Author: kono
Date: 2009-08-11 13:29:03 -0700 (Tue, 11 Aug 2009)
New Revision: 17773
Added:
csplugins/trunk/ucsd/kono/CPDBClient/build.xml
csplugins/trunk/ucsd/kono/CPDBClient/jar/
csplugins/trunk/ucsd/kono/CPDBClient/jar/cpdbClient.jar
csplugins/trunk/ucsd/kono/CPDBClient/junitLib/
csplugins/trunk/ucsd/kono/CPDBClient/junitLib/junit-4.7.jar
csplugins/trunk/ucsd/kono/CPDBClient/lib/
csplugins/trunk/ucsd/kono/CPDBClient/lib/CPDBClientGenerated.jar
csplugins/trunk/ucsd/kono/CPDBClient/resources/
csplugins/trunk/ucsd/kono/CPDBClient/resources/plugin.props
csplugins/trunk/ucsd/kono/CPDBClient/src/
csplugins/trunk/ucsd/kono/CPDBClient/src/org/
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClient.java
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClientPlugin.java
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/test/
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/test/BasicServiceTest.java
csplugins/trunk/ucsd/kono/CPDBClient/wsdl/
csplugins/trunk/ucsd/kono/CPDBClient/wsdl/CPDB.wsdl
Log:
Start writing skeleton of CPDB Client.
Added: csplugins/trunk/ucsd/kono/CPDBClient/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/CPDBClient/build.xml
(rev 0)
+++ csplugins/trunk/ucsd/kono/CPDBClient/build.xml 2009-08-11 20:29:03 UTC
(rev 17773)
@@ -0,0 +1,88 @@
+<?xml version = "1.0"?>
+<project name="cpdbClient" default="all" basedir=".">
+
+ <property name="src" location="src" />
+ <property name="build" location="build" />
+ <property name="build.compiler" value="modern" />
+ <!-- path to Cytoscape under development (CVS) -->
+ <property name="cylib" location="../cytoscape" />
+ <property name="lib" location="lib" />
+ <property name="testlib" location="junitLib" />
+ <property name="jar" location="jar" />
+ <property name="doc" location="doc" />
+ <property name="projectName" value="cpdbClient" />
+
+ <property name="cytoscape.plugin" value="${lib}/plugins" />
+
+ <path id="classpath">
+ <fileset dir="${cylib}">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${lib}">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${testlib}">
+ <include name="**/*.jar" />
+ </fileset>
+ </path>
+
+ <target name="prepare" depends="clean">
+ <mkdir dir="${build}" />
+ </target>
+
+ <target name="compile" depends="prepare"
+ description="Compile with Cytoscape under development">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac source="1.5" debug="true" deprecation="true"
srcdir="${src}"
+ destdir="${build}">
+ <classpath refid="classpath" />
+ </javac>
+ </target>
+
+ <target name="clean" description="clean up">
+ <!-- Delete the ${build} and ${src} directory trees -->
+ <delete dir="${build}" />
+ <delete dir="${jar}" />
+ </target>
+
+ <target name="jar" depends="compile"
+ description="makes a jar for Cytoscape under development">
+ <mkdir dir="${jar}" />
+ <unzip dest="${build}">
+ <fileset dir="${lib}" includes="*" />
+ </unzip>
+ <copy todir="build/org/cytoscape/webservice/cpdb"
file="resources/plugin.props" />
+
+ <jar jarfile="${jar}/${projectName}.jar">
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
+
value="org.cytoscape.webservice.cpdb.CPDBClientPlugin" />
+ </manifest>
+ <fileset dir="${build}" />
+ </jar>
+ </target>
+
+ <target name="all" depends="jar" />
+
+ <target name="run" depends="jar" description="Run under development">
+ <java classname="cytoscape.CyMain" classpathref="classpath"
fork="true"
+ maxmemory="1g">
+ <arg line="--JLD" />
+ <arg line="${jar}/${projectName}.jar" />
+ <arg line="-vt" />
+ <arg line="5000" />
+ </java>
+ </target>
+
+
+ <!-- Target to Run JavaDoc -->
+ <target name="doc" description="Runs JavaDoc.">
+ <javadoc packagenames="cytoscape.groups.results.*"
sourcepath="src"
+ source="1.5" destdir="doc"
classpathref="classpath_release">
+ <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; />
+ <link href="http://csbi.sourceforge.net/API/"; />
+ <link
href="http://chianti.ucsd.edu/Cyto-2_6_3/javadoc/"; />
+ </javadoc>
+ </target>
+
+</project>
\ No newline at end of file
Added: csplugins/trunk/ucsd/kono/CPDBClient/jar/cpdbClient.jar
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsd/kono/CPDBClient/jar/cpdbClient.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/CPDBClient/junitLib/junit-4.7.jar
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsd/kono/CPDBClient/junitLib/junit-4.7.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/CPDBClient/lib/CPDBClientGenerated.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/CPDBClient/lib/CPDBClientGenerated.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/CPDBClient/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/CPDBClient/resources/plugin.props
(rev 0)
+++ csplugins/trunk/ucsd/kono/CPDBClient/resources/plugin.props 2009-08-11
20:29:03 UTC (rev 17773)
@@ -0,0 +1,34 @@
+#plugin.props
+
+# This props file should be filled out and included in the plugin jar file.
