Author: mes
Date: 2011-09-15 14:13:46 -0700 (Thu, 15 Sep 2011)
New Revision: 26824
Added:
core3/impl/branches/no-spring/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/CyActivator.java
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
Removed:
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml
Modified:
core3/impl/branches/no-spring/table-import-impl/osgi.bnd
core3/impl/branches/no-spring/table-import-impl/pom.xml
Log:
removed use of spring
Modified: core3/impl/branches/no-spring/table-import-impl/osgi.bnd
===================================================================
--- core3/impl/branches/no-spring/table-import-impl/osgi.bnd 2011-09-15
21:00:24 UTC (rev 26823)
+++ core3/impl/branches/no-spring/table-import-impl/osgi.bnd 2011-09-15
21:13:46 UTC (rev 26824)
@@ -4,3 +4,4 @@
Import-Package: *
Private-Package: ${bundle.namespace}.internal.*
+Bundle-Activator: ${bundle.namespace}.internal.CyActivator
Modified: core3/impl/branches/no-spring/table-import-impl/pom.xml
===================================================================
--- core3/impl/branches/no-spring/table-import-impl/pom.xml 2011-09-15
21:00:24 UTC (rev 26823)
+++ core3/impl/branches/no-spring/table-import-impl/pom.xml 2011-09-15
21:13:46 UTC (rev 26824)
@@ -222,11 +222,6 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
- <artifactId>service-api</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
<artifactId>event-api</artifactId>
<type>test-jar</type>
<scope>test</scope>
Added:
core3/impl/branches/no-spring/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/CyActivator.java
(rev 0)
+++
core3/impl/branches/no-spring/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/CyActivator.java
2011-09-15 21:13:46 UTC (rev 26824)
@@ -0,0 +1,117 @@
+
+
+
+
+package org.cytoscape.tableimport.internal;
+
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.property.bookmark.BookmarksUtil;
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.work.swing.GUITaskManager;
+import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.util.swing.FileUtil;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.util.swing.OpenBrowser;
+
+import org.cytoscape.tableimport.internal.ImportAttributeTableReaderFactory;
+import static org.cytoscape.io.DataCategory.*;
+import org.cytoscape.tableimport.internal.ImportNetworkTableReaderFactory;
+import
org.cytoscape.tableimport.internal.task.ImportOntologyAndAnnotationAction;
+import org.cytoscape.io.BasicCyFileFilter;
+import
org.cytoscape.tableimport.internal.reader.ontology.OBONetworkReaderFactory;
+
+import org.cytoscape.io.read.InputStreamTaskFactory;
+import org.cytoscape.application.swing.CyAction;
+
+
+import org.osgi.framework.BundleContext;
+
+import org.cytoscape.service.util.AbstractCyActivator;
+
+import java.util.Properties;
+
+
+
+public class CyActivator extends AbstractCyActivator {
+ public CyActivator() {
+ super();
+ }
+
+
+ public void start(BundleContext bc) {
+
+ CyLayoutAlgorithmManager cyLayoutsServiceRef =
getService(bc,CyLayoutAlgorithmManager.class);
+ CyNetworkFactory cyNetworkFactoryServiceRef =
getService(bc,CyNetworkFactory.class);
+ CyNetworkViewFactory cyNetworkViewFactoryServiceRef =
getService(bc,CyNetworkViewFactory.class);
+ CySwingApplication cytoscapeDesktopService =
getService(bc,CySwingApplication.class);
+ CyApplicationManager cyApplicationManagerRef =
getService(bc,CyApplicationManager.class);
+ CyNetworkManager cyNetworkManagerServiceRef =
getService(bc,CyNetworkManager.class);
+ CyTableManager cyTableManagerServiceRef =
getService(bc,CyTableManager.class);
+ GUITaskManager guiTaskManagerServiceRef =
getService(bc,GUITaskManager.class);
+ CyProperty bookmarkServiceRef =
getService(bc,CyProperty.class,"(cyPropertyName=bookmarks)");
+ BookmarksUtil bookmarksUtilServiceRef =
getService(bc,BookmarksUtil.class);
+ CyProperty cytoscapePropertiesServiceRef =
getService(bc,CyProperty.class,"(cyPropertyName=cytoscape3.props)");
+ FileUtil fileUtilService = getService(bc,FileUtil.class);
+ OpenBrowser openBrowserService =
getService(bc,OpenBrowser.class);
+ CyNetworkNaming cyNetworkNamingServiceRef =
