Author: rodche
Date: 2012-05-24 14:13:30 -0700 (Thu, 24 May 2012)
New Revision: 29345
Removed:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
Log:
now dynamically generates lists of available data sources and organisms (for
filtering); lists contain names, are sorted, multi-select, and with checkboxes
(actual filter values will be set to corresponding taxonomy or Provenance URIs)
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-05-24
20:55:50 UTC (rev 29344)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-05-24
21:13:30 UTC (rev 29345)
@@ -7,6 +7,8 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<bundle.symbolicName>org.cytoscape.cpathsquared-impl</bundle.symbolicName>
+ <cytoscape.version>3.0.0-beta1</cytoscape.version>
+ <spring.version>3.0.5.RELEASE</spring.version>
</properties>
<modelVersion>4.0.0</modelVersion>
<artifactId>cpathsquared-impl</artifactId>
@@ -121,68 +123,65 @@
</repositories>
-
-
-
<dependencies>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>model-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>viewmodel-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>layout-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>presentation-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-util-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>vizmap-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>webservice-swing-api</artifactId>
- <version>[3.0.0-alpha8-SNAPSHOT, 4.0.0)</version>
+ <version>[${cytoscape.version}, 4.0.0)</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.logging</groupId>
<artifactId>pax-logging-api</artifactId>
- <version>1.5.2</version>
+ <version>[1.5.2, 2.0.0)</version>
<scope>provided</scope>
</dependency>
@@ -194,7 +193,7 @@
<dependency>
<groupId>pathwaycommons.cpath</groupId>
<artifactId>cpath-client</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.2.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biopax.paxtools</groupId>
@@ -211,31 +210,31 @@
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
- <version>3.0.5.RELEASE</version>
+ <version>${spring.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
- <version>3.0.5.RELEASE</version>
+ <version>${spring.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-oxm</artifactId>
- <version>3.0.5.RELEASE</version>
+ <version>${spring.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
- <version>3.0.5.RELEASE</version>
+ <version>${spring.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
- <version>3.0.5.RELEASE</version>
+ <version>${spring.version}</version>
<scope>runtime</scope>
</dependency>
</dependencies>
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
2012-05-24 21:13:30 UTC (rev 29345)
@@ -3,7 +3,7 @@
import java.io.ByteArrayOutputStream;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.List;
+import java.util.Map;
import java.util.Set;
import org.biopax.paxtools.model.Model;
@@ -54,15 +54,16 @@
listener.searchInitiated(keyword, organism, datasource);
}
- CPath2Client client = CPath2Client.newInstance();
- client.setEndPointURL("http://awabi.cbio.mskcc.org/cpath2/";);
+ CPath2Client client = newClient();
if(LOGGER.isDebugEnabled())
LOGGER.debug("cPath2Url=" + client.getEndPointURL());
if(organism != null)
client.setOrganisms(organism);
- client.setType("Entity"); //TODO make sure: we want Entity type hits
only, because UtilityClass elements can be retrieved via sub-queries
+ //TODO design choice: search for interactions right away (cpath2 cool!
index allows it) vs. get physical entities first (then get processes...)
+// client.setType("PhysicalEntity");
+ client.setType("Interaction");
if(datasource != null)
client.setDataSources(datasource);
@@ -76,8 +77,14 @@
return res;
}
+ private static CPath2Client newClient() {
+ CPath2Client client = CPath2Client.newInstance();
+// client.setEndPointURL("http://localhost:8080/cpath-web-service/";);
+ client.setEndPointURL("http://awabi.cbio.mskcc.org/cpath2/";);
+ return client;
+ }
- /**
+ /**
* Gets One or more records by Primary ID.
* @param ids Array of URIs.
