location where the VIVO application will store the data that it creates.
+# This includes uploaded files (usually images) and the Lucene search index.
+#
+vitro.home.directory = C:/Users/hjk54/vivodata
+
+#
+# SMTP host which the "Contact Us" form can use to send mail. If this is left 
+# empty, the "Contact Us" form will be disabled.
+#
+Vitro.smtpHost =appsmtp.mail.cornell.edu
+#Added these per Jim's instructions, TO DO: try without smtpHost line
+email.smtpHost = appsmtp.mail.cornell.edu
+email.replyTo = hjk54@cornell.edu
+
+#
+# The basic parameters for a database connection. Change the end of the 
+# URL to reflect your database name (if it is not "vitro"). Change the username 
+# and password to match the authorized database user you created. Increase the
+# maximum size of the database connection pool if you need to serve a greater
+# number of concurrent page requests.
+#
+#Test Empty database
+#VitroConnection.DataSource.url = jdbc:mysql://localhost/testvivo
+
+VitroConnection.DataSource.url = jdbc:mysql://localhost/vivodb
+VitroConnection.DataSource.username = vivouser
+VitroConnection.DataSource.password = vivopass
+#test migration
+#VitroConnection.DataSource.url = jdbc:mysql://localhost/migratetest
+#VitroConnection.DataSource.username = migrateuser
+#VitroConnection.DataSource.password = migratepassword
+
+#
+# The Jena triple store technology to use.  SDB is Jena's SPARQL database;
+# this setting allows RDF data to scale beyond the limits of the JVM heap.
+# Set to RDB to use the older Jena RDB store with in-memory caching. 
+#
+VitroConnection.DataSource.tripleStoreType = SDB
+
+#
+# The maximum number of active connections in the database connection pool.
+# Increase this value to support a greater number of concurrent page requests
+# with SDB.  It is not necessary to adjust this value when using the
+# RDB configuration.
+#
+VitroConnection.DataSource.pool.maxActive = 40
+
+#
+# The maximum number of database connections that will be allowed
+# to remain idle in the connection pool.  Default is 25%
+# of the maximum number of active connections.
+#
+VitroConnection.DataSource.pool.maxIdle = 10
+
+#
+# Parameters to change in order to use VIVO with a database other than 
+# MySQL.
+#
+VitroConnection.DataSource.dbtype = MySQL
+VitroConnection.DataSource.driver = com.mysql.jdbc.Driver
+VitroConnection.DataSource.validationQuery = SELECT 1
+
+#
+# The name of your first admin user for the VIVO application. The password 
+# for this user is initially set to "defaultAdmin", but you will be asked to 
+# change the password the first time you log in.
+#
+initialAdminUser = defaultAdmin
+rootUser.emailAddress = hjk54@cornell.edu
+#
+# How is a logged-in user associated with a particular Individual? One way is 
+# for the Individual to have a property whose value is the username of the user.
+# This value should be the URI for that property.
+#
+selfEditing.idMatchingProperty = http://vivo.mannlib.cornell.edu/ns#networkId
+
+#
+# If an external authentication system like Shibboleth or CUWebAuth is to be
+# used, these properties say how the login button should be labeled, and which
+# HTTP header will contain the user ID from the authentication system. If such
+# a system is not to be used, leave these commented out. Consult the 
+# installation instructions for more details. 
+#
+#externalAuth.buttonText = Log in using BearCat Shibboleth
+#externalAuth.netIdHeaderName = remote_userID 
+
+#
+# The temporal graph visualization can require extensive machine resources.
+# This can have a particularly noticable impact on memory usage if
+# - VIVO is configured to use Jena SDB,
+# - The organization tree is deep,
+# - The number of grants and publications is large.
+# VIVO release 1.2 guards against this impact by disabling the temporal graph
+# visualization unless the "visualization.temporal" flag is set to "enabled".
+#
+# visualization.temporal = enabled 
+
+#
+# The temporal graph visualization is used to compare different organizations/people
+# within an organization on parameters like number of publications or grants.
+# By default, the app will attempt to make its best guess at the top level
+# organization in your instance. If you're unhappy with this selection, uncomment out
+# the property below and set it to the URI of the organization individual you want to
+# identify as the top level organization. It will be used as the default whenever the
+# temporal graph visualization is rendered without being passed an explicit org.
+# For example, to use "Ponce School of Medicine" as the top organization:
+# visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862
+#
+# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI
+
+#
+# Default type(s) for Google Refine Reconciliation Service
+# The format for this property is id, name; id1, name1; id2, name2 etc.
+# See Service Metadata from this page http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi
+# for more information.
+Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Course, Course; http://vivoweb.org/ontology/core#Grant, Grant; http://aims.fao.org/aos/geopolitical.owl, Location; http://xmlns.com/foaf/0.1/Organization, Organization; http://xmlns.com/foaf/0.1/Person, Person; http://purl.org/ontology/bibo/Article, Publication
+#solr
+vitro.local.solr.url = http://localhost:8080/vivosolr

ontology/public/catalog-v001.xml

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri id="User Entered Import Resolution" name="http://vivoweb.org/ontology/core/vivo-c4o-public-1.5.owl" uri="vivo-core-public-1.5.owl"/>
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
+</catalog>

productMods/templates/freemarker/body/partials/individual/individual-positions.ftl

@@ -1,6 +1,6 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
-<#-- List of positions for the individual -->
+<#-- List of positions for the individual --> <h3>Positions!${core}personInPosition</h3>
 <#assign positions = propertyGroups.pullProperty("${core}personInPosition")!>
 <#if positions?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
     <#assign localName = positions.localName>

productMods/templates/freemarker/body/partials/individual/individual-researchAreas.ftl

@@ -2,6 +2,9 @@
 
 <#-- List of research areas for the individual -->
 <#assign researchAreas = propertyGroups.pullProperty("${core}hasResearchArea")!> 
+<#assign concepts = propertyGroups.pullProperty("${core}hasAssociatedConcept")!> 
+<#if concepts?has_content> concepts has content <#else> concepts dont have content</#if>
+<h2>RESEARCH AREAS: ${core}hasResearchArea</h2>
 <#if researchAreas?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
     <#assign localName = researchAreas.localName>
     <h2 id="${localName}" class="mainPropGroup">
@@ -11,5 +14,5 @@
     </h2>
     <ul id="individual-${localName}" role="list" >
         <@p.objectProperty researchAreas editable />
-    </ul>
+    </ul> <#else> Research areas does not have content
 </#if>   

productMods/templates/freemarker/edit/forms/addAssociatedConcept.ftl

@@ -96,6 +96,9 @@
     <input type="hidden" id="conceptNode" name="conceptNode" value=""/> <!-- Field value populated by JavaScript -->
     <input type="hidden" id="conceptLabel" name="conceptLabel" value="" />  <!-- Field value populated by JavaScript -->
 		<input type="hidden" id="conceptSource" name="conceptSource" value="" /> <!-- Field value populated by JavaScript -->
+    		<input type="hidden" id="conceptSemanticTypeURI" name="conceptSemanticTypeURI" value="" /> <!-- Field value populated by JavaScript -->
+        		<input type="hidden" id="conceptSemanticTypeLabel" name="conceptSemanticTypeLabel" value="" /> <!-- Field value populated by JavaScript -->
+    
     <div id="selectedConcept" name="selectedConcept" class="acSelection">
         <p class="inline">
         </p>

productMods/templates/freemarker/edit/forms/js/addConcept.js

@@ -54,6 +54,7 @@ var addConceptForm = {
         this.externalConceptURI = $('#conceptNode');
         this.externalConceptLabel = $('#conceptLabel');
         this.externalConceptSource = $('#conceptSource');
+        this.externalConceptSemanticTypeLabel = $("#conceptSemanticTypeLabel");
         //remove links
         this.removeConceptLinks = $('a.remove');
         this.errors = $('#errors');
@@ -236,23 +237,27 @@ var addConceptForm = {
     	}
     	var i;
     	var len = checkedElements.length;
-    	var checkedConcept, checkedConceptElement, conceptLabel, conceptSource;
+    	var checkedConcept, checkedConceptElement, conceptLabel, conceptSource, conceptSemanticType;
     	var conceptNodes = [];
     	var conceptLabels = [];
     	var conceptSources = [];
+    	var conceptSemanticTypes = [];
     	