getService(bc,CyNetworkNaming.class);
+ CyNetworkViewManager cyNetworkViewManagerServiceRef =
getService(bc,CyNetworkViewManager.class);
+ CyTableFactory cyDataTableFactoryServiceRef =
getService(bc,CyTableFactory.class);
+ StreamUtil streamUtilService = getService(bc,StreamUtil.class);
+ CyEventHelper cyEventHelperRef =
getService(bc,CyEventHelper.class);
+
+ BasicCyFileFilter attrsTableFilter_txt = new
BasicCyFileFilter(new String[]{"csv","tsv"}, new
String[]{"text/plain","text/tab-separated-values"},"Comma or Tab Separated
Value Files",TABLE,streamUtilService);
+ BasicCyFileFilter attrsTableFilter_xls = new
BasicCyFileFilter(new String[]{"xls","xlsx"}, new
String[]{"application/excel"},"Excel Files",TABLE,streamUtilService);
+ BasicCyFileFilter oboFilter = new BasicCyFileFilter(new
String[]{"obo"}, new String[]{"text/obo"},"OBO
Files",NETWORK,streamUtilService);
+ OBONetworkReaderFactory oboReaderFactory = new
OBONetworkReaderFactory(oboFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyEventHelperRef);
+ ImportAttributeTableReaderFactory
importAttributeTableReaderFactory_txt = new
ImportAttributeTableReaderFactory(attrsTableFilter_txt,cytoscapeDesktopService,cyApplicationManagerRef,cyNetworkManagerServiceRef,bookmarkServiceRef,bookmarksUtilServiceRef,guiTaskManagerServiceRef,cytoscapePropertiesServiceRef,cyTableManagerServiceRef,fileUtilService,openBrowserService,cyDataTableFactoryServiceRef,".txt");
+ ImportAttributeTableReaderFactory
importAttributeTableReaderFactory_xls = new
ImportAttributeTableReaderFactory(attrsTableFilter_xls,cytoscapeDesktopService,cyApplicationManagerRef,cyNetworkManagerServiceRef,bookmarkServiceRef,bookmarksUtilServiceRef,guiTaskManagerServiceRef,cytoscapePropertiesServiceRef,cyTableManagerServiceRef,fileUtilService,openBrowserService,cyDataTableFactoryServiceRef,".xls");
+ ImportOntologyAndAnnotationAction ontologyAction = new
ImportOntologyAndAnnotationAction(cyApplicationManagerRef,bookmarkServiceRef,bookmarksUtilServiceRef,guiTaskManagerServiceRef,oboReaderFactory,cyNetworkManagerServiceRef,cyDataTableFactoryServiceRef,cyTableManagerServiceRef);
+ BasicCyFileFilter networkTableFilter_txt = new
BasicCyFileFilter(new String[]{"csv","tsv"}, new
String[]{"text/plain","text/tab-separated-values"},"Comma or Tab Separated
Value Files",NETWORK,streamUtilService);
+ BasicCyFileFilter networkTableFilter_xls = new
BasicCyFileFilter(new String[]{"xls","xlsx"}, new
String[]{"application/excel"},"Excel Files",NETWORK,streamUtilService);
+ ImportNetworkTableReaderFactory
importNetworkTableReaderFactory_txt = new
ImportNetworkTableReaderFactory(networkTableFilter_txt,cytoscapeDesktopService,cyApplicationManagerRef,cyNetworkManagerServiceRef,guiTaskManagerServiceRef,cytoscapePropertiesServiceRef,fileUtilService,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,".txt",cyNetworkNamingServiceRef,cyNetworkViewManagerServiceRef,cyTableManagerServiceRef);
+ ImportNetworkTableReaderFactory
importNetworkTableReaderFactory_xls = new
ImportNetworkTableReaderFactory(networkTableFilter_xls,cytoscapeDesktopService,cyApplicationManagerRef,cyNetworkManagerServiceRef,guiTaskManagerServiceRef,cytoscapePropertiesServiceRef,fileUtilService,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,".xls",cyNetworkNamingServiceRef,cyNetworkViewManagerServiceRef,cyTableManagerServiceRef);
+
+
+ Properties importAttributeTableReaderFactory_xlsProps = new
Properties();
+
importAttributeTableReaderFactory_xlsProps.setProperty("serviceType","importAttributeTableTaskFactory");
+
importAttributeTableReaderFactory_xlsProps.setProperty("readerDescription","Attribute
Table file reader");
+
importAttributeTableReaderFactory_xlsProps.setProperty("readerId","attributeTableReader");
+
registerService(bc,importAttributeTableReaderFactory_xls,InputStreamTaskFactory.class,
importAttributeTableReaderFactory_xlsProps);
+
+ Properties importAttributeTableReaderFactory_txtProps = new
Properties();
+
importAttributeTableReaderFactory_txtProps.setProperty("serviceType","importAttributeTableTaskFactory");
+
importAttributeTableReaderFactory_txtProps.setProperty("readerDescription","Attribute
