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Merge revisions 4706 4715 4724 4726 4731 4733 4734 4735 4739 to the trunk. For bjl23 and bdc34. Also web.xml from 4719, but not EntityController.java, which causes SVN to barf.

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jeb228 2010-04-13 19:51:58 +00:00
parent 10bf357d5e
commit b88ed19ed0
6 changed files with 292 additions and 193 deletions
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4
webapp/config/web.xml
View file

@ -1044,6 +1044,10 @@
<servlet-name>entity</servlet-name> <servlet-name>entity</servlet-name>
<url-pattern>/individual/*</url-pattern> <url-pattern>/individual/*</url-pattern>
</servlet-mapping> </servlet-mapping>
<servlet-mapping>
<servlet-name>entity</servlet-name>
<url-pattern>/display/*</url-pattern>
</servlet-mapping>
<servlet-mapping> <servlet-mapping>
<servlet-name>updateEntityFlags</servlet-name> <servlet-name>updateEntityFlags</servlet-name>
<url-pattern>/updateEntityFlags</url-pattern> <url-pattern>/updateEntityFlags</url-pattern>

303
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/ContactMailServlet.java
View file

@ -22,21 +22,24 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties; import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.beans.Portal; import edu.cornell.mannlib.vitro.webapp.beans.Portal;
public class ContactMailServlet extends VitroHttpServlet { public class ContactMailServlet extends VitroHttpServlet {
private static final Logger LOG = Logger.getLogger(ContactMailServlet.class); private static final Logger LOG = Logger.getLogger(ContactMailServlet.class);
public static HttpServletRequest request; private final static String CONFIRM_PAGE = "/thankyou.jsp";
public static HttpServletRequest response; private final static String ERR_PAGE = "/contact_err.jsp";
private final static String SPAM_MESSAGE = "Your message was flagged as spam.";
private final static String EMAIL_BACKUP_FILE_PATH = "/WEB-INF/LatestMessage.html";
private final static String WEB_USERNAME_PARAM = "webusername";
private final static String WEB_USEREMAIL_PARAM = "webuseremail";
private final static String COMMENTS_PARAM = "s34gfd88p9x1";
private static String smtpHost = null; private static String smtpHost = null;
private static final Log log = LogFactory.getLog(ContactMailServlet.class.getName());
public void init(ServletConfig servletConfig) throws javax.servlet.ServletException { public void init(ServletConfig servletConfig) throws javax.servlet.ServletException {
super.init(servletConfig); super.init(servletConfig);
@ -62,38 +65,56 @@ public class ContactMailServlet extends VitroHttpServlet {
public void doGet( HttpServletRequest request, HttpServletResponse response ) public void doGet( HttpServletRequest request, HttpServletResponse response )
throws ServletException, IOException { throws ServletException, IOException {
VitroRequest vreq = new VitroRequest(request); VitroRequest vreq = new VitroRequest(request);
Portal portal = vreq.getPortal(); Portal portal = vreq.getPortal();
String statusMsg = null; // holds the error status
String confirmpage = "/thankyou.jsp";
String errpage = "/contact_err.jsp";
String status = null; // holds the error status
if (smtpHost==null || smtpHost.equals("")){ if (smtpHost==null || smtpHost.equals("")){
status = "This application has not yet been configured to send mail " + statusMsg = "This application has not yet been configured to send mail " +
"-- smtp host has not been identified in the Configuration Properties file."; "-- smtp host has not been identified in the Configuration Properties file.";
response.sendRedirect( "test?bodyJsp=" + errpage + "&ERR=" + status + "&home=" + portal.getPortalId() ); redirectToError(response, statusMsg, portal);
return; return;
} }
String SPAM_MESSAGE = "Your message was flagged as spam."; String webusername = vreq.getParameter(WEB_USERNAME_PARAM);
String webuseremail = vreq.getParameter(WEB_USEREMAIL_PARAM);
String comments = vreq.getParameter(COMMENTS_PARAM);
boolean probablySpam = false; String validationMessage = validateInput(webusername, webuseremail,
String spamReason = ""; comments);
if (validationMessage != null) {
redirectToError(response, validationMessage, portal);
return;
}
webusername = webusername.trim();
webuseremail = webuseremail.trim();
comments = comments.trim();
String originalReferer = (String) request.getSession().getAttribute("commentsFormReferer"); String spamReason = null;
String originalReferer = (String) request.getSession()