* @param format Output format. TODO
@@ -87,10 +94,8 @@
*/
public static String getRecordsByIds(String[] ids, OutputFormat format)
{
- CPath2Client client = CPath2Client.newInstance();
-
//TODO client must return other formats, if requested
- Model res = client.get(Arrays.asList(ids));
+ Model res = newClient().get(Arrays.asList(ids));
ByteArrayOutputStream baos = new ByteArrayOutputStream();
BioPaxUtil.getBiopaxIO().convertToOWL(res, baos);
@@ -99,15 +104,13 @@
}
- //TODO
- public static List<String> getOrganisms() {
- throw new UnsupportedOperationException("Not implemented.");
+ public static Map<String, String> getAvailableOrganisms() {
+ return newClient().getValidOrganisms();
}
- //TODO
- public static List<String> getDataSources() {
- throw new UnsupportedOperationException("Not implemented.");
+ public static Map<String, String> getLoadedDataSources() {
+ return newClient().getValidDataSources();
}
@@ -141,7 +144,6 @@
public static SearchResponse topPathways(String keyword, Set<String>
organism,
Set<String> datasource) {
- // TODO Auto-generated method stub
- return null;
+ return newClient().getTopPathways();
}
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
2012-05-24 21:13:30 UTC (rev 29345)
@@ -1,7 +1,7 @@
package org.cytoscape.cpathsquared.internal.view;
-public class FilterBoxItem {
+public class FilterBoxItem implements Comparable<FilterBoxItem> {
private String name;
private String value;
@@ -23,4 +23,11 @@
public String toString() {
return name;
}
+
+
+ //in order to order by name
+ @Override
+ public int compareTo(FilterBoxItem o) {
+ return this.name.compareTo(o.getName());
+ }
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
2012-05-24 21:13:30 UTC (rev 29345)
@@ -10,19 +10,15 @@
import java.awt.event.FocusEvent;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
-import java.net.URL;
-import java.util.HashSet;
-import java.util.Set;
+import javax.swing.AbstractListModel;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.DefaultListModel;
-import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
-import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
@@ -31,30 +27,32 @@
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkListener;
+import org.cytoscape.cpathsquared.internal.CPath2;
import org.cytoscape.cpathsquared.internal.CPath2Factory;
import org.cytoscape.cpathsquared.internal.task.ExecuteSearchTask;
import org.cytoscape.cpathsquared.internal.task.ResultHandler;
+import org.cytoscape.util.swing.CheckBoxJList;
import org.cytoscape.work.TaskFactory;
+import java.util.*;
/**
* Search Box Panel.
*
*/
public class SearchQueryPanel extends JPanel {
- private JButton searchButton;
private static final String ENTER_TEXT = "Enter Gene Name or ID";
- private final JList organismBox;
- private final JList dataSourceBox;
+ private final CheckBoxJList organismList;
+ private final CheckBoxJList dataSourceList;
private final JTextField searchField;
/**
* Constructor.
*/
public SearchQueryPanel() {
- this.organismBox = new JList();
- this.dataSourceBox = new JList();
- this.searchField = createSearchField();
+ this.organismList = new CheckBoxJList();
+ this.dataSourceList = new CheckBoxJList();
+ this.searchField = createSearchField();
GradientHeader header = new GradientHeader("Search");
header.setAlignmentX(Component.LEFT_ALIGNMENT);
@@ -63,19 +61,22 @@
add(header);
add(Box.createVerticalStrut(5));
- JPanel centerPanel = new JPanel();
- BoxLayout boxLayoutMain = new BoxLayout(centerPanel, BoxLayout.X_AXIS);
- centerPanel.setLayout(boxLayoutMain);
- centerPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
+ JPanel queryPanel = new JPanel();
+ queryPanel.setLayout(new BoxLayout(queryPanel, BoxLayout.Y_AXIS));
+ queryPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