Table file reader");
+
importAttributeTableReaderFactory_txtProps.setProperty("readerId","attributeTableReader_txt");
+
registerService(bc,importAttributeTableReaderFactory_txt,InputStreamTaskFactory.class,
importAttributeTableReaderFactory_txtProps);
+
+ Properties oboReaderFactoryProps = new Properties();
+
oboReaderFactoryProps.setProperty("serviceType","oboReaderFactory");
+ oboReaderFactoryProps.setProperty("readerDescription","Open
Biomedical Ontology (OBO) file reader");
+ oboReaderFactoryProps.setProperty("readerId","oboReader");
+
registerService(bc,oboReaderFactory,InputStreamTaskFactory.class,
oboReaderFactoryProps);
+ registerService(bc,ontologyAction,CyAction.class, new
Properties());
+
+ Properties importNetworkTableReaderFactory_txtProps = new
Properties();
+
importNetworkTableReaderFactory_txtProps.setProperty("serviceType","importNetworkTableTaskFactory");
+
importNetworkTableReaderFactory_txtProps.setProperty("readerDescription","Network
Table file reader");
+
importNetworkTableReaderFactory_txtProps.setProperty("readerId","networkTableReader_txt");
+
registerService(bc,importNetworkTableReaderFactory_txt,InputStreamTaskFactory.class,
importNetworkTableReaderFactory_txtProps);
+
+ Properties importNetworkTableReaderFactory_xlsProps = new
Properties();
+
importNetworkTableReaderFactory_xlsProps.setProperty("serviceType","importNetworkTableTaskFactory");
+
importNetworkTableReaderFactory_xlsProps.setProperty("readerDescription","Network
Table file reader");
+
importNetworkTableReaderFactory_xlsProps.setProperty("readerId","networkTableReader_xls");
+
registerService(bc,importNetworkTableReaderFactory_xls,InputStreamTaskFactory.class,
importNetworkTableReaderFactory_xlsProps);
+
+ }
+}
+
Deleted:
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-15 21:00:24 UTC (rev 26823)
+++
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-15 21:13:46 UTC (rev 26824)
@@ -1,105 +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-3.0.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="cyLayoutsServiceRef"
interface="org.cytoscape.view.layout.CyLayoutAlgorithmManager" />
- <osgi:reference id="cyNetworkFactoryServiceRef"
interface="org.cytoscape.model.CyNetworkFactory" />
- <osgi:reference id="cyNetworkViewFactoryServiceRef"
interface="org.cytoscape.view.model.CyNetworkViewFactory" />
-
- <osgi:reference id="cytoscapeDesktopService"
- interface="org.cytoscape.application.swing.CySwingApplication"
/>
- <osgi:reference id="cyApplicationManagerRef"
interface="org.cytoscape.application.CyApplicationManager" />
- <osgi:reference id="cyNetworkManagerServiceRef"
interface="org.cytoscape.model.CyNetworkManager" />
- <osgi:reference id="cyTableManagerServiceRef"
interface="org.cytoscape.model.CyTableManager" />
- <osgi:reference id="guiTaskManagerServiceRef"
interface="org.cytoscape.work.swing.GUITaskManager" />
- <osgi:reference id="bookmarkServiceRef"
interface="org.cytoscape.property.CyProperty"
- filter="(cyPropertyName=bookmarks)" />
-
- <osgi:reference id="bookmarksUtilServiceRef"
- interface="org.cytoscape.property.bookmark.BookmarksUtil" />
-
- <osgi:reference id="cytoscapePropertiesServiceRef"
- interface="org.cytoscape.property.CyProperty"
- filter="(cyPropertyName=cytoscape3.props)" />
-
- <osgi:reference id="fileUtilService"
interface="org.cytoscape.util.swing.FileUtil" />
- <osgi:reference id="openBrowserService"
interface="org.cytoscape.util.swing.OpenBrowser" />
-
- <osgi:reference id="cyNetworkNamingServiceRef"
interface="org.cytoscape.session.CyNetworkNaming" />
- <osgi:reference id="cyNetworkViewManagerServiceRef"
interface="org.cytoscape.view.model.CyNetworkViewManager" />
-
- <osgi:reference id="cyDataTableFactoryServiceRef"
interface="org.cytoscape.model.CyTableFactory" />
-
- <osgi:reference id="streamUtilService"
interface="org.cytoscape.io.util.StreamUtil" />
-
- <osgi:reference id="cyEventHelperRef"
interface="org.cytoscape.event.CyEventHelper" />
-
- <!--
- This code registers the bean we just created "sampleTaskFactory" as an
- OSGi service of a particular type
(org.cytoscape.task.NetworkTaskFactory).
