Author: mes
Date: 2011-09-15 13:00:16 -0700 (Thu, 15 Sep 2011)
New Revision: 26818
Added:
core3/impl/branches/no-spring/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
Removed:
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml
Modified:
core3/impl/branches/no-spring/psi-mi-impl/osgi.bnd
core3/impl/branches/no-spring/psi-mi-impl/pom.xml
Log:
removed use of spring
Modified: core3/impl/branches/no-spring/psi-mi-impl/osgi.bnd
===================================================================
--- core3/impl/branches/no-spring/psi-mi-impl/osgi.bnd 2011-09-15 19:55:30 UTC
(rev 26817)
+++ core3/impl/branches/no-spring/psi-mi-impl/osgi.bnd 2011-09-15 20:00:16 UTC
(rev 26818)
@@ -1,4 +1,4 @@
-Spring-Context: META-INF/spring/*.xml
+Bundle-Activator: ${bundle.namespace}.internal.CyActivator
Private-Package: ${bundle.namespace}.internal.*
Export-Package:
!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${pom.version}"
-Import-Package: com.sun.xml.internal.bind,*
\ No newline at end of file
+Import-Package: com.sun.xml.internal.bind,*
Modified: core3/impl/branches/no-spring/psi-mi-impl/pom.xml
===================================================================
--- core3/impl/branches/no-spring/psi-mi-impl/pom.xml 2011-09-15 19:55:30 UTC
(rev 26817)
+++ core3/impl/branches/no-spring/psi-mi-impl/pom.xml 2011-09-15 20:00:16 UTC
(rev 26818)
@@ -102,11 +102,6 @@
</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/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
(rev 0)
+++
core3/impl/branches/no-spring/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
2011-09-15 20:00:16 UTC (rev 26818)
@@ -0,0 +1,63 @@
+
+package org.cytoscape.psi_mi.internal;
+
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+
+import org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkViewTaskFactory;
+import org.cytoscape.psi_mi.internal.plugin.PsiMiTabReaderFactory;
+import org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter;
+import static org.cytoscape.psi_mi.internal.plugin.SchemaVersion.*;
+import org.cytoscape.psi_mi.internal.plugin.PsiMiTabCyFileFilter;
+import org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkWriterFactory;
+
+import org.cytoscape.io.write.CyNetworkViewWriterFactory;
+import org.cytoscape.io.read.InputStreamTaskFactory;
+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);
+ StreamUtil streamUtilRef = getService(bc,StreamUtil.class);
+
+ PsiMiCyFileFilter psiMiFilter = new PsiMiCyFileFilter("PSI-MI
files (*.xml)",streamUtilRef);
+ PsiMiCyFileFilter psiMi1Filter = new PsiMiCyFileFilter("PSI-MI
Level 1",streamUtilRef);
+ PsiMiCyFileFilter psiMi25Filter = new PsiMiCyFileFilter("PSI-MI
Level 2.5",streamUtilRef);
+ PsiMiTabCyFileFilter psiMiTabFilter = new
PsiMiTabCyFileFilter();
+ PsiMiNetworkViewTaskFactory psiMiNetworkViewTaskFactory = new
PsiMiNetworkViewTaskFactory(psiMiFilter,cyNetworkFactoryServiceRef,cyNetworkViewFactoryServiceRef,cyLayoutsServiceRef);
+ PsiMiNetworkWriterFactory psiMi1NetworkViewWriterFactory = new
PsiMiNetworkWriterFactory(LEVEL_1,psiMi1Filter);
+ PsiMiNetworkWriterFactory psiMi25NetworkViewWriterFactory = new
PsiMiNetworkWriterFactory(LEVEL_2_5,psiMi25Filter);
+ PsiMiTabReaderFactory psiMiTabReaderFactory = new
PsiMiTabReaderFactory(psiMiTabFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyLayoutsServiceRef);
+
+
+ Properties psiMiNetworkViewTaskFactoryProps = new Properties();
+
psiMiNetworkViewTaskFactoryProps.setProperty("serviceType","psiMiNetworkViewTaskFactory");
+
psiMiNetworkViewTaskFactoryProps.setProperty("readerDescription","PSI-MI Level
1/2.5 file reader");
+
psiMiNetworkViewTaskFactoryProps.setProperty("readerId","psiMiNetworkViewReader");
+
registerService(bc,psiMiNetworkViewTaskFactory,InputStreamTaskFactory.class,
psiMiNetworkViewTaskFactoryProps);
+
+ Properties psiMiTabReaderFactoryProps = new Properties();
+
psiMiTabReaderFactoryProps.setProperty("serviceType","psiMiTabReaderFactory");
+
psiMiTabReaderFactoryProps.setProperty("readerDescription","PSI-MI tab file
reader");
+
psiMiTabReaderFactoryProps.setProperty("readerId","psiMiTabReader");
+
registerService(bc,psiMiTabReaderFactory,InputStreamTaskFactory.class,
psiMiTabReaderFactoryProps);
+
registerService(bc,psiMi1NetworkViewWriterFactory,CyNetworkViewWriterFactory.class,
new Properties());
+
registerService(bc,psiMi25NetworkViewWriterFactory,CyNetworkViewWriterFactory.class,
new Properties());
+
+ }
+}
+
Deleted:
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-15 19:55:30 UTC (rev 26817)
+++
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-15 20:00:16 UTC (rev 26818)