This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=CPDBClient
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=CPDB web service client.
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=0.1
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Network and Attribute I/O
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin, Ex.
http://my-lab-site.org
+projectURL=http://cytoscape.org
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD
+
+# Date this plugin/plugin version was released
+releaseDate=August 11, 2009
Added:
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClient.java
===================================================================
---
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClient.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClient.java
2009-08-11 20:29:03 UTC (rev 17773)
@@ -0,0 +1,133 @@
+package org.cytoscape.webservice.cpdb;
+
+import javax.swing.JPanel;
+
+import soap.cpdb.CPDB;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.CyWebServiceException;
+import cytoscape.data.webservice.NetworkImportWebServiceClient;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientImplWithGUI;
+import cytoscape.data.webservice.WebServiceClientManager.ClientType;
+import cytoscape.layout.Tunable;
+import cytoscape.util.ModulePropertiesImpl;
+import cytoscape.visual.VisualStyle;
+
+/*
+ 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.
+ */
+
+/**
+ * CPDB web service client.
+ *
+ * @author atanas, kono
+ * @version 0.1
+ * @since Cytoscape 2.6.3
+ *
+ */
+public class CPDBClient extends WebServiceClientImplWithGUI<CPDB, JPanel>
+ implements NetworkImportWebServiceClient {
+
+ // Display name of this client.
+ private static final String DISPLAY_NAME = "IntAct Web Service Client";
+
+ // Client ID. This should be unique.
+ private static final String CLIENT_ID = "intact";
+
+ // Instance of this client. This is a singleton.
+ private static WebServiceClient<CPDB> client = new CPDBClient();
+
+ // Visual Style name for the networks generated by this client.
+ private static final String DEF_VS_NAME = "CPDB Style";
+ private VisualStyle defaultVS = null;
+
+ // Attributes.
+ private final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ private final CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
+
+ private void setDescription() {
+ description = "Test";
+ }
+
+ /**
+ * Return instance of this client.
+ *
+ * @return
+ */
+ public static WebServiceClient<CPDB> getClient() {
+ return client;
+ }
+
+ /**
+ * Creates a new IntactClient object.
+ */
+ private CPDBClient() {
+ super(CLIENT_ID, DISPLAY_NAME, new ClientType[] {
ClientType.NETWORK },
+ null, new CPDB(), null);
+ setDescription();
+ // Set properties for this client.
+ setProperty();
+ }
+
+ /**
+ * Set props for this client.
+ */
+ private void setProperty() {
+ props = new ModulePropertiesImpl(clientID, "wsc");
+
+ props.add(new Tunable("max_interactions", "Maximum number of
records",
+ Tunable.INTEGER, new Integer(50000)));
+
+ props.add(new Tunable("timeout", "Timeout (sec.)",
Tunable.INTEGER,
+ new Integer(1200)));
+ // props.add(new Tunable("select_interaction",
+ // "Import only selected interactions",
+ // Tunable.BOOLEAN, new Boolean(false)));
+ }
+
+ @Override
+ public void executeService(CyWebServiceEvent arg0)
+ throws CyWebServiceException {
+ // TODO Auto-generated method stub
+
+ }
+
+ public VisualStyle getDefaultVisualStyle() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Added:
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClientPlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClientPlugin.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/CPDBClientPlugin.java
2009-08-11 20:29:03 UTC (rev 17773)
@@ -0,0 +1,24 @@
+package org.cytoscape.webservice.cpdb;
+
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ * Intact Web Service Client Plugin.<br>
+ *
+ * @author kono
+ * @version 0.5
+ * @since Cytoscape 2.6
+ */
+public class CPDBClientPlugin extends CytoscapePlugin {
+ /**
+ * Register IntAct client to the web service client manager
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public CPDBClientPlugin() throws Exception {
+ // Register this client to the manager.