     	checkedElements.each(function() {
     		checkedConceptElement = $(this);
     		checkedConcept = checkedConceptElement.val();
     		conceptLabel = checkedConceptElement.attr("label");
     		conceptSource = checkedConceptElement.attr("conceptDefinedBy");
+    		conceptSemanticType = checkedConceptElement.attr("conceptType");
     		conceptNodes.push(checkedConcept);
     		conceptLabels.push(conceptLabel);
     		conceptSources.push(conceptSource);
+    		conceptSemanticTypes.push(conceptSemanticType);
     	});
     	this.externalConceptURI.val(conceptNodes);
     	this.externalConceptLabel.val(conceptLabels);
     	this.externalConceptSource.val(conceptSources);
+    	this.externalConceptSemanticTypeLabel.val(conceptSemanticTypes);
     	return true;
     }, 
     generateIndividualConceptDisplay: function(cuiURI, label, definition, type, definedBy, isBestMatch) {

src/edu/cornell/mannlib/semservices/bo/BaseObject.java

@@ -0,0 +1,27 @@
+package edu.cornell.mannlib.semservices.bo;
+
+public class BaseObject {
+   /**
+    * Simple JavaBean domain object with an id property.
+    * Used as a base class for objects needing this property.
+    *
+    * @author Ken Krebs
+    * @author Juergen Hoeller
+    */
+   private Integer id;
+
+   public void setId(Integer id) {
+      this.id = id;
+   }
+
+   public Integer getId() {
+      return id;
+   }
+
+   public boolean isNew() {
+      return (this.id == null);
+   }
+
+
+
+}

src/edu/cornell/mannlib/semservices/bo/Concept.java

@@ -1,7 +1,8 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.bo;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class Concept {
 
    private String definedBy;
@@ -11,13 +12,22 @@ public class Concept {
    private String type;
    private String definition;
    private String uri;
+   private String schemeURI;
+   private List<String> broaderURIList;
+   private List<String> narrowerURIList;
+   private List<String> exactMatchURIList;
+   private List<String> closeMatchURIList;
 
    /**
     * default constructor
     */
    public Concept() {
-
+      this.broaderURIList = new ArrayList<String>();
+      this.narrowerURIList = new ArrayList<String>();
+      this.exactMatchURIList = new ArrayList<String>();
+      this.closeMatchURIList = new ArrayList<String>();
    }
+   
    /**
     * @return the conceptId
     */
@@ -90,6 +100,18 @@ public class Concept {
    public void setDefinedBy(String definedBy) {
       this.definedBy = definedBy;
    }
+   /**
+    * @return the schemeURI
+    */
+   public String getSchemeURI() {
+      return schemeURI;
+   }
+   /**
+    * @param schemeURI the schemeURI to set
+    */
+   public void setSchemeURI(String schemeURI) {
+      this.schemeURI = schemeURI;
+   }
    /**
     * @return the bestMatch
     */
@@ -102,5 +124,29 @@ public class Concept {
    public void setBestMatch(String bestMatch) {
       this.bestMatch = bestMatch;
    }
+public List<String> getBroaderURIList() {
+	return broaderURIList;
+}
+public void setBroaderURIList(List<String> broaderURIList) {
+	this.broaderURIList = broaderURIList;
+}
+public List<String> getNarrowerURIList() {
+	return narrowerURIList;
+}
+public void setNarrowerURIList(List<String> narrowerURIList) {
+	this.narrowerURIList = narrowerURIList;
+}
+public List<String> getExactMatchURIList() {
+	return exactMatchURIList;
+}
+public void setExactMatchURIList(List<String> exactMatchURIList) {
+	this.exactMatchURIList = exactMatchURIList;
+}
+public List<String> getCloseMatchURIList() {
+	return closeMatchURIList;
+}
+public void setCloseMatchURIList(List<String> closeMatchURIList) {
+	this.closeMatchURIList = closeMatchURIList;
+}
 
 }

src/edu/cornell/mannlib/semservices/bo/ConceptInfo.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.bo;
 
 
@@ -8,8 +6,7 @@ import java.util.List;
 
 public class ConceptInfo extends SemanticServicesInfoBase {
 
-    private List<Concept> conceptList;
+    private List<?> conceptList;
-
     /**
      *
      */
@@ -18,17 +15,16 @@ public class ConceptInfo extends SemanticServicesInfoBase {
     }
 
     /**
-     * @return the vivoDepartmentList
+     * @return the conceptList
      */
-    public List<Concept> getConceptList() {
+    public List<?> getConceptList() {
         return conceptList;
     }
 
     /**
-     * @param vivoDepartmentList the vivoDepartmentList to set
+     * @param conceptList the conceptList to set
      */
-    public void setConceptList(List<Concept> inputConceptList) {
+    public void setConceptList(List<?> conceptList) {
-        this.conceptList = inputConceptList;
+        this.conceptList = conceptList;
     }
-
 }

src/edu/cornell/mannlib/semservices/bo/Day.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.bo;
 
 import java.util.Calendar;

src/edu/cornell/mannlib/semservices/bo/SemanticServicesError.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.bo;
 
 public class SemanticServicesError {

src/edu/cornell/mannlib/semservices/bo/SemanticServicesInfoBase.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.bo;
 
 public class SemanticServicesInfoBase {

src/edu/cornell/mannlib/semservices/bo/SparqlFeed.java

@@ -0,0 +1,208 @@
+package edu.cornell.mannlib.semservices.bo;
+
+import java.io.Serializable;
+import java.util.HashMap;
+import java.util.Map;
+
+public class SparqlFeed extends BaseObject implements Serializable {
+
+
+   /**
+    *
+    */
+   private static final long serialVersionUID = 6024170338796859330L;
+   private String name;
+   private String endpoint;
+   private String repository;
+   private String query;
+   private int mapperId;
+   private int fetcherId;
+   private Map<String, String> parameterMap;
+
+   /**
+    * Constructor
+    */
+   public SparqlFeed() {
+      super();
+      parameterMap = new HashMap<String, String>();
+   }
+
+   /**
+    * @return the name
+    */
+   public String getName() {
+      return name;
+   }
+
+   /**
+    * @param name the name to set
+    */
+   public void setName(String name) {
+      this.name = name;
+   }
+
+   /**
+    * @return the endpoint
+    */
+   public String getEndpoint() {
+      return endpoint;
+   }
+
+   /**
+    * @param endpoint the endpoint to set
+    */
+   public void setEndpoint(String endpoint) {
+      this.endpoint = endpoint;
+   }
+
+   /**
+    * @return the repository
+    */
+   public String getRepository() {
+      return repository;
+   }
+
+   /**
+    * @param repository the repository to set
+    */
+   public void setRepository(String repository) {
+      this.repository = repository;
+   }
+
+   /**
+    * @return the query
+    */
+   public String getQuery() {
+      return query;
+   }
+
+   /**
+    * @param query the query to set
+    */
+   public void setQuery(String query) {
+      this.query = query;
+   }
+
+   /**
+    * @return the mapperId
+    */
+   public int getMapperId() {
+      return mapperId;
+   }
+
+   /**
+    * @param mapperId the mapperId to set
+    */
+   public void setMapperId(int mapperId) {
+      this.mapperId = mapperId;
+   }
+
+   /**
+    * @return the fetcherId
+    */
+   public int getFetcherId() {
+      return fetcherId;
+   }
+
+   /**
+    * @param fetcherId the fetcherId to set
+    */
+   public void setFetcherId(int fetcherId) {
+      this.fetcherId = fetcherId;
+   }
+
+   /**
+    * @return the parameterMap
+    */
+   public Map<String, String> getParameterMap() {
+      return parameterMap;
+   }
+
+   /**
+    * @param parameterMap the parameterMap to set
+    */
+   public void setParameterMap(Map<String, String> parameterMap) {
+      this.parameterMap = parameterMap;
+   }
+
+   /* (non-Javadoc)
+    * @see java.lang.Object#hashCode()
+    */
+   @Override
+   public int hashCode() {
+      final int prime = 31;
+      int result = 1;
+      result = prime * result + ((endpoint == null) ? 0 : endpoint.hashCode());
+      result = prime * result + fetcherId;
+      result = prime * result + mapperId;
+      result = prime * result + ((name == null) ? 0 : name.hashCode());
+      result = prime * result
+            + ((parameterMap == null) ? 0 : parameterMap.hashCode());
+      result = prime * result + ((query == null) ? 0 : query.hashCode());
+      result = prime * result
+            + ((repository == null) ? 0 : repository.hashCode());
+      return result;
+   }
+
+   /* (non-Javadoc)
+    * @see java.lang.Object#equals(java.lang.Object)
+    */
+   @Override
+   public boolean equals(Object obj) {
+      if (this == obj) {
+         return true;
+      }
+      if (obj == null) {
+         return false;
+      }
+      if (getClass() != obj.getClass()) {
+         return false;
+      }
+      SparqlFeed other = (SparqlFeed) obj;
+      if (endpoint == null) {
+         if (other.endpoint != null) {
+            return false;
+         }
+      } else if (!endpoint.equals(other.endpoint)) {
+         return false;
+      }
+      if (fetcherId != other.fetcherId) {
+         return false;
+      }
+      if (mapperId != other.mapperId) {
+         return false;
+      }
+      if (name == null) {
+         if (other.name != null) {
+            return false;
+         }
+      } else if (!name.equals(other.name)) {
+         return false;
+      }
+      if (parameterMap == null) {
+         if (other.parameterMap != null) {
+            return false;
+         }
+      } else if (!parameterMap.equals(other.parameterMap)) {
+         return false;
+      }
+      if (query == null) {
+         if (other.query != null) {
+            return false;
+         }
+      } else if (!query.equals(other.query)) {
+         return false;
+      }
+      if (repository == null) {
+         if (other.repository != null) {
+            return false;
+         }
+      } else if (!repository.equals(other.repository)) {
+         return false;
+      }
+      return true;
+   }
+
+
+
+}

