NIHVIVO-1510 Collation of properties using default list view. NIHVIVO-1569 Fixed a bug in BaseObjectPropertyDataPostProcessor.removeDuplicates()

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/BaseObjectPropertyDataPostProcessor.java

@@ -2,6 +2,7 @@
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Matcher;
@@ -58,11 +59,14 @@ public abstract class BaseObjectPropertyDataPostProcessor implements
             return;
         }
         List<String> foundObjects = new ArrayList<String>();
-        for (Map<String, String> map : data) {
+        log.debug("Processing property: " + objectPropertyTemplateModel.getUri());
+        Iterator<Map<String, String>> dataIterator = data.iterator();
+        while (dataIterator.hasNext()) {
+            Map<String, String> map = dataIterator.next();
             String objectValue = map.get(objectVariableName);
             // We arbitrarily remove all but the first. Not sure what selection criteria could be brought to bear on this.
             if (foundObjects.contains(objectValue)) {
-                data.remove(map);
+                dataIterator.remove();
             } else {
                 foundObjects.add(objectValue);
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/CollatedObjectPropertyTemplateModel.java

@@ -26,36 +26,27 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateModel {
 
     private static final Log log = LogFactory.getLog(CollatedObjectPropertyTemplateModel.class);  
+    private static final String DEFAULT_CONFIG_FILE = "listViewConfig-default-collated.xml";
     
     private SortedMap<String, List<ObjectPropertyStatementTemplateModel>> subclasses;
     
     CollatedObjectPropertyTemplateModel(ObjectProperty op, Individual subject, VitroRequest vreq) throws Exception {
         super(op, subject, vreq); 
 
-        // RY Temporarily throw an error because collation hasn't been implemented yet.
+        /* Get the data */
-//        boolean error = true;
-//        if (error) {
-//            throw new Exception("Collated object property not implemented yet");
-//        }
-        
-        /* Change the approach to collation:
-         * Custom views can get the subclasses in the query. Must use a term ?subclass - throw error if not.
-         * Default view: we may be able to figure out the  class to get subclasses of by inspecting the property.
-         * If not, use getDirectClasses etc of the object term.
-         * We need a subclassed and nonsubclassed default query for the default view: collated-query and uncollated-query.
-         * We can also use these for custom views. Throw error if property is collated but there's no subclass term
-         * in the query. (The reverse is okay - uncollated property with a subclass term in the query.     
-         */
-        
         WebappDaoFactory wdf = vreq.getWebappDaoFactory();
         ObjectPropertyStatementDao opDao = wdf.getObjectPropertyStatementDao();
         String subjectUri = subject.getURI();
         String propertyUri = op.getURI();
-        List<Map<String, String>> statementData = opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getQueryString());
+        List<Map<String, String>> statementData = 
+            opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getQueryString());
 
-        Map<String, List<ObjectPropertyStatementTemplateModel>> unsortedSubclasses = hasDefaultListView() ?
+        /* Apply postprocessing */
-                collateDefaultListView(subjectUri, propertyUri, statementData, vreq) :
+        postprocess(statementData, wdf);
-                collateCustomListView(subjectUri, propertyUri, statementData, vreq);
+        
+        /* Collate the data */
+        Map<String, List<ObjectPropertyStatementTemplateModel>> unsortedSubclasses = 
+            collate(subjectUri, propertyUri, statementData, vreq);
 
         /* Sort by subclass name */
         Comparator<String> comparer = new Comparator<String>() {
@@ -67,10 +58,10 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
         subclasses.putAll(unsortedSubclasses);        
     }
     
-    private Map<String, List<ObjectPropertyStatementTemplateModel>> collateCustomListView(String subjectUri, 
+    private Map<String, List<ObjectPropertyStatementTemplateModel>> collate(String subjectUri, 
             String propertyUri, List<Map<String, String>> statementData, VitroRequest vreq) {
     