@@ -1,47 +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 OSGi 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="streamUtilRef"
- interface="org.cytoscape.io.util.StreamUtil" />
-
- <osgi:service id="psiNetworkViewReaderFactoryService"
ref="psiMiNetworkViewTaskFactory"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType"
value="psiMiNetworkViewTaskFactory" />
- <entry key="readerId" value="psiMiNetworkViewReader" />
- <entry key="readerDescription" value="PSI-MI Level
1/2.5 file reader" />
- </osgi:service-properties>
- </osgi:service>
-
- <osgi:service id="psiMiTabReaderFactoryService"
ref="psiMiTabReaderFactory"
- interface="org.cytoscape.io.read.InputStreamTaskFactory">
- <osgi:service-properties>
- <entry key="serviceType" value="psiMiTabReaderFactory"
/>
- <entry key="readerId" value="psiMiTabReader" />
- <entry key="readerDescription" value="PSI-MI tab file
reader" />
- </osgi:service-properties>
- </osgi:service>
-
- <osgi:service id="psiMi1NetworkViewWriterFactoryService"
ref="psiMi1NetworkViewWriterFactory"
- interface="org.cytoscape.io.write.CyNetworkViewWriterFactory">
- </osgi:service>
-
- <osgi:service id="psiMi25NetworkViewWriterFactoryService"
ref="psiMi25NetworkViewWriterFactory"
- interface="org.cytoscape.io.write.CyNetworkViewWriterFactory">
- </osgi:service>
-</beans>
Copied:
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml)
===================================================================
---
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2011-09-15 20:00:16 UTC (rev 26818)
@@ -0,0 +1,47 @@
+<?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 OSGi 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="streamUtilRef"
+ interface="org.cytoscape.io.util.StreamUtil" />
+
+ <osgi:service id="psiNetworkViewReaderFactoryService"
ref="psiMiNetworkViewTaskFactory"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType"
value="psiMiNetworkViewTaskFactory" />
+ <entry key="readerId" value="psiMiNetworkViewReader" />
+ <entry key="readerDescription" value="PSI-MI Level
1/2.5 file reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="psiMiTabReaderFactoryService"
ref="psiMiTabReaderFactory"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory">
+ <osgi:service-properties>
+ <entry key="serviceType" value="psiMiTabReaderFactory"
/>
+ <entry key="readerId" value="psiMiTabReader" />
+ <entry key="readerDescription" value="PSI-MI tab file
reader" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="psiMi1NetworkViewWriterFactoryService"
ref="psiMi1NetworkViewWriterFactory"
+ interface="org.cytoscape.io.write.CyNetworkViewWriterFactory">
+ </osgi:service>
+
+ <osgi:service id="psiMi25NetworkViewWriterFactoryService"
ref="psiMi25NetworkViewWriterFactory"
+ interface="org.cytoscape.io.write.CyNetworkViewWriterFactory">
+ </osgi:service>
+</beans>
Deleted:
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-15 19:55:30 UTC (rev 26817)
+++
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-15 20:00:16 UTC (rev 26818)
@@ -1,64 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans";
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:aop="http://www.springframework.org/schema/aop";
- xmlns:context="http://www.springframework.org/schema/context";
- xmlns:lang="http://www.springframework.org/schema/lang";
xmlns:osgi="http://www.springframework.org/schema/osgi";
- xmlns:util="http://www.springframework.org/schema/util";
- xsi:schemaLocation="
- http://www.springframework.org/schema/beans
-
http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
- http://www.springframework.org/schema/aop
-
http://www.springframework.org/schema/aop/spring-aop-3.0.xsd
- http://www.springframework.org/schema/context
-
http://www.springframework.org/schema/context/spring-context-3.0.xsd
- http://www.springframework.org/schema/util
-
http://www.springframework.org/schema/util/spring-util-3.0.xsd
- http://www.springframework.org/schema/lang
-
http://www.springframework.org/schema/lang/spring-lang-3.0.xsd
- http://www.springframework.org/schema/osgi
-
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
- default-lazy-init="false">
-
- <context:annotation-config />
-
- <bean id="psiMiFilter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter">
- <constructor-arg value="PSI-MI files (*.xml)" />
- <constructor-arg ref="streamUtilRef" />
- </bean>
-
- <bean id="psiMi1Filter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter">
- <constructor-arg value="PSI-MI Level 1" />
- <constructor-arg ref="streamUtilRef" />
- </bean>
-
