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[Treebase-guts] SF.net SVN: treebase:[731] trunk/treebase-web
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From: <yo...@us...> - 2010-07-13 16:38:10
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Revision: 731
http://treebase.svn.sourceforge.net/treebase/?rev=731&view=rev
Author: youjun
Date: 2010-07-13 16:38:00 +0000 (Tue, 13 Jul 2010)
Log Message:
-----------
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2010-07-07 19:32:38 UTC (rev 730)
+++ trunk/treebase-web/pom.xml 2010-07-13 16:38:00 UTC (rev 731)
@@ -21,6 +21,9 @@
</resource>
</resources>
<finalName>treebase-web</finalName>
+
+
+
<plugins>
<!-- Ant Task plugin-->
@@ -80,26 +83,20 @@
<repository>
<id>org.tuckey.urlrewritefilter</id>
<url>http://repository.jboss.org/maven2/org/tuckey/urlrewritefilter/</url>
- </repository>
-
+ </repository>
+ <repository>
+ <id>java.net</id>
+ <url>http://download.java.net/maven/2</url>
+ </repository>
+
+
</repositories>
+
- <pluginRepositories>
- <pluginRepository>
- <id>Maven Snapshots</id>
- <url>http://snapshots.maven.codehaus.org/maven2</url>
- <snapshots>
- <enabled>true</enabled>
- </snapshots>
- <releases>
- <enabled>false</enabled>
- </releases>
- </pluginRepository>
- </pluginRepositories>
- <dependencies>
-
-
+
+
+ <dependencies>
<dependency>
<groupId>org.nexml.model</groupId>
@@ -341,5 +338,36 @@
<artifactId>velocity-tools-view</artifactId>
<version>1.1</version>
</dependency>
- </dependencies>
+
+<dependency>
+<groupId>com.sun.jersey</groupId>
+<artifactId>jersey-client</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>com.sun.jersey</groupId>
+<artifactId>jersey-server</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>com.sun.jersey.contribs</groupId>
+<artifactId>jersey-multipart</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>com.sun.jersey</groupId>
+<artifactId>jersey-bundle</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>javax.ws.rs</groupId>
+<artifactId>jsr311-api</artifactId>
+<version>1.0</version>
+</dependency>
+</dependencies>
+
</project>
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java 2010-07-13 16:38:00 UTC (rev 731)
@@ -0,0 +1,69 @@
+package org.cipres.treebase.web.util;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.zip.GZIPInputStream;
+
+import org.apache.tools.tar.TarEntry;
+import org.apache.tools.tar.TarInputStream;
+
+public class UnTarTool
+{
+
+ public static void unTarGz(File file,File outDir) throws IOException{
+
+ TarInputStream tarIn = null;
+
+ try{
+
+ tarIn = new TarInputStream(new GZIPInputStream(
+ new BufferedInputStream(new FileInputStream(file))),
+ 1024);
+
+ TarEntry entry = null;
+ //tarIn.getNextEntry();
+ //File outputDir = new File(outDir, "myBag");
+ //outputDir.mkdirs();
+ while( (entry = tarIn.getNextEntry()) != null ){
+ File f = new File(outDir,entry.getName());
+ if(entry.isDirectory()){
+ f.mkdirs();
+ }else{
+ f.getParentFile().mkdirs();
+ f.createNewFile();
+ OutputStream out = null;
+ try{
+ out = new FileOutputStream(f);
+ int length = 0;
+ byte[] b = new byte[1024];
+ while((length = tarIn.read(b)) != -1){
+ out.write(b, 0, length);
+ }
+
+ }catch(IOException ex){
+ throw ex;
+ }finally{
+ if(out!=null)
+ out.close();
+ }
+ }
+ }
+ }catch(IOException ex){
+ throw ex;
+ } finally{
+ try{
+ if(tarIn != null){
+ tarIn.close();
+ }
+ }catch(IOException ex){
+ throw ex;
+ }
+ }
+
+ }
+
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java 2010-07-13 16:38:00 UTC (rev 731)
@@ -0,0 +1,104 @@
+package org.cipres.treebase.web.webservices;
+
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+import com.sun.jersey.multipart.*;
+import javax.servlet.http.HttpServletRequest;
+import javax.ws.rs.Consumes;
+//import javax.ws.rs.POST;
+import javax.ws.rs.PUT;
+import javax.ws.rs.Path;
+import javax.ws.rs.core.Context;
+
+import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.web.util.UnTarTool;
+
+
+
+@Path("/dryadImport")
+
+public class DryadImportor {
+
+ @Context
+ HttpServletRequest httpRequest;
+
+ @PUT
+ //@POST
+ //@GET
+
+ @Consumes("multipart/mixed")
+
+public String processMultiparts(MultiPart multiPart) {
+
+ String ip = httpRequest.getRemoteAddr();
