The Annozilla project is designed to view and create annotations associated with a web page, as defined by the W3C Annotea project. The idea is to store annotations as RDF on a server, using XPointer (or at least XPointer-like constructs) to identify the region of the document being annotated. The intention of Annozilla is to use Mozilla's native facilities to manipulate annotation data - its built-in RDF handling to parse the annotations, and nsIXmlHttpRequest to submit data when creating annotations..
In this example: firefox opened the NCBI home page (right side). Once the page is loaded, annozilla fetches the bookmarks about NCBI from connotea (top left). Double clicking in the annotations makes annozilla download the body of those bookmarks (bottom left).
The JAVA servlet I wrote is available at :
But wait, there is a problem: For "security reasons" Annozilla does not use the "GET" parameters in an URL (I really understand that). So when the following URL is submited:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14870871
Annozilla ignores all the parameters and inserts the comments for:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
which is really less interesting !!!... Anyway, this was still a nice to write and it was proof of concept on how to use the connotea API.
update: 2010-08-12: source code
/*
Copyright (c) 2006 Pierre Lindenbaum PhD
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
``Software''), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.
The name of the authors when specified in the source files shall be
kept unmodified.
THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL 4XT.ORG BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
$Id: $
$Author: $
$Revision: $
$Date: $
$Locker: $
$RCSfile: $
$Source: $
$State: $
$Name: $
$Log: $
*************************************************************************/
package org.lindenb.annotea.server;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.io.StreamTokenizer;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.MalformedURLException;
import java.net.Socket;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import java.security.MessageDigest;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Iterator;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.Result;
import javax.xml.transform.Source;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.w3c.dom.CDATASection;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.Text;
import org.xml.sax.SAXException;
import com.oreilly.servlet.Base64Decoder;
/**
* @author lindenb
* http://islande:8080/annotea/Annotea
*/
public class AnnoteaServer extends HttpServlet
{
/**
* serialVersionUID
*/
private static final long serialVersionUID = 1L;
/** flag for debugging on/off */
private static boolean DEBUG=false;
//static declaration of xml namespaces
static public final String RDF = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
static public final String RDFS = "http://www.w3.org/2000/01/rdf-schema#";
static public final String DC = "http://purl.org/dc/elements/1.1/";
static public final String XMLNS= "http://www.w3.org/2000/xmlns/";
static public final String AN = "http://www.w3.org/2000/10/annotation-ns#";
static public final String XHTML = "http://www.w3.org/1999/xhtml" ;
static public final String HTTP = "http://www.w3.org/1999/xx/http#";
static public final String CONNOTEA ="http://www.connotea.org/2005/01/schema#";
static public final String TERMS = "http://purl.org/dc/terms/";
/** query parameter name as specified in the spec */
static final String QUERY_ANNOTATION_PARAMETER="w3c_annotates";
/** default number of rows to fetch from http://www.connotea.org */
static final int CONNOTEA_DEFAULT_NUM_ROWS=10;
/** number of rows to fetch from http://www.connotea.org */
int connoteaNumRowsToFetch =CONNOTEA_DEFAULT_NUM_ROWS;
/** @see javax.servlet.GenericServlet#init() */
public void init() throws ServletException
{
//init number of rows
String s = getInitParameter("connoteaNumRowsToFetch");
if(s!=null)
{
try
{
this.connoteaNumRowsToFetch=Integer.parseInt(s);
if(this.connoteaNumRowsToFetch<=0) this.connoteaNumRowsToFetch=CONNOTEA_DEFAULT_NUM_ROWS;
}
catch(Exception err)
{
throw new ServletException(err);
}
}
}
/** convert a string to MD5 */
static String toMD5(String url) throws ServletException
{
StringBuffer result= new StringBuffer();
try
{
MessageDigest md = MessageDigest.getInstance("MD5");
md.update(url.getBytes());
byte[] digest = md.digest();
for (int k=0; k<digest.length; k++)
{
String hex = Integer.toHexString(digest[k]);
if (hex.length() == 1) hex = "0" + hex;
result.append(hex.substring(hex.length()-2));
}
}
catch(Exception err)
{
throw new ServletException(err);
}
return result.toString();
}
/** @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse) */
protected void doGet(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException
{
res.setContentType("text/xml");
String urlquery= req.getParameter(QUERY_ANNOTATION_PARAMETER);
PrintWriter out=res.getWriter();
String pathInfo = req.getPathInfo(); // /a/b;c=123
/**
*
* WE FOUND URLQUERY
*
*/
if(urlquery!=null)
{
debug("query is "+urlquery);
String authorizationUTF8= URLEncoder.encode(getAuthorization(req),"UTF-8");
String md5=toMD5(urlquery);
Document doc= getConnoteaRDF(
"http://www.connotea.org/data/bookmarks/uri/"+md5,
req
);
String postCount=null;
String created=null;
if(doc!=null)
{
Element root= doc.getDocumentElement();
if(root==null || !isA(root,RDF,"RDF")) throw new ServletException("Bad XML root from connotea");
for(Node n1= root.getFirstChild();n1!=null;n1=n1.getNextSibling())