- By registering your bean as a service, it will become available to all
- users interested in services of that particular type.
- The service properties are metadata that can be used elsewhere in the
- system to identify and otherwise control how the service gets use
- (like determining which menu to put the service in).
- -->
-
- <osgi:service id="importAttributeTableReaderFactoryService_xls"
ref="importAttributeTableReaderFactory_xls"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType"
value="importAttributeTableTaskFactory" />
- <entry key="readerId" value="attributeTableReader" />
- <entry key="readerDescription" value="Attribute Table
file reader" />
- </osgi:service-properties>
- </osgi:service>
-
- <osgi:service id="importAttributeTableReaderFactoryService_txt"
ref="importAttributeTableReaderFactory_txt"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType"
value="importAttributeTableTaskFactory" />
- <entry key="readerId" value="attributeTableReader_txt"
/>
- <entry key="readerDescription" value="Attribute Table
file reader" />
- </osgi:service-properties>
- </osgi:service>
-
- <!-- Export OBO support as a regular network reader factory -->
- <osgi:service id="oboReaderFactoryService" ref="oboReaderFactory"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType" value="oboReaderFactory" />
- <entry key="readerId" value="oboReader" />
- <entry key="readerDescription" value="Open Biomedical
Ontology (OBO) file reader" />
- </osgi:service-properties>
- </osgi:service>
-
- <osgi:service id="ontologyActionService" ref="ontologyAction"
- interface="org.cytoscape.application.swing.CyAction" />
-
-
- <osgi:service id="importNetworkTableReaderFactoryService_txt"
ref="importNetworkTableReaderFactory_txt"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType"
value="importNetworkTableTaskFactory" />
- <entry key="readerId" value="networkTableReader_txt" />
- <entry key="readerDescription" value="Network Table
file reader" />
- </osgi:service-properties>
- </osgi:service>
-
- <osgi:service id="importNetworkTableReaderFactoryService_xls"
ref="importNetworkTableReaderFactory_xls"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType"
value="importNetworkTableTaskFactory" />
- <entry key="readerId" value="networkTableReader_xls" />
- <entry key="readerDescription" value="Network Table
file reader" />
- </osgi:service-properties>
- </osgi:service>
-
-</beans>
Copied:
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml)
===================================================================
---
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2011-09-15 21:13:46 UTC (rev 26824)
@@ -0,0 +1,105 @@
+<?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-3.0.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="cyLayoutsServiceRef"
interface="org.cytoscape.view.layout.CyLayoutAlgorithmManager" />
+ <osgi:reference id="cyNetworkFactoryServiceRef"
interface="org.cytoscape.model.CyNetworkFactory" />
+ <osgi:reference id="cyNetworkViewFactoryServiceRef"
interface="org.cytoscape.view.model.CyNetworkViewFactory" />
+
+ <osgi:reference id="cytoscapeDesktopService"
+ interface="org.cytoscape.application.swing.CySwingApplication"
/>
+ <osgi:reference id="cyApplicationManagerRef"
interface="org.cytoscape.application.CyApplicationManager" />
+ <osgi:reference id="cyNetworkManagerServiceRef"
interface="org.cytoscape.model.CyNetworkManager" />
+ <osgi:reference id="cyTableManagerServiceRef"
interface="org.cytoscape.model.CyTableManager" />
+ <osgi:reference id="guiTaskManagerServiceRef"
interface="org.cytoscape.work.swing.GUITaskManager" />
+ <osgi:reference id="bookmarkServiceRef"
interface="org.cytoscape.property.CyProperty"
+ filter="(cyPropertyName=bookmarks)" />
+
+ <osgi:reference id="bookmarksUtilServiceRef"
+ interface="org.cytoscape.property.bookmark.BookmarksUtil" />
+
+ <osgi:reference id="cytoscapePropertiesServiceRef"
+ interface="org.cytoscape.property.CyProperty"
+ filter="(cyPropertyName=cytoscape3.props)" />
+
+ <osgi:reference id="fileUtilService"
interface="org.cytoscape.util.swing.FileUtil" />
+ <osgi:reference id="openBrowserService"
interface="org.cytoscape.util.swing.OpenBrowser" />
+
+ <osgi:reference id="cyNetworkNamingServiceRef"
interface="org.cytoscape.session.CyNetworkNaming" />