src/edu/cornell/mannlib/semservices/bo/SparqlFeedParam.java

@@ -0,0 +1,61 @@
+package edu.cornell.mannlib.semservices.bo;
+
+import java.io.Serializable;
+
+public class SparqlFeedParam extends BaseObject implements Serializable {
+
+   /**
+    *
+    */
+   private static final long serialVersionUID = 4602167398212576479L;
+   private int sparqlFeedId;
+   private String param;
+   private String value;
+
+   public SparqlFeedParam()  {
+      //  default constructor
+   }
+
+   /**
+    * @return the sparqlFeedId
+    */
+   public int getSparqlFeedId() {
+      return sparqlFeedId;
+   }
+
+   /**
+    * @param sparqlFeedId the sparqlFeedId to set
+    */
+   public void setSparqlFeedId(int sparqlFeedId) {
+      this.sparqlFeedId = sparqlFeedId;
+   }
+
+   /**
+    * @return the param
+    */
+   public String getParam() {
+      return param;
+   }
+
+   /**
+    * @param param the param to set
+    */
+   public void setParam(String param) {
+      this.param = param;
+   }
+
+   /**
+    * @return the value
+    */
+   public String getValue() {
+      return value;
+   }
+
+   /**
+    * @param value the value to set
+    */
+   public void setValue(String value) {
+      this.value = value;
+   }
+
+}

src/edu/cornell/mannlib/semservices/bo/SparqlPlugin.java

@@ -0,0 +1,54 @@
+package edu.cornell.mannlib.semservices.bo;
+
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class SparqlPlugin extends BaseObject {
+   private String type;
+   private String name;
+   private String classname;
+
+   /**
+    *
+    */
+   public SparqlPlugin() {
+      super();
+   }
+   /**
+    * @return the name
+    */
+   public String getName() {
+      return name;
+   }
+   /**
+    * @param name the name to set
+    */
+   public void setName(String name) {
+      this.name = name;
+   }
+   /**
+    * @return the type
+    */
+   public String getType() {
+      return type;
+   }
+   /**
+    * @param type the type to set
+    */
+   public void setType(String type) {
+      this.type = type;
+   }
+   /**
+    * @return the classname
+    */
+   public String getClassname() {
+      return classname;
+   }
+   /**
+    * @param classname the classname to set
+    */
+   public void setClassname(String classname) {
+      this.classname = classname;
+   }
+}

src/edu/cornell/mannlib/semservices/bo/Time.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.bo;
 
 import java.util.Date;

src/edu/cornell/mannlib/semservices/exceptions/ConceptsNotFoundException.java

@@ -0,0 +1,13 @@
+package edu.cornell.mannlib.semservices.exceptions;
+
+public class ConceptsNotFoundException extends Exception {
+   /**
+    * An exception that indicates a service could not find a Concept
+    */
+   private static final long serialVersionUID = -4729465393290022840L;
+   public ConceptsNotFoundException() { }
+   public ConceptsNotFoundException(String message) { super(message); }
+   public ConceptsNotFoundException(Throwable cause) { super(cause); }
+   public ConceptsNotFoundException(String message, Throwable cause) { super(message, cause); }
+
+}

src/edu/cornell/mannlib/semservices/service/ExternalConceptService.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.service;
 
 import java.util.List;
@@ -7,7 +5,24 @@ import java.util.List;
 import edu.cornell.mannlib.semservices.bo.Concept;
 
 public interface ExternalConceptService {
-   // this is the only method that needs to be exposed
+
+	/**
+	 * @param term
+	 * @return
+	 */
 	List<Concept> processResults(String term) throws Exception;
 
+	/**
+	 * @param term
+	 * @return
+	 * @throws Exception
+	 */
+	List<Concept> getConcepts(String term) throws Exception;
+
+	/**
+	 * @param uri
+	 * @return
+	 */
+	List<Concept> getConceptsByURIWithSparql(String uri) throws Exception;
+
 }

src/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java

@@ -8,18 +8,30 @@ import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.StringWriter;
 import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.rmi.RemoteException;
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 
-
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.rpc.ServiceException;
+
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.fao.gilw.aims.webservices.AgrovocWS;
+import org.fao.www.webservices.AgrovocWS.ACSWWebService;
-import org.fao.gilw.aims.webservices.AgrovocWSServiceLocator;
+import org.fao.www.webservices.AgrovocWS.ACSWWebServiceServiceLocator;
+import org.semanticweb.skos.SKOSAnnotation;
+import org.semanticweb.skos.SKOSConcept;
+import org.semanticweb.skos.SKOSDataset;
+import org.semanticweb.skos.SKOSEntity;
+import org.semanticweb.skos.SKOSLiteral;
+import org.semanticweb.skos.SKOSUntypedLiteral;
+import org.semanticweb.skosapibinding.SKOSManager;
 import org.w3c.dom.Attr;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
@@ -27,95 +39,190 @@ import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+
 import edu.cornell.mannlib.semservices.bo.Concept;
 import edu.cornell.mannlib.semservices.service.ExternalConceptService;
 import edu.cornell.mannlib.semservices.util.XMLUtils;
 
 public class AgrovocService implements ExternalConceptService  {
+	
    protected final Log logger = LogFactory.getLog(getClass());
-   private java.lang.String AgrovocWS_address = "http://www.fao.org/webservices/AgrovocWS";
+   private java.lang.String AgrovocWS_address = "http://agrovoc.fao.org/axis/services/SKOSWS";
+   private final String schemeUri = "http://aims.fao.org/aos/agrovoc/agrovocScheme";
+   private final String baseUri = "http://aims.fao.org/aos/agrovoc/";
+   private final String ontologyName = "agrovoc";
+   private final String format = "SKOS";
+   private final String lang = "en";
+   private final String codeName = "hasCodeAgrovoc";
+   private final String searchMode = "Exact Match";
+   protected final String dbpedia_endpoint = " http://dbpedia.org/sparql";
 
-   public List<Concept> processResults(String term) throws Exception {
+  
+   
+	@Override
+	public List<Concept> getConcepts(String term) throws Exception {
 		List<Concept> conceptList = new ArrayList<Concept>();
-
+		//System.out.println("Searching for term: "+ term);
-      String termcode;
+		String result = getURIByTermAndLangXML(this.ontologyName, term, this.searchMode, this.format, this.lang);
-      try {
+		// return empty conceptList if conceptUri is empty
-         termcode = getTermcodeByTerm(term);
+        if (StringUtils.isEmpty(result)) {
-      } catch (Exception e1) {
+        	return conceptList;
-         logger.error("Could not get termcode from service", e1);
-         throw e1;
         }
 		
-      String format = "SKOS";
+		// First create a new SKOSManager
-      // if the termcode is null it means that either the service is not responding
+		String conceptUri = getConceptURIFromRDF(result);
-      // or there was not a match for the string
+        SKOSManager manager = new SKOSManager();
-      //System.out.println("Got termcode: "+termcode);
-
-      String results = getConceptInfoByTermcodeXML(termcode, format);
-
-      //XMLUtils.prettyPrint(results);
         
+        // return empty conceptList if conceptUri is empty
+        if (StringUtils.isEmpty(conceptUri)) {
+        	return conceptList;
+        }
+        URI uri = null;
 		try {
-         Document doc = XMLUtils.parse(results);
+			uri = new URI(conceptUri);
-         String prefLabelQuery = "child::*[@xml:lang='EN']";
+		} catch (URISyntaxException e) { 
-         NodeList nodes = doc.getElementsByTagName("skos:Concept");
+			e.printStackTrace();
-         //System.out.println("Found this many nodes: "+ nodes.getLength());
+			return conceptList;
-         for (int i=0; i < nodes.getLength(); i++) {
+		}
 		
-            Node node = nodes.item(i);
+		System.out.println("uri: "+uri); 
-            //XMLUtils.serializeNode(node); System.out.println();
+        SKOSDataset dataset = manager.loadDataset(uri);
         