.getAttribute("commentsFormReferer");
if (originalReferer != null) {
request.getSession().removeAttribute("commentsFormReferer"); request.getSession().removeAttribute("commentsFormReferer");
if (originalReferer == null) { /* does not support legitimate clients that don't send the Referer header
originalReferer = "none";
// (the following does not support cookie-less browsing:)
// probablySpam = true;
// status = SPAM_MESSAGE;
} else {
String referer = request.getHeader("Referer"); String referer = request.getHeader("Referer");
if (referer.indexOf("comments")<0 && referer.indexOf("correction")<0) { if (referer == null ||
probablySpam=true; (referer.indexOf("comments") <0
status = SPAM_MESSAGE ; && referer.indexOf("correction") <0) ) {
spamReason = "The form was not submitted from the Contact Us or Corrections page."; spamReason = "The form was not submitted from the " +
"Contact Us or Corrections page.";
statusMsg = SPAM_MESSAGE;
}
*/
} else {
originalReferer = "none";
}
if (spamReason == null) {
spamReason = checkForSpam(comments);
if (spamReason != null) {
statusMsg = SPAM_MESSAGE;
} }
} }
@ -104,19 +125,19 @@ public class ContactMailServlet extends VitroHttpServlet {
if ("comment".equals(formType)) { if ("comment".equals(formType)) {
if (portal.getContactMail() == null || portal.getContactMail().trim().length()==0) { if (portal.getContactMail() == null || portal.getContactMail().trim().length()==0) {
log.error("No contact mail address defined in current portal "+portal.getPortalId()); LOG.error("No contact mail address defined in current portal "+portal.getPortalId());
throw new Error( throw new Error(
"To establish the Contact Us mail capability the system administrators must " "To establish the Contact Us mail capability the system administrators must "
+ "specify an email address in the current portal."); + "specify an email address in the current portal.");
} else { } else {
deliverToArray = portal.getContactMail().split(","); deliverToArray = portal.getContactMail().split(",");
} }
deliveryfrom = "Message from the "+portal.getAppName()+" Contact Form (ARMANN-nospam)"; deliveryfrom = "Message from the "+portal.getAppName()+" Contact Form";
} else if ("correction".equals(formType)) { } else if ("correction".equals(formType)) {
if (portal.getCorrectionMail() == null || portal.getCorrectionMail().trim().length()==0) { if (portal.getCorrectionMail() == null || portal.getCorrectionMail().trim().length()==0) {
log.error("Expecting one or more correction email addresses to be specified in current portal "+portal.getPortalId()+"; will attempt to use contact mail address"); LOG.error("Expecting one or more correction email addresses to be specified in current portal "+portal.getPortalId()+"; will attempt to use contact mail address");
if (portal.getContactMail() == null || portal.getContactMail().trim().length()==0) { if (portal.getContactMail() == null || portal.getContactMail().trim().length()==0) {
log.error("No contact mail address or correction mail address defined in current portal "+portal.getPortalId()); LOG.error("No contact mail address or correction mail address defined in current portal "+portal.getPortalId());
} else { } else {
deliverToArray = portal.getContactMail().split(","); deliverToArray = portal.getContactMail().split(",");
} }
@ -126,78 +147,104 @@ public class ContactMailServlet extends VitroHttpServlet {
deliveryfrom = "Message from the "+portal.getAppName()+" Correction Form (ARMANN-nospam)"; deliveryfrom = "Message from the "+portal.getAppName()+" Correction Form (ARMANN-nospam)";
} else { } else {
deliverToArray = portal.getContactMail().split(","); deliverToArray = portal.getContactMail().split(",");
status = SPAM_MESSAGE ; statusMsg = SPAM_MESSAGE ;
spamReason = "The form specifies no delivery type."; spamReason = "The form specifies no delivery type.";
} }
recipientCount=(deliverToArray == null) ? 0 : deliverToArray.length; recipientCount=(deliverToArray == null) ? 0 : deliverToArray.length;
if (recipientCount == 0) { if (recipientCount == 0) {
log.error("recipientCount is 0 when DeliveryType specified as \""+formType+"\""); LOG.error("recipientCount is 0 when DeliveryType specified as \""+formType+"\"");
throw new Error( throw new Error(
"To establish the Contact Us mail capability the system administrators must " "To establish the Contact Us mail capability the system administrators must "
+ "specify at least one email address in the current portal."); + "specify at least one email address in the current portal.");
} }