+ <osgi:reference id="cyNetworkViewManagerServiceRef"
interface="org.cytoscape.view.model.CyNetworkViewManager" />
+
+ <osgi:reference id="cyDataTableFactoryServiceRef"
interface="org.cytoscape.model.CyTableFactory" />
+
+ <osgi:reference id="streamUtilService"
interface="org.cytoscape.io.util.StreamUtil" />
+
+ <osgi:reference id="cyEventHelperRef"
interface="org.cytoscape.event.CyEventHelper" />
+
+ <!--
+ This code registers the bean we just created "sampleTaskFactory" as an
+ OSGi service of a particular type
(org.cytoscape.task.NetworkTaskFactory).
+ By registering your bean as a service, it will become available to all
+ users interested in services of that particular type.
+ The service properties are metadata that can be used elsewhere in the
+ system to identify and otherwise control how the service gets use
+ (like determining which menu to put the service in).
+ -->
+
+ <osgi:service id="importAttributeTableReaderFactoryService_xls"
ref="importAttributeTableReaderFactory_xls"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType"
value="importAttributeTableTaskFactory" />
+ <entry key="readerId" value="attributeTableReader" />
+ <entry key="readerDescription" value="Attribute Table
file reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="importAttributeTableReaderFactoryService_txt"
ref="importAttributeTableReaderFactory_txt"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType"
value="importAttributeTableTaskFactory" />
+ <entry key="readerId" value="attributeTableReader_txt"
/>
+ <entry key="readerDescription" value="Attribute Table
file reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <!-- Export OBO support as a regular network reader factory -->
+ <osgi:service id="oboReaderFactoryService" ref="oboReaderFactory"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType" value="oboReaderFactory" />
+ <entry key="readerId" value="oboReader" />
+ <entry key="readerDescription" value="Open Biomedical
Ontology (OBO) file reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="ontologyActionService" ref="ontologyAction"
+ interface="org.cytoscape.application.swing.CyAction" />
+
+
+ <osgi:service id="importNetworkTableReaderFactoryService_txt"
ref="importNetworkTableReaderFactory_txt"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType"
value="importNetworkTableTaskFactory" />
+ <entry key="readerId" value="networkTableReader_txt" />
+ <entry key="readerDescription" value="Network Table
file reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="importNetworkTableReaderFactoryService_xls"
ref="importNetworkTableReaderFactory_xls"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType"
value="importNetworkTableTaskFactory" />
+ <entry key="readerId" value="networkTableReader_xls" />
+ <entry key="readerDescription" value="Network Table
file reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+</beans>
Deleted:
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-15 21:00:24 UTC (rev 26823)
+++
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-15 21:13:46 UTC (rev 26824)
@@ -1,200 +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:context="http://www.springframework.org/schema/context";
- xsi:schemaLocation="
- http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
- http://www.springframework.org/schema/context
-
http://www.springframework.org/schema/context/spring-context-3.0.xsd";>
-
- <!-- This simply constructs an object (or bean) called
"sampleTaskFactory"
- of type org.example.internal.SampleTaskFactory. The name
"sampleTaskFactory"
- is used to identify this particular object in this and the
bundle-context-osgi.xml
- file. -->
-
- <bean id="attrsTableFilter_txt"
class="org.cytoscape.io.BasicCyFileFilter">
- <constructor-arg index="0">
- <set>
- <value>csv</value>
- <value>tsv</value>
- </set>
- </constructor-arg>
- <constructor-arg index="1">
- <set>
- <value>text/plain</value>
- <value>text/tab-separated-values</value>
- </set>
- </constructor-arg>
- <constructor-arg value="Any text file" />
- <constructor-arg type="org.cytoscape.io.DataCategory"
- value="TABLE" />
- <constructor-arg ref="streamUtilService" />
- </bean>
-
- <bean id="attrsTableFilter_xls"
class="org.cytoscape.io.BasicCyFileFilter">
- <constructor-arg index="0">
