added new summary file where for a given publication the distinct set…

… of locations are computed. Each unique location for a given publication is added to the publication/citation counts. This summary is called distinct location.

Change from the JFileChooser to Cytoscape FileUtil for file loading in the UserPanel.

SocialNetwork/pom.xml

@@ -330,6 +330,12 @@
 			<version>${cytoscape.api.version}</version>
 			<type>bundle</type>
 		</dependency>
+		<dependency>
+			<groupId>org.mockito</groupId>
+			<artifactId>mockito-all</artifactId>
+			<version>1.9.5</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<packaging>bundle</packaging>

SocialNetwork/src/main/java/org/baderlab/csapps/socialnetwork/CyActivator.java

@@ -18,6 +18,7 @@
 import org.cytoscape.application.swing.CyAction;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.util.swing.FileUtil;
 import org.cytoscape.util.swing.OpenBrowser;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewManager;
@@ -65,6 +66,8 @@ public void start(BundleContext bc) {
 
 		VisualStyleFactory visualStyleFactoryServiceRef = getService(bc,VisualStyleFactory.class);
 
+		FileUtil fileUtil = getService(bc, FileUtil.class);
+
 		//open browser used by about  panel,
 		OpenBrowser openBrowserRef = getService(bc, OpenBrowser.class);
 
@@ -138,7 +141,7 @@ public void start(BundleContext bc) {
 		appManager.setCyAppManagerServiceRef(cyApplicationManagerServiceRef);
 
 		// Create & register new menu item (for opening /closing main app panel)
-		UserPanel userPanel = new UserPanel(appManager);
+		UserPanel userPanel = new UserPanel(appManager,fileUtil,cySwingApplicationServiceRef);
 
 		Map<String, String> serviceProperties = new HashMap<String, String>();
 		serviceProperties.put("inMenuBar", "true");

SocialNetwork/src/main/java/org/baderlab/csapps/socialnetwork/panels/AcademiaPanel.java

@@ -5,6 +5,7 @@
 import java.awt.event.ActionListener;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.HashSet;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -14,13 +15,16 @@
 import javax.swing.JButton;
 import javax.swing.JFileChooser;
 import javax.swing.JPanel;
+
 import javax.swing.JRadioButton;
 import javax.swing.JTextField;
 
 import org.baderlab.csapps.socialnetwork.CytoscapeUtilities;
 import org.baderlab.csapps.socialnetwork.model.SocialNetworkAppManager;
 import org.baderlab.csapps.socialnetwork.model.academia.Incites_InstitutionLocationMap;
 import org.baderlab.csapps.socialnetwork.model.academia.Scopus;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.util.swing.FileChooserFilter;
 import org.cytoscape.util.swing.FileUtil;
 
 
@@ -57,12 +61,16 @@ public class AcademiaPanel {
 	 * A reference to the app Manager
 	 */
 	private SocialNetworkAppManager appManager = null;
+	private FileUtil fileUtil = null;
+	protected CySwingApplication cySwingAppRef = null;
 
 
 
-	public AcademiaPanel(SocialNetworkAppManager appManager) {
+	public AcademiaPanel(SocialNetworkAppManager appManager,FileUtil fileUtil, CySwingApplication cySwingAppRef) {
 		super();
 		this.appManager = appManager;
+		this.fileUtil = fileUtil;
+		this.cySwingAppRef = cySwingAppRef;
 	}
 
 	/**
@@ -166,24 +174,24 @@ public  JButton createLoadButton() {
 		loadButton.addActionListener(new ActionListener() {
 
