Tree view for post analysis web loader. Refs #306

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/io/ModelSerializer.java

@@ -106,7 +106,7 @@ public ImmutableSet<Integer> deserialize(JsonElement json, Type type, JsonDeseri
 		}
 	}
 
-	private static class PathAdapter implements JsonDeserializer<Path>, JsonSerializer<Path> {
+	public static class PathAdapter implements JsonDeserializer<Path>, JsonSerializer<Path> {
 		@Override
 		public Path deserialize(JsonElement jsonElement, Type type, JsonDeserializationContext context) {
 			return Paths.get(jsonElement.getAsString());

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/PADialogPage.java

@@ -34,7 +34,7 @@
 import org.baderlab.csplugins.enrichmentmap.util.NamingUtil;
 import org.baderlab.csplugins.enrichmentmap.view.creation.NamePanel;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.web.DownloadGMTFileTask;
-import org.baderlab.csplugins.enrichmentmap.view.postanalysis.web.WebLoadDialogParameters;
+import org.baderlab.csplugins.enrichmentmap.view.postanalysis.web.DialogParameters;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialog;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogCallback;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogPage;
@@ -282,7 +282,7 @@ private void openSelectFileDialog() {
 
 	private void openLoadFromWebDialog() {
 		JDialog parent = callback.getDialogFrame();
-		WebLoadDialogParameters params = new WebLoadDialogParameters(this);
+		DialogParameters params = new DialogParameters(this);
 		CardDialog dialog = new CardDialog(parent, params);
 		dialog.open();
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/BaderlabDialogPage.java

@@ -5,7 +5,7 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Comparator;
-import java.util.List;
+import java.util.Optional;
 import java.util.concurrent.Callable;
 import java.util.function.Consumer;
 
@@ -17,12 +17,8 @@
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
 import javax.swing.LayoutStyle;
-import javax.swing.ListSelectionModel;
 import javax.swing.SwingWorker;
-import javax.swing.table.TableColumnModel;
 
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.PADialogPage;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogCallback;
@@ -39,7 +35,7 @@ public class BaderlabDialogPage implements CardDialogPage {
 	private CardDialogCallback callback;
 	private JComboBox<ComboItem<DateDir>> dateCombo;
 	private JLabel spinnerLabel;
-	private JTable table;
+	private FileChooserPanel fileChooserPanel;
 	private ActionListener dateActionListener;
 	private boolean openCalled = false;
 
@@ -61,13 +57,13 @@ public String getPageComboText() {
 	@Override
 	public void finish() {
 		String dateFolder = getDateFolder();
-		String filePath = getGmtFilePath();
-		if(dateFolder == null || filePath == null) {
+		Optional<String> filePath = fileChooserPanel.getSelectedFilePath();
+		if(dateFolder == null || !filePath.isPresent()) {
 			return;
 		}
 
 		try {
-			URL url = BaderlabRequests.buildUrl(dateFolder, filePath);
+			URL url = BaderlabRequests.buildUrl(dateFolder, filePath.get());
 			parent.runLoadFromUrlTasks(url, callback.getDialog());
 
 		} catch (MalformedURLException e) {
@@ -88,14 +84,19 @@ public JPanel createBodyPanel(CardDialogCallback callback) {
 		this.callback = callback;
 		callback.setFinishButtonEnabled(false);
 
+		fileChooserPanel = new TreeFileChooserPanel();
+		fileChooserPanel.getPanel().setBorder(BorderFactory.createEmptyBorder(0, 8, 8, 8));
+		fileChooserPanel.setSelectionListener(s -> callback.setFinishButtonEnabled(s.isPresent()));
+		
 		JPanel datePanel = createDatePanel();
-		JPanel listPanel = createTablePanel();
+		JPanel listPanel = fileChooserPanel.getPanel();
 
 		JPanel panel = new JPanel(new BorderLayout());
 		panel.add(datePanel, BorderLayout.NORTH);
 		panel.add(listPanel, BorderLayout.CENTER);
 		return panel;
 	}
+	
 
 	private JPanel createDatePanel() {
 		JLabel title = new JLabel("Download gene set files from download.baderlab.org");
@@ -149,53 +150,17 @@ private JPanel createDatePanel() {
 		return panel;
 	}
 
-	private JPanel createTablePanel() {
-		table = new JTable();
-		
-		JScrollPane scrollPane = new JScrollPane(table);
-		scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
-		scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
-		table.setFillsViewportHeight(true);
-		table.setCellSelectionEnabled(false);
-		table.setRowSelectionAllowed(true);
-		table.setAutoCreateRowSorter(true);
-		table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-		
-		table.getSelectionModel().addListSelectionListener(e -> updateFinishButton());
-		
-		FileSizeCellRenderer fileSizeRenderer = new FileSizeCellRenderer();
-		fileSizeRenderer.setHorizontalAlignment(JLabel.RIGHT);
-		table.setDefaultRenderer(Integer.class, fileSizeRenderer);
-		
-		updateTable(null);
-		
-		JPanel panel = new JPanel(new BorderLayout());
-		panel.add(scrollPane, BorderLayout.CENTER);
-		panel.setBorder(BorderFactory.createEmptyBorder(0, 8, 8, 8));
-		return panel;
-	}
+
 
 	private void updateFinishButton() {
-		callback.setFinishButtonEnabled(table.getSelectionModel().getMinSelectionIndex() >= 0);
+		callback.setFinishButtonEnabled(fileChooserPanel.getSelectedFilePath().isPresent());
 	}
 