+ queryPanel.setAlignmentY(Component.TOP_ALIGNMENT);
+ JPanel queryFiltersPanel = new JPanel();
+ queryFiltersPanel.setLayout(new BoxLayout(queryFiltersPanel,
BoxLayout.X_AXIS));
+ queryFiltersPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
+ queryFiltersPanel.setAlignmentY(Component.TOP_ALIGNMENT);
+
// create query field, examples/label, and button
- URL url = GradientHeader.class.getResource("resources/run_tool.gif");
- ImageIcon icon = new ImageIcon(url);
- searchButton = new JButton("Search");
+ JButton searchButton = new JButton("Search");
searchButton.setToolTipText("Execute Search");
searchButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
- executeSearch(searchField.getText(),
organismBox.getSelectedValues(), dataSourceBox.getSelectedValues());
+ executeSearch(searchField.getText(),
organismList.getSelectedValues(), dataSourceList.getSelectedValues());
}
});
searchButton.setAlignmentX(Component.LEFT_ALIGNMENT);
@@ -84,8 +85,10 @@
searchField.setBorder
(BorderFactory.createCompoundBorder(searchField.getBorder(),
pulsatingBorder));
searchField.setAlignmentX(Component.LEFT_ALIGNMENT);
+ searchField.setMaximumSize(new Dimension(1000, 100));
- JEditorPane label = new JEditorPane ("text/html", "Examples: <a
href='TP53'>TP53</a>, " +
+ JEditorPane label = new JEditorPane (
+ "text/html", "Examples: <a href='TP53'>TP53</a>, " +
"<a href='BRCA1'>BRCA1</a>, or <a href='SRY'>SRY</a>.");
label.setEditable(false);
label.setOpaque(false);
@@ -105,57 +108,44 @@
label.setBorder(new EmptyBorder(5,3,3,3));
label.setAlignmentX(Component.LEFT_ALIGNMENT);
- centerPanel.add(searchField);
- centerPanel.add(createOrganismFilterBox());
- centerPanel.add(createDataSourceFilterBox());
-
- JButton clearButton = new JButton("Clear");
- clearButton.setToolTipText("Clear");
- clearButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent actionEvent) {
- searchField.setText(null);
- organismBox.clearSelection();
- dataSourceBox.clearSelection();
- }
- });
-
- centerPanel.add(clearButton);
- centerPanel.add(searchButton);
-
- add(centerPanel);
- add(label);
+ queryPanel.add(searchField);
+ queryPanel.add(label);
+ queryPanel.add(searchButton);
+ queryFiltersPanel.add(queryPanel);
+ queryFiltersPanel.add(createOrganismFilterBox());
+ queryFiltersPanel.add(createDataSourceFilterBox());
+
+ add(queryFiltersPanel);
}
- private final JComponent createOrganismFilterBox() {
- //TODO fill the lists dynamically (from the web service)
- DefaultListModel organismBoxModel = new DefaultListModel();
- organismBoxModel.addElement(new FilterBoxItem("Human",
"urn:miriam:taxonomy:9606"));
- organismBoxModel.addElement(new FilterBoxItem("Mouse",
"urn:miriam:taxonomy:10090"));
- organismBoxModel.addElement(new FilterBoxItem("Rat",
"urn:miriam:taxonomy:10116"));
- organismBoxModel.addElement(new FilterBoxItem("S. cerevisiae",
"urn:miriam:taxonomy:4932"));
- organismBox.setModel(organismBoxModel);
- organismBox.setToolTipText("Select Organisms");
- organismBox.setMaximumSize(new Dimension(200, 9999));
- organismBox.setAlignmentX(Component.LEFT_ALIGNMENT);
- JScrollPane scroll = new JScrollPane(organismBox);
- scroll.setSize(100, 100);
+ private final JComponent createOrganismFilterBox() {
+ SortedJListModel<FilterBoxItem> model = new
SortedJListModel<FilterBoxItem>();
+ Map<String,String> map = CPath2.getAvailableOrganisms();
+ for(String o : map.keySet()) {
+ model.addElement(new FilterBoxItem(map.get(o), o));
+ }
+ organismList.setModel(model);
+ organismList.setToolTipText("Select Organisms");
+ organismList.setAlignmentX(Component.LEFT_ALIGNMENT);
+ JScrollPane scroll = new JScrollPane(organismList,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
return scroll;
}
private final JComponent createDataSourceFilterBox() {
- //TODO fill the lists dynamically (from the web service)