+        for (SKOSConcept skosConcept : dataset.getSKOSConcepts()) {
         	Concept concept = new Concept();
-            concept.setDefinedBy("http://aims.fao.org/aos/agrovoc/agrovocScheme");
+            System.out.println("Concept: " + skosConcept.getURI());
-            concept.setConceptId(termcode);
+            concept.setUri(skosConcept.getURI().toString());
+            concept.setConceptId(stripConceptId(skosConcept.getURI().toString()));
+            concept.setBestMatch("true");
+            concept.setDefinedBy(this.schemeUri);
+            concept.setSchemeURI(this.schemeUri);
+            concept.setType("");
+            String lang = "";
             
-            NamedNodeMap attrs = node.getAttributes();
+            for (SKOSLiteral literal : skosConcept.getSKOSRelatedConstantByProperty(dataset, manager.getSKOSDataFactory().getSKOSPrefLabelProperty())) {
-            Attr idAttr = (Attr) attrs.getNamedItem("rdf:about");
-            String conceptUri = idAttr.getTextContent();
-            concept.setUri(conceptUri);
               
-            Node prefLabelNode = XMLUtils.getNodeWithXpath(node, prefLabelQuery);
+              if (!literal.isTyped()) {
-            if (prefLabelNode != null) {
+                  // if it has  language
-               String prefLabel = prefLabelNode.getTextContent();
+                  SKOSUntypedLiteral untypedLiteral = literal.getAsSKOSUntypedLiteral();
-               concept.setLabel(prefLabel);
+                  if (untypedLiteral.hasLang()) {
+                      lang = untypedLiteral.getLang();
+                  } else {
+                	  lang = "";
                   }
+              }
+              if (lang.equals("en")) {
+                 //System.out.println("prefLabel: " + literal.getLiteral());
+                 
+                 concept.setLabel(literal.getLiteral());
+              }
+            }
+            
+            // get the broader property URI
+            List<String> broaderURIList = new ArrayList<String>();
+            for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSBroaderProperty().getURI())) {
+            	String value = new String();
+            	if (annotation.isAnnotationByConstant()) {
+                   SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
+                   value = literal.getLiteral(); 
+            	   //System.out.println("broder uri: "+ value);
+            	} else {
+                    // annotation is some resource
+                    SKOSEntity entity = annotation.getAnnotationValue();
+                    value = entity.getURI().toString();
+                }
+            	//System.out.println("broader uri: "+value);
+            	broaderURIList.add(value);
+            }
+            concept.setBroaderURIList(broaderURIList);
+            
+            // get the narrower property URI
+            List<String> narrowerURIList = new ArrayList<String>();
+            for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSNarrowerProperty().getURI())) {
+            	String value = new String();
+            	if (annotation.isAnnotationByConstant()) {
+                   SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
+                   value = literal.getLiteral(); 
+            	   //System.out.println("narrower uri: "+ value);
+            	} else {
+                    // annotation is some resource
+                    SKOSEntity entity = annotation.getAnnotationValue();
+                    value = entity.getURI().toString();
+                }
+            	//System.out.println("narrower uri: "+value);
+            	narrowerURIList.add(value);
+            }
+            concept.setNarrowerURIList(narrowerURIList);
+            
+            // exact match
+            List<String> exactMatchURIList = new ArrayList<String>();
+            for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSExactMatchProperty().getURI())) {
+            	String value = new String();
+            	if (annotation.isAnnotationByConstant()) {
+                   SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
+                   value = literal.getLiteral(); 
+            	   //System.out.println("exact match: "+ value);
+            	} else {
+                    // annotation is some resource
+                    SKOSEntity entity = annotation.getAnnotationValue();
+                    value = entity.getURI().toString();
+                }
+            	//System.out.println("exact match: "+value);
+            	exactMatchURIList.add(value);
+            }
+            concept.setExactMatchURIList(exactMatchURIList);
+            
+            // close match
+            List<String> closeMatchURIList = new ArrayList<String>();
+            for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSCloseMatchProperty().getURI())) {
+            	String value = new String();
+            	if (annotation.isAnnotationByConstant()) {
+                   SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
+                   value = literal.getLiteral(); 
+            	   //System.out.println("close match: "+ value);
+            	} else {
+                    // annotation is some resource
+                    SKOSEntity entity = annotation.getAnnotationValue();
+                    value = entity.getURI().toString();
+                }
+            	//System.out.println("close match: "+value);
+            	closeMatchURIList.add(value);
+            	if (value.startsWith("http://dbpedia.org")) {
+            		String description = getDbpediaDescription(value);
+            		//System.out.println("description: "+ description);
+            		concept.setDefinition(description);
+            	}
+            }
+            concept.setCloseMatchURIList(closeMatchURIList);
+            
             conceptList.add(concept);
-         }
+             
-      } catch (IOException e) {
+
-         e.printStackTrace();
-      } catch (SAXException e) {
-         e.printStackTrace();
-      } catch (ParserConfigurationException e) {
-         e.printStackTrace();
         }
 		return conceptList;
 	}
 
-
+   public List<Concept> processResults(String term) throws Exception {
-   protected String getAgrovocLanguages() {
+       return getConcepts(term);
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getAgrovocLanguages();
-      } catch (ServiceException e) {
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
    }
    
-      return result;
-   }
    
+   
+   @Deprecated
    protected String getTermcodeByTerm(String term) throws Exception {
       String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
+      ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
       try {
          URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
+         ACSWWebService agrovoc_service = locator.getACSWWebService(url);
          result = agrovoc_service.getTermcodeByTerm(term);
       } catch (ServiceException e) {
          logger.error("service exception", e);
@@ -130,13 +237,15 @@ public class AgrovocService implements ExternalConceptService  {
       return result;
    }
 
-   protected String getTermcodeByTermXML(String term, String format) {
+    
+   
+   protected String getTermCodeByTermAndLangXML(String ontologyName, String searchString, String lang, String codeName, String format) {
 	      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
+	      ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
 	      try {
 	         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
+	         ACSWWebService agrovoc_service = locator.getACSWWebService(url);
-         result = agrovoc_service.getTermcodeByTermXML(term, format);
+	         result = agrovoc_service.getTermCodeByTermAndLangXML(ontologyName, searchString, lang, codeName, format);
 	      } catch (ServiceException e) {
 	         logger.error("service exception", e);
 	         e.printStackTrace();
@@ -148,33 +257,18 @@ public class AgrovocService implements ExternalConceptService  {
 	      return result;
 	   }
 
-   protected String getTermByLanguage(int termcode, String language) {
+    
+
+	protected String getURIByTermAndLangXML(String ontologyName, String term,
+			String searchMode, String format, String lang) {
 		String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
+		ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
 		try {
 			URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
+			ACSWWebService agrovoc_service = locator.getACSWWebService(url);
-         result = agrovoc_service.getTermByLanguage(termcode, language);
+			result = agrovoc_service.getURIByTermAndLangXML(ontologyName, term,
+					searchMode, format, lang);
 		} catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-      return result;
-   }
-
-   protected String getTermByLanguageXML(int termcode, String language, String format) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getTermByLanguageXML(termcode, language, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
 			e.printStackTrace();
 		} catch (RemoteException e) {
 			e.printStackTrace();
@@ -185,220 +279,16 @@ public class AgrovocService implements ExternalConceptService  {
 		return result;
 	}
 
-   protected String getTermsListByLanguage2(String termcodes, String language, String sep) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getTermsListByLanguage2(termcodes, language, sep);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-      return result;
-   }
    
-   protected String getTermsListByLanguageXML(String termcodes, String language, String format) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getTermsListByLanguageXML(termcodes, language, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
  
-      return result;
-   }
     
-   protected String getAllLabelsByTermcode2(int termcode, String sep) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getAllLabelsByTermcode2(termcode, sep);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String getAllLabelsByTermcodeXML(int termcode, String format) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getAllLabelsByTermcodeXML(termcode, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String simpleSearchByMode2(String term, String mode, String sep ) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.simpleSearchByMode2(term, mode, sep);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String simpleSearchByModeXML(String term, String mode, String format) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.simpleSearchByModeXML(term, mode, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String searchByTerm2(String term, String sep) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.searchByTerm2(term, sep);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String searchByTermXML(String term, String format) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.searchByTermXML(term, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String searchCategoryByMode(String term, String lang, String schemeid, String mode, String sep) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.searchCategoryByMode(term, lang, schemeid, mode, sep);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String searchCategoryByModeXML(String term, String mode, String schemeid, String lang, String format) {
-      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.searchCategoryByModeXML(term, mode, schemeid, lang, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String[] getConceptInfoByTermcode(String termcode) {
-      String result[] = null;
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getConceptInfoByTermcode(termcode);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
 
    protected String getConceptInfoByTermcodeXML(String termcode, String format) {
       String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
+      ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
       try {
          URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
+         ACSWWebService agrovoc_service = locator.getACSWWebService(url);
          result = agrovoc_service.getConceptInfoByTermcodeXML(termcode, format);
       } catch (ServiceException e) {
          logger.error("service exception", e);
@@ -412,51 +302,13 @@ public class AgrovocService implements ExternalConceptService  {
       return result;
    }
    