// obtain passed in form data with a simple trim on the values String msgText = composeEmail(webusername, webuseremail, comments,
String webusername = vreq.getParameter("webusername");// Null.trim(); will give you an exception deliveryfrom, originalReferer, request.getRemoteAddr());
String webuseremail = vreq.getParameter("webuseremail");//.trim();
String comments = vreq.getParameter("s34gfd88p9x1");
if( webusername == null || "".equals(webusername) ){ // debugging
probablySpam=true; PrintWriter outFile = new PrintWriter
status = SPAM_MESSAGE; (new FileWriter(request.getSession().getServletContext()
spamReason = "A proper webusername field was not found in the form submitted."; .getRealPath(EMAIL_BACKUP_FILE_PATH),true)); //autoflush
webusername=""; writeBackupCopy(outFile, msgText, spamReason);
} else
webusername=webusername.trim();
if( webuseremail == null || "".equals(webuseremail) ){ // Set the smtp host
probablySpam=true; Properties props = System.getProperties();
status = SPAM_MESSAGE; props.put("mail.smtp.host", smtpHost);
spamReason = "A proper webuser email field was not found in the form submitted."; Session s = Session.getDefaultInstance(props,null); // was Session.getInstance(props,null);
webuseremail=""; //s.setDebug(true);
} else try {
webuseremail=webuseremail.trim();
if (comments==null || comments.equals("")) { // to avoid error messages in log due to null comments String if (spamReason == null) {
probablySpam=true; sendMessage(s, webuseremail, deliverToArray, deliveryfrom,
status = SPAM_MESSAGE; recipientCount, msgText);
spamReason = "The proper comments field was not found in the form submitted."; }
} catch (AddressException e) {
statusMsg = "Please supply a valid email address.";
outFile.println( statusMsg );
outFile.println( e.getMessage() );
} catch (SendFailedException e) {
statusMsg = "The system was unable to deliver your mail. Please try again later. [SEND FAILED]";
outFile.println( statusMsg );
outFile.println( e.getMessage() );
} catch (MessagingException e) {
statusMsg = "The system was unable to deliver your mail. Please try again later. [MESSAGING]";
outFile.println( statusMsg );
outFile.println( e.getMessage() );
e.printStackTrace();
}
outFile.flush();
outFile.close();
// Redirect to the appropriate confirmation page
if (statusMsg == null && spamReason == null) {
// message was sent successfully
redirectToConfirmation(response, statusMsg, portal);
} else { } else {
comments=comments.trim(); // exception occurred
redirectToError( response, statusMsg, portal);
} }
/* *************************** The following chunk code is for blocking specific types of spam messages. It should be removed from a more generalized codebase. */
/* if this blog markup is found, treat comment as blog spam */
if (!probablySpam
&& (comments.indexOf("[/url]") > -1
|| comments.indexOf("[/URL]") > -1
|| comments.indexOf("[url=") > -1
|| comments.indexOf("[URL=") > -1)) {
probablySpam = true;
status = SPAM_MESSAGE;
spamReason = "The message contained blog link markup.";
} }
/* if message is absurdly short, treat as blog spam */ public void doPost( HttpServletRequest request, HttpServletResponse response )
if (!probablySpam && comments.length()<15) { throws ServletException, IOException
probablySpam=true; {
status = SPAM_MESSAGE; doGet( request, response );
spamReason="The message was too short.";
} }
/* if contact form was requested directly, and message contains 'phentermine', treat as spam */ private void redirectToConfirmation(HttpServletResponse response,
if (!probablySpam && originalReferer.equals("none") && (comments.indexOf("phentermine")>-1 || comments.indexOf("Phentermine")>-1)) { String statusMsg, Portal portal) throws IOException {
probablySpam=true; response.sendRedirect( "test?bodyJsp=" + CONFIRM_PAGE + "&home=" +
status = SPAM_MESSAGE; portal.getPortalId() );
spamReason = "The comments form was requested directly, and the message contains the word 'Phentermine.'";
} }
/* ************************** end spam filtering code */ private void redirectToError(HttpServletResponse response, String statusMsg,
Portal portal) throws IOException {
response.sendRedirect( "test?bodyJsp=" + ERR_PAGE + "&ERR=" + statusMsg
+ "&home=" + portal.getPortalId() );
}
/** Intended to mangle url so it can get through spam filtering
* http://host/dir/servlet?param=value -> host: dir/servlet?param=value */
public String stripProtocol( String in ){
if( in == null )
return "";
else
return in.replaceAll("http://", "host: " );
}
private String composeEmail(String webusername, String webuseremail,