- <set>
- <value>xls</value>
- <value>xlsx</value>
- </set>
- </constructor-arg>
- <constructor-arg index="1">
- <set>
- <value>application/excel</value>
- </set>
- </constructor-arg>
- <constructor-arg value="Any text file" />
- <constructor-arg type="org.cytoscape.io.DataCategory"
- value="TABLE" />
- <constructor-arg ref="streamUtilService" />
- </bean>
-
-
- <!-- Filter for OBO Flat File -->
- <bean id="oboFilter" class="org.cytoscape.io.BasicCyFileFilter">
- <constructor-arg index="0">
- <set>
- <value>obo</value>
- </set>
- </constructor-arg>
- <constructor-arg index="1">
- <set>
- <value>text/obo</value>
- <!-- content types should be exact - don't add
possible matches! <value>text/plain</value> -->
- </set>
- </constructor-arg>
- <constructor-arg value="OBO files" />
- <constructor-arg type="org.cytoscape.io.DataCategory"
- value="NETWORK" />
- <constructor-arg type="org.cytoscape.io.util.StreamUtil"
- ref="streamUtilService" />
- </bean>
-
- <bean id="oboReaderFactory"
-
class="org.cytoscape.tableimport.internal.reader.ontology.OBONetworkReaderFactory">
- <constructor-arg ref="oboFilter" />
- <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
- <constructor-arg ref="cyNetworkFactoryServiceRef" />
- <constructor-arg ref="cyEventHelperRef" />
- </bean>
-
-
- <bean id="importAttributeTableReaderFactory_txt"
-
class="org.cytoscape.tableimport.internal.ImportAttributeTableReaderFactory">
- <constructor-arg ref="attrsTableFilter_txt" />
- <constructor-arg ref="cytoscapeDesktopService" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="bookmarkServiceRef" />
- <constructor-arg ref="bookmarksUtilServiceRef" />
- <constructor-arg ref="guiTaskManagerServiceRef" />
- <constructor-arg ref="cytoscapePropertiesServiceRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
- <constructor-arg ref="fileUtilService" />
- <constructor-arg ref="openBrowserService" />
- <constructor-arg ref="cyDataTableFactoryServiceRef" />
- <constructor-arg value=".txt" />
- </bean>
-
-
- <bean id="importAttributeTableReaderFactory_xls"
-
class="org.cytoscape.tableimport.internal.ImportAttributeTableReaderFactory">
- <constructor-arg ref="attrsTableFilter_xls" />
- <constructor-arg ref="cytoscapeDesktopService" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="bookmarkServiceRef" />
- <constructor-arg ref="bookmarksUtilServiceRef" />
- <constructor-arg ref="guiTaskManagerServiceRef" />
- <constructor-arg ref="cytoscapePropertiesServiceRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
- <constructor-arg ref="fileUtilService" />
- <constructor-arg ref="openBrowserService" />
- <constructor-arg ref="cyDataTableFactoryServiceRef" />
- <constructor-arg value=".xls" />
- </bean>
-
-
- <bean id="ontologyAction"
class="org.cytoscape.tableimport.internal.task.ImportOntologyAndAnnotationAction">
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="bookmarkServiceRef" />
- <constructor-arg ref="bookmarksUtilServiceRef" />
- <constructor-arg ref="guiTaskManagerServiceRef" />
- <constructor-arg ref="oboReaderFactory" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="cyDataTableFactoryServiceRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
- </bean>
-
- <bean id="networkTableFilter_txt"
class="org.cytoscape.io.BasicCyFileFilter">
- <constructor-arg index="0">
- <set>
- <value>csv</value>
- <value>tsv</value>
- </set>
- </constructor-arg>
- <constructor-arg index="1">
- <set>
- <value>text/plain</value>
- </set>
- </constructor-arg>
- <constructor-arg value="csv,tsv files" />
- <constructor-arg type="org.cytoscape.io.DataCategory"
- value="NETWORK" />
- <constructor-arg type="org.cytoscape.io.util.StreamUtil">
- <ref bean="streamUtilService" />
- </constructor-arg>
- </bean>
-
- <bean id="networkTableFilter_xls"
class="org.cytoscape.io.BasicCyFileFilter">
- <constructor-arg index="0">
- <set>
- <value>xls</value>
- <value>xlsx</value>
- </set>
- </constructor-arg>
- <constructor-arg index="1">
- <set>
- <value>application/excel</value>
- </set>
- </constructor-arg>
- <constructor-arg value="Excel file" />
- <constructor-arg type="org.cytoscape.io.DataCategory"
- value="NETWORK" />
- <constructor-arg ref="streamUtilService" />
- </bean>
-
- <bean id="importNetworkTableReaderFactory_txt"
-