- <bean id="psiMi25Filter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter">
- <constructor-arg value="PSI-MI Level 2.5" />
- <constructor-arg ref="streamUtilRef" />
- </bean>
-
- <bean id="psiMiTabFilter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiTabCyFileFilter" />
-
- <bean id="psiMiNetworkViewTaskFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkViewTaskFactory">
- <constructor-arg ref="psiMiFilter" />
- <constructor-arg ref="cyNetworkFactoryServiceRef" />
- <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
- <constructor-arg ref="cyLayoutsServiceRef" />
- </bean>
-
- <bean id="psiMi1NetworkViewWriterFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkWriterFactory">
- <constructor-arg
type="org.cytoscape.psi_mi.internal.plugin.SchemaVersion" value="LEVEL_1" />
- <constructor-arg ref="psiMi1Filter"/>
- </bean>
-
- <bean id="psiMi25NetworkViewWriterFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkWriterFactory">
- <constructor-arg
type="org.cytoscape.psi_mi.internal.plugin.SchemaVersion" value="LEVEL_2_5" />
- <constructor-arg ref="psiMi25Filter"/>
- </bean>
-
- <bean id="psiMiTabReaderFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiTabReaderFactory">
- <constructor-arg ref="psiMiTabFilter" />
- <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
- <constructor-arg ref="cyNetworkFactoryServiceRef" />
- <constructor-arg ref="cyLayoutsServiceRef" />
- </bean>
-</beans>
Copied:
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml)
===================================================================
---
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/psi-mi-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
2011-09-15 20:00:16 UTC (rev 26818)
@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:aop="http://www.springframework.org/schema/aop";
+ xmlns:context="http://www.springframework.org/schema/context";
+ xmlns:lang="http://www.springframework.org/schema/lang";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xmlns:util="http://www.springframework.org/schema/util";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+
http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
+ http://www.springframework.org/schema/aop
+
http://www.springframework.org/schema/aop/spring-aop-3.0.xsd
+ http://www.springframework.org/schema/context
+
http://www.springframework.org/schema/context/spring-context-3.0.xsd
+ http://www.springframework.org/schema/util
+
http://www.springframework.org/schema/util/spring-util-3.0.xsd
+ http://www.springframework.org/schema/lang
+
http://www.springframework.org/schema/lang/spring-lang-3.0.xsd
+ http://www.springframework.org/schema/osgi
+
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+ <context:annotation-config />
+
+ <bean id="psiMiFilter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter">
+ <constructor-arg value="PSI-MI files (*.xml)" />
+ <constructor-arg ref="streamUtilRef" />
+ </bean>
+
+ <bean id="psiMi1Filter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter">
+ <constructor-arg value="PSI-MI Level 1" />
+ <constructor-arg ref="streamUtilRef" />
+ </bean>
+
+ <bean id="psiMi25Filter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter">
+ <constructor-arg value="PSI-MI Level 2.5" />
+ <constructor-arg ref="streamUtilRef" />
+ </bean>
+
+ <bean id="psiMiTabFilter"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiTabCyFileFilter" />
+
+ <bean id="psiMiNetworkViewTaskFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkViewTaskFactory">
+ <constructor-arg ref="psiMiFilter" />
+ <constructor-arg ref="cyNetworkFactoryServiceRef" />
+ <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
+ <constructor-arg ref="cyLayoutsServiceRef" />
+ </bean>
+
+ <bean id="psiMi1NetworkViewWriterFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkWriterFactory">
+ <constructor-arg
type="org.cytoscape.psi_mi.internal.plugin.SchemaVersion" value="LEVEL_1" />
+ <constructor-arg ref="psiMi1Filter"/>
+ </bean>
+
+ <bean id="psiMi25NetworkViewWriterFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkWriterFactory">
+ <constructor-arg
type="org.cytoscape.psi_mi.internal.plugin.SchemaVersion" value="LEVEL_2_5" />
+ <constructor-arg ref="psiMi25Filter"/>
+ </bean>
+
+ <bean id="psiMiTabReaderFactory"
class="org.cytoscape.psi_mi.internal.plugin.PsiMiTabReaderFactory">
+ <constructor-arg ref="psiMiTabFilter" />
+ <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
+ <constructor-arg ref="cyNetworkFactoryServiceRef" />
+ <constructor-arg ref="cyLayoutsServiceRef" />
+ </bean>
+</beans>
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