Author: jgao Date: 2011-11-08 06:28:26 -0800 (Tue, 08 Nov 2011) New Revision: 27429
Added: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImpl.java Modified: csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClient.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.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/service/IDMappingServiceSuppport.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/FileIDMappingClientConfigDialog.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/RDBIDMappingClientConfigDialog.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.java Log: cythesaurus: disable session property Modified: csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props 2011-11-08 14:28:26 UTC (rev 27429) @@ -13,7 +13,7 @@ pluginDescription=Provides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin";>Click for more information</a>. # Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03 -pluginVersion=1.30 +pluginVersion=1.31 # Compatible Cytoscape version. If there are more than one version, seperate by ",". cytoscapeVersion=2.8 Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -65,7 +65,7 @@ */ public final class CyThesaurusPlugin extends CytoscapePlugin { public static Map mapSrcAttrIDTypes = null; - public static double VERSION = 1.20; + public static double VERSION = 1.31; public CyThesaurusPlugin() { try { @@ -136,39 +136,39 @@ } }); - pcs.addPropertyChangeListener(Cytoscape.SESSION_SAVED, - new PropertyChangeListener() { - public void propertyChange(PropertyChangeEvent evt) { - // remove the old client but not the session properties - IDMapperClientManager.removeAllClients(false); +// pcs.addPropertyChangeListener(Cytoscape.SESSION_SAVED, +// new PropertyChangeListener() { +// public void propertyChange(PropertyChangeEvent evt) { +// // remove the old client but not the session properties +// IDMapperClientManager.removeAllClients(false); +// +// // reload the clients for this session (change the prop prefix) +// IDMapperClientManager.reloadFromCytoscapeSessionProperties(); +// IDMapperClientManager.reCache(); +// } +// }); - // reload the clients for this session (change the prop prefix) - IDMapperClientManager.reloadFromCytoscapeSessionProperties(); - IDMapperClientManager.reCache(); - } - }); +// pcs.addPropertyChangeListener(Cytoscape.SESSION_LOADED, +// new PropertyChangeListener() { +// public void propertyChange(PropertyChangeEvent evt) { +// // remove the old client include session properties +// IDMapperClientManager.removeAllClients(true); +// +// // reload the clients for this session +// IDMapperClientManager.reloadFromCytoscapeSessionProperties(); +// +// if (IDMapperClientManager.countClients()==0) { +// // load the default clients if no client +//// IDMapperClientManager.reloadFromCytoscapeGlobalProperties(); +// registerDefaultClients(); +// } +// +// IDMapperClientManager.reCache(); +// +// mapSrcAttrIDTypes = null; +// } +// }); - pcs.addPropertyChangeListener(Cytoscape.SESSION_LOADED, - new PropertyChangeListener() { - public void propertyChange(PropertyChangeEvent evt) { - // remove the old client include session properties - IDMapperClientManager.removeAllClients(true); - - // reload the clients for this session - IDMapperClientManager.reloadFromCytoscapeSessionProperties(); - - if (IDMapperClientManager.countClients()==0) { - // load the default clients if no client -// IDMapperClientManager.reloadFromCytoscapeGlobalProperties(); - registerDefaultClients(); - } - - IDMapperClientManager.reCache(); - - mapSrcAttrIDTypes = null; - } - }); - // pcs.addPropertyChangeListener(Cytoscape.PREFERENCE_MODIFIED, // new PropertyChangeListener() { // public void propertyChange(PropertyChangeEvent evt) { @@ -183,9 +183,6 @@ private void registerDefaultClients() { IDMapperClientManager.reloadFromCytoscapeGlobalProperties(); -// if (IDMapperClientManager.countClients()==0) { -// IDMapperClientManager.registerDefaultClient(); -// } } class IDMappingAction extends CytoscapeAction { Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClient.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClient.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClient.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -81,7 +81,7 @@ public ClientType getClientType(); -// boolean isSelected(); -// -// void setSelected(boolean selected); + boolean isSelected(); + + void setSelected(boolean selected); } Copied: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImpl.java (from rev 27337, csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java) =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImpl.java (rev 0) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImpl.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -0,0 +1,243 @@ +/* + 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; + +import java.util.HashSet; +import java.util.Set; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.TimeUnit; + +import org.bridgedb.BridgeDb; +import org.bridgedb.DataSource; +import org.bridgedb.IDMapper; +import org.bridgedb.IDMapperCapabilities; +import org.bridgedb.IDMapperException; + +/** + * + * @author gjj + */ +public class IDMapperClientImpl implements IDMapperClient { + protected IDMapper mapper = null; + + protected String connectionString; + protected final String classString; + protected final String id; + protected final String displayName; + protected boolean selected; + protected final ClientType clientType; + + protected static int clientNo = 0; + + protected static final String CLIENT_ID = "id"; + protected static final String CLIENT_DISPLAYNAME = "display-name"; + protected static final String CLASS_STRING = "class-name"; + protected static final String CONNECTION_STRING = "connection-string"; + protected static final String SELECTED = "selected"; + protected static final String CLIENT_TYPE = "client-type"; + + public static class Builder { + private String connectionString; + private String classString; + + // optional parameters + private String displayName = null; + private String id = null; + private boolean selected = true; + private ClientType clientType = null; + + public Builder(String connectionString, String classString) { + if (connectionString==null || classString==null) { + throw new IllegalArgumentException(); + } + this.connectionString = connectionString; + this.classString = classString; + } + + public Builder displayName(String displayName) { + this.displayName = displayName; + return this; + } + + public Builder id(String id) { + this.id = id; + return this; + } + + public Builder selected(boolean selected) { + this.selected = selected; + return this; + } + + public Builder clientType(ClientType clientType) { + this.clientType = clientType; + return this; + } + + public IDMapperClientImpl build() + throws IDMapperException, ClassNotFoundException { + return new IDMapperClientImpl(this); + } + } + + private IDMapperClientImpl(Builder builder) + throws IDMapperException, ClassNotFoundException { + + //Class.forName(classString); + //mapper = BridgeDb.connect(connectionString); + + String defId = builder.id==null?""+clientNo+"-" + +System.currentTimeMillis():builder.id; + + ClientType defClientType = builder.clientType; + if (defClientType==null) { + Class.forName(builder.classString); + mapper = BridgeDb.connect(builder.connectionString); + defClientType = ClientType.getClientType(mapper); + } + + this.id = defId; + this.displayName = builder.displayName; + this.classString = builder.classString; + this.connectionString = builder.connectionString; + this.selected= builder.selected; + this.clientType = defClientType; + + clientNo++; + } + + public String getId() { + return id; + } + + public String getDisplayName() { + return displayName; + } + + public ClientType getClientType() { + return clientType; + } + + public IDMapper getIDMapper() { + if (mapper==null) { + try { + Class.forName(getClassString()); + + ExecutorService executor = Executors.newSingleThreadExecutor(); + executor.execute(new Runnable() { + public void run() { + try { + mapper = BridgeDb.connect(getConnectionString()); + } catch (Exception e) { + e.printStackTrace(); + } + } + }); + + //TODO: how to set waiting time? + if (executor.awaitTermination(5, TimeUnit.SECONDS)) { + executor.shutdown(); + } + + if (mapper == null) { + System.err.println("Failed to connect to " + this.toString()); + return null; + } + + preprocess(mapper); + } catch (Exception e) { + e.printStackTrace(); + return null; + } + } + return mapper; + } + + /** + * set fullname of datasource as syscode if it is null + * in this plugin, fullname represents the datasource + * @param mapper + */ + private static void preprocess(final IDMapper mapper) { + if (mapper==null) + return; + + IDMapperCapabilities caps = mapper.getCapabilities(); + Set<DataSource> dss = new HashSet(); + try { + dss.addAll(caps.getSupportedSrcDataSources()); + dss.addAll(caps.getSupportedTgtDataSources()); + } catch (Exception e) { + e.printStackTrace(); + return; + } + +// for (DataSource ds : dss) { +// if (ds.getFullName()==null) { +// String sysCode = ds.getSystemCode(); +// DataSource.register(sysCode, sysCode); +// } +// } + } + + public String getConnectionString() { + return connectionString; + } + + public void setConnectionString(String connectionString) + throws IDMapperException { + this.connectionString = connectionString; + mapper = null; + } + + public String getClassString() { + return classString; + } + + @Override + public String toString() { + return this.getDisplayName(); + } + + public boolean isSelected() { + return selected; + } + + public void setSelected(boolean selected) { + this.selected = selected; + } +} Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -303,11 +303,11 @@ return props; } - boolean isSelected() { + public boolean isSelected() { return (Boolean)selected.getValue(); } - void setSelected(boolean selected) { + public void setSelected(boolean selected) { this.selected.setValue(selected); props.saveProperties(this.selected); } Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -111,7 +111,7 @@ private static ExecutorService executor = null; - private static int waitSeconds = 1; + private static int waitSeconds = 5; static { // new IDMapperClientManager(); @@ -216,7 +216,7 @@ } else if (line.compareTo(CLIENT_END)==0) { if (classStr!=null && connStr!=null) { try { - IDMapperClient client = new IDMapperClientImplTunables + IDMapperClient client = new IDMapperClientImpl .Builder(connStr, classStr) .displayName(display) .id(clientId) @@ -285,7 +285,7 @@ String connStr = "idmapper-bridgerest:"+BridgeRestUtil.defaultBaseUrl+"/"+newDefaultSpecies; IDMapperClient client; try { - client = new IDMapperClientImplTunables + client = new IDMapperClientImpl .Builder(connStr, classPath) .displayName("BridgeDb("+BridgeRestUtil.defaultBaseUrl+"/"+newDefaultSpecies+")") .selected(true) @@ -455,9 +455,7 @@ changed = selectedClients.remove(client); if (changed) { - if (client instanceof IDMapperClientImplTunables) { - ((IDMapperClientImplTunables)client).setSelected(select); - } + client.setSelected(select); fireIDMapperChange(); } } @@ -521,127 +519,134 @@ } public static void cache() { - if (cacheStatus == CacheStatus.CACHED) - return; + synchronized(cacheStatus) { + if (cacheStatus == CacheStatus.CACHED) + return; - if (cacheStatus == CacheStatus.CACHING) { - if (executor.isTerminated()) { - cacheStatus = CacheStatus.CACHED; + if (cacheStatus == CacheStatus.CACHING) { + if (executor.isTerminated()) { + cacheStatus = CacheStatus.CACHED; + } + return; } - return; + + cacheStatus = CacheStatus.CACHING; } - cacheStatus = CacheStatus.CACHING; - selectedIDMapperStack = new IDMapperStack(); srcTypes = Collections.synchronizedSet(new HashSet<DataSourceWrapper>()); tgtTypes = Collections.synchronizedSet(new HashSet<DataSourceWrapper>()); supportedMapping = Collections.synchronizedSet(new HashSet<List<DataSourceWrapper>>()); - executor = Executors.newCachedThreadPool(); + try { + executor = Executors.newCachedThreadPool(); - for (IDMapperClient client : selectedClients()) { - final IDMapper idMapper = client.getIDMapper(); - if (idMapper==null) - continue; + for (IDMapperClient client : selectedClients()) { + final IDMapper idMapper = client.getIDMapper(); + if (idMapper==null) + continue; - //selectedIDMapperStack - selectedIDMapperStack.addIDMapper(idMapper); + //selectedIDMapperStack + selectedIDMapperStack.addIDMapper(idMapper); - executor.execute(new Runnable() { - public void run() { - IDMapperCapabilities caps = idMapper.getCapabilities(); + executor.execute(new Runnable() { + public void run() { + IDMapperCapabilities caps = idMapper.getCapabilities(); - Set<DataSource> srcs, tgts; - try { - srcs = caps.getSupportedSrcDataSources(); - tgts = caps.getSupportedTgtDataSources(); - } catch (Exception e) { - e.printStackTrace(); - return; - } + Set<DataSource> srcs, tgts; + try { + srcs = caps.getSupportedSrcDataSources(); + tgts = caps.getSupportedTgtDataSources(); + } catch (Exception e) { + e.printStackTrace(); + return; + } - // srcTypes - if (srcs!=null) { - for (DataSource ds : srcs) { - srcTypes.add(DataSourceWrapper.getInstance( - DataSourceUtil.getName(ds), DataSourceWrapper.DsAttr.DATASOURCE)); + // srcTypes + if (srcs!