Author: jgao
Date: 2011-10-10 13:50:23 -0700 (Mon, 10 Oct 2011)
New Revision: 27115
Added:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceUtil.java
Modified:
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.bio.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.rdb.construct.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.rdb.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.biomart.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.bridgerest.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.cronos.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.picr.jar
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.synergizer.jar
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/CyThesaurusDialog.form
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/SourceAttributeSelectionTable.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/TargetAttributeSelectionTable.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceWrapper.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/XrefWrapper.java
Log:
CyThesaurus: new bridgedb libs and bug fixes
Modified: csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.bio.jar
===================================================================
(Binary files differ)
Modified: csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.jar
===================================================================
(Binary files differ)
Modified: csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.rdb.construct.jar
===================================================================
(Binary files differ)
Modified: csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.rdb.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.biomart.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.bridgerest.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.cronos.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.picr.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/jgao/IDMapping/lib/org.bridgedb.webservice.synergizer.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -270,12 +270,12 @@
return;
}
- for (DataSource ds : dss) {
- if (ds.getFullName()==null) {
- String sysCode = ds.getSystemCode();
- DataSource.register(sysCode, sysCode);
- }
- }
+// for (DataSource ds : dss) {
+// if (ds.getFullName()==null) {
+// String sysCode = ds.getSystemCode();
+// DataSource.register(sysCode, sysCode);
+// }
+// }
}
public String getConnectionString() {
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -36,6 +36,7 @@
package csplugins.id.mapping;
import csplugins.id.mapping.util.BridgeRestUtil;
+import csplugins.id.mapping.util.DataSourceUtil;
import csplugins.id.mapping.util.DataSourceWrapper;
import cytoscape.CytoscapeInit;
@@ -562,7 +563,7 @@
if (srcs!=null) {
for (DataSource ds : srcs) {
srcTypes.add(DataSourceWrapper.getInstance(
- ds.getFullName(),
DataSourceWrapper.DsAttr.DATASOURCE));
+ DataSourceUtil.getName(ds),
DataSourceWrapper.DsAttr.DATASOURCE));
}
}
@@ -570,7 +571,7 @@
if (tgts!=null) {
for (DataSource ds : tgts) {
tgtTypes.add(DataSourceWrapper.getInstance(
- ds.getFullName(),
DataSourceWrapper.DsAttr.DATASOURCE));
+ DataSourceUtil.getName(ds),
DataSourceWrapper.DsAttr.DATASOURCE));
}
}
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
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -38,6 +38,7 @@
import csplugins.id.mapping.ui.IDMappingSourceConfigDialog;
import csplugins.id.mapping.ui.CyThesaurusDialog;
import csplugins.id.mapping.AttributeBasedIDMappingImpl;
+import csplugins.id.mapping.util.DataSourceUtil;
import csplugins.id.mapping.util.DataSourceWrapper;
import csplugins.id.mapping.util.IDMapperWrapper;
import csplugins.id.mapping.util.XrefWrapper;
@@ -771,7 +772,7 @@
Set<DataSource> dss = DataSourcePatterns.getDataSourceMatches(id);
dss.retainAll(selectedDss);
for (DataSource ds : dss)
- types.add(ds.getFullName());
+ types.add(DataSourceUtil.getName(ds));
}
result.addResult(types);
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
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -41,6 +41,7 @@
import csplugins.id.mapping.IDMapperClient;
import csplugins.id.mapping.IDMapperClientImplTunables;
import csplugins.id.mapping.IDMapperClientManager;
+import csplugins.id.mapping.util.DataSourceUtil;
import csplugins.id.mapping.util.DataSourceWrapper;
import csplugins.id.mapping.ui.CyThesaurusDialog;
@@ -401,13 +402,13 @@
Set<String> srcTypes = new HashSet();
for(DataSource ds : srcDataSources) {
- srcTypes.add(ds.getFullName());
+ srcTypes.add(DataSourceUtil.getName(ds));
}
content.put(SOURCE_ID_TYPE, srcTypes);
Set<String> tgtTypes = new HashSet();
for(DataSource ds : tgtDataSources) {
- tgtTypes.add(ds.getFullName());
+ tgtTypes.add(DataSourceUtil.getName(ds));
}
content.put(TARGET_ID_TYPE, tgtTypes);
@@ -477,7 +478,7 @@
for (String id : srcIDs) {
Set<DataSource> dss = DataSourcePatterns.getDataSourceMatches(id);
for (DataSource ds : dss)
- types.add(ds.getFullName());
+ types.add(DataSourceUtil.getName(ds));
}
Map content = new HashMap();
@@ -627,9 +628,9 @@
} else {
Set<String> supportedSrcTypes = new
HashSet(srcDataSources.size());
for (DataSource ds : srcDataSources) {
- String fullName = ds.getFullName();
+ String fullName = DataSourceUtil.getName(ds);
if (fullName!=null) {
- supportedSrcTypes.add(ds.getFullName());
+ supportedSrcTypes.add(DataSourceUtil.getName(ds));
} else {
// TODO: how to deal?