DefaultListModel dataSourceBoxModel = new DefaultListModel();
- dataSourceBoxModel.addElement(new FilterBoxItem("Reactome",
"urn:miriam:reactome"));
- dataSourceBoxModel.addElement(new FilterBoxItem("NCI_Nature Curated",
"urn:miriam:pid.pathway"));
- dataSourceBox.setModel(dataSourceBoxModel);
- dataSourceBox.setToolTipText("Select Datasources");
- dataSourceBox.setMaximumSize(new Dimension(200, 9999));
- dataSourceBox.setAlignmentX(Component.LEFT_ALIGNMENT);
- JScrollPane scroll = new JScrollPane(dataSourceBox);
- scroll.setSize(100, 100);
+ Map<String,String> map = CPath2.getLoadedDataSources();
+ for(String d : map.keySet()) {
+ dataSourceBoxModel.addElement(new FilterBoxItem(map.get(d), d));
+ }
+
+ dataSourceList.setModel(dataSourceBoxModel);
+ dataSourceList.setToolTipText("Select Datasources");
+ dataSourceList.setAlignmentX(Component.LEFT_ALIGNMENT);
+ JScrollPane scroll = new JScrollPane(dataSourceList,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
return scroll;
}
@@ -183,7 +173,7 @@
int keyCode = e.getKeyCode();
if (keyCode == 10) {
executeSearch(searchField.getText(),
- organismBox.getSelectedValues(),
dataSourceBox.getSelectedValues());
+ organismList.getSelectedValues(),
dataSourceList.getSelectedValues());
}
}
});
@@ -224,12 +214,63 @@
CPath2Factory.getTaskManager().execute(search.createTaskIterator());
}
}
+
+ static class SortedJListModel<E> extends AbstractListModel {
+ SortedSet<E> items;
-
- /**
- * Initializes Focus to the Search Button.
- */
- public final void initFocus() {
- searchButton.requestFocusInWindow();
- }
+ public SortedJListModel() {
+ super();
+ items = new TreeSet<E>();
+ }
+
+ @Override
+ public Object getElementAt(int index) {
+ return items.toArray()[index];
+ }
+
+ @Override
+ public int getSize() {
+ return items.size();
+ }
+
+ public void addAll(Object elements[]) {
+ Collection c = Arrays.asList(elements);
+ items.addAll(c);
+ fireContentsChanged(this, 0, getSize());
+ }
+
+ public void addElement(E o) {
+ items.add(o);
+ fireContentsChanged(this, 0, getSize());
+ }
+
+ public boolean removeElement(Object element) {
+ boolean removed = items.remove(element);
+ if (removed) {
+ fireContentsChanged(this, 0, getSize());
+ }
+ return removed;
+ }
+
+ public void clear() {
+ items.clear();
+ fireContentsChanged(this, 0, getSize());
+ }
+
+ public boolean contains(Object element) {
+ return items.contains(element);
+ }
+
+ public Object firstElement() {
+ return items.first();
+ }
+
+ public Iterator iterator() {
+ return items.iterator();
+ }
+
+ public Object lastElement() {
+ return items.last();
+ }
+ }
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
2012-05-24 21:13:30 UTC (rev 29345)
@@ -85,7 +85,7 @@
header.setAlignmentX(Component.LEFT_ALIGNMENT);
hitListPane.add(header, BorderLayout.NORTH);
JSplitPane internalPanel = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
hitListScrollPane, detailsPanel);
- internalPanel.setDividerLocation(100);
+ internalPanel.setDividerLocation(200);
hitListPane.add(internalPanel, BorderLayout.CENTER);
// Create search results extra filtering panel
@@ -104,7 +104,7 @@
// Create the Split Pane
JSplitPane splitPane = new JSplitPane (JSplitPane.HORIZONTAL_SPLIT,
hitListPane, networksPanel);
- splitPane.setDividerLocation(200);
+ splitPane.setDividerLocation(400);
splitPane.setAlignmentX(Component.LEFT_ALIGNMENT);
this.add(splitPane);
@@ -181,8 +181,7 @@
// Ignore the "unselect" event.
if (!listSelectionEvent.getValueIsAdjusting()) {
if (selectedIndex >=0) {
- SelectEntity selectTask = new SelectEntity();
- selectTask.selectItem(
+ (new SelectEntity()).selectItem(
(SearchHit)resList.getModel().getElementAt(selectedIndex),
summaryDocument, summaryTextPane,
appLayeredPane);
}
@@ -206,27 +205,27 @@
* @param pathwayModel Pathway Model.