{
if(!isA(n1,TERMS,"URI")) continue;
for(Node n2= n1.getFirstChild();n2!=null;n2=n2.getNextSibling())
{
if(isA(n2,CONNOTEA,"postCount"))
{
postCount=textContent(n2).replace('\n',' ').trim();
}
else if(isA(n2,CONNOTEA,"created"))
{
created=textContent(n2).replace('\n',' ').trim();
}
}
break;
}
}
debug("postcount="+postCount);
out.print(
"<?xml version=\"1.0\" ?>\n" +
"<r:RDF xmlns:r=\""+RDF+"\"\n" +
" xmlns:a=\""+AN+"\"\n" +
" xmlns:d=\""+DC+"\">\n"
);
if(postCount!=null)
{
out.print(
" <r:Description r:about=\""+getBaseURL(req)+"/"+md5+"\">\n" +
" <r:type r:resource=\""+ AN +"Annotation\"/>\n" +
" <r:type r:resource=\"http://www.w3.org/2000/10/annotationType#Comment\"/>\n" +
" <a:annotates r:resource=\""+urlquery+"\"/>\n" +
" <d:title>"+postCount+" Annotation(s) of "+urlquery+" on connotea</d:title>\n" +
" <a:context>" + urlquery+"#xpointer(/html[1])</a:context>\n" +
" <d:creator>Connotea</d:creator>\n" +
" <a:created>"+created+"</a:created>\n" +
" <d:date>"+created+"</d:date>\n" +
" <a:body r:resource=\""+getBaseURL(req)+"/body/"+md5+"?authorization="+authorizationUTF8+"\">"+
"</r:Description>"
);
}
out.print("</r:RDF>\n");
}
/**
*
* /BODY/ in pathinfo
*
*/
else if(pathInfo!=null && pathInfo.startsWith("/body/"))
{
String md5=pathInfo.substring(6);
Document doc=getConnoteaRDF("http://www.connotea.org/data/uri/"+md5+
"?num="+this.connoteaNumRowsToFetch,
req);
if(doc==null)
{
throw new ServletException("Cannot get http://www.connotea.org/data/uri/"+md5);
}
Element root= doc.getDocumentElement();
if(root==null || !isA(root,RDF,"RDF")) throw new ServletException("Bad XML root from connotea");
out.print("<?xml version=\"1.0\" ?>\n"+
"<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">"
);
printHTMLBodyFromConnotea(new PrintWriter(new FileWriter("/tmp/logAnnotea.txt")),md5,root);
printHTMLBodyFromConnotea(out,md5,root);
}
/**
*
* other
*
*/
else
{
debug("pathinfo not handled ?");
out.print(
"<?xml version=\"1.0\" ?>\n" +
"<r:RDF xmlns:r=\""+RDF+"\"\n" +
" xmlns:a=\""+AN+"\"\n" +
" xmlns:d=\""+DC+"\">\n" +
"<a:annotates r:resource=\""+
req.getRequestURL()+ "\"/>"+
"</r:RDF>\n"
);
}
out.flush();
}
/** return and parse an HTML annotation from connotea */
private void printHTMLBodyFromConnotea(PrintWriter out,String md5,Element root)
{
out.print("<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\">"+
"<body>");
out.print("<img src=\"http://www.connotea.org/connotealogo.gif\" alt=\"connotea\"/><br/>");
for(Node n1= root.getFirstChild();n1!=null;n1=n1.getNextSibling())
{
if(isA(n1,CONNOTEA,"Post"))
{
String title=null;
String user=null;
String uri=null;
String created=null;
HashSet subject= new HashSet();
for(Node n2= n1.getFirstChild();n2!=null;n2=n2.getNextSibling())
{
if(isA(n2,DC,"creator")) { user=textContent(n2).trim();}
else if(isA(n2,CONNOTEA,"title")) { title=textContent(n2).trim();}
else if(isA(n2,CONNOTEA,"created")) {
created=textContent(n2).trim();
int T=created.indexOf('T');
if(T!=-1) created= created.substring(0,T);
}
else if(isA(n2,DC,"subject")) { subject.add(textContent(n2).trim());}
else if(isA(n2,CONNOTEA,"uri"))
{
for(Node n3= n2.getFirstChild();n3!=null;n3=n3.getNextSibling())
{
if(isA(n3,TERMS,"URI"))
{
Element e3=(Element)n3;
uri=e3.getAttributeNS(RDF,"about").trim();
}
}
}
}
out.print("<div>");
if(title!=null)
{
if(uri!=null) out.print("<h4><a target=\"ext\" title=\""+escape(uri)+"\" href=\""+escape(uri)+"\">");
out.print(""+escape(title));
if(uri!=null) out.print("</a>");
out.print(" (<a target=\"ext\" title=\"http://www.connotea.org/uri/"+md5+"\" href=\"http://www.connotea.org/uri/"+md5+"\">info</a>)");
out.print("</h4>");
}
if(user!=null)
{
out.print("Posted by <a target=\"ext\" href=\"http://www.connotea.org/user/"+user+"\">"+user+"</a>");
if(!subject.isEmpty())
{
out.print(" to");
for (Iterator iter = subject.iterator(); iter.hasNext();)
{
String sbj=escape((String)iter.next());
out.print(" <a target=\"ext\" href=\"http://www.connotea.org/tag/"+sbj+"\">"+sbj+"</a>");
}
}
if(created!=null ) out.print(" on <a target=\"ext\" href=\"http://www.connotea.org/date/"+created+"\">"+created+"</a>");
out.print("<br/>");
}
out.print("</div><hr/>");
}
}
out.print("<a title=\"mailto:plindenbaum@yahoo.fr\" href=\"mailto:plindenbaum@yahoo.fr\">plindenbaum@yahoo.fr</a> Pierre Lindenbaum PhD<br/>");
out.print("<div align=\"center\"><img border=\"1\" src=\"http://www.integragen.com/img/title.png\"/></div>");
out.print("</body></html>");
out.flush();
}
/**
* @see javax.servlet.http.HttpServlet#doPost(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse) */
protected void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException
{
Document doc=null;
try
{
doc= newDocumentBuilder().parse(req.getInputStream());
}
catch(SAXException err)
{
debug("cannot get document from input stream");
throw new ServletException(err);
}
String context=null;
String content=null;
Element root= doc.getDocumentElement();
if(root==null) throw new ServletException("Cannot find root element of input");
debug("DOM1 content is "+DOM2String(root));
for(Node c1= root.getFirstChild();c1!=null;c1=c1.getNextSibling())
{
if(!isA(c1,RDF,"Description")) continue;
for(Node c2= c1.getFirstChild();c2!=null;c2=c2.getNextSibling())
{
if(c2.hasChildNodes()&& isA(c2,AN,"context"))
{
Element e2=(Element)c2;
context=textContent(e2).trim();
int xpointer=context.indexOf("#xpointer");
if(xpointer!=-1) context=context.substring(0,xpointer);
}
else if(c2.hasChildNodes()&& isA(c2,AN,"body"))
{
for(Node c3= c2.getFirstChild();c3!=null;c3=c3.getNextSibling())
{
if(!(c3.hasChildNodes()&& isA(c3,HTTP,"Message"))) continue;