-	private void updateTable(List<GmtFile> gmtFiles) {
-		GmtFileTableModel tableModel = new GmtFileTableModel(gmtFiles);
-		table.setModel(tableModel);
-		
-		TableColumnModel columnModel = table.getColumnModel();
-		columnModel.getColumn(1).setMaxWidth(150);
-	}
 
 	private String getDateFolder() {
 		return dateCombo.getItemAt(dateCombo.getSelectedIndex()).getValue().getFolder();
 	}
 
-	private String getGmtFilePath() {
-		int row = table.getSelectionModel().getMinSelectionIndex();
-		String gmtFilePath = (String) table.getModel().getValueAt(row, 0);
-		return gmtFilePath;
-	}
 
 	private <T> void doRequest(Callable<T> doInBackground, Consumer<T> done) {
 		SwingWorker<T,Void> worker = new SwingWorker<T, Void>() {
@@ -249,12 +214,12 @@ private void requestDates() {
 	}
 
 	private void requestFiles() {
-		updateTable(null);
+		fileChooserPanel.setFiles(null);
 		String dateFolder = getDateFolder();
 
 		doRequest(
 			() -> BaderlabRequests.requestFiles(dateFolder),
-			this::updateTable
+			fileChooserPanel::setFiles
 		);
 	}
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/BaderlabRequests.java

@@ -10,11 +10,15 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLEncoder;
+import java.nio.file.Path;
 import java.util.List;
 
 import javax.ws.rs.core.UriBuilder;
 
+import org.baderlab.csplugins.enrichmentmap.model.io.ModelSerializer;
+
 import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
 import com.google.gson.reflect.TypeToken;
 
 public class BaderlabRequests {
@@ -46,9 +50,13 @@ private static <T> T requestAndParse(URL url, Type type) throws IOException {
 			throw new RuntimeException("Request error, status: " + code);
 		}
 
+		Gson gson = new GsonBuilder()
+				.registerTypeHierarchyAdapter(Path.class, new ModelSerializer.PathAdapter())
+				.create();
+		
 		try(InputStream in = connection.getInputStream()) {
 			Reader reader = new BufferedReader(new InputStreamReader(in));
-			T results = new Gson().fromJson(reader, type);
+			T results = gson.fromJson(reader, type);
 			return results;
 		}
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/WebLoadDialogParameters.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/DialogParameters.java

@@ -8,14 +8,14 @@
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogPage;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogParameters;
 
-public class WebLoadDialogParameters implements CardDialogParameters {
+public class DialogParameters implements CardDialogParameters {
 
 	public static final String TITLE = "Signature Gene Sets";
 
 	private final PADialogPage parent;
 
 
-	public WebLoadDialogParameters(PADialogPage parent) {
+	public DialogParameters(PADialogPage parent) {
 		this.parent = parent;
 	}
 
@@ -34,7 +34,7 @@ public List<CardDialogPage> getPages() {
 
 	@Override
 	public Dimension getPreferredSize() {
-		return new Dimension(800, 500);
+		return new Dimension(600, 500);
 	}
 
 	@Override

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/FileChooserPanel.java

@@ -0,0 +1,19 @@
+package org.baderlab.csplugins.enrichmentmap.view.postanalysis.web;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.function.Consumer;
+
+import javax.swing.JPanel;
+
+public interface FileChooserPanel {
+
+	JPanel getPanel();
+	
+	void setFiles(List<GmtFile> gmtFiles);
+	
+	Optional<String> getSelectedFilePath();
+	
+	void setSelectionListener(Consumer<Optional<String>> listener);
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/FileSizeCellRenderer.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/FileSizeRenderer.java

@@ -3,7 +3,7 @@
 import javax.swing.table.DefaultTableCellRenderer;
 
 @SuppressWarnings("serial")
-public class FileSizeCellRenderer extends DefaultTableCellRenderer {
+public class FileSizeRenderer extends DefaultTableCellRenderer {
 
 	@Override
 	protected void setValue(Object value) {
@@ -16,7 +16,7 @@ protected void setValue(Object value) {
 		}
 	}
 
-	private static String humanReadableByteCount(long bytes, boolean si) {
+	public static String humanReadableByteCount(long bytes, boolean si) {
 		int unit = si ? 1000 : 1024;
 		if (bytes < unit)
 			return bytes + " B";
@@ -25,4 +25,4 @@ private static String humanReadableByteCount(long bytes, boolean si) {
 		return String.format("%.1f %sB", bytes / Math.pow(unit, exp), pre);
 	}
 
-}
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/web/GmtFile.java

@@ -1,21 +1,23 @@
 package org.baderlab.csplugins.enrichmentmap.view.postanalysis.web;
 
+import java.nio.file.Path;
+
 public class GmtFile {
 
-	private final String filePath;
+	private final Path filePath;
 	private final int size;
 
-	public GmtFile(String filePath, int size) {
+	public GmtFile(Path filePath, int size) {
 		this.filePath = filePath;
 		this.size = size;
 	}
 
-	public String getFilePath() {
+	public Path getPath() {
 		return filePath;
 	}
 
 	public int getSize() {
 		return size;
 	}
-
+	
 }