*/
private final void downloadPathway(int[] rows, DefaultTableModel model) {
- try {
- SearchHit hit = (SearchHit) model.getDataVector().get(rows[0]);
- String internalId = hit.getUri();
- String title = model.getValueAt(rows[0], 0)
- + " (" + model.getValueAt(rows[0], 1) + ")";
+ if(rows.length < 1) {
+ return;
+ }
+
+ int i= rows[0];
+ SearchHit hit = (SearchHit) model.getDataVector().get(i);
+ String internalId = hit.getUri();
+ String title = model.getValueAt(i, 0)
+ + " (" + model.getValueAt(i, 1) + ")";
- OutputFormat format;
- //TODO add EXTENDED_BINARY_SIF
- if (CPath2Properties.downloadMode ==
CPath2Properties.DOWNLOAD_BIOPAX) {
- format = OutputFormat.BIOPAX;
- } else {
- format = OutputFormat.BINARY_SIF;
- }
-
- TaskFactory taskFactory = CPath2Factory.newTaskFactory(new
ExecuteGetRecordByCPathIdTask(
- new String[]{internalId}, format, title));
-
CPath2Factory.getTaskManager().execute(taskFactory.createTaskIterator());
-
- } catch (IndexOutOfBoundsException e) {
- // Ignore TODO strange...
+ OutputFormat format;
+ //TODO add EXTENDED_BINARY_SIF
+ if (CPath2Properties.downloadMode == CPath2Properties.DOWNLOAD_BIOPAX)
{
+ format = OutputFormat.BIOPAX;
+ } else {
+ format = OutputFormat.BINARY_SIF;
}
+
+ TaskFactory taskFactory = CPath2Factory.newTaskFactory(new
ExecuteGetRecordByCPathIdTask(
+ new String[]{internalId}, format, title));
+
CPath2Factory.getTaskManager().execute(taskFactory.createTaskIterator());
}
}
\ No newline at end of file
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
2012-05-24 21:13:30 UTC (rev 29345)
@@ -24,7 +24,8 @@
StringBuffer html = new StringBuffer();
html.append("<html>");
- html.append ("<h2>" + item.getName() + "</h2>");
+ if(item.getName() != null)
+ html.append ("<h2>" + item.getName() + "</h2>");
html.append ("<h3>Class: " + item.getBiopaxClass() + "</h3>");
html.append ("<h3>URI: " + item.getUri() + "</h3>");
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2012-05-24 21:13:30 UTC (rev 29345)
@@ -1,67 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans";
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
- xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
- default-lazy-init="false">
-
-
- <!-- Import services -->
- <osgi:reference id="cySwingApplicationRef"
- interface="org.cytoscape.application.swing.CySwingApplication"
/>
-
- <osgi:reference id="taskManagerRef"
- interface="org.cytoscape.work.TaskManager" />
-
- <osgi:reference id="openBrowserRef"
- interface="org.cytoscape.util.swing.OpenBrowser" />
-
- <osgi:reference id="cyNetworkManagerRef"
- interface="org.cytoscape.model.CyNetworkManager" />
-
- <osgi:reference id="cyApplicationManagerRef"
- interface="org.cytoscape.session.CyApplicationManager" />
-
- <osgi:reference id="cyNetworkViewManagerRef"
- interface="org.cytoscape.view.model.CyNetworkViewManager" />
-
- <osgi:reference id="cyNetworkViewReaderManagerRef"
- interface="org.cytoscape.io.read.CyNetworkReaderManager" />
-
- <osgi:reference id="cyNetworkNamingRef"
- interface="org.cytoscape.session.CyNetworkNaming" />
-
- <osgi:reference id="cyNetworkFactoryRef"
- interface="org.cytoscape.model.CyNetworkFactory" />
-
- <osgi:reference id="cyLayoutsRef"
- interface="org.cytoscape.view.layout.CyLayoutAlgorithmManager"
/>
-
- <osgi:reference id="undoSupportRef"
- interface="org.cytoscape.work.undo.UndoSupport" />
-
- <osgi:reference id="bioPaxContainerRef"