for(Node c4= c3.getFirstChild();c4!=null;c4=c4.getNextSibling())
{
if(!(c4.hasChildNodes()&& isA(c4,HTTP,"Body"))) continue;
content= textContent(c4).trim().replaceAll("[ ]+"," ");
debug("DOM content is "+DOM2String(c4));
}
}
}
}
}
if(context==null)
{
throw new ServletException("Cannot find context in "+root);
}
if(content==null)
{
throw new ServletException("Cannot find content in "+DOM2String(root));
}
/** check if boomarks already exists */
try
{
String usertitle=null;
String comment=null;
StringBuffer description=new StringBuffer();
HashSet tags= new HashSet();
doc= getConnoteaRDF(
"http://www.connotea.org/data/user/"+
getLogin(req)+"/uri/"+
toMD5(context),req
);
if(doc!=null)
{
root= doc.getDocumentElement();
if(root!=null)
{
for(Node n1= root.getFirstChild();n1!=null;n1=n1.getNextSibling())
{
if(isA(n1,CONNOTEA,"Post"))
{
for(Node n2= n1.getFirstChild();n2!=null;n2=n2.getNextSibling())
{
if(isA(n2,CONNOTEA,"title")) { usertitle=textContent(n2).trim();}
else if(isA(n2,DC,"subject")) { tags.add(textContent(n2).trim().toLowerCase());}
else if(isA(n2,CONNOTEA,"description")) { description= new StringBuffer(textContent(n2).trim()+"\n");}
}
break;
}
}
}
debug("existed: title="+usertitle+" subject="+tags+ " desc="+description);
}
/* construct URL to connotea */
BufferedReader buffReader= new BufferedReader(new StringReader(content));
debug("content is "+content);
String line=null;
while((line=buffReader.readLine())!=null)
{
line= line.trim();
String upper= line.toUpperCase();
//parse tags
if(upper.startsWith("TAG:"))
{
try
{
StreamTokenizer parser= new StreamTokenizer(
new StringReader(line.substring(4))
);
parser.quoteChar('"');
parser.quoteChar('\'');
parser.eolIsSignificant(false);
parser.lowerCaseMode(true);
parser.ordinaryChars('0','9');
parser.wordChars('0','9');
parser.whitespaceChars(',',',');
parser.whitespaceChars(';',';');
parser.whitespaceChars('(','(');
parser.whitespaceChars(')',')');
while ( parser.nextToken() != StreamTokenizer.TT_EOF )
{
if ( parser.ttype == StreamTokenizer.TT_WORD)
{
tags.add(parser.sval.toLowerCase());
}
else if ( parser.ttype == StreamTokenizer.TT_NUMBER )
{
//hum... ignoring number
//items.add(""+parser.nval);
}
else if ( parser.ttype == StreamTokenizer.TT_EOL )
{
continue;
}
else if(parser.sval!=null)
{
tags.add(parser.sval.toLowerCase()) ;
}
}
}
catch(Exception ex)
{
}
}
else if(upper.startsWith("TI:"))
{
usertitle= line.substring(3).trim();
if(usertitle.length()==0) usertitle=null;
}
else if(upper.startsWith("COM:"))
{
comment= line.substring(4).trim();
if(comment.length()==0) comment=null;
}
else
{
description.append(line+"\n");
}
}
//put one tag if no tags was declared
if(tags.isEmpty()) tags.add("annoteated");
if(description.length()==0) description= new StringBuffer(context);
//build tags parameter
StringBuffer tagStr= new StringBuffer();
for (Iterator iter = tags.iterator(); iter.hasNext();)
{
if(tagStr.length()!=0) tagStr.append(",");
tagStr.append(iter.next().toString());
}
debug("tagstr="+tagStr);
URL url=new URL("http://www.connotea.org:80/data/add");
String postbody=
"uri=" + URLEncoder.encode(context,"UTF-8")+
(usertitle==null?"":"&usertitle="+URLEncoder.encode(usertitle,"UTF-8"))+
"&description="+URLEncoder.encode(description.toString(),"UTF-8")+
(comment==null?"":"&comment="+URLEncoder.encode(comment,"UTF-8"))+
"&tags=" + URLEncoder.encode(tagStr.toString(),"UTF-8")+
"&annoteaflag=hiBenThisIsPierre"
;
StringBuffer poststring= new StringBuffer();
poststring.append("POST "+url.getFile()+" HTTP/1.1\n");
poststring.append("Host: "+url.getHost()+"\n");
poststring.append("authorization: "+getAuthorization(req)+"\n");
poststring.append("Content-length: "+postbody.length()+"\n");
poststring.append("\n");
poststring.append(postbody.toString());
Socket socket= new Socket(url.getHost(),url.getPort());
InputStream from_server= socket.getInputStream();
PrintWriter to_server= new PrintWriter(
new OutputStreamWriter(socket.getOutputStream()));
to_server.print(poststring.toString());
to_server.flush();
StringBuffer response= new StringBuffer();
int c; while((c=from_server.read())!=-1) { response.append((char)c);}
to_server.close();
from_server.close();
debug("sent "+ poststring+" response is:\n"+response+"\n");
}
catch(Exception err)
{
debug("error "+err);
throw new ServletException(err);
}
{
String msg="<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n" +
"<rdf:RDF xmlns:rdf=\""+RDF+"\"\n" +
" xmlns:a=\""+AN+"\"\n" +
" xmlns:dc=\""+DC+"\">\n" +
" <rdf:Description rdf:about=\""+
getBaseURL(req)+"/"+toMD5(context)
+"\">\n" +
" <dc:creator>connotea user</dc:creator>\n"+
" <a:created>2006-01-31</a:created>\n"+
" <dc:date>2006-01-31</dc:date>\n"+
" <a:annotates rdf:resource=\""+escape(context)+"\"/>\n" +
" <rdf:type rdf:resource=\""+ AN +"Annotation\"/>\n" +
" <rdf:type rdf:resource=\"http://www.w3.org/2000/10/annotationType#Comment\"/>\n" +
//" <a:body rdf:resource=\""+getBaseURL(req)+"/body/"+toMD5(context) +"\"/>\n" +
" </rdf:Description>\n" +
"</rdf:RDF>";
res.setStatus(HttpServletResponse.SC_CREATED);
res.setHeader("Connection","close");
res.setHeader("Pragma","no-cache");
res.setContentType("text/xml");
res.setContentLength(msg.length());
PrintWriter out= res.getWriter();
out.print(msg);
debug("message sent is "+msg);
out.flush();
}
}
/** return the BASE URL of this servet */
private static String getBaseURL(HttpServletRequest req) throws ServletException
{
String scheme = req.getScheme(); // http
String serverName = req.getServerName(); // hostname.com
int serverPort = req.getServerPort(); // 80
String contextPath = req.getContextPath(); // /mywebapp