-   protected String[] getDefinitions(int termcode, String lang) {
+   protected String getConceptByKeyword(String ontologyName, String searchString, String format, String searchMode, String lang) {
-      String[] result = null;
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getDefinitions(termcode, lang);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String getDefinitionsXML(int termcode, String lang, String format) {
-      String result = null;
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
-      try {
-         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
-         result = agrovoc_service.getDefinitionsXML(termcode, lang, format);
-      } catch (ServiceException e) {
-         logger.error("service exception", e);
-         e.printStackTrace();
-      }  catch (RemoteException e) {
-         e.printStackTrace();
-      } catch (MalformedURLException e) {
-         e.printStackTrace();
-      }
-
-      return result;
-   }
-
-   protected String getTermExpansion(String aQuery, String langugage) {
 	      String result = new String();
-      AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
+	      ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
 	      try {
 	         URL url = new URL(AgrovocWS_address);
-         AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
+	         ACSWWebService agrovoc_service = locator.getACSWWebService(url);
-         result = agrovoc_service.getTermExpansion(aQuery, langugage);
+	         result = agrovoc_service.getConceptByKeyword(ontologyName, searchString, format, searchMode, lang);
 	      } catch (ServiceException e) {
 	         logger.error("service exception", e);
 	         e.printStackTrace();
@@ -469,12 +321,14 @@ public class AgrovocService implements ExternalConceptService  {
 	      return result;
 	   }
    
+    
+
    protected String getWsdl() {
       String result = new String();
       try {
 
          StringWriter sw = new StringWriter();
-         URL rss = new URL(AgrovocWS_address + "?wsdl");
+         URL rss = new URL(this.AgrovocWS_address + "?wsdl");
 
          BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
          String inputLine;
@@ -490,4 +344,139 @@ public class AgrovocService implements ExternalConceptService  {
       }
       return result;
    }
+
+
+   public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
+	 //John Ferreira's original code has implementation
+	      List<Concept> newConceptList = new ArrayList<Concept>();
+	      return newConceptList;
+   }
+   
+   protected String getAgrovocTermCode(String rdf) throws Exception {
+	   String termcode = new String();
+	   try {
+	      Document doc = XMLUtils.parse(rdf);
+	      NodeList nodes = doc.getElementsByTagName("hasCodeAgrovoc");
+	      if (nodes.item(0) != null) {
+	         Node node = nodes.item(0);
+	         termcode = node.getTextContent();
+	      }
+	         
+	   } catch (SAXException e) {
+	      //e.printStackTrace();
+	      throw e;
+	   } catch (ParserConfigurationException e) {
+	      //e.printStackTrace();
+	      throw e;
+	   } catch (IOException e) { 
+		  //e.printStackTrace();
+		  throw e;
+	   }
+	   return termcode;
+   }
+   
+	protected String getConceptURIFromRDF(String rdf) {
+		String conceptUri = new String();
+		try {
+			Document doc = XMLUtils.parse(rdf);
+			NodeList nodes = doc.getElementsByTagName("skos:Concept");
+			Node node = nodes.item(0);
+
+			NamedNodeMap attrs = node.getAttributes();
+			Attr idAttr = (Attr) attrs.getNamedItem("rdf:about");
+			conceptUri = idAttr.getTextContent();
+		} catch (IOException e) { 
+			e.printStackTrace();
+			System.err.println("rdf: "+rdf);
+		} catch (SAXException e) { 
+			e.printStackTrace();
+			System.err.println("rdf: "+rdf);
+		} catch (ParserConfigurationException e) { 
+			e.printStackTrace();
+			System.err.println("rdf: "+rdf);
+		}
+		return conceptUri;
+
+	}
+	
+	protected String getDbpediaDescription(String uri) throws Exception{
+		String description = new String();
+		String qs = ""
+				+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
+				+ "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n"
+				+ "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
+				+ "PREFIX dbpedia-owl: <http://dbpedia.org/ontology/>\n"
+				+ "SELECT DISTINCT ?description WHERE { \n" + "<" + uri
+				+ "> rdfs:comment ?description . \n"
+				+ "FILTER (LANG(?description)='en' ) \n" + "}";
+		//System.out.println(qs);
+		List<HashMap> resultList = new ArrayList<HashMap>();
+		QueryExecution qexec = null;
+		try {
+
+			Query query = QueryFactory.create(qs);
+			qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint,
+					query);
+			resultList = new ArrayList<HashMap>();
+			ResultSet resultSet = qexec.execSelect();
+			int resultSetSize = 0;
+			while (resultSet.hasNext()) {
+				resultSetSize++;
+				QuerySolution solution = resultSet.nextSolution();
+				Iterator varnames = solution.varNames();
+				HashMap<String, String> hm = new HashMap<String, String>();
+				while (varnames.hasNext()) {
+					String name = (String) varnames.next();
+					RDFNode rdfnode = solution.get(name);
+					// logger.info("rdf node name, type: "+ name
+					// +", "+getRDFNodeType(rdfnode));
+					if (rdfnode.isLiteral()) {
+						Literal literal = rdfnode.asLiteral();
+						String nodeval = literal.getString();
+						hm.put(name, nodeval);
+					} else if (rdfnode.isResource()) {
+						Resource resource = rdfnode.asResource();
+						String nodeval = resource.toString();
+						hm.put(name, nodeval);
+					}
+				}
+				resultList.add(hm);
+			}
+			description = "";
+			for (HashMap map : resultList) {
+				if (map.containsKey("description")) {
+					description = (String) map.get("description");
+				}
+			}
+		} catch (Exception ex) {
+			throw ex;
+		}
+		return description;
+	}
+   
+   /**
+    * @param uri
+    * @return
+    */
+   protected String stripConceptId(String uri) {
+      String conceptId = new String();
+      int lastslash = uri.lastIndexOf('/');
+      conceptId = uri.substring(lastslash + 1, uri.length());
+      return conceptId;
+   }
+
+   /**
+    * @param str
+    * @return
+    */
+   protected String extractConceptId(String str) {
+      try {
+         return str.substring(1, str.length() - 1);
+      } catch (Exception ex) {
+         return "";
+      }
+   }
+   
+   
+
 }

src/edu/cornell/mannlib/semservices/service/impl/GemetService.java

@@ -1,41 +1,23 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.service.impl;
 
 
 import java.io.BufferedReader;
-import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.StringWriter;
-import java.net.MalformedURLException;
 import java.net.URL;
-import java.rmi.RemoteException;
 import java.util.ArrayList;
 import java.util.List;
 
-
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.rpc.ServiceException;
-
 import net.sf.json.JSONArray;
 import net.sf.json.JSONObject;
 import net.sf.json.JSONSerializer;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.fao.gilw.aims.webservices.AgrovocWS;
-import org.fao.gilw.aims.webservices.AgrovocWSServiceLocator;
-import org.w3c.dom.Attr;
-import org.w3c.dom.Document;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
 
 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.semservices.util.XMLUtils;
-import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
 
 public class GemetService implements ExternalConceptService  {
    protected final Log logger = LogFactory.getLog(getClass());
@@ -49,38 +31,70 @@ public class GemetService implements ExternalConceptService  {
    private final String altLabelUri = "http://www.w3.org/2004/02/skos/core%23altLabel";
    private final String exampleUri = "http://www.w3.org/2004/02/skos/core%23example";
    private final String acronymLabelUri = "http://www.w3.org/2004/02/skos/core%23acronymLabel";
+   private final String endpoint = "http://cr.eionet.europa.eu/sparql";
+   private final String schemeURI = "http://www.eionet.europa.eu/gemet/gemetThesaurus";
+
+
+  
+	@Override
+	public List<Concept> getConcepts(String term) throws Exception {
+		List<Concept> conceptList = new ArrayList<Concept>();
+	      try {
+	         String results = getConceptsMatchingKeyword(term);
+	         //System.out.println(results);
+	         conceptList = processOutput(results);         
+	          
+	      } catch (Exception ex) {
+	         return new ArrayList<Concept>();
+	         //ex.printStackTrace();
+	         //throw ex;
+	      }
+	      return conceptList;
+	}
 
    public List<Concept> processResults(String term) throws Exception {
-      List<Concept> conceptList = processConceptsAndRelatedMatchingKeyword(term);
+      List<Concept> conceptList = new ArrayList<Concept>();
+      try {
+         String results = getConceptsMatchingKeyword(term);
+         conceptList = processOutput(results);
+      } catch (Exception ex) {
+         //ex.printStackTrace();
+         throw ex;
+      }
       return conceptList;
 
