[Treebase-devel] Fwd: [Treebase-guts] SF.net SVN: treebase:[731] trunk/treebase-web

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Begin forwarded message:

> From: yo...@us...
> Date: July 13, 2010 12:38:00 PM EDT
> To: tre...@li...
> Subject: [Treebase-guts] SF.net SVN: treebase:[731] trunk/treebase-web
>
> 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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