Author: jgao
Date: 2010-09-10 14:20:04 -0700 (Fri, 10 Sep 2010)
New Revision: 21799
Added:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/BridgeRestUtil.java
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/FinalStaticValues.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.form
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.java
Log:
CyThesaurus: forbid saving target ids into existing attribute; set default
resource
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java
2010-09-10 20:31:35 UTC (rev 21798)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java
2010-09-10 21:20:04 UTC (rev 21799)
@@ -65,7 +65,8 @@
public CyThesaurusPlugin() {
try {
BioDataSource.init();
- IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
+// IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
+ registerDefaultClients();
listenToSessionEvent();
IDMappingServiceSuppport.addService();
@@ -84,8 +85,8 @@
pcs.addPropertyChangeListener(Cytoscape.CYTOSCAPE_INITIALIZED,
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
- IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
-
+// IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
+ registerDefaultClients();
mapSrcAttrIDTypes = null;
}
});
@@ -112,7 +113,8 @@
if (IDMapperClientManager.countClients()==0) {
// load the default clients if no client
-
IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
+//
IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
+ registerDefaultClients();
}
mapSrcAttrIDTypes = null;
@@ -120,6 +122,13 @@
});
}
+ private void registerDefaultClients() {
+ IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
+ if (IDMapperClientManager.countClients()==0) {
+ IDMapperClientManager.registerDefaultClient();
+ }
+ }
+
class IDMappingAction extends CytoscapeAction {
public IDMappingAction() {
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/FinalStaticValues.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/FinalStaticValues.java
2010-09-10 20:31:35 UTC (rev 21798)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/FinalStaticValues.java
2010-09-10 21:20:04 UTC (rev 21799)
@@ -43,5 +43,5 @@
public static final String PLUGIN_NAME = "CyThesaurus";
public static final String CLIENT_GLOBAL_PROPS =
"cythesaurus.clients.props";
public static final String CLIENT_SESSION_PROPS = "cythesaurus.client";
-
+ public static final String DEFAULT_SPECIES_NAME = "defaultSpeciesName";
}
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
2010-09-10 20:31:35 UTC (rev 21798)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
2010-09-10 21:20:04 UTC (rev 21799)
@@ -35,6 +35,8 @@
package csplugins.id.mapping;
+import csplugins.id.mapping.util.BridgeRestUtil;
+
import cytoscape.CytoscapeInit;
import java.io.BufferedReader;
@@ -47,14 +49,12 @@
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
-import org.bridgedb.DataSource;
import org.bridgedb.IDMapper;
-import org.bridgedb.IDMapperCapabilities;
-import org.bridgedb.IDMapperException;
import org.bridgedb.IDMapperStack;
/**
@@ -66,11 +66,11 @@
private static Map<String, IDMapperClient> clientConnectionStringMap;
static {
- new IDMapperClientManager();
+// new IDMapperClientManager();
+ clientConnectionStringMap = new HashMap();
}
private IDMapperClientManager() {
- clientConnectionStringMap = new HashMap();
//reloadFromCytoscapeSessionProperties();
}
@@ -187,6 +187,33 @@
return true;
}
+ static boolean registerDefaultClient() {
+ Properties props = CytoscapeInit.getProperties();
+ String defaultSpecies =
props.getProperty(FinalStaticValues.DEFAULT_SPECIES_NAME);
+
+ List<String> orgs =
BridgeRestUtil.supportedOrganisms(BridgeRestUtil.defaultBaseUrl);
+ if (!orgs.contains(defaultSpecies))
+ return false;
+
+ String classPath = "org.bridgedb.webservice.bridgerest.BridgeRest";
+ String connStr =
"idmapper-bridgerest:"+BridgeRestUtil.defaultBaseUrl+"/"+defaultSpecies;
+ IDMapperClient client;
+ try {
+ client = new IDMapperClientImplTunables
+ .Builder(connStr, classPath)
+
.displayName("BridgeDb("+BridgeRestUtil.defaultBaseUrl+"/"+defaultSpecies+")")
+ .selected(true)
+
.clientType(IDMapperClient.ClientType.WEBSERVICE)
+ .build();
+ } catch (Exception e) {
+ e.printStackTrace();
+ return false;
+ }
+
+ registerClient(client);
+ return true;
+ }
+