String servletPath = req.getServletPath(); // /servlet/MyServlet
//String pathInfo = req.getPathInfo(); // /a/b;c=123
//String queryString = req.getQueryString(); // d=789
return scheme+"://"+serverName+":"+serverPort+contextPath+servletPath;
}
/** creates a new namespace aware DocumentBuilder parsing DOM */
private static DocumentBuilder newDocumentBuilder() throws ServletException
{
DocumentBuilderFactory factory= DocumentBuilderFactory.newInstance();
factory.setCoalescing(true);
factory.setNamespaceAware(true);
factory.setExpandEntityReferences(true);
factory.setIgnoringComments(true);
factory.setValidating(false);
try
{
return factory.newDocumentBuilder();
} catch (ParserConfigurationException error)
{
throw new ServletException(error);
}
}
/** simple escape XML function */
public static String escape(String s)
{
if(s==null) return s;
StringBuffer buff= new StringBuffer();
for(int i=0;i< s.length();++i)
{
switch(s.charAt(i))
{
case('\"') : buff.append("""); break;
case('\'') : buff.append("'"); break;
case('&') : buff.append("&"); break;
case('<') : buff.append("<"); break;
case('>') : buff.append(">"); break;
default: buff.append(s.charAt(i)); break;
}
}
return buff.toString();
}
/** simple test for XML element */
static public boolean isA(Node e,String ns, String localname)
{
if(e==null) return false;
return ns.equals(e.getNamespaceURI()) && e.getLocalName().equals(localname);
}
/** get text content of a DOM node */
static public String textContent(Node node)
{
return textContent(node,new StringBuffer()).toString();
}
/** get text content of a DOM node */
static private StringBuffer textContent(Node node,StringBuffer s)
{
if(node==null) return s;
for(Node c= node.getFirstChild();c!=null;c=c.getNextSibling())
{
if(isA(c,XHTML,"br"))
{
s.append("\n");
}
else if(c.getNodeType()==Node.CDATA_SECTION_NODE)
{
s.append(((CDATASection)c).getNodeValue());
}
else if(c.getNodeType()==Node.TEXT_NODE)
{
s.append(((Text)c).getNodeValue());
}
else
{
textContent(c,s);
}
}
return s;
}
/** download a document from connotea or null if the url was not found */
private Document getConnoteaRDF(String url,HttpServletRequest req) throws ServletException
{
DocumentBuilder builder= newDocumentBuilder();
try
{
return builder.parse(
openSecureURLInputStream(
url,
req
)
);
}
catch (FileNotFoundException e)
{
debug("file not found for "+url+" returning empty rdf document");
return null;
}
catch(Exception err)
{
debug("cannot download :"+url+ " "+err);
throw new ServletException(err);
}
}
/** get login from header authorization */
static private String getLogin(HttpServletRequest req) throws ServletException
{
return getLoginAndPassword(req)[0];
}
/** get login and passord from header authorization */
static private String[] getLoginAndPassword(HttpServletRequest req) throws ServletException
{
String s64= getAuthorization(req);
if(!s64.startsWith("Basic ")) throw new ServletException("header \"authorization\" does not start with \"Basic \" ");
s64=s64.substring(6);
String decoded= Base64Decoder.decode(s64);
int loc= decoded.indexOf(':');
if(loc==-1) throw new ServletException("no \":\" in decoded authorization "+s64);
return new String[]{decoded.substring(0,loc),decoded.substring(loc+1)};
}
/** find parameter authorization in http request */
static String getAuthorization(HttpServletRequest req) throws ServletException
{
String s64= req.getHeader("authorization");
if(s64==null)
{
s64=req.getParameter("authorization");
}
if(s64==null)
{
s64=req.getParameter("Authorization");
}
if(s64==null)
{
Enumeration e= req.getHeaderNames();
StringBuffer headers= new StringBuffer();
while(e.hasMoreElements())
{
String key=(String)e.nextElement();
headers.append(key).append("=").append(req.getHeader(key)).append(";\n");
}
throw new ServletException("no header \"authorization\" was found in\n"+headers);
}
return s64;
}
/** open a URL, filling authorization header */
static private InputStream openSecureURLInputStream(String urlstr,HttpServletRequest req)
throws ServletException,FileNotFoundException
{
URL url=null;
String s64=null;
try
{
s64= getAuthorization(req);
url= new URL(urlstr);
URLConnection uc = url.openConnection();
uc.setRequestProperty("Authorization", s64);
InputStream content = uc.getInputStream();
return content;
}
catch (MalformedURLException e)
{
throw new ServletException(e);
}
catch (FileNotFoundException e)
{
throw e;
}
catch (IOException e)
{
throw new ServletException(e);
}
}
/** quick n dirty debugging function: append the message to "/tmp/logAnnotea.txt" */
static private void debug(Object o)
{
if(!DEBUG) return;
try
{
File f= new File("/tmp/logAnnotea.txt");
PrintWriter pout= new PrintWriter(new FileWriter(f,true));
pout.println("###"+System.currentTimeMillis()+"########");
pout.println(o);
pout.flush();
pout.close();
}
catch (Exception err)
{
err.printStackTrace();
}
}
private String DOM2String(Node doc)throws ServletException
{
StringWriter out= new StringWriter();
printDOM(new PrintWriter(out,true),doc);
return out.toString();
}
/* print DOM document for debugging purpose...*/
private static void printDOM(PrintWriter log,Node doc) throws ServletException
{
Source source = new DOMSource(doc);
Result result = new StreamResult(log);
try
{
Transformer xformer = TransformerFactory.newInstance().newTransformer();
xformer.transform(source, result);
}
catch(TransformerException error)
{
error.printStackTrace();
error.printStackTrace(log);
log.flush();
throw new ServletException(error);
}
}
}
Copyright (c) 2006 Pierre Lindenbaum PhD
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
``Software''), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.