+ WebServiceClientManager.registerClient(CPDBClient.getClient());
+ }
+}
Added:
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/test/BasicServiceTest.java
===================================================================
---
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/test/BasicServiceTest.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/CPDBClient/src/org/cytoscape/webservice/cpdb/test/BasicServiceTest.java
2009-08-11 20:29:03 UTC (rev 17773)
@@ -0,0 +1,17 @@
+package org.cytoscape.webservice.cpdb.test;
+
+
+import org.junit.After;
+import org.junit.Before;
+
+public class BasicServiceTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+}
Added: csplugins/trunk/ucsd/kono/CPDBClient/wsdl/CPDB.wsdl
===================================================================
--- csplugins/trunk/ucsd/kono/CPDBClient/wsdl/CPDB.wsdl
(rev 0)
+++ csplugins/trunk/ucsd/kono/CPDBClient/wsdl/CPDB.wsdl 2009-08-11 20:29:03 UTC
(rev 17773)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<definitions name="CPDB_CS" targetNamespace="SOAP/CPDB"
+ xmlns:tns="SOAP/CPDB" xmlns="http://schemas.xmlsoap.org/wsdl/";
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema";
xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/";>
+
+ <types>
+ <xsd:schema elementFormDefault="qualified"
targetNamespace="SOAP/CPDB"
+ xmlns:tns="SOAP/CPDB"
xmlns:xsd="http://www.w3.org/2001/XMLSchema";>
+
+ <xsd:element name="evidenceInteractions">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element name="entities"
type="xsd:string"
+ minOccurs="0"
maxOccurs="unbounded" />
+ <xsd:element
name="interactions" type="xsd:string"
+ minOccurs="0"
maxOccurs="unbounded" />
+ <xsd:element
name="exactMatchEntities" type="xsd:boolean"
+ minOccurs="0"
maxOccurs="1" />
+ <xsd:element
name="exactMatchInteractions" type="xsd:boolean"
+ minOccurs="0"
maxOccurs="1" />
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ <xsd:element name="evidenceInteractionsResponse">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element
name="interactionAttributes" type="xsd:string"
+ minOccurs="0"
maxOccurs="unbounded" />
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:element>
+ </xsd:schema>
+ </types>
+
+
+ <message name="evidenceInteractionsRequest">
+ <part name="arg" element="tns:evidenceInteractions" />
+ </message>
+ <message name="evidenceInteractionsResponse">
+ <part name="res" element="tns:evidenceInteractionsResponse" />
+ </message>
+
+
+ <!-- port -->
+ <portType name="CPDBportTp">
+ <operation name="evidenceInteractions">
+ <input name="evidenceInteractions_input"
message="tns:evidenceInteractionsRequest" />
+ <output name="evidenceInteractions_output"
message="tns:evidenceInteractionsResponse" />
+ </operation>
+ </portType>
+
+
+ <!-- binding -->
+ <binding name="CPDB_WS_http_binding" type="tns:CPDBportTp">
+ <soap:binding style="document"
+ transport="http://schemas.xmlsoap.org/soap/http"; />
+ <operation name="evidenceInteractions">
+ <soap:operation
soapAction="SOAP/CPDB#evidenceInteractions" />
+ <input name="evidenceInteractions_input">
+ <soap:body
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/";
+ use="literal" />
+ </input>
+ <output name="evidenceInteractions_output">
+ <soap:body
encodingStyle="http://schemas.xmlsoap.org/soap/encoding/";
+ use="literal" />
+ </output>
+ </operation>
+ </binding>
+
+
+ <!-- service -->
+ <service name="CPDB">
+ <port name="CPDBport" binding="tns:CPDB_WS_http_binding">
+ <soap:address
location="http://cpdb.molgen.mpg.de/csplugin"; />
+ </port>
+ </service>
+
+</definitions>
--~--~---------~--~----~------------~-------~--~----~
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
-~----------~----~----~----~------~----~------~--~---