String comments, String deliveryfrom,
String originalReferer, String ipAddr) {
StringBuffer msgBuf = new StringBuffer();
// contains the intro copy for the body of the email message
String lineSeparator = System.getProperty("line.separator");
// \r\n on windows, \n on unix
StringBuffer msgBuf = new StringBuffer(); // contains the intro copy for the body of the email message
String lineSeparator = System.getProperty("line.separator"); // \r\n on windows, \n on unix
// from MyLibrary // from MyLibrary
msgBuf.setLength(0); msgBuf.setLength(0);
msgBuf.append("Content-Type: text/html; charset='us-ascii'" + lineSeparator); msgBuf.append("Content-Type: text/html; charset='us-ascii'" + lineSeparator);
@ -208,7 +255,8 @@ public class ContactMailServlet extends VitroHttpServlet {
msgBuf.append("</head>" + lineSeparator ); msgBuf.append("</head>" + lineSeparator );
msgBuf.append("<body>" + lineSeparator ); msgBuf.append("<body>" + lineSeparator );
msgBuf.append("<h4>" + deliveryfrom + "</h4>" + lineSeparator ); msgBuf.append("<h4>" + deliveryfrom + "</h4>" + lineSeparator );
msgBuf.append("<h4>From: "+webusername +" (" + webuseremail + ")"+" at IP address "+request.getRemoteAddr()+"</h4>"+lineSeparator); msgBuf.append("<h4>From: "+webusername +" (" + webuseremail + ")" +
" at IP address " + ipAddr + "</h4>"+lineSeparator);
if (!(originalReferer == null || originalReferer.equals("none"))){ if (!(originalReferer == null || originalReferer.equals("none"))){
//The spam filter that is being used by the listsrv is rejecting <a href="... //The spam filter that is being used by the listsrv is rejecting <a href="...
@ -227,17 +275,18 @@ public class ContactMailServlet extends VitroHttpServlet {
msgBuf.append("</body>" + lineSeparator ); msgBuf.append("</body>" + lineSeparator );
msgBuf.append("</html>" + lineSeparator ); msgBuf.append("</html>" + lineSeparator );
String msgText = msgBuf.toString(); return msgBuf.toString();
// debugging
PrintWriter outFile = new PrintWriter (new FileWriter(request.getSession().getServletContext().getRealPath("/WEB-INF/LatestMessage.html"),true)); //autoflush
}
private void writeBackupCopy(PrintWriter outFile, String msgText,
String spamReason) {
Calendar cal = Calendar.getInstance(); Calendar cal = Calendar.getInstance();
outFile.println("<hr/>"); outFile.println("<hr/>");
outFile.println(); outFile.println();
outFile.println("<p>"+cal.getTime()+"</p>"); outFile.println("<p>"+cal.getTime()+"</p>");
outFile.println(); outFile.println();
if (probablySpam) { if (spamReason != null) {
outFile.println("<p>REJECTED - SPAM</p>"); outFile.println("<p>REJECTED - SPAM</p>");
outFile.println("<p>"+spamReason+"</p>"); outFile.println("<p>"+spamReason+"</p>");
outFile.println(); outFile.println();
@ -247,13 +296,12 @@ public class ContactMailServlet extends VitroHttpServlet {
outFile.println(); outFile.println();
outFile.flush(); outFile.flush();
// outFile.close(); // outFile.close();
}
// Set the smtp host private void sendMessage(Session s, String webuseremail,
Properties props = System.getProperties(); String[] deliverToArray, String deliveryfrom, int recipientCount,
props.put("mail.smtp.host", smtpHost); String msgText)
Session s = Session.getDefaultInstance(props,null); // was Session.getInstance(props,null); throws AddressException, SendFailedException, MessagingException {
//s.setDebug(true);
try {
// Construct the message // Construct the message
MimeMessage msg = new MimeMessage( s ); MimeMessage msg = new MimeMessage( s );
//System.out.println("trying to send message from servlet"); //System.out.println("trying to send message from servlet");
@ -280,53 +328,50 @@ public class ContactMailServlet extends VitroHttpServlet {
// set the Date: header // set the Date: header
msg.setSentDate( new Date() ); msg.setSentDate( new Date() );
//System.out.println("sending from servlet");
if (!probablySpam)
Transport.send( msg ); // try to send the message via smtp - catch error exceptions Transport.send( msg ); // try to send the message via smtp - catch error exceptions
} catch (AddressException e) {
status = "Please supply a valid email address.";
outFile.println( status );
outFile.println( e.getMessage() );
} catch (SendFailedException e) {
status = "The system was unable to deliver your mail. Please try again later. [SEND FAILED]";
outFile.println( status );
outFile.println( e.getMessage() );
} catch (MessagingException e) {
status = "The system was unable to deliver your mail. Please try again later. [MESSAGING]";