The name of the authors when specified in the source files shall be
kept unmodified.
THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL 4XT.ORG BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
$Id: $
$Author: $
$Revision: $
$Date: $
$Locker: $
$RCSfile: $
$Source: $
$State: $
$Name: $
$Log: $
*************************************************************************/
package org.lindenb.annotea.server;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.io.StreamTokenizer;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.MalformedURLException;
import java.net.Socket;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import java.security.MessageDigest;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Iterator;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.Result;
import javax.xml.transform.Source;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.w3c.dom.CDATASection;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.Text;
import org.xml.sax.SAXException;
import com.oreilly.servlet.Base64Decoder;
/**
* @author lindenb
* http://islande:8080/annotea/Annotea
*/
public class AnnoteaServer extends HttpServlet
{
/**
* serialVersionUID
*/
private static final long serialVersionUID = 1L;
/** flag for debugging on/off */
private static boolean DEBUG=false;
//static declaration of xml namespaces
static public final String RDF = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
static public final String RDFS = "http://www.w3.org/2000/01/rdf-schema#";
static public final String DC = "http://purl.org/dc/elements/1.1/";
static public final String XMLNS= "http://www.w3.org/2000/xmlns/";
static public final String AN = "http://www.w3.org/2000/10/annotation-ns#";
static public final String XHTML = "http://www.w3.org/1999/xhtml" ;
static public final String HTTP = "http://www.w3.org/1999/xx/http#";
static public final String CONNOTEA ="http://www.connotea.org/2005/01/schema#";
static public final String TERMS = "http://purl.org/dc/terms/";
/** query parameter name as specified in the spec */
static final String QUERY_ANNOTATION_PARAMETER="w3c_annotates";
/** default number of rows to fetch from http://www.connotea.org */
static final int CONNOTEA_DEFAULT_NUM_ROWS=10;
/** number of rows to fetch from http://www.connotea.org */
int connoteaNumRowsToFetch =CONNOTEA_DEFAULT_NUM_ROWS;
/** @see javax.servlet.GenericServlet#init() */
public void init() throws ServletException
{
//init number of rows
String s = getInitParameter("connoteaNumRowsToFetch");
if(s!=null)
{
try
{
this.connoteaNumRowsToFetch=Integer.parseInt(s);
if(this.connoteaNumRowsToFetch<=0) this.connoteaNumRowsToFetch=CONNOTEA_DEFAULT_NUM_ROWS;
}
catch(Exception err)
{
throw new ServletException(err);
}
}
}
/** convert a string to MD5 */
static String toMD5(String url) throws ServletException
{
StringBuffer result= new StringBuffer();
try
{
MessageDigest md = MessageDigest.getInstance("MD5");
md.update(url.getBytes());
byte[] digest = md.digest();
for (int k=0; k<digest.length; k++)
{
String hex = Integer.toHexString(digest[k]);
if (hex.length() == 1) hex = "0" + hex;
result.append(hex.substring(hex.length()-2));
}
}
catch(Exception err)
{
throw new ServletException(err);
}
return result.toString();
}
/** @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse) */
protected void doGet(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException
{
res.setContentType("text/xml");
String urlquery= req.getParameter(QUERY_ANNOTATION_PARAMETER);
PrintWriter out=res.getWriter();
String pathInfo = req.getPathInfo(); // /a/b;c=123
/**
*
* WE FOUND URLQUERY
*
*/
if(urlquery!=null)
{
debug("query is "+urlquery);
String authorizationUTF8= URLEncoder.encode(getAuthorization(req),"UTF-8");
String md5=toMD5(urlquery);
Document doc= getConnoteaRDF(
"http://www.connotea.org/data/bookmarks/uri/"+md5,
req
);
String postCount=null;
String created=null;
if(doc!=null)
{
Element root= doc.getDocumentElement();
if(root==null || !isA(root,RDF,"RDF")) throw new ServletException("Bad XML root from connotea");
for(Node n1= root.getFirstChild();n1!=null;n1=n1.getNextSibling())
{
if(!isA(n1,TERMS,"URI")) continue;
for(Node n2= n1.getFirstChild();n2!=null;n2=n2.getNextSibling())
{
if(isA(n2,CONNOTEA,"postCount"))
{
postCount=textContent(n2).replace('\n',' ').trim();
}
else if(isA(n2,CONNOTEA,"created"))
{
created=textContent(n2).replace('\n',' ').trim();
}
}
break;
}
}
debug("postcount="+postCount);
out.print(
"<?xml version=\"1.0\" ?>\n" +
"<r:RDF xmlns:r=\""+RDF+"\"\n" +
" xmlns:a=\""+AN+"\"\n" +
" xmlns:d=\""+DC+"\">\n"
);
if(postCount!=null)
{
out.print(
" <r:Description r:about=\""+getBaseURL(req)+"/"+md5+"\">\n" +
" <r:type r:resource=\""+ AN +"Annotation\"/>\n" +
" <r:type r:resource=\"http://www.w3.org/2000/10/annotationType#Comment\"/>\n" +
" <a:annotates r:resource=\""+urlquery+"\"/>\n" +
" <d:title>"+postCount+" Annotation(s) of "+urlquery+" on connotea</d:title>\n" +
" <a:context>" + urlquery+"#xpointer(/html[1])</a:context>\n" +
" <d:creator>Connotea</d:creator>\n" +
" <a:created>"+created+"</a:created>\n" +
" <d:date>"+created+"</d:date>\n" +
" <a:body r:resource=\""+getBaseURL(req)+"/body/"+md5+"?authorization="+authorizationUTF8+"\">"+