    }
 
+   public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
+     //John Ferreira's original code has implementation
+      List<Concept> newConceptList = new ArrayList<Concept>();
+      return newConceptList;
+   }
+
    /**
     * @param results
     * @return
-    * By default, concepts set with best match = true
     */
-   private List<Concept> processOutput(String results) {
+   private List<Concept> processOutput(String results) throws Exception  {
-     return processOutput(results, "true");
 
-   }
-   
-   private List<Concept> processOutput(String results, String bestMatch) {
       List<Concept> conceptList = new ArrayList<Concept>();
+
       try {
          JSONArray jsonArray = (JSONArray) JSONSerializer.toJSON( results );
+         if (jsonArray.size() == 0) {
+            throw new ConceptsNotFoundException();
+         }
 
          for (int i = 0; i < jsonArray.size(); i++) {
             Concept concept = new Concept();
-				concept
+            concept.setDefinedBy(this.schemeURI);
-						.setDefinedBy("http://www.eionet.europa.eu/gemet/gemetThesaurus");
+            concept.setBestMatch("true");
-				concept.setBestMatch(bestMatch);
             JSONObject json = jsonArray.getJSONObject(i);
             String uri = getJsonValue(json, "uri");
 
             concept.setUri(uri);
-				concept.setConceptId(uri);
+            concept.setConceptId(stripConceptId(uri));
+            concept.setSchemeURI(schemeURI);
             if (json.has("preferredLabel")) {
                JSONObject preferredLabelObj = json
                      .getJSONObject("preferredLabel");
@@ -96,16 +110,33 @@ public class GemetService implements ExternalConceptService  {
                         "string"));
                }
             }
+            
+            String narrower = getRelatedConcepts(uri, "narrower");
+            List<String> narrowerURIList = getRelatedUris(narrower);
+            concept.setNarrowerURIList(narrowerURIList);            
+            
+            String broader = getRelatedConcepts(uri, "broader");
+            List<String> broaderURIList = getRelatedUris(broader);
+            concept.setBroaderURIList(broaderURIList); 
+            
+            /*String related = getRelatedConcepts(uri, "related");
+            List<String> relatedURIList = getRelatedUris(related);
+            for (String s: relatedURIList) {
+            	System.out.println("related uri: "+s);
+            }*/
+            
+            
             conceptList.add(concept);
 
          }
 
-
       } catch (Exception ex ) {
-         ex.printStackTrace();
+         //ex.printStackTrace();
          logger.error("Could not get concepts", ex);
+         throw ex;
       }
       return conceptList;
+
    }
 
    /**
@@ -123,22 +154,49 @@ public class GemetService implements ExternalConceptService  {
    }
 
 
+   /**
+    * @param concept_uri
+    * @return
+    * @throws Exception
+    */
    protected String getAvailableLangs(String concept_uri) throws Exception {
       String result = new String();
       String serviceUrl = GemetWS_address + "getAvailableLanguages" +
       "?concept_uri=" + concept_uri;
+      try {
          result = getGemetResults(serviceUrl);
+      } catch (Exception e) {
+         e.printStackTrace();
+         throw e;
+      }
       return result;
    }
 
+   /**
+    * @param concept_uri
+    * @return
+    * @throws Exception
+    */
    protected String getConcept(String concept_uri) throws Exception {
       String result = new String();
       String serviceUrl = GemetWS_address + "getConcept" +
       "?concept_uri=" + concept_uri +
       "&language=en";
+      try {
          result = getGemetResults(serviceUrl);
+      } catch (Exception e) {
+         e.printStackTrace();
+         throw e;
+      }
       return result;
    }
+
+   /**
+    * @param concept_uri
+    * @param property
+    * @return
+    * @throws Exception
+    */
    protected String getAllTranslationsForConcept(String concept_uri, String property) throws Exception {
       String result = new String();
       String property_uri = new String();
@@ -160,11 +218,23 @@ public class GemetService implements ExternalConceptService  {
       "?concept_uri=" + concept_uri +
       "&property_uri=" + property_uri +
       "&language=en";
+
+      try {
          result = getGemetResults(serviceUrl);
+      } catch (Exception e) {
+         e.printStackTrace();
+         throw e;
+      }
       return result;
    }
 
 
+   /**
+    * @param concept_uri
+    * @param relation
+    * @return
+    * @throws Exception
+    */
    protected String getRelatedConcepts(String concept_uri, String relation) throws Exception {
       String result = new String();
       String relation_uri = new String();
@@ -179,40 +249,42 @@ public class GemetService implements ExternalConceptService  {
       "?concept_uri=" + concept_uri +
       "&relation_uri=" + relation_uri +
       "&language=en";
+      try {
          result = getGemetResults(serviceUrl);
+      } catch (Exception e) {
+         e.printStackTrace();
+         throw e;
+      }
       return result;
    }
 
 
 
+   /**
+    * @param keyword
+    * @return
+    * @throws Exception
+    */
    protected String getConceptsMatchingKeyword(String keyword) throws Exception {
       String result = new String();
       String serviceUrl = GemetWS_address + "getConceptsMatchingKeyword" +
-      "?keyword="  + URLEncoder.encode(keyword) +
+      "?keyword="  + keyword +
       "&search_mode=0" +
       "&thesaurus_uri=http://www.eionet.europa.eu/gemet/concept/" +
       "&language=en";
-
+      try {
          result = getGemetResults(serviceUrl);
+      } catch (Exception ex) {
+         throw ex;
+      }
       return result;
 
    }
 
-   //Get concepts matching keyword plus any related concepts
+   /**
-   protected List<Concept> processConceptsAndRelatedMatchingKeyword(String keyword) throws Exception {
+    * @param url
-	      String result = getConceptsMatchingKeyword(keyword);
+    * @return
-	      //iterate through each of the concepts and add related concepts a well
+    */
-	      List<Concept> bestMatchConceptList = processOutput(result);
-	      List<Concept> relatedConceptList = new ArrayList<Concept>();
-	      for(Concept c: bestMatchConceptList) {
-	    	  String conceptUri = c.getUri();
-	    	  String resultsRelated = getRelatedConcepts(conceptUri, "related");
-	    	  relatedConceptList.addAll(processOutput(resultsRelated, "false"));
-	      }
-	      bestMatchConceptList.addAll(relatedConceptList);
-	      return bestMatchConceptList;
-	   }
-
    protected String getGemetResults(String url) throws Exception  {
       String results = new String();
       //System.out.println("url: "+url);
@@ -232,9 +304,36 @@ public class GemetService implements ExternalConceptService  {
 
       } catch (Exception ex) {
          logger.error("error occurred in servlet", ex);
+         ex.printStackTrace();
          throw ex;
       }
       return results;
    }
    
+   protected List<String> getRelatedUris(String json) {
+	   List<String> uriList = new ArrayList<String>();
+	   String uri = new String();
+	   JSONArray jsonArray = (JSONArray) JSONSerializer.toJSON( json );
+	    if (jsonArray.size() == 0) {
+           return new ArrayList<String>();
+        }
+	    for (int i = 0; i < jsonArray.size(); i++) {
+	    	JSONObject jsonObj = jsonArray.getJSONObject(i);	    	
+            uri = getJsonValue(jsonObj, "uri");	
+            uriList.add(uri);
+	    }
+       
+	   return uriList;
+	   
+   }
+   
+   protected String stripConceptId(String uri) {
+	     String conceptId = new String();
+	     int lastslash = uri.lastIndexOf('/');
+	     conceptId = uri.substring(lastslash + 1, uri.length());
+	     return conceptId;
+	  }
+   
+   
+
 }

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

@@ -1,11 +1,10 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.service.impl;
 
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
 import java.io.StringWriter;
 import java.net.URL;
+import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -17,8 +16,8 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 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.web.URLEncoder;
 
 /**
  * @author jaf30
@@ -28,11 +27,48 @@ public class UMLSService implements ExternalConceptService {
    protected final Log logger = LogFactory.getLog(getClass());
    private static final String submissionUrl = "http://link.informatics.stonybrook.edu/MeaningLookup/MlServiceServlet?";
    private static final String baseUri = "http://link.informatics.stonybrook.edu/umls/CUI/";
+   private static final String endpoint = "http://link.informatics.stonybrook.edu/sparql/";
+   private static final String schemeURI = "http://link.informatics.stonybrook.edu/umls";
 