+ if(!AllowIP.isAllowIP(ip))return "not authorized";
+
+ BodyPartEntity bpe = (BodyPartEntity) multiPart.getBodyParts().get(0).getEntity();
+ File unzipFold;
+ String systemTime;
+
+ do{
+ systemTime = "" + System.currentTimeMillis();
+ String uploadDir = httpRequest.getSession().getServletContext()
+ .getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
+ + TreebaseUtil.FILESEP + systemTime;
+ unzipFold = new File(uploadDir);
+ }while(unzipFold.exists());
+
+
+ File zipfile = new File(unzipFold,"data.tar.gz");
+
+ try {
+ unzipFold.mkdirs();
+ zipfile.createNewFile();
+ InputStream in = bpe.getInputStream();
+ OutputStream out=new FileOutputStream(zipfile);
+
+ byte[] buf = new byte[1024];
+ int len;
+ while ((len = in.read(buf)) > 0){
+ out.write(buf, 0, len);
+ }
+ in.close();
+ out.close();
+ UnTarTool.unTarGz(zipfile,unzipFold);
+
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ StringWriter sw = new StringWriter();
+ e.printStackTrace(new PrintWriter(sw));
+ return sw.getBuffer().toString();
+ }
+ String[] baseURL=httpRequest.getRequestURL().toString().split("handshaking");
+ String importURL= baseURL[0] + "login.jsp?importKey=" + systemTime;
+
+ return importURL;
+
+ }
+
+}
+
+class AllowIP{
+ private static final String dryad1 = "152.1.24.8";
+ private static final String dryad2 = "152.3.105.16";
+ private static final String yale1 = "130.132.27.141";
+ private static final String yale2 = "130.132.27.212";
+
+ static boolean isAllowIP(String ip){
+
+ if (ip.compareTo(dryad1)==0) return true;
+ if (ip.compareTo(dryad2)==0) return true;
+ if (ip.compareTo(yale1)==0)return true;
+ if (ip.compareTo(yale2)==0)return true;
+
+ return false;
+ }
+
+}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-07-07 19:32:38 UTC (rev 730)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-07-13 16:38:00 UTC (rev 731)
@@ -120,13 +120,67 @@
<!-- ========================================================== -->
<filter-mapping>
<filter-name>securityFilter</filter-name>
- <url-pattern>/*</url-pattern>
+ <url-pattern>/*</url-pattern>
</filter-mapping>
- <filter-mapping>
+
+ <filter-mapping>
<filter-name>sitemesh</filter-name>
- <url-pattern>/*</url-pattern>
+ <url-pattern>*.html</url-pattern>
<dispatcher>REQUEST</dispatcher>
<dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>*.jsp</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>*.htm</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>*.rdf</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/phylows/*</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/top/*</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/services/*</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>hibernateFilter</filter-name>
+ <url-pattern>*.html</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>hibernateFilter</filter-name>
@@ -197,8 +251,22 @@
</servlet-class>
</servlet>
-
+ <!-- ========================================================== -->
+ <!-- Processed by Jersey -->
+ <!-- ========================================================== -->
+ <servlet>
+ <servlet-name>HandshakingServlet</servlet-name>
+ <servlet-class>
+ com.sun.jersey.spi.container.servlet.ServletContainer
+ </servlet-class>
+ <init-param>
+ <param-name>com.sun.jersey.config.property.packages</param-name>
+ <param-value>org.cipres.treebase.web.webservices</param-value>
+ </init-param>
+ <load-on-startup>1</load-on-startup>
+ </servlet>
+
<!-- ========================================================== -->
<!-- url pattern that will be processed by DispatcherServlet -->
<!-- ========================================================== -->
@@ -239,6 +307,14 @@
<servlet-mapping>
<servlet-name>CXFServlet</servlet-name>
<url-pattern>/services/*</url-pattern>
+ </servlet-mapping>
+
+ <!-- ========================================================== -->
+ <!-- url pattern that will be processed by CXFServlet -->
+ <!-- ========================================================== -->
+ <servlet-mapping>
+ <servlet-name>HandshakingServlet</servlet-name>
+ <url-pattern>/handshaking/*</url-pattern>
</servlet-mapping>
<!-- ========================================================== -->
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