class="org.cytoscape.tableimport.internal.ImportNetworkTableReaderFactory">
- <constructor-arg ref="networkTableFilter_txt" />
- <constructor-arg ref="cytoscapeDesktopService" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="guiTaskManagerServiceRef" />
- <constructor-arg ref="cytoscapePropertiesServiceRef" />
- <constructor-arg ref="fileUtilService" />
- <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
- <constructor-arg ref="cyNetworkFactoryServiceRef" />
- <constructor-arg value=".txt" />
- <constructor-arg ref="cyNetworkNamingServiceRef" />
- <constructor-arg ref="cyNetworkViewManagerServiceRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
- </bean>
-
- <bean id="importNetworkTableReaderFactory_xls"
-
class="org.cytoscape.tableimport.internal.ImportNetworkTableReaderFactory">
- <constructor-arg ref="networkTableFilter_xls" />
- <constructor-arg ref="cytoscapeDesktopService" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="guiTaskManagerServiceRef" />
- <constructor-arg ref="cytoscapePropertiesServiceRef" />
- <constructor-arg ref="fileUtilService" />
- <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
- <constructor-arg ref="cyNetworkFactoryServiceRef" />
- <constructor-arg value=".xls" />
- <constructor-arg ref="cyNetworkNamingServiceRef" />
- <constructor-arg ref="cyNetworkViewManagerServiceRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
- </bean>
-</beans>
Copied:
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml)
===================================================================
---
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/table-import-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
2011-09-15 21:13:46 UTC (rev 26824)
@@ -0,0 +1,200 @@
+<?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:context="http://www.springframework.org/schema/context";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
+ http://www.springframework.org/schema/context
+
http://www.springframework.org/schema/context/spring-context-3.0.xsd";>
+
+ <!-- This simply constructs an object (or bean) called
"sampleTaskFactory"
+ of type org.example.internal.SampleTaskFactory. The name
"sampleTaskFactory"
+ is used to identify this particular object in this and the
bundle-context-osgi.xml
+ file. -->
+
+ <bean id="attrsTableFilter_txt"
class="org.cytoscape.io.BasicCyFileFilter">
+ <constructor-arg index="0">
+ <set>
+ <value>csv</value>
+ <value>tsv</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg index="1">
+ <set>
+ <value>text/plain</value>
+ <value>text/tab-separated-values</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg value="Any text file" />
+ <constructor-arg type="org.cytoscape.io.DataCategory"
+ value="TABLE" />
+ <constructor-arg ref="streamUtilService" />
+ </bean>
+
+ <bean id="attrsTableFilter_xls"
class="org.cytoscape.io.BasicCyFileFilter">
+ <constructor-arg index="0">
+ <set>
+ <value>xls</value>
+ <value>xlsx</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg index="1">
+ <set>
+ <value>application/excel</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg value="Any text file" />
+ <constructor-arg type="org.cytoscape.io.DataCategory"
+ value="TABLE" />
+ <constructor-arg ref="streamUtilService" />
+ </bean>
+
+
+ <!-- Filter for OBO Flat File -->
+ <bean id="oboFilter" class="org.cytoscape.io.BasicCyFileFilter">
+ <constructor-arg index="0">
+ <set>
+ <value>obo</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg index="1">
+ <set>
+ <value>text/obo</value>
+ <!-- content types should be exact - don't add
possible matches! <value>text/plain</value> -->
+ </set>
+ </constructor-arg>
+ <constructor-arg value="OBO files" />
+ <constructor-arg type="org.cytoscape.io.DataCategory"
+ value="NETWORK" />
+ <constructor-arg type="org.cytoscape.io.util.StreamUtil"
+ ref="streamUtilService" />
+ </bean>
+
+ <bean id="oboReaderFactory"
+
class="org.cytoscape.tableimport.internal.reader.ontology.OBONetworkReaderFactory">
+ <constructor-arg ref="oboFilter" />
+ <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
+ <constructor-arg ref="cyNetworkFactoryServiceRef" />
+ <constructor-arg ref="cyEventHelperRef" />
+ </bean>
+
+
+ <bean id="importAttributeTableReaderFactory_txt"
+
class="org.cytoscape.tableimport.internal.ImportAttributeTableReaderFactory">