"</r:Description>"
);
}
out.print("</r:RDF>\n");
}
/**
*
* /BODY/ in pathinfo
*
*/
else if(pathInfo!=null && pathInfo.startsWith("/body/"))
{
String md5=pathInfo.substring(6);
Document doc=getConnoteaRDF("http://www.connotea.org/data/uri/"+md5+
"?num="+this.connoteaNumRowsToFetch,
req);
if(doc==null)
{
throw new ServletException("Cannot get http://www.connotea.org/data/uri/"+md5);
}
Element root= doc.getDocumentElement();
if(root==null || !isA(root,RDF,"RDF")) throw new ServletException("Bad XML root from connotea");
out.print("<?xml version=\"1.0\" ?>\n"+
"<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">"
);
printHTMLBodyFromConnotea(new PrintWriter(new FileWriter("/tmp/logAnnotea.txt")),md5,root);
printHTMLBodyFromConnotea(out,md5,root);
}
/**
*
* other
*
*/
else
{
debug("pathinfo not handled ?");
out.print(
"<?xml version=\"1.0\" ?>\n" +
"<r:RDF xmlns:r=\""+RDF+"\"\n" +
" xmlns:a=\""+AN+"\"\n" +
" xmlns:d=\""+DC+"\">\n" +
"<a:annotates r:resource=\""+
req.getRequestURL()+ "\"/>"+
"</r:RDF>\n"
);
}
out.flush();
}
/** return and parse an HTML annotation from connotea */
private void printHTMLBodyFromConnotea(PrintWriter out,String md5,Element root)
{
out.print("<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\">"+
"<body>");
out.print("<img src=\"http://www.connotea.org/connotealogo.gif\" alt=\"connotea\"/><br/>");
for(Node n1= root.getFirstChild();n1!=null;n1=n1.getNextSibling())
{
if(isA(n1,CONNOTEA,"Post"))
{
String title=null;
String user=null;
String uri=null;
String created=null;
HashSet subject= new HashSet();
for(Node n2= n1.getFirstChild();n2!=null;n2=n2.getNextSibling())
{
if(isA(n2,DC,"creator")) { user=textContent(n2).trim();}
else if(isA(n2,CONNOTEA,"title")) { title=textContent(n2).trim();}
else if(isA(n2,CONNOTEA,"created")) {
created=textContent(n2).trim();
int T=created.indexOf('T');
if(T!=-1) created= created.substring(0,T);
}
else if(isA(n2,DC,"subject")) { subject.add(textContent(n2).trim());}
else if(isA(n2,CONNOTEA,"uri"))
{
for(Node n3= n2.getFirstChild();n3!=null;n3=n3.getNextSibling())
{
if(isA(n3,TERMS,"URI"))
{
Element e3=(Element)n3;
uri=e3.getAttributeNS(RDF,"about").trim();
}
}
}
}
out.print("<div>");
if(title!=null)
{
if(uri!=null) out.print("<h4><a target=\"ext\" title=\""+escape(uri)+"\" href=\""+escape(uri)+"\">");
out.print(""+escape(title));
if(uri!=null) out.print("</a>");
out.print(" (<a target=\"ext\" title=\"http://www.connotea.org/uri/"+md5+"\" href=\"http://www.connotea.org/uri/"+md5+"\">info</a>)");
out.print("</h4>");
}
if(user!=null)
{
out.print("Posted by <a target=\"ext\" href=\"http://www.connotea.org/user/"+user+"\">"+user+"</a>");
if(!subject.isEmpty())
{
out.print(" to");
for (Iterator iter = subject.iterator(); iter.hasNext();)
{
String sbj=escape((String)iter.next());
out.print(" <a target=\"ext\" href=\"http://www.connotea.org/tag/"+sbj+"\">"+sbj+"</a>");
}
}
if(created!=null ) out.print(" on <a target=\"ext\" href=\"http://www.connotea.org/date/"+created+"\">"+created+"</a>");
out.print("<br/>");
}
out.print("</div><hr/>");
}
}
out.print("<a title=\"mailto:plindenbaum@yahoo.fr\" href=\"mailto:plindenbaum@yahoo.fr\">plindenbaum@yahoo.fr</a> Pierre Lindenbaum PhD<br/>");
out.print("<div align=\"center\"><img border=\"1\" src=\"http://www.integragen.com/img/title.png\"/></div>");
out.print("</body></html>");
out.flush();
}
/**
* @see javax.servlet.http.HttpServlet#doPost(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse) */
protected void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException
{
Document doc=null;
try
{
doc= newDocumentBuilder().parse(req.getInputStream());
}
catch(SAXException err)
{
debug("cannot get document from input stream");
throw new ServletException(err);
}
String context=null;
String content=null;
Element root= doc.getDocumentElement();
if(root==null) throw new ServletException("Cannot find root element of input");
debug("DOM1 content is "+DOM2String(root));
for(Node c1= root.getFirstChild();c1!=null;c1=c1.getNextSibling())
{
if(!isA(c1,RDF,"Description")) continue;
for(Node c2= c1.getFirstChild();c2!=null;c2=c2.getNextSibling())
{
if(c2.hasChildNodes()&& isA(c2,AN,"context"))
{
Element e2=(Element)c2;
context=textContent(e2).trim();
int xpointer=context.indexOf("#xpointer");
if(xpointer!=-1) context=context.substring(0,xpointer);
}
else if(c2.hasChildNodes()&& isA(c2,AN,"body"))
{
for(Node c3= c2.getFirstChild();c3!=null;c3=c3.getNextSibling())
{
if(!(c3.hasChildNodes()&& isA(c3,HTTP,"Message"))) continue;
for(Node c4= c3.getFirstChild();c4!=null;c4=c4.getNextSibling())
{
if(!(c4.hasChildNodes()&& isA(c4,HTTP,"Body"))) continue;
content= textContent(c4).trim().replaceAll("[ ]+"," ");
debug("DOM content is "+DOM2String(c4));
}
}
}
}
}
if(context==null)
{
throw new ServletException("Cannot find context in "+root);
}
if(content==null)
{
throw new ServletException("Cannot find content in "+DOM2String(root));
}
/** check if boomarks already exists */
try
{
String usertitle=null;
String comment=null;
StringBuffer description=new StringBuffer();
HashSet tags= new HashSet();
doc= getConnoteaRDF(
"http://www.connotea.org/data/user/"+
getLogin(req)+"/uri/"+
toMD5(context),req
);
if(doc!=null)
{
root= doc.getDocumentElement();