-   public List<Concept> processResults(String term) throws Exception{
+   
+	@Override
+	public List<Concept> getConcepts(String term) throws Exception {
+		List<Concept> conceptList = new ArrayList<Concept>();
+
+		String results = null;
+		//Format in rdf/xml is possible but would require separate processing method
+		String dataUrl = submissionUrl + "textToProcess="
+				+ URLEncoder.encode(term, "UTF-8") 
+				+ "&format=json";
+
+		try {
+
+			StringWriter sw = new StringWriter();
+			URL rss = new URL(dataUrl);
+
+			BufferedReader in = new BufferedReader(new InputStreamReader(
+					rss.openStream()));
+			String inputLine;
+			while ((inputLine = in.readLine()) != null) {
+				sw.write(inputLine);
+			}
+			in.close();
+
+			results = sw.toString();
+			//System.out.println("results before processing: "+results);
+			conceptList = processOutput(results);
+			return conceptList;
+
+		} catch (Exception ex) {
+			logger.error("error occurred in servlet", ex);
+			return null;
+		}
+	}
+
+   public List<Concept> processResults(String term) throws Exception {
       String results = null;
       String dataUrl = submissionUrl + "textToProcess="
-            + URLEncoder.encode(term) + "&format=json";
+            + URLEncoder.encode(term, "UTF-8") + "&format=json";
 
       try {
 
@@ -47,41 +83,57 @@ public class UMLSService implements ExternalConceptService {
          in.close();
 
          results = sw.toString();
+         //System.out.println("results before processing: "+results);
+         List<Concept> conceptList = processOutput(results);
+         return conceptList;
 
       } catch (Exception ex) {
          logger.error("error occurred in servlet", ex);
-         throw ex;
+         return null;
       }
-      List<Concept> conceptList = processOutput(results);
+
-      return conceptList;
+   }
+
+   /**
+    * @param uri
+    * @return
+    */
+   public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
+	 //John Ferreira's original code has implementation
+	      List<Concept> newConceptList = new ArrayList<Concept>();
+	      return newConceptList;
    }
 
    /**
     * @param results
     * @return
     */
-   private List<Concept> processOutput(String results) {
+   private List<Concept> processOutput(String results) throws Exception {
 
       List<Concept> conceptList = new ArrayList<Concept>();
       List<String> bestMatchIdList = new ArrayList<String>();
       String bestMatchId = new String();
+      boolean bestMatchFound = false;
+      boolean allFound = false;
+
       try {
          JSONObject json = (JSONObject) JSONSerializer.toJSON( results );
-
+         //System.out.println(json.toString());
          if (json.has("Best Match")) {
+            bestMatchFound = true;
             //System.out.println("Best Match");
 
             JSONArray bestMatchArray = json.getJSONArray("Best Match");
             int len = bestMatchArray.size();
             if (len > 1) {
-               System.out.println("Found this many best matches: "+ len);
+               logger.debug("Found this many best matches: "+ len);
             }
             int i;
             for (i = 0; i < len; i++) {
                JSONObject o = bestMatchArray.getJSONObject(i);
                //System.out.println(o.toString());
                Concept concept = new Concept();
-               concept.setDefinedBy("http://link.informatics.stonybrook.edu/umls");
+               concept.setDefinedBy(schemeURI);
                concept.setBestMatch("true");
                String cui = getJsonValue(o, "CUI");
                bestMatchIdList.add(cui);
@@ -91,11 +143,12 @@ public class UMLSService implements ExternalConceptService {
                concept.setType(getJsonValue(o, "type"));
                concept.setDefinition(getJsonValue(o, "definition"));
                concept.setUri(baseUri + cui);
+               concept.setSchemeURI(schemeURI);
                conceptList.add(concept);
             }
          }
          if (json.has("All")) {
-
+            allFound = true;
             JSONArray allArray = json.getJSONArray("All");
             int len = allArray.size();
             //System.out.println("size of best match array: "+ len);
@@ -104,7 +157,7 @@ public class UMLSService implements ExternalConceptService {
                JSONObject o = allArray.getJSONObject(i);
                //System.out.println(o.toString());
                Concept concept = new Concept();
-               concept.setDefinedBy("http://link.informatics.stonybrook.edu/umls");
+               concept.setDefinedBy(schemeURI);
                String cui = getJsonValue(o, "CUI");
                concept.setConceptId(cui);
 
@@ -112,6 +165,7 @@ public class UMLSService implements ExternalConceptService {
                concept.setType(getJsonValue(o, "type"));
                concept.setDefinition(getJsonValue(o, "definition"));
                concept.setUri(baseUri + cui);
+               concept.setSchemeURI(schemeURI);
                // prevent duplicate concepts in list
                if (! bestMatchIdList.contains(cui)) {
                   concept.setBestMatch("false");
@@ -122,20 +176,18 @@ public class UMLSService implements ExternalConceptService {
       } catch (Exception ex ) {
          ex.printStackTrace();
          logger.error("Could not get concepts", ex);
+         throw ex;
       }
+      if (! bestMatchFound && !allFound) {
+         // we did not get a bestMatch or All element
+         throw new ConceptsNotFoundException();
+      }
+
+      //
       return conceptList;
 
-      //
-      // now serialize the list of Concepts to a JSON String
-      //
-      //JSONObject jsonObject = null;
-      //jsonObject = BeanToJsonSerializer.serializeToJsonObject(conceptList);
-      //System.out.println(jsonObject.toString());
-      //return jsonObject.toString();
-
    }
 
-
    /**
     * Get a string from a json object or an empty string if there is no value for the given key
    * @param obj
@@ -150,4 +202,13 @@ public class UMLSService implements ExternalConceptService {
       }
    }
 
+
+
+  protected String stripConceptId(String uri) {
+     String conceptId = new String();
+     int lastslash = uri.lastIndexOf('/');
+     conceptId = uri.substring(lastslash + 1, uri.length());
+     return conceptId;
+  }
+
 }

src/edu/cornell/mannlib/semservices/util/ClassUtils.java

@@ -1,7 +1,4 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 /*
-
  * $Id$
  * CONFIDENTIAL AND PROPRIETARY. ? 2007 Revolution Health Group LLC. All rights reserved.
  * This source code may not be disclosed to others, used or reproduced without the written permission of Revolution Health Group.

src/edu/cornell/mannlib/semservices/util/DateConverter.java

@@ -1,7 +1,4 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 /*
-
  * $Id: DateConverter.java 50408 2007-03-28 19:14:46Z jdamick $
  *
  * Copyright 2006- Revolution Health Group.  All rights reserved.

src/edu/cornell/mannlib/semservices/util/DateUtils.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.util;
 
 import java.text.ParsePosition;

src/edu/cornell/mannlib/semservices/util/DayConverter.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.util;
 
 

src/edu/cornell/mannlib/semservices/util/MetadataNamespaceContext.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.util;
 import java.util.Iterator;
 import javax.xml.XMLConstants;

src/edu/cornell/mannlib/semservices/util/ObjectUtils.java

@@ -264,5 +264,10 @@ public class ObjectUtils {
       }
    }
 
+   public static String nl2br(String text) {
+      return text.replaceAll("\n\n", "<p>").replaceAll("\n", "<br>");
+   }
+
+
 
 }

src/edu/cornell/mannlib/semservices/util/TimeConverter.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.util;
 import edu.cornell.mannlib.semservices.bo.Time;
 import java.util.Date;

src/edu/cornell/mannlib/semservices/util/TimestampConverter.java

@@ -1,5 +1,3 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.util;
 import java.sql.Timestamp;
 import java.text.SimpleDateFormat;

src/edu/cornell/mannlib/semservices/util/XMLGregorianCalendarConverter.java

@@ -1,5 +1,4 @@
 /*
-
  * $Id: XMLGregorianCalendarConverter.java 28642 2006-10-25 13:41:54Z jdamick $
  *
  * Copyright 2006- Revolution Health Group.  All rights reserved.

src/edu/cornell/mannlib/semservices/util/XMLUtils.java

@@ -1,8 +1,7 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
 package edu.cornell.mannlib.semservices.util;
 
 import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStreamWriter;
@@ -122,6 +121,15 @@ public class XMLUtils {
        serializer.serialize(doc);
     }
 
+   public static String serializeDoctoString(Document doc) throws IOException {
+      XMLSerializer serializer = new XMLSerializer();
+      ByteArrayOutputStream bout = new ByteArrayOutputStream();
+
+      serializer.setOutputByteStream(bout);
+      serializer.serialize(doc);
+      return bout.toString();
+   }
+
     /**
     * @param xml
     */
@@ -152,6 +160,36 @@ public class XMLUtils {
 