-        Map<String, List<ObjectPropertyStatementTemplateModel>> unsortedSubclasses = 
+        Map<String, List<ObjectPropertyStatementTemplateModel>> subclassMap = 
             new HashMap<String, List<ObjectPropertyStatementTemplateModel>>();
         String currentSubclassUri = null;
         List<ObjectPropertyStatementTemplateModel> currentList = null;
@@ -80,19 +71,11 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
                 currentSubclassUri = subclassUri;
                 currentList = new ArrayList<ObjectPropertyStatementTemplateModel>();
                 String subclassName = getSubclassName(subclassUri, vreq);
-                unsortedSubclasses.put(subclassName, currentList);
+                subclassMap.put(subclassName, currentList);
             }
             currentList.add(new ObjectPropertyStatementTemplateModel(subjectUri, propertyUri, map));
         }   
-        return unsortedSubclasses; 
+        return subclassMap; 
-    }
-    
-    private Map<String, List<ObjectPropertyStatementTemplateModel>> collateDefaultListView(String subjectUri, 
-            String propertyUri, List<Map<String, String>> statementData, VitroRequest vreq) {
-        
-        Map<String, List<ObjectPropertyStatementTemplateModel>> unsortedSubclasses = 
-            new HashMap<String, List<ObjectPropertyStatementTemplateModel>>();
-        return unsortedSubclasses;
     }
     
     private String getSubclassName(String subclassUri, VitroRequest vreq) {
@@ -101,27 +84,9 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
         return vclass.getName();
     }
 
-    private String getCollationTargetError() {
+    @Override
-        String errorMessage = null;
+    protected String getDefaultConfigFileName() {
-        String collationTarget = getCollationTarget();
+        return DEFAULT_CONFIG_FILE;
-        // Make sure the collation target is not null or empty.
-        if (collationTarget == null || collationTarget.trim().isEmpty()) {
-            errorMessage = "No collation target specified.";
-        } else {
-            // Make sure the collation target is one of the select terms in the query.
-            String queryString = getQueryString();
-            String selectClause = queryString.substring(0, queryString.indexOf("{"));
-            Pattern collationTargetPattern = Pattern.compile("\\b\\\\?" + collationTarget + "\\b");
-            Matcher matcher = collationTargetPattern.matcher(selectClause);
-            if (! matcher.find()) {
-                errorMessage = "Invalid collation target.";
-            }
-        }   
-        return errorMessage;
-    }
-    
-    private List<VClass> getDirectVClasses(String key, List<Map<String, Object>> data) {
-        return null;
     }
     
     /* Access methods for templates */

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/ObjectPropertyTemplateModel.java

@@ -56,10 +56,6 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         return config.queryString;
     }
 
-    protected String getCollationTarget() {
-        return config.collationTarget;
-    }
-    
     protected boolean hasDefaultListView() {
         return config.isDefaultConfig;
     }
@@ -95,19 +91,18 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         }
     }
     
+    protected abstract String getDefaultConfigFileName();
+    
     private class PropertyListConfig {
 
-        private static final String DEFAULT_CONFIG_FILE = "listViewConfig-default.xml";
         private static final String CONFIG_FILE_PATH = "/config/";
         private static final String NODE_NAME_QUERY = "query";
         private static final String NODE_NAME_TEMPLATE = "template";
-        private static final String NODE_NAME_COLLATION_TARGET = "collation-target";
         private static final String NODE_NAME_POSTPROCESSOR = "postprocessor";
         
         private boolean isDefaultConfig;
         private String queryString;
         private String templateName;
-        private String collationTarget;
         private String postprocessor;
 
         PropertyListConfig(ObjectProperty op, VitroRequest vreq) throws Exception {
@@ -117,7 +112,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
             ObjectPropertyDao opDao = wdf.getObjectPropertyDao();
             String configFileName = opDao.getCustomListConfigFileName(op);
             if (configFileName == null) { // no custom config; use default config
-                configFileName = DEFAULT_CONFIG_FILE;
+                configFileName = getDefaultConfigFileName();
             }
             log.debug("Using list view config file " + configFileName + " for object property " + op.getURI());
             
@@ -127,7 +122,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
                 if ( ! isDefaultConfig(configFileName) && ! config.exists() ) {
                     log.warn("Can't find config file " + configFilePath + " for object property " + op.getURI() + "\n" +
                             ". Using default config file instead.");
-                    configFilePath = getConfigFilePath(DEFAULT_CONFIG_FILE);
+                    configFilePath = getConfigFilePath(getDefaultConfigFileName());
                     // Should we test for the existence of the default, and throw an error if it doesn't exist?
                 }                   
                 setValuesFromConfigFile(configFilePath);           
@@ -143,7 +138,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
                     log.warn("Invalid list view config for object property " + op.getURI() + 
                             " in " + configFilePath + ":\n" +                            
                             invalidConfigMessage + " Using default config instead.");
-                    configFilePath = getConfigFilePath(DEFAULT_CONFIG_FILE);
+                    configFilePath = getConfigFilePath(getDefaultConfigFileName());
                     setValuesFromConfigFile(configFilePath);                    
                 }
             }
@@ -152,7 +147,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         }
         
         private boolean isDefaultConfig(String configFileName) {
-            return configFileName.equals(DEFAULT_CONFIG_FILE);
+            return configFileName.equals(getDefaultConfigFileName());
         }
         
         private String checkForInvalidConfig(VitroRequest vreq) {
@@ -189,7 +184,6 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
                 templateName = getConfigValue(doc, NODE_NAME_TEMPLATE); 
                 