public static void saveCurrentToCytoscapeGlobalProperties() throws
IOException {
String fileName = FinalStaticValues.CLIENT_GLOBAL_PROPS;
File file = cytoscape.CytoscapeInit.getConfigFile(fileName);
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
2010-09-10 20:31:35 UTC (rev 21798)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
2010-09-10 21:20:04 UTC (rev 21799)
@@ -487,10 +487,10 @@
throw new CyCommandException(NETWORK_LIST+" must be String or
Collection<String> "
+ "or CyNetwork or Collection<CyNetwork>.\n");
}
+ }
- if (networks.isEmpty()) {
- throw new CyCommandException("No network to work on.");
- }
+ if (networks.isEmpty()) {
+ throw new CyCommandException("No network to work on.");
}
Set<String> attributes = new HashSet();
@@ -505,26 +505,24 @@
}else{
if (obj instanceof String) {
String attr = (String)obj;
- if (attributes.contains(attr)) {
- srcAttrs.add(attr);
- } else {
+ if (!attributes.contains(attr)) {
throw new CyCommandException("Node attribute "+attr+" does
not exist.");
}
+ srcAttrs.add(attr);
} else if (obj instanceof Collection) {
Collection<String> attrs = (Collection)obj;
for (String attr : attrs) {
if (attributes.contains(attr)) {
- srcAttrs.add(attr);
- } else {
throw new CyCommandException("Node attribute "+attr+"
does not exist.");
}
+ srcAttrs.add(attr);
}
} else {
throw new CyCommandException(SOURCE_ATTR+" must be String or
Collection<String>.\n");
}
if (srcAttrs.isEmpty()) {
- throw new CyCommandException("No network to work on.");
+ throw new CyCommandException("No source attribute to work
on.");
}
}
@@ -602,18 +600,20 @@
String tgtAttr = getArg(command, TARGET_ATTR, args);
if (tgtAttr==null) {
- Set<String> usedName = new HashSet();
- usedName.add("ID"); //TODO remove in Cy3
-
usedName.addAll(java.util.Arrays.asList(Cytoscape.getNodeAttributes().getAttributeNames()));
- if (usedName.contains(tgtType)) {
+ if (attributes.contains(tgtType)) {
int num = 1;
- while (usedName.contains(tgtType+"."+num)) {
+ while (attributes.contains(tgtType+"."+num)) {
num ++;
}
tgtAttr = tgtType+"."+num;
} else {
tgtAttr = tgtType;
}
+ } else {
+ if (attributes.contains(tgtAttr)) {
+ throw new CyCommandException(tgtAttr+" is an existing
attribute "
+ + "and hence cannot be used as target attribute
name.");
+ }
}
obj = args.get(FIRST_ONLY);
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.form
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.form
2010-09-10 20:31:35 UTC (rev 21798)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.form
2010-09-10 21:20:04 UTC (rev 21799)
@@ -102,7 +102,7 @@
</Properties>
<AuxValues>
<AuxValue name="JavaCodeGenerator_DeclarationPost"
type="java.lang.String" value="private TextComboBoxEditor
bridgedbComboBoxEditor;"/>
- <AuxValue name="JavaCodeGenerator_InitCodePre"
type="java.lang.String" value="DefaultComboBoxModel bridgeComboBoxModel = new
DefaultComboBoxModel();
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Arabidopsis
thaliana");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Bacillus
subtilis");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Caenorhabditis
elegans");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Chicken");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Cow");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Danio
rerio");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Dog");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Escherichia
coli");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Frui!
t
fly");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Horse");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Mouse");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Human");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Mosquito");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Populus
trichocarpa");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Rat");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Rice");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Saccharomyces
cerevisiae");
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Xenopus
tropicalis");
bridgedbBaseUrlComboBox.setModel(bridgeComboBoxModel);
bridgedbComboBoxEditor
= new TextComboBoxEditor("http://webservice.bridgedb.org/Human&;!
quot;);
bridgedbBaseUrlComboBox.setEditor(bridgedbComboBox!