     }
 
+   /**
+    * @param xml
+    */
+   public static String prettyPrintToString(String xml) {
+       Source xmlInput = new StreamSource(new StringReader(xml));
+       StreamResult xmlOutput = new StreamResult(new StringWriter());
+       Transformer transformer = null;
+      try {
+         transformer = TransformerFactory.newInstance().newTransformer();
+      } catch (TransformerConfigurationException e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      } catch (TransformerFactoryConfigurationError e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      }
+       //transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "testing.dtd");
+       transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+       transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
+       try {
+         transformer.transform(xmlInput, xmlOutput);
+      } catch (TransformerException e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      }
+       String formattedxml=xmlOutput.getWriter().toString();
+       return formattedxml;
+
+    }
+
     /**
     * @param node
     */

src/edu/cornell/mannlib/semservices/view/BeanToJsonSerializer.java

@@ -1,4 +1,16 @@
-package edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService;
+/*
+ * $Id: BeanToJsonSerializer.java 66350 2007-08-20 21:11:41Z xluan $
+ *
+ * Copyright 2006- Revolution Health Group.  All rights reserved.
+ *
+ * This software is the confidential and proprietary information
+ * of Revolution Health Group.  (Confidential Information).
+ * You shall not disclose such Confidential Information and shall
+ * use it only in accordance with the terms of the license
+ * agreement you entered into with Revolution Health Group.
+ *
+ */
+package edu.cornell.mannlib.semservices.view;
 
 import java.beans.PropertyDescriptor;
 import java.lang.reflect.InvocationTargetException;

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

@@ -46,7 +46,8 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 	private Log log = LogFactory.getLog(AddAssociatedConceptGenerator.class);
 	private String template = "addAssociatedConcept.ftl";
 	private static String SKOSConceptType = "http://www.w3.org/2004/02/skos/core#Concept";
-	
+	//TODO: Set this to a dynamic mechanism
+	private static String VIVOCore = "http://vivoweb.org/ontology/core#";
 		
     @Override
     public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {
@@ -168,10 +169,13 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 		return n3Required;
     }
     
-   //Don't think there's any n3 optional here
+   //Optional N3, includes possibility of semantic type which may or may not be included
+    //label and source are independent of semantic type
 	private List<String> generateN3Optional() {
 		return list("?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" + 
-    	        "?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource ."  	            	        
+    	        "?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource .", 
+				"?conceptNode <" + VIVOCore + "conceptSemanticType> ?conceptSemanticTypeURI ." + 
+    	        "?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ."
     	);
     }
 	
@@ -185,6 +189,8 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			HashMap<String, String> newResources = new HashMap<String, String>();
 			//There are no new resources here, the concept node uri doesn't
 			//get created but already exists, and vocab uri should already exist as well
+			//Adding concept semantic type uri just to test - note this isn't really on the form at all
+			newResources.put("conceptSemanticTypeURI", null);
 			return newResources;
 		}
     
@@ -233,9 +239,12 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
     	//The URI of the node that defines the concept
     	urisOnForm.add("conceptNode");
     	urisOnForm.add("conceptSource");
+    	urisOnForm.add("conceptSemanticTypeURI");
     	editConfiguration.setUrisOnform(urisOnForm);
     	//Also need to add the label of the concept
     	literalsOnForm.add("conceptLabel");
+    	literalsOnForm.add("conceptSemanticTypeLabel");
+
     	editConfiguration.setLiteralsOnForm(literalsOnForm);
     }
     
@@ -263,6 +272,8 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
     	setConceptNodeField(editConfiguration, vreq);
     	setConceptLabelField(editConfiguration, vreq);
     	setVocabURIField(editConfiguration, vreq);
+    	setConceptSemanticTypeURIField(editConfiguration,vreq);
+    	setConceptSemanticTypeLabelField(editConfiguration,vreq);
     }
     
 	//this field will be hidden and include the concept node URI
@@ -291,6 +302,22 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 				);
 	}
 	
+	//This will also be a URI
+	private void setConceptSemanticTypeURIField(EditConfigurationVTwo editConfiguration,
+			VitroRequest vreq) {
+		editConfiguration.addField(new FieldVTwo().
+				setName("conceptSemanticTypeURI")
+				);
+	}
+	
+	private void setConceptSemanticTypeLabelField(EditConfigurationVTwo editConfiguration,
+			VitroRequest vreq) {
+		editConfiguration.addField(new FieldVTwo().
+				setName("conceptSemanticTypeLabel").
+				setRangeDatatypeUri(XSD.xstring.toString())
+				);
+	}
+    
    
     //Add preprocessor
 	
@@ -357,6 +384,7 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			 	boolean isSKOSConcept = false;
 			 	String conceptUri =  conceptIndividual.getURI();
 			 	String conceptLabel = conceptIndividual.getName();
+
 			 	//Check if SKOS Concept type
 			 	List<ObjectPropertyStatement> osl = conceptIndividual.getObjectPropertyStatements(RDF.type.getURI());
 			 	for(ObjectPropertyStatement os: osl) {
@@ -367,7 +395,8 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			 	}
 			 	
 			 	if(isSKOSConcept) {
-			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, null, null, SKOSConceptType));
+			 		//if the concept in question is skos - which would imply a user generated concept
+			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, null, null, SKOSConceptType, null, null));
 			 	} else {
 			 		//Get the vocab source and vocab label
 			 		List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
@@ -379,7 +408,19 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			 			//Assuming name will get label
 			 			vocabLabel = sourceIndividual.getName();
 			 		}
-			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null));
+			 		String conceptSemanticTypeURI = null;
+			 		String conceptSemanticTypeLabel = null;
+			 		//Can a concept have multiple semantic types?  Currently we are only returning the first one
+			 		List<ObjectPropertyStatement> semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "conceptSemanticType");
+				 	if(semanticTypeStatements.size() > 0) {
+				 		conceptSemanticTypeURI = semanticTypeStatements.get(0).getObjectURI();
+					 	Individual conceptSemanticTypeIndividual = EditConfigurationUtils.getIndividual(vreq, conceptSemanticTypeURI);
+					 	conceptSemanticTypeLabel = conceptSemanticTypeIndividual.getName();
+				 	}
+				 	//get label
+
+			 		//Assuming this is from an external vocabulary source
+			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null, conceptSemanticTypeURI, conceptSemanticTypeLabel));
 
 			 	}
 		 }
@@ -392,12 +433,16 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 		private String vocabURI;
 		private String vocabLabel;
 		private String type; //In case of SKOS concept, will have skos concept type
-		public AssociatedConceptInfo(String inputLabel, String inputURI, String inputVocabURI, String inputVocabLabel, String inputType) {
+		private String conceptSemanticTypeURI; //For some services, such as UMLS, we have a semantic type associated
+		private String conceptSemanticTypeLabel;
+		public AssociatedConceptInfo(String inputLabel, String inputURI, String inputVocabURI, String inputVocabLabel, String inputType, String inputConceptSemanticTypeURI, String inputConceptSemanticTypeLabel) {
 			this.conceptLabel = inputLabel;
 			this.conceptURI = inputURI;
 			this.vocabURI = inputVocabURI;
 			this.vocabLabel = inputVocabLabel;
 			this.type = inputType;
+			this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
+			this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
 		}
 		
 		//Getters
@@ -421,6 +466,14 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			return type;
 		}
 		
+		public  String getConceptSemanticTypeURI(){
+			return conceptSemanticTypeURI;
+		}
+		
+		public  String getConceptSemanticTypeLabel(){
+			return conceptSemanticTypeLabel;
+		}
+		
 	}
 	
 	public class AssociatedConceptInfoComparator implements Comparator<AssociatedConceptInfo>{

src/edu/cornell/mannlib/vitro/webapp/servlet/ConceptSearchServlet.java

@@ -20,9 +20,9 @@ import org.apache.commons.logging.LogFactory;
 import edu.cornell.mannlib.semservices.bo.Concept;
 import edu.cornell.mannlib.semservices.bo.ConceptInfo;
 import edu.cornell.mannlib.semservices.bo.SemanticServicesError;
+import edu.cornell.mannlib.semservices.view.BeanToJsonSerializer;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.BeanToJsonSerializer;
 import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.ConceptSearchServiceUtils;
 
 public class ConceptSearchServlet extends VitroHttpServlet {

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

@@ -39,7 +39,7 @@ public class ConceptSearchServiceUtils {
 		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"));
     	//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(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"));
     	return map;
 	}
@@ -82,7 +82,7 @@ public class ConceptSearchServiceUtils {
 	    
 	    //Get search
 	    String searchTerm = getSearchTerm(vreq);
-	    List<Concept> conceptResults =  conceptServiceClass.processResults(searchTerm);
+	    List<Concept> conceptResults =  conceptServiceClass.getConcepts(searchTerm);
 	    return conceptResults;
     }