if(root!=null)
{
for(Node n1= root.getFirstChild();n1!=null;n1=n1.getNextSibling())
{
if(isA(n1,CONNOTEA,"Post"))
{
for(Node n2= n1.getFirstChild();n2!=null;n2=n2.getNextSibling())
{
if(isA(n2,CONNOTEA,"title")) { usertitle=textContent(n2).trim();}
else if(isA(n2,DC,"subject")) { tags.add(textContent(n2).trim().toLowerCase());}
else if(isA(n2,CONNOTEA,"description")) { description= new StringBuffer(textContent(n2).trim()+"\n");}
}
break;
}
}
}
debug("existed: title="+usertitle+" subject="+tags+ " desc="+description);
}
/* construct URL to connotea */
BufferedReader buffReader= new BufferedReader(new StringReader(content));
debug("content is "+content);
String line=null;
while((line=buffReader.readLine())!=null)
{
line= line.trim();
String upper= line.toUpperCase();
//parse tags
if(upper.startsWith("TAG:"))
{
try
{
StreamTokenizer parser= new StreamTokenizer(
new StringReader(line.substring(4))
);
parser.quoteChar('"');
parser.quoteChar('\'');
parser.eolIsSignificant(false);
parser.lowerCaseMode(true);
parser.ordinaryChars('0','9');
parser.wordChars('0','9');
parser.whitespaceChars(',',',');
parser.whitespaceChars(';',';');
parser.whitespaceChars('(','(');
parser.whitespaceChars(')',')');
while ( parser.nextToken() != StreamTokenizer.TT_EOF )
{
if ( parser.ttype == StreamTokenizer.TT_WORD)
{
tags.add(parser.sval.toLowerCase());
}
else if ( parser.ttype == StreamTokenizer.TT_NUMBER )
{
//hum... ignoring number
//items.add(""+parser.nval);
}
else if ( parser.ttype == StreamTokenizer.TT_EOL )
{
continue;
}
else if(parser.sval!=null)
{
tags.add(parser.sval.toLowerCase()) ;
}
}
}
catch(Exception ex)
{
}
}
else if(upper.startsWith("TI:"))
{
usertitle= line.substring(3).trim();
if(usertitle.length()==0) usertitle=null;
}
else if(upper.startsWith("COM:"))
{
comment= line.substring(4).trim();
if(comment.length()==0) comment=null;
}
else
{
description.append(line+"\n");
}
}
//put one tag if no tags was declared
if(tags.isEmpty()) tags.add("annoteated");
if(description.length()==0) description= new StringBuffer(context);
//build tags parameter
StringBuffer tagStr= new StringBuffer();
for (Iterator iter = tags.iterator(); iter.hasNext();)
{
if(tagStr.length()!=0) tagStr.append(",");
tagStr.append(iter.next().toString());
}
debug("tagstr="+tagStr);
URL url=new URL("http://www.connotea.org:80/data/add");
String postbody=
"uri=" + URLEncoder.encode(context,"UTF-8")+
(usertitle==null?"":"&usertitle="+URLEncoder.encode(usertitle,"UTF-8"))+
"&description="+URLEncoder.encode(description.toString(),"UTF-8")+
(comment==null?"":"&comment="+URLEncoder.encode(comment,"UTF-8"))+
"&tags=" + URLEncoder.encode(tagStr.toString(),"UTF-8")+
"&annoteaflag=hiBenThisIsPierre"
;
StringBuffer poststring= new StringBuffer();
poststring.append("POST "+url.getFile()+" HTTP/1.1\n");
poststring.append("Host: "+url.getHost()+"\n");
poststring.append("authorization: "+getAuthorization(req)+"\n");
poststring.append("Content-length: "+postbody.length()+"\n");
poststring.append("\n");
poststring.append(postbody.toString());
Socket socket= new Socket(url.getHost(),url.getPort());
InputStream from_server= socket.getInputStream();
PrintWriter to_server= new PrintWriter(
new OutputStreamWriter(socket.getOutputStream()));
to_server.print(poststring.toString());
to_server.flush();
StringBuffer response= new StringBuffer();
int c; while((c=from_server.read())!=-1) { response.append((char)c);}
to_server.close();
from_server.close();
debug("sent "+ poststring+" response is:\n"+response+"\n");
}
catch(Exception err)
{
debug("error "+err);
throw new ServletException(err);
}
{
String msg="<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n" +
"<rdf:RDF xmlns:rdf=\""+RDF+"\"\n" +
" xmlns:a=\""+AN+"\"\n" +
" xmlns:dc=\""+DC+"\">\n" +
" <rdf:Description rdf:about=\""+
getBaseURL(req)+"/"+toMD5(context)
+"\">\n" +
" <dc:creator>connotea user</dc:creator>\n"+
" <a:created>2006-01-31</a:created>\n"+
" <dc:date>2006-01-31</dc:date>\n"+
" <a:annotates rdf:resource=\""+escape(context)+"\"/>\n" +
" <rdf:type rdf:resource=\""+ AN +"Annotation\"/>\n" +
" <rdf:type rdf:resource=\"http://www.w3.org/2000/10/annotationType#Comment\"/>\n" +
//" <a:body rdf:resource=\""+getBaseURL(req)+"/body/"+toMD5(context) +"\"/>\n" +
" </rdf:Description>\n" +
"</rdf:RDF>";
res.setStatus(HttpServletResponse.SC_CREATED);
res.setHeader("Connection","close");
res.setHeader("Pragma","no-cache");
res.setContentType("text/xml");
res.setContentLength(msg.length());
PrintWriter out= res.getWriter();
out.print(msg);
debug("message sent is "+msg);
out.flush();
}
}
/** return the BASE URL of this servet */
private static String getBaseURL(HttpServletRequest req) throws ServletException
{
String scheme = req.getScheme(); // http
String serverName = req.getServerName(); // hostname.com
int serverPort = req.getServerPort(); // 80
String contextPath = req.getContextPath(); // /mywebapp
String servletPath = req.getServletPath(); // /servlet/MyServlet
//String pathInfo = req.getPathInfo(); // /a/b;c=123
//String queryString = req.getQueryString(); // d=789
return scheme+"://"+serverName+":"+serverPort+contextPath+servletPath;
}
/** creates a new namespace aware DocumentBuilder parsing DOM */