+ <constructor-arg ref="attrsTableFilter_txt" />
+ <constructor-arg ref="cytoscapeDesktopService" />
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="bookmarkServiceRef" />
+ <constructor-arg ref="bookmarksUtilServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
+ <constructor-arg ref="cytoscapePropertiesServiceRef" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
+ <constructor-arg ref="fileUtilService" />
+ <constructor-arg ref="openBrowserService" />
+ <constructor-arg ref="cyDataTableFactoryServiceRef" />
+ <constructor-arg value=".txt" />
+ </bean>
+
+
+ <bean id="importAttributeTableReaderFactory_xls"
+
class="org.cytoscape.tableimport.internal.ImportAttributeTableReaderFactory">
+ <constructor-arg ref="attrsTableFilter_xls" />
+ <constructor-arg ref="cytoscapeDesktopService" />
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="bookmarkServiceRef" />
+ <constructor-arg ref="bookmarksUtilServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
+ <constructor-arg ref="cytoscapePropertiesServiceRef" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
+ <constructor-arg ref="fileUtilService" />
+ <constructor-arg ref="openBrowserService" />
+ <constructor-arg ref="cyDataTableFactoryServiceRef" />
+ <constructor-arg value=".xls" />
+ </bean>
+
+
+ <bean id="ontologyAction"
class="org.cytoscape.tableimport.internal.task.ImportOntologyAndAnnotationAction">
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="bookmarkServiceRef" />
+ <constructor-arg ref="bookmarksUtilServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
+ <constructor-arg ref="oboReaderFactory" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="cyDataTableFactoryServiceRef" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
+ </bean>
+
+ <bean id="networkTableFilter_txt"
class="org.cytoscape.io.BasicCyFileFilter">
+ <constructor-arg index="0">
+ <set>
+ <value>csv</value>
+ <value>tsv</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg index="1">
+ <set>
+ <value>text/plain</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg value="csv,tsv files" />
+ <constructor-arg type="org.cytoscape.io.DataCategory"
+ value="NETWORK" />
+ <constructor-arg type="org.cytoscape.io.util.StreamUtil">
+ <ref bean="streamUtilService" />
+ </constructor-arg>
+ </bean>
+
+ <bean id="networkTableFilter_xls"
class="org.cytoscape.io.BasicCyFileFilter">
+ <constructor-arg index="0">
+ <set>
+ <value>xls</value>
+ <value>xlsx</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg index="1">
+ <set>
+ <value>application/excel</value>
+ </set>
+ </constructor-arg>
+ <constructor-arg value="Excel file" />
+ <constructor-arg type="org.cytoscape.io.DataCategory"
+ value="NETWORK" />
+ <constructor-arg ref="streamUtilService" />
+ </bean>
+
+ <bean id="importNetworkTableReaderFactory_txt"
+
class="org.cytoscape.tableimport.internal.ImportNetworkTableReaderFactory">
+ <constructor-arg ref="networkTableFilter_txt" />
+ <constructor-arg ref="cytoscapeDesktopService" />
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
+ <constructor-arg ref="cytoscapePropertiesServiceRef" />
+ <constructor-arg ref="fileUtilService" />
+ <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
+ <constructor-arg ref="cyNetworkFactoryServiceRef" />
+ <constructor-arg value=".txt" />
+ <constructor-arg ref="cyNetworkNamingServiceRef" />
+ <constructor-arg ref="cyNetworkViewManagerServiceRef" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
+ </bean>
+
+ <bean id="importNetworkTableReaderFactory_xls"
+
class="org.cytoscape.tableimport.internal.ImportNetworkTableReaderFactory">
+ <constructor-arg ref="networkTableFilter_xls" />
+ <constructor-arg ref="cytoscapeDesktopService" />
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
+ <constructor-arg ref="cytoscapePropertiesServiceRef" />
+ <constructor-arg ref="fileUtilService" />
+ <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
+ <constructor-arg ref="cyNetworkFactoryServiceRef" />
+ <constructor-arg value=".xls" />
+ <constructor-arg ref="cyNetworkNamingServiceRef" />
+ <constructor-arg ref="cyNetworkViewManagerServiceRef" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
+ </bean>
+</beans>
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