 			public void actionPerformed(ActionEvent event) {
-				// Ask user to select the appropriate data file.
-				JFileChooser chooser = new JFileChooser();
-				// Initialize the chooser dialog box to desktop
-				File directory = new File(FileUtil.LAST_DIRECTORY);
-				chooser.setCurrentDirectory(directory);
-				chooser.setDialogTitle("Data Selection");
-				chooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
-				int check = chooser.showDialog(null, "OK");
-				// Only attempt to read data file if user clicks "OK"
-				if (check == JFileChooser.APPROVE_OPTION) {
-					File textFile = chooser.getSelectedFile();
-					setDataFile(textFile);
-					getPathTextFieldRef().setText(textFile.getAbsolutePath());
-					getFacultyTextFieldRef().setText(parseFileName(textFile.getAbsolutePath()));
-				} else {
-					setDataFile(null);
-					getPathTextFieldRef().setText(null);
-				}
+
+				//Use Cytoscape File util package for the file chooser instead of Java's so 
+				//we navigate to last cytoscape known directory. 
+				//Filter - only enable txt, and excel files. 
+				FileChooserFilter filter1 = new FileChooserFilter("text file","txt");
+				FileChooserFilter filter2 = new FileChooserFilter("excel spreadsheet","xls");
+				FileChooserFilter filter3 = new FileChooserFilter("excel spreadsheet","xlsx");
+				FileChooserFilter filter4 = new FileChooserFilter("excel spreadsheet","csv");
+				HashSet<FileChooserFilter> filters = new HashSet<FileChooserFilter>();
+				filters.add(filter1);
+				filters.add(filter2);
+				filters.add(filter3);
+				filters.add(filter4);
+				File textFile = fileUtil.getFile( cySwingAppRef.getJFrame(), "Data File Selection",FileUtil.LOAD, filters);
+
+				setDataFile(textFile);
+				getPathTextFieldRef().setText(textFile.getAbsolutePath());
+				getFacultyTextFieldRef().setText(parseFileName(textFile.getAbsolutePath()));
 			}
 		});
 		return loadButton;

SocialNetwork/src/main/java/org/baderlab/csapps/socialnetwork/panels/UserPanel.java

@@ -46,9 +46,11 @@
 import org.baderlab.csapps.socialnetwork.model.SocialNetwork;
 import org.baderlab.csapps.socialnetwork.model.VisualStyles;
 import org.baderlab.csapps.socialnetwork.util.GenerateReports;
+import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
 import org.cytoscape.model.CyNetwork;
+import org.cytoscape.util.swing.FileUtil;
 
 import javax.swing.border.TitledBorder;
 import javax.swing.table.DefaultTableModel;
@@ -137,6 +139,8 @@ public class UserPanel extends JPanel implements CytoPanelComponent {
 	 * Reference to the main appManager
 	 */
 	private SocialNetworkAppManager appManager = null;
+	private FileUtil fileUtil = null;
+	private CySwingApplication cySwingAppRef = null;
 
 	/*
 	 * instance of academia panel
@@ -148,10 +152,12 @@ public class UserPanel extends JPanel implements CytoPanelComponent {
 	 * @param null
 	 * @return null
 	 */
-	public UserPanel(SocialNetworkAppManager appManager) {
+	public UserPanel(SocialNetworkAppManager appManager, FileUtil fileUtil, CySwingApplication cySwingAppRef ) {
 
 		// Save a reference to this panel object
 		this.appManager = appManager;
+		this.fileUtil = fileUtil;
+		this.cySwingAppRef = cySwingAppRef;
 		this.appManager.setUserPanelRef(this);
 
 		this.setLayout(new BorderLayout());
@@ -165,7 +171,7 @@ public UserPanel(SocialNetworkAppManager appManager) {
 		this.add(this.topPanelRef, BorderLayout.NORTH);
 
 		// Add the default info panel (Academia)
-		this.academiaPanel = new AcademiaPanel(appManager);
+		this.academiaPanel = new AcademiaPanel(appManager,this.fileUtil, this.cySwingAppRef);
 		this.setSelectedInfoPanel(this.academiaPanel.createAcademiaInfoPanel());
 		this.add(this.infoPanelRef, BorderLayout.CENTER);
 

SocialNetwork/src/main/java/org/baderlab/csapps/socialnetwork/util/GenerateReports.java