}
@@ -637,9 +638,9 @@
Set<String> supportedTgtTypes = new
HashSet(tgtDataSources.size());
for (DataSource ds : tgtDataSources) {
- String fullName = ds.getFullName();
+ String fullName = DataSourceUtil.getName(ds);
if (fullName!=null) {
- supportedTgtTypes.add(ds.getFullName());
+ supportedTgtTypes.add(DataSourceUtil.getName(ds));
} else {
// TODO: how to deal?
}
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.form
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.form
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.form
2011-10-10 20:50:23 UTC (rev 27115)
@@ -293,9 +293,7 @@
<SubComponents>
<Component class="javax.swing.JButton" name="rightButton">
<Properties>
- <Property name="icon" type="javax.swing.Icon"
editor="org.netbeans.modules.form.editors2.IconEditor">
- <Image iconType="3" name="/images/right16.gif"/>
- </Property>
+ <Property name="text" type="java.lang.String" value=">"/>
<Property name="enabled" type="boolean" value="false"/>
</Properties>
<AuxValues>
@@ -304,9 +302,7 @@
</Component>
<Component class="javax.swing.JButton" name="leftButton">
<Properties>
- <Property name="icon" type="javax.swing.Icon"
editor="org.netbeans.modules.form.editors2.IconEditor">
- <Image iconType="3" name="/images/left16.gif"/>
- </Property>
+ <Property name="text" type="java.lang.String" value="<"/>
<Property name="enabled" type="boolean" value="false"/>
</Properties>
<AuxValues>
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -298,7 +298,7 @@
lrButtonPanel.setLayout(new java.awt.GridLayout(0, 1, 0, 2));
- rightButton.setIcon(new
javax.swing.ImageIcon(getClass().getResource("/images/right16.gif"))); // NOI18N
+ rightButton.setText(">");
rightButton.setEnabled(false);
rightButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
@@ -333,7 +333,7 @@
});
lrButtonPanel.add(rightButton);
- leftButton.setIcon(new
javax.swing.ImageIcon(getClass().getResource("/images/left16.gif"))); // NOI18N
+ leftButton.setText("<");
leftButton.setEnabled(false);
leftButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/SourceAttributeSelectionTable.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/SourceAttributeSelectionTable.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/SourceAttributeSelectionTable.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -41,6 +41,7 @@
import cytoscape.data.CyAttributes;
import csplugins.id.mapping.IDMapperClientManager;
+import csplugins.id.mapping.util.DataSourceUtil;
import csplugins.id.mapping.util.DataSourceWrapper;
import giny.model.Node;
@@ -239,7 +240,7 @@
for (String id : srcIds) {
Set<DataSource> dss = DataSourcePatterns.getDataSourceMatches(id);
for (DataSource ds : dss) {
- DataSourceWrapper dsw =
DataSourceWrapper.getInstance(ds.getFullName(),
+ DataSourceWrapper dsw =
DataSourceWrapper.getInstance(DataSourceUtil.getName(ds),
DataSourceWrapper.DsAttr.DATASOURCE, false);
if (dsw!=null && supportedIDType.contains(dsw)) {
result.add(dsw);
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/TargetAttributeSelectionTable.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/TargetAttributeSelectionTable.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/TargetAttributeSelectionTable.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -234,6 +234,9 @@
if (attr.length()==0) {
DataSourceWrapper dsw = (DataSourceWrapper)idTypeComboBoxes
.get(row).getSelectedItem();
+ if (dsw==null) {
+ System.err.println();
+ }
attr = dsw.toString();
if (usedName.contains(attr)) {
Added:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceUtil.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceUtil.java
(rev 0)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceUtil.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -0,0 +1,55 @@
+/*
+ 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 org.bridgedb.DataSource;
+
+/**
+ *
+ * @author jgao
+ */
+public final class DataSourceUtil {
+ private DataSourceUtil() {}
+
+ public static String getName(DataSource ds) {
+ if (ds==null) {
+ return null;
+ }
+
+ String name = ds.getFullName();
+ return name!=null ? name : ds.getSystemCode();
+ }
+}
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceWrapper.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceWrapper.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/DataSourceWrapper.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -100,6 +100,9 @@
attributeWrappers.put(value, wrapper);
}
}
+
+ if (wrapper==null)
+ return null;
return wrapper;
}
@@ -123,6 +126,8 @@
}
public int compareTo(DataSourceWrapper dsw) {
+ if(dsw==null)
+ return 1;
if (da != dsw.da)
return da==DsAttr.DATASOURCE?-1:1;
return value.compareTo(dsw.value);
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/XrefWrapper.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/XrefWrapper.java
2011-10-08 21:09:00 UTC (rev 27114)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/util/XrefWrapper.java
2011-10-10 20:50:23 UTC (rev 27115)
@@ -48,7 +48,7 @@
public XrefWrapper(final Xref xref) {
this(xref.getId(),DataSourceWrapper.getInstance(
- xref.getDataSource().getFullName(),
+ DataSourceUtil.getName(xref.getDataSource()),
DataSourceWrapper.DsAttr.DATASOURCE));
}
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