- interface="org.cytoscape.biopax.internal.BioPaxContainer" />
-
- <osgi:reference id="mapBioPaxToCytoscapeFactoryRef"
- interface="org.cytoscape.biopax.internal.BioPaxMapperFactory" />
-
- <osgi:reference id="networkListenerRef"
- interface="org.cytoscape.biopax.internal.BioPaxViewTracker" />
-
- <osgi:reference id="visualMappingManagerRef"
- interface="org.cytoscape.view.vizmap.VisualMappingManager"/>
-
- <osgi:reference id="visualStyleFactoryRef"
- interface="org.cytoscape.view.vizmap.VisualStyleFactory"/>
-
- <osgi:reference id="discreteMappingFactoryRef"
-
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
- filter="(mapping.type=discrete)"/>
-
- <osgi:reference id="passthroughMappingFactoryRef"
-
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
- filter="(mapping.type=passthrough)"/>
-
- <osgi:service ref="cPathWebService" auto-export="interfaces" />
-</beans>
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
2012-05-24 20:55:50 UTC (rev 29344)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
2012-05-24 21:13:30 UTC (rev 29345)
@@ -1,48 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans";
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:aop="http://www.springframework.org/schema/aop";
- xmlns:context="http://www.springframework.org/schema/context";
- xmlns:lang="http://www.springframework.org/schema/lang";
xmlns:osgi="http://www.springframework.org/schema/osgi";
- xsi:schemaLocation="
- http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://www.springframework.org/schema/aop
- http://www.springframework.org/schema/aop/spring-aop-2.5.xsd
- http://www.springframework.org/schema/context
- http://www.springframework.org/schema/context/spring-context-2.5.xsd
- http://www.springframework.org/schema/lang
http://www.springframework.org/schema/lang/spring-lang-2.5.xsd
- http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
- default-lazy-init="true">
-
- <context:annotation-config />
-
- <bean id="cPath2Factory"
class="org.cytoscape.cpathsquared.internal.CPath2Factory">
- <constructor-arg ref="cySwingApplicationRef" />
- <constructor-arg ref="taskManagerRef" />
- <constructor-arg ref="openBrowserRef" />
- <constructor-arg ref="cyNetworkManagerRef" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyNetworkViewManagerRef" />
- <constructor-arg ref="cyNetworkViewReaderManagerRef" />
- <constructor-arg ref="cyNetworkNamingRef" />
- <constructor-arg ref="cyNetworkFactoryRef" />
- <constructor-arg ref="cyLayoutsRef" />
- <constructor-arg ref="undoSupportRef" />
- <constructor-arg ref="bioPaxContainerRef" />
- <constructor-arg ref="mapBioPaxToCytoscapeFactoryRef" />
- <constructor-arg ref="networkListenerRef" />
- <constructor-arg ref="binarySifVisualStyleUtil" />
- <constructor-arg ref="visualMappingManagerRef" />
- </bean>
-
- <bean id="cPathWebService"
class="org.cytoscape.cpathsquared.internal.CPath2CytoscapeWebService">
- <constructor-arg ref="cPath2Factory" />
- </bean>
-
- <bean id="binarySifVisualStyleUtil"
class="org.cytoscape.cpathsquared.internal.view.BinarySifVisualStyleFactory">
- <constructor-arg ref="visualStyleFactoryRef" />
- <constructor-arg ref="visualMappingManagerRef" />
- <constructor-arg ref="discreteMappingFactoryRef" />
- <constructor-arg ref="passthroughMappingFactoryRef" />
- </bean>
-</beans>
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