adding licence to classes, removing sparql feed related classes

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

@@ -203,7 +203,9 @@ var addConceptForm = {
     	var definedBy = conceptResult.definedBy;
     	var type = conceptResult.type;
     	var uri = conceptResult.uri;
-    	return addConceptForm.generateIndividualConceptDisplay(uri, label, definition, type, definedBy, isBestMatch);
+    	//this will be null if there are no alternate labels
+    	var altLabels = conceptResult.altLabelList;
+    	return addConceptForm.generateIndividualConceptDisplay(uri, label, altLabels, definition, type, definedBy, isBestMatch);
     },
     //This should now return all best matches in one array and other results in another
     parseResults:function(resultsArray) {
@@ -260,12 +262,12 @@ var addConceptForm = {
     	this.externalConceptSemanticTypeLabel.val(conceptSemanticTypes);
     	return true;
     }, 
-    generateIndividualConceptDisplay: function(cuiURI, label, definition, type, definedBy, isBestMatch) {
+    generateIndividualConceptDisplay: function(cuiURI, label, altLabels, definition, type, definedBy, isBestMatch) {
     	var htmlAdd = "<li class='concepts'>" + 
     	"<div class='row'>" + 
     	"<div class='column conceptLabel'>" +
     	addConceptForm.generateIndividualCUIInput(cuiURI, label, type, definedBy) +  
-    	label + addConceptForm.generateIndividualTypeDisplay(type) + "</div>" + 
+    	addConceptForm.generateIndividualLabelsDisplay(label, altLabels) + addConceptForm.generateIndividualTypeDisplay(type) + "</div>" + 
     	addConceptForm.generateIndividualDefinitionDisplay(definition) + 
     	addConceptForm.generateBestOrAlternate(isBestMatch) +
     	"</div>" +  
@@ -275,6 +277,14 @@ var addConceptForm = {
     generateIndividualCUIInput:function(cuiURI, label, type, definedBy) {
     	return 	"<input type='checkbox'  name='CUI' value='" + cuiURI + "' label='" + label + "' conceptType='" + type + "' conceptDefinedBy='" + definedBy + "'/>";
     },
+    //In case there are multiple labels display those
+    generateIndividualLabelsDisplay:function(label, altLabels) {
+    	var labelDisplay = label;
+    	if(altLabels != null && altLabels.length > 0) {
+    		labelDisplay += "<br>(" + altLabels + ")";
+    	}
+    	return labelDisplay;
+    },
     generateIndividualTypeDisplay:function(type) {
     	if(type != null && type.length > 0) {
     		return " (" + type + ")";

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

@@ -1,3 +1,4 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
 package edu.cornell.mannlib.semservices.bo;
 
 public class BaseObject {

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

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

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

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

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

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

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

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

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

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

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

@@ -1,208 +0,0 @@
-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

@@ -1,61 +0,0 @@
-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

@@ -1,54 +0,0 @@
-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

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

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

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

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

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

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

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

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

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

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 /*
  * $Id$
  * CONFIDENTIAL AND PROPRIETARY. ? 2007 Revolution Health Group LLC. All rights reserved.

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 /*
  * $Id: DateConverter.java 50408 2007-03-28 19:14:46Z jdamick $
  *

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

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

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

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

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

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

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

@@ -1,4 +1,7 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 /*
+
  * $Id$
  * 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/TimeConverter.java

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 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

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

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

@@ -1,4 +1,7 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 /*
+
  * $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

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

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

@@ -1,3 +1,5 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
 /*
  * $Id: BeanToJsonSerializer.java 66350 2007-08-20 21:11:41Z xluan $
  *