Editor);

bridgedbBaseUrlComboBox.setSelectedItem("http://webservice.bridgedb.org/Human");"/>
+ <AuxValue name="JavaCodeGenerator_InitCodePre"
type="java.lang.String" value="List<String> orgs =
BridgeRestUtil.supportedOrganismsNr(BridgeRestUtil.defaultBaseUrl);
String[]
orgUrls = new String[orgs.size()];
int iorg = 0;
for (String org :
orgs) {
 orgUrls[iorg++] = BridgeRestUtil.defaultBaseUrl + "/"
+org;
}
DefaultComboBoxModel bridgeComboBoxModel = new
DefaultComboBoxModel(orgUrls);
bridgedbBaseUrlComboBox.setModel(bridgeComboBoxModel);
String
textInEditor = orgUrls.length==0?"No organism available, please specify
yours.":orgUrls[0];
bridgedbComboBoxEditor = new
TextComboBoxEditor(textInEditor);
bridgedbBaseUrlComboBox.setEditor(bridgedbComboBoxEditor);
//bridgedbBaseUrlComboBox.setSelectedItem("http://webservice.bridgedb.org/Human");"/>
</AuxValues>
<Constraints>
<Constraint
layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout"
value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.java
2010-09-10 20:31:35 UTC (rev 21798)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.java
2010-09-10 21:20:04 UTC (rev 21799)
@@ -37,6 +37,7 @@
import csplugins.id.mapping.IDMapperClient;
import csplugins.id.mapping.IDMapperClientImplTunables;
+import csplugins.id.mapping.util.BridgeRestUtil;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
@@ -49,6 +50,7 @@
import org.bridgedb.webservice.biomart.BiomartStub;
import org.bridgedb.webservice.synergizer.SynergizerStub;
+import java.util.List;
import java.util.Set;
import java.util.HashSet;
import java.util.Vector;
@@ -237,29 +239,18 @@
bridgedbBaseUrlPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Base
URL of BridgeDb web service"));
bridgedbBaseUrlPanel.setLayout(new java.awt.GridBagLayout());
- DefaultComboBoxModel bridgeComboBoxModel = new DefaultComboBoxModel();
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Arabidopsis
thaliana");
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Bacillus
subtilis");
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Caenorhabditis
elegans");
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Chicken";);
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Cow";);
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Danio
rerio");
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Dog";);
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Escherichia
coli");
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Fruit
fly");
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Horse";);
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Mouse";);
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Human";);
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Mosquito";);
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Populus
trichocarpa");
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Rat";);
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Rice";);
-
bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Saccharomyces
cerevisiae");
- bridgeComboBoxModel.addElement("http://webservice.bridgedb.org/Xenopus
tropicalis");
+ List<String> orgs =
BridgeRestUtil.supportedOrganismsNr(BridgeRestUtil.defaultBaseUrl);
+ String[] orgUrls = new String[orgs.size()];
+ int iorg = 0;
+ for (String org : orgs) {
+ orgUrls[iorg++] = BridgeRestUtil.defaultBaseUrl + "/" +org;
+ }
+ DefaultComboBoxModel bridgeComboBoxModel = new
DefaultComboBoxModel(orgUrls);
bridgedbBaseUrlComboBox.setModel(bridgeComboBoxModel);
- bridgedbComboBoxEditor = new
TextComboBoxEditor("http://webservice.bridgedb.org/Human";);
+ String textInEditor = orgUrls.length==0?"No organism available, please
specify yours.":orgUrls[0];
+ bridgedbComboBoxEditor = new TextComboBoxEditor(textInEditor);
bridgedbBaseUrlComboBox.setEditor(bridgedbComboBoxEditor);
-
bridgedbBaseUrlComboBox.setSelectedItem("http://webservice.bridgedb.org/Human";);
+
//bridgedbBaseUrlComboBox.setSelectedItem("http://webservice.bridgedb.org/Human";);
bridgedbBaseUrlComboBox.setEditable(true);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
Added:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/BridgeRestUtil.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/BridgeRestUtil.java
(rev 0)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/BridgeRestUtil.java
2010-09-10 21:20:04 UTC (rev 21799)
@@ -0,0 +1,107 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.id.mapping.util;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.io.IOException;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+
+/**
+ *
+ * @author gjj
+ */
+public class BridgeRestUtil {
+ private BridgeRestUtil(){}
+
+ public static String defaultBaseUrl = "http://webservice.bridgedb.org";;
+
+ public static List<String> supportedOrganisms(String baseUrl) {
+ return supportedOrganisms(baseUrl, -1);
+ }
+
+ public static List<String> supportedOrganismsNr(String baseUrl) {
+ return supportedOrganisms(baseUrl, 0);
+ }
+
+ public static List<String> supportedOrganismsLatin(String baseUrl) {
+ return supportedOrganisms(baseUrl, 1);
+ }
+
+ private static List<String> supportedOrganisms(String baseUrl, int column)
{
+ String contentUrl = baseUrl + "/contents";
+ List<String> lines;
+ try {
+ lines = readUrl(contentUrl);
+ } catch (IOException e) {
+ e.printStackTrace();
+ return Collections.emptyList();
+ }
+
+ List<String> ret = new ArrayList<String>(lines.size());
+ for (String line : lines) {
+ String[] strs = line.split("\t");
+ if (column>=0)
+ ret.add(strs[strs.length>column?column:0]);
+ else
+ ret.addAll(Arrays.asList(strs));
+ }
+ return ret;
+ }
+
+ private static List<String> readUrl(String strUrl) throws IOException {
+ URL url = new URL(strUrl);
+ URLConnection yc = url.openConnection();
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(
+ yc.getInputStream()));
+ List<String> ret = new ArrayList<String>();
+ String inputLine;
+ while ((inputLine = in.readLine()) != null)
+ ret.add(inputLine);
+ in.close();
+
+ return ret;
+ }
+}
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