@@ -8,6 +8,7 @@
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Iterator;
 
 import org.baderlab.csapps.socialnetwork.CytoscapeUtilities;
@@ -40,10 +41,16 @@ public class GenerateReports {
 	private HashMap<String,Integer> pubByLocation = new HashMap<String, Integer>();
 	//location -> number of publication (unique location for each publication
 	private HashMap<String,Integer> pubByLocation_unique = new HashMap<String, Integer>();
+	//location -> number of publication (count each distinct location for each publication once.
+	//i.e. publication has a total of 10 authors, 2 from US, 5 from Canada and 3 international add publication count of 1 to US, Canada and international)
+	private HashMap<String,Integer> pubByLocation_distinct = new HashMap<String, Integer>();
 	//location -> number of total citations
-	private HashMap<String,Integer> citationByLocation = new HashMap<String, Integer>();
+	private HashMap<String,Integer> citationsByLocation = new HashMap<String, Integer>();
 	//location -> number of total citations (unique location for each publication
 	private HashMap<String,Integer> citationsByLocation_unique = new HashMap<String, Integer>();
+	//location -> number of total citations (count each distinct location for each publication once. 
+	//i.e. publication has a total of 10 authors, 2 from US, 5 from Canada and 3 international add publication count of 1 to US, Canada and international)
+	private HashMap<String,Integer> citationsByLocation_distinct = new HashMap<String, Integer>();
 
 
 	public GenerateReports(ArrayList<Publication> pubs, String outputDir,String networkName) {
@@ -66,22 +73,29 @@ public HashMap<String,String> createReports(){
 
 		this.calculateTotals();
 		this.calculateTotals_unique();
+		this.calculateTotals_distinct();
 		HashMap<String, String> filenames = new HashMap<String, String>();
 
 		String basename = this.outputDir + System.getProperty("file.separator") + this.networkName;
 
+		this.generateFiles(this.outputDir,this.networkName + "_pubByLocation_distinct", this.pubByLocation_distinct,"Publications by Location - counting publications once for every distinct location");
+		filenames.put("1a. Pub by location(txt) - distinct locations publication counts", basename + "_pubByLocation_distinct.txt");
+		filenames.put("1b. Pub by location(html) - distinct locations publication counts", basename + "_pubByLocation_distinct.html");		
 		this.generateFiles(this.outputDir,this.networkName + "_pubByLocation", this.pubByLocation,"Publications by Location");
-		filenames.put("1. Pub by location(txt)", basename + "_pubByLocation.txt");
-		filenames.put("2. Pub by location(html)", basename + "_pubByLocation.html");
+		filenames.put("2a. Pub by location(txt)", basename + "_pubByLocation.txt");
+		filenames.put("2b. Pub by location(html)", basename + "_pubByLocation.html");
 		this.generateFiles(this.outputDir,this.networkName + "_pubByLocation_unique", this.pubByLocation_unique,"Publications by Location - counting publications only once");
-		filenames.put("3. Pub by location(txt) - unique publication counts",basename + "_pubByLocation_unique.txt");
-		filenames.put("4. Pub by location(html) - unique publication counts", basename + "_pubByLocation_unique.html");
-		this.generateFiles(this.outputDir,this.networkName + "_citationByLocation", this.citationByLocation,"Citations by Location");
-		filenames.put("5. Citation by location(txt)",basename + "_citationByLocation.txt");
-		filenames.put("6. Citation by location(html)", basename + "_citationByLocation.html");
+		filenames.put("3a. Pub by location(txt) - unique publication counts",basename + "_pubByLocation_unique.txt");
+		filenames.put("3b. Pub by location(html) - unique publication counts", basename + "_pubByLocation_unique.html");
+		this.generateFiles(this.outputDir,this.networkName + "_citationByLocation_distinct", this.citationsByLocation_distinct,"Citations by Location - counting citations once for every distinct location");
+		filenames.put("4a. Citation by location(txt) - distinct locations citation count",basename + "_citationByLocation_distinct.txt");
+		filenames.put("4b. Citation by location(html) - distinct locations citation counts", basename + "_citationByLocation_distinct.html");
+		this.generateFiles(this.outputDir,this.networkName + "_citationByLocation", this.citationsByLocation,"Citations by Location");
+		filenames.put("5a. Citation by location(txt)",basename + "_citationByLocation.txt");
+		filenames.put("5b. Citation by location(html)", basename + "_citationByLocation.html");
 		this.generateFiles(this.outputDir,this.networkName + "_citationByLocation_unique", this.citationsByLocation_unique,"Citations by Location - counting publications only once");
-		filenames.put("7. Citation by location(txt)- unique publication counts",  basename + "_citationByLocation_unique.txt");
-		filenames.put("8. Citation by location(html)- unique publication counts",  basename + "_citationByLocation_unique.html");
+		filenames.put("6a. Citation by location(txt)- unique publication counts",  basename + "_citationByLocation_unique.txt");
+		filenames.put("6b. Citation by location(html)- unique publication counts",  basename + "_citationByLocation_unique.html");
 