=null) { + for (DataSource ds : srcs) { + srcTypes.add(DataSourceWrapper.getInstance( + DataSourceUtil.getName(ds), DataSourceWrapper.DsAttr.DATASOURCE)); + } } - } - // tgtTypes - if (tgts!=null) { - for (DataSource ds : tgts) { - tgtTypes.add(DataSourceWrapper.getInstance( - DataSourceUtil.getName(ds), DataSourceWrapper.DsAttr.DATASOURCE)); + // tgtTypes + if (tgts!=null) { + for (DataSource ds : tgts) { + tgtTypes.add(DataSourceWrapper.getInstance( + DataSourceUtil.getName(ds), DataSourceWrapper.DsAttr.DATASOURCE)); + } } - } - // mapping from type to type - if (srcs!=null && tgts!=null) { - for (DataSource src : srcs) { - for (DataSource tgt : tgts) { - boolean spt = false; - try { - spt = caps.isMappingSupported(src, tgt); - } catch (Exception e) { - e.printStackTrace(); + // mapping from type to type + if (srcs!=null && tgts!=null) { + for (DataSource src : srcs) { + for (DataSource tgt : tgts) { + boolean spt = false; + try { + spt = caps.isMappingSupported(src, tgt); + } catch (Exception e) { + e.printStackTrace(); + } + if (spt) { + List<DataSourceWrapper> dsws = new ArrayList<DataSourceWrapper>(2); + dsws.add(DataSourceWrapper.getInstance( + DataSourceUtil.getName(src), DataSourceWrapper.DsAttr.DATASOURCE)); + dsws.add(DataSourceWrapper.getInstance( + DataSourceUtil.getName(tgt), DataSourceWrapper.DsAttr.DATASOURCE)); + supportedMapping.add(dsws); + } } - if (spt) { - List<DataSourceWrapper> dsws = new ArrayList<DataSourceWrapper>(2); - dsws.add(DataSourceWrapper.getInstance( - DataSourceUtil.getName(src), DataSourceWrapper.DsAttr.DATASOURCE)); - dsws.add(DataSourceWrapper.getInstance( - DataSourceUtil.getName(tgt), DataSourceWrapper.DsAttr.DATASOURCE)); - supportedMapping.add(dsws); - } } } - } - // AttributeMapper - if (!(idMapper instanceof AttributeMapper)) - return; + // AttributeMapper + if (!(idMapper instanceof AttributeMapper)) + return; - AttributeMapper attrMapper = (AttributeMapper)idMapper; - Set<String> attrs = null; - try { - attrs = attrMapper.getAttributeSet(); - } catch (Exception e) { - e.printStackTrace(); - } + AttributeMapper attrMapper = (AttributeMapper)idMapper; + Set<String> attrs = null; + try { + attrs = attrMapper.getAttributeSet(); + } catch (Exception e) { + e.printStackTrace(); + } - if (attrs==null) - return; - - for (String attr : attrs) { - DataSourceWrapper dsw = DataSourceWrapper.getInstance(attr, DataSourceWrapper.DsAttr.ATTRIBUTE); - if (attrMapper.isFreeAttributeSearchSupported()) { - srcTypes.add(dsw); - if (tgts!=null) { - for (DataSource tgt : tgts) { + if (attrs==null) + return; + + for (String attr : attrs) { + DataSourceWrapper dsw = DataSourceWrapper.getInstance(attr, DataSourceWrapper.DsAttr.ATTRIBUTE); + if (attrMapper.isFreeAttributeSearchSupported()) { + srcTypes.add(dsw); + if (tgts!=null) { + for (DataSource tgt : tgts) { + List<DataSourceWrapper> dsws = new ArrayList<DataSourceWrapper>(2); + dsws.add(dsw); + dsws.add(DataSourceWrapper.getInstance( + tgt.getFullName(), DataSourceWrapper.DsAttr.DATASOURCE)); + supportedMapping.add(dsws); + } + } + } + + tgtTypes.add(dsw); + if (srcs!=null) { + for (DataSource src : srcs) { List<DataSourceWrapper> dsws = new ArrayList<DataSourceWrapper>(2); + dsws.add(DataSourceWrapper.getInstance( + src.getFullName(), DataSourceWrapper.DsAttr.DATASOURCE)); dsws.add(dsw); - dsws.add(DataSourceWrapper.getInstance( - tgt.getFullName(), DataSourceWrapper.DsAttr.DATASOURCE)); supportedMapping.add(dsws); } } } - - tgtTypes.add(dsw); - if (srcs!=null) { - for (DataSource src : srcs) { - List<DataSourceWrapper> dsws = new ArrayList<DataSourceWrapper>(2); - dsws.add(DataSourceWrapper.getInstance( - src.getFullName(), DataSourceWrapper.DsAttr.DATASOURCE)); - dsws.add(dsw); - supportedMapping.add(dsws); - } - } } - } - }); + }); + } + } catch (Exception e) { + e.printStackTrace(); + cacheStatus = CacheStatus.UNCACHED; } } } 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 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -33,7 +33,7 @@ import csplugins.id.mapping.CyThesaurusPlugin; import csplugins.id.mapping.IDMapperClient; -import csplugins.id.mapping.IDMapperClientImplTunables; +import csplugins.id.mapping.IDMapperClientImpl; import csplugins.id.mapping.IDMapperClientManager; import csplugins.id.mapping.ui.IDMappingSourceConfigDialog; import csplugins.id.mapping.ui.CyThesaurusDialog; @@ -292,7 +292,7 @@ displayName = connString; try { - IDMapperClient client = new IDMapperClientImplTunables + IDMapperClient client = new IDMapperClientImpl .Builder(connString, classPath) .displayName(displayName) .build(); Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -39,7 +39,7 @@ import csplugins.id.mapping.CyThesaurusPlugin; import csplugins.id.mapping.FinalStaticValues; import csplugins.id.mapping.IDMapperClient; -import csplugins.id.mapping.IDMapperClientImplTunables; +import csplugins.id.mapping.IDMapperClientImpl; import csplugins.id.mapping.IDMapperClientManager; import csplugins.id.mapping.util.DataSourceUtil; import csplugins.id.mapping.util.DataSourceWrapper; @@ -265,7 +265,7 @@ } else { IDMapperClient client = null; try { - client = new IDMapperClientImplTunables + client = new IDMapperClientImpl .Builder(connStr, classPath) .displayName(display) .build(); Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/FileIDMappingClientConfigDialog.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/FileIDMappingClientConfigDialog.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/FileIDMappingClientConfigDialog.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -36,7 +36,7 @@ package csplugins.id.mapping.ui; import csplugins.id.mapping.IDMapperClient; -import csplugins.id.mapping.IDMapperClientImplTunables; +import csplugins.id.mapping.IDMapperClientImpl; import cytoscape.util.CyFileFilter; import cytoscape.util.FileUtil; @@ -836,7 +836,7 @@ throws IDMapperException, ClassNotFoundException { String url = textFileTextField.getText(); - return new IDMapperClientImplTunables + return new IDMapperClientImpl .Builder(getConnectionString(), "org.bridgedb.file.IDMapperText") .displayName(url) .build(); Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form 2011-11-08 14:28:26 UTC (rev 27429) @@ -123,6 +123,7 @@ </Container> <Container class="javax.swing.JPanel" name="defaultPanel"> <AuxValues> + <AuxValue name="JavaCodeGenerator_InitCodePre" type="java.lang.String" value="defaultPanel.setVisible(false);"/> <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/> <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/> </AuxValues> Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -193,6 +193,8 @@ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5); getContentPane().add(sourceConfPanel, gridBagConstraints); + defaultPanel.setVisible(false); + loadDefaultButton.setText("Load default resources"); loadDefaultButton.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { @@ -241,6 +243,13 @@ private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_closeButtonActionPerformed setVisible(false); this.dispose(); + try { + if (srcTree.isModified()) + IDMapperClientManager.saveCurrentToCytoscapeGlobalProperties(); + } catch (Exception e) { + e.printStackTrace(); + JOptionPane.showMessageDialog(this, "Failed to save the current resources."); + } }//GEN-LAST:event_closeButtonActionPerformed private void saveAsDefaultButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_saveAsDefaultButtonActionPerformed Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/RDBIDMappingClientConfigDialog.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/RDBIDMappingClientConfigDialog.java 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/RDBIDMappingClientConfigDialog.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -36,7 +36,7 @@ package csplugins.id.mapping.ui; import csplugins.id.mapping.IDMapperClient; -import csplugins.id.mapping.IDMapperClientImplTunables; +import csplugins.id.mapping.IDMapperClientImpl; import org.bridgedb.IDMapperException; import org.bridgedb.rdb.IDMapperRdb; @@ -218,7 +218,7 @@ String className = strs[1]; String displayName = strs[2]; - return new IDMapperClientImplTunables + return new IDMapperClientImpl .Builder(connStr, className) .displayName(displayName) .build(); 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 2011-11-08 01:33:05 UTC (rev 27428) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/WebserviceIDMappingClientConfigDialog.java 2011-11-08 14:28:26 UTC (rev 27429) @@ -36,7 +36,7 @@ package csplugins.id.mapping.ui; import csplugins.id.mapping.IDMapperClient; -import csplugins.id.mapping.IDMapperClientImplTunables; +import csplugins.id.mapping.IDMapperClientImpl; import csplugins.id.mapping.util.BridgeRestUtil; import cytoscape.task.Task; @@ -979,7 +979,7 @@ String className = strs[1]; String displayName = strs[2]; - return new IDMapperClientImplTunables + return new IDMapperClientImpl .Builder(connStr, className) .displayName(displayName) .build(); -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