private static DocumentBuilder newDocumentBuilder() throws ServletException
{
DocumentBuilderFactory factory= DocumentBuilderFactory.newInstance();
factory.setCoalescing(true);
factory.setNamespaceAware(true);
factory.setExpandEntityReferences(true);
factory.setIgnoringComments(true);
factory.setValidating(false);
try
{
return factory.newDocumentBuilder();
} catch (ParserConfigurationException error)
{
throw new ServletException(error);
}
}
/** simple escape XML function */
public static String escape(String s)
{
if(s==null) return s;
StringBuffer buff= new StringBuffer();
for(int i=0;i< s.length();++i)
{
switch(s.charAt(i))
{
case('\"') : buff.append("""); break;
case('\'') : buff.append("'"); break;
case('&') : buff.append("&"); break;
case('<') : buff.append("<"); break;
case('>') : buff.append(">"); break;
default: buff.append(s.charAt(i)); break;
}
}
return buff.toString();
}
/** simple test for XML element */
static public boolean isA(Node e,String ns, String localname)
{
if(e==null) return false;
return ns.equals(e.getNamespaceURI()) && e.getLocalName().equals(localname);
}
/** get text content of a DOM node */
static public String textContent(Node node)
{
return textContent(node,new StringBuffer()).toString();
}
/** get text content of a DOM node */
static private StringBuffer textContent(Node node,StringBuffer s)
{
if(node==null) return s;
for(Node c= node.getFirstChild();c!=null;c=c.getNextSibling())
{
if(isA(c,XHTML,"br"))
{
s.append("\n");
}
else if(c.getNodeType()==Node.CDATA_SECTION_NODE)
{
s.append(((CDATASection)c).getNodeValue());
}
else if(c.getNodeType()==Node.TEXT_NODE)
{
s.append(((Text)c).getNodeValue());
}
else
{
textContent(c,s);
}
}
return s;
}
/** download a document from connotea or null if the url was not found */
private Document getConnoteaRDF(String url,HttpServletRequest req) throws ServletException
{
DocumentBuilder builder= newDocumentBuilder();
try
{
return builder.parse(
openSecureURLInputStream(
url,
req
)
);
}
catch (FileNotFoundException e)
{
debug("file not found for "+url+" returning empty rdf document");
return null;
}
catch(Exception err)
{
debug("cannot download :"+url+ " "+err);
throw new ServletException(err);
}
}
/** get login from header authorization */
static private String getLogin(HttpServletRequest req) throws ServletException
{
return getLoginAndPassword(req)[0];
}
/** get login and passord from header authorization */
static private String[] getLoginAndPassword(HttpServletRequest req) throws ServletException
{
String s64= getAuthorization(req);
if(!s64.startsWith("Basic ")) throw new ServletException("header \"authorization\" does not start with \"Basic \" ");
s64=s64.substring(6);
String decoded= Base64Decoder.decode(s64);
int loc= decoded.indexOf(':');
if(loc==-1) throw new ServletException("no \":\" in decoded authorization "+s64);
return new String[]{decoded.substring(0,loc),decoded.substring(loc+1)};
}
/** find parameter authorization in http request */
static String getAuthorization(HttpServletRequest req) throws ServletException
{
String s64= req.getHeader("authorization");
if(s64==null)
{
s64=req.getParameter("authorization");
}
if(s64==null)
{
s64=req.getParameter("Authorization");
}
if(s64==null)
{
Enumeration e= req.getHeaderNames();
StringBuffer headers= new StringBuffer();
while(e.hasMoreElements())
{
String key=(String)e.nextElement();
headers.append(key).append("=").append(req.getHeader(key)).append(";\n");
}
throw new ServletException("no header \"authorization\" was found in\n"+headers);
}
return s64;
}
/** open a URL, filling authorization header */
static private InputStream openSecureURLInputStream(String urlstr,HttpServletRequest req)
throws ServletException,FileNotFoundException
{
URL url=null;
String s64=null;
try
{
s64= getAuthorization(req);
url= new URL(urlstr);
URLConnection uc = url.openConnection();
uc.setRequestProperty("Authorization", s64);
InputStream content = uc.getInputStream();
return content;
}
catch (MalformedURLException e)
{
throw new ServletException(e);
}
catch (FileNotFoundException e)
{
throw e;
}
catch (IOException e)
{
throw new ServletException(e);
}
}
/** quick n dirty debugging function: append the message to "/tmp/logAnnotea.txt" */
static private void debug(Object o)
{
if(!DEBUG) return;
try
{
File f= new File("/tmp/logAnnotea.txt");
PrintWriter pout= new PrintWriter(new FileWriter(f,true));
pout.println("###"+System.currentTimeMillis()+"########");
pout.println(o);
pout.flush();
pout.close();
}
catch (Exception err)
{
err.printStackTrace();
}
}
private String DOM2String(Node doc)throws ServletException
{
StringWriter out= new StringWriter();
printDOM(new PrintWriter(out,true),doc);
return out.toString();
}
/* print DOM document for debugging purpose...*/
private static void printDOM(PrintWriter log,Node doc) throws ServletException
{
Source source = new DOMSource(doc);
Result result = new StreamResult(log);
try
{
Transformer xformer = TransformerFactory.newInstance().newTransformer();
xformer.transform(source, result);
}
catch(TransformerException error)
{
error.printStackTrace();
error.printStackTrace(log);
log.flush();
throw new ServletException(error);
}
}
}
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