 		return filenames;
 	}
@@ -120,10 +134,54 @@ private void calculateTotals(){
 				}
 			}			
 		}
-		this.citationByLocation = citations_summary;
+		this.citationsByLocation = citations_summary;
 		this.pubByLocation = pubs_summary;
 
 	}
+	/*
+	 * for each publication in the set of publications for this network
+	 * For each publication get its set of Authors.  For each Author get their location 
+	 * For each unique location on the given publication add a count to that location
+	 * (counts will be duplicated but only once per location for each publication.) 
+	 * Do the same for the times cited
+	 * Add up the publications based on distinct locations of a given publication.
+	 */
+	private void calculateTotals_distinct(){
+		HashMap<String,Integer> pubs_summary = new HashMap<String, Integer>();
+		HashMap<String,Integer> citations_summary = new HashMap<String, Integer>();
+
+		if(this.publications != null){
+			for(Publication pub:this.publications){
+
+
+				//for each publication the set of Authors
+				HashSet<String> all_locations = new HashSet<String>();
+				for(Author author:pub.getAuthorList()){
+
+					String current_location = author.getLocation();
+					if(!all_locations.contains(current_location))  
+						all_locations.add(current_location);
+				}
+
+				for(String current:all_locations){
+					if(pubs_summary.containsKey(current) && citations_summary.containsKey(current)){
+						Integer pub_count = pubs_summary.get(current) +1;
+						pubs_summary.put(current, pub_count);
+						Integer cit_count = citations_summary.get(current) + pub.getTimesCited();
+						citations_summary.put(current, cit_count);
+
+					}
+					else{
+						pubs_summary.put(current, 1);
+						citations_summary.put(current,pub.getTimesCited());
+					}
+				}
+			}			
+		}
+		this.citationsByLocation_distinct = citations_summary;
+		this.pubByLocation_distinct = pubs_summary;
+
+	}
 
 
 	/*

SocialNetwork/src/test/java/org/baderlab/csapps/socialnetwork/TestSearch.java

@@ -2,11 +2,14 @@
 
 import static org.junit.Assert.*;
 
+import static org.mockito.Mockito.mock;
 
 import org.baderlab.csapps.socialnetwork.model.Category;
 import org.baderlab.csapps.socialnetwork.model.Search;
 import org.baderlab.csapps.socialnetwork.model.SocialNetworkAppManager;
 import org.baderlab.csapps.socialnetwork.panels.UserPanel;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.util.swing.FileUtil;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -17,6 +20,9 @@
  */
 public class TestSearch {
 
+	private FileUtil fileUtil = mock(FileUtil.class);
+	private CySwingApplication cySwingAppRef = mock(CySwingApplication.class);
+
 	@Before
 	public void setUp() throws Exception {
 	}
@@ -32,7 +38,7 @@ public void tearDown() throws Exception {
 	 */
 	public void testPubmedSearch() {
 		SocialNetworkAppManager appManager = new SocialNetworkAppManager ();
-		appManager.setUserPanelRef(new UserPanel(appManager));
+		appManager.setUserPanelRef(new UserPanel(appManager,fileUtil,cySwingAppRef));
 		Search search = new Search("emili a", Category.ACADEMIA,appManager);
 		int hits = search.getTotalHits();
 		int results = search.getResults().size();