                 // Optional values
-                collationTarget = getConfigValue(doc, NODE_NAME_COLLATION_TARGET);
                 postprocessor = getConfigValue(doc, NODE_NAME_POSTPROCESSOR);
             } catch (Exception e) {
                 log.error("Error processing config file " + configFilePath, e);

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/UncollatedObjectPropertyTemplateModel.java

@@ -18,23 +18,35 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 public class UncollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateModel {
 
     private static final Log log = LogFactory.getLog(UncollatedObjectPropertyTemplateModel.class);  
+    private static final String DEFAULT_CONFIG_FILE = "listViewConfig-default-uncollated.xml";
     
     private List<ObjectPropertyStatementTemplateModel> statements;
     
     UncollatedObjectPropertyTemplateModel(ObjectProperty op, Individual subject, VitroRequest vreq) {
         super(op, subject, vreq);
+        
+        /* Get the data */
         WebappDaoFactory wdf = vreq.getWebappDaoFactory();
         ObjectPropertyStatementDao opDao = wdf.getObjectPropertyStatementDao();
         String subjectUri = subject.getURI();
         String propertyUri = op.getURI();
         List<Map<String, String>> statementData = opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getQueryString());
+        
+        /* Apply postprocessing */
         postprocess(statementData, wdf);
+        
+        /* Put into data structure to send to template */
         statements = new ArrayList<ObjectPropertyStatementTemplateModel>(statementData.size());
         for (Map<String, String> map : statementData) {
             statements.add(new ObjectPropertyStatementTemplateModel(subjectUri, propertyUri, map));
         }
     }
     
+    @Override
+    protected String getDefaultConfigFileName() {
+        return DEFAULT_CONFIG_FILE;
+    }
+    
     /* Access methods for templates */
 
     public List<ObjectPropertyStatementTemplateModel> getStatements() {

webapp/web/config/listViewConfig-default-collated.xml

@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<!-- 
+    Default list view config file for collated object properties 
+
+    Required elements: 
+        - query: the sparql query used to retrieve the data
+        - template: the name of the template used to display a single property statement
+    
+    Optional elements: 
+        - postprocessor: a Java class that postprocesses the data retrieved from the query before
+                       sending it to the template
+    
+    Query requirements:
+        - WHERE clause must contain a statement ?subject ?property ?object, with the variables
+          ?subject and ?property named as such. The object can be given any name, but it must be 
+          included in the SELECT terms retrieved by the query. This is the statement that will be edited 
+          from the edit links.
+        - Each assertion or set of optional assertions must reference a different graph variable, so that
+          we do not impose a requirement about which assertions are in the same graph.           
+-->
+
+<list-view-config>
+    <query>    
+        PREFIX vitro: &lt;http://vitro.mannlib.cornell.edu/ns/vitro/0.7#&gt;
+        PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;  
+          
+        SELECT ?subclass ?object ?name ?moniker {
+            GRAPH ?g1 { ?subject ?property ?object }
+            OPTIONAL { GRAPH ?g2 { ?object rdfs:label ?name } }
+            OPTIONAL { GRAPH ?g3 { ?object vitro:moniker ?moniker } }
+            OPTIONAL { GRAPH ?g4 { ?object a ?subclass } 
+                       FILTER (?g4 != &lt;http://vitro.mannlib.cornell.edu/default/inferred-tbox&gt; &amp;&amp; 
+                               ?g4 != &lt;http://vitro.mannlib.cornell.edu/default/vitro-kb-inf&gt; )             
+                     }
+        }       
+    </query>
+
+    <postprocessor>edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.DefaultListViewDataPostProcessor</postprocessor>
+    
+    <template>propStatement-default.ftl</template>
+</list-view-config>

webapp/web/config/listViewConfig-default-uncollated.xml

@@ -2,6 +2,8 @@
 <!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
 <!-- 
+    Default list view config file for uncollated object properties 
+    
     Required elements: 
         - query: the sparql query used to retrieve the data
         - template: the name of the template used to display a single property statement