outFile.println( status );
outFile.println( e.getMessage() );
e.printStackTrace();
} }
outFile.flush(); private String validateInput(String webusername, String webuseremail,
outFile.close(); String comments) {
// Redirect to the appropriate confirmation page if( webusername == null || "".equals(webusername.trim()) ){
if (status == null && !probablySpam) { return "A proper webusername field was not found in the form submitted.";
// message was sent successfully
response.sendRedirect( "test?bodyJsp=" + confirmpage + "&home=" + portal.getPortalId() );
} else {
// exception occurred
response.sendRedirect( "test?bodyJsp=" + errpage + "&ERR=" + status + "&home=" + portal.getPortalId() );
} }
if( webuseremail == null || "".equals(webuseremail.trim()) ){
return "A proper webuser email field was not found in the form submitted.";
} }
public void doPost( HttpServletRequest request, HttpServletResponse response ) if (comments==null || "".equals(comments.trim())) {
throws ServletException, IOException return "The proper comments field was not found in the form submitted.";
{
doGet( request, response );
} }
/** Intended to mangle url so it can get through spam filtering return null;
* http://host/dir/servlet?param=value -> host: dir/servlet?param=value */ }
public String stripProtocol( String in ){
if( in == null ) /**
return ""; * @param request
else * @return null if message not judged to be spam, otherwise a String
return in.replaceAll("http://", "host: " ); * containing the reason the message was flagged as spam.
*/
private String checkForSpam(String comments) {
/* if this blog markup is found, treat comment as blog spam */
if (
(comments.indexOf("[/url]") > -1
|| comments.indexOf("[/URL]") > -1
|| comments.indexOf("[url=") > -1
|| comments.indexOf("[URL=") > -1)) {
return "The message contained blog link markup.";
}
/* if message is absurdly short, treat as blog spam */
if (comments.length()<15) {
return "The message was too short.";
}
return null;
} }
} }

21
webapp/src/edu/cornell/mannlib/vitro/webapp/filters/URLRewritingHttpServletResponse.java
View file

@ -27,6 +27,7 @@ import org.openrdf.model.URI;
import org.openrdf.model.impl.URIImpl; import org.openrdf.model.impl.URIImpl;
import edu.cornell.mannlib.vitro.webapp.beans.Portal; import edu.cornell.mannlib.vitro.webapp.beans.Portal;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper; import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapperFactory; import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapperFactory;
@ -37,12 +38,14 @@ public class URLRewritingHttpServletResponse implements HttpServletResponse {
private HttpServletResponse _response; private HttpServletResponse _response;
private HttpServletRequest _request; private HttpServletRequest _request;
private ServletContext _context; private ServletContext _context;
private WebappDaoFactory wadf;
private int contextPathDepth; private int contextPathDepth;
private Pattern slashPattern = Pattern.compile("/"); private Pattern slashPattern = Pattern.compile("/");
public URLRewritingHttpServletResponse(HttpServletResponse response, HttpServletRequest request, ServletContext context) { public URLRewritingHttpServletResponse(HttpServletResponse response, HttpServletRequest request, ServletContext context) {
this._response = response; this._response = response;
this._context = context; this._context = context;
this.wadf = (WebappDaoFactory) context.getAttribute("webappDaoFactory");
this.contextPathDepth = slashPattern.split(request.getContextPath()).length-1; this.contextPathDepth = slashPattern.split(request.getContextPath()).length-1;
} }
@ -94,8 +97,11 @@ public class URLRewritingHttpServletResponse implements HttpServletResponse {
return _response.encodeURL(inUrl); return _response.encodeURL(inUrl);
} }
// rewrite home parameters as portal prefixes for URLs not relative to the current location // rewrite home parameters as portal prefixes or remove
if (url.pathBeginsWithSlash && PortalPickerFilter.isPortalPickingActive) { // if there is only one portal
if ( url.pathBeginsWithSlash &&
(PortalPickerFilter.isPortalPickingActive ||
wadf.getPortalDao().isSinglePortal()) ) {
PortalPickerFilter ppf = PortalPickerFilter.getPortalPickerFilter(this._context); PortalPickerFilter ppf = PortalPickerFilter.getPortalPickerFilter(this._context);
if ( (ppf != null) && (url.queryParams != null) ) { if ( (ppf != null) && (url.queryParams != null) ) {
Iterator<String[]> qpIt = url.queryParams.iterator(); Iterator<String[]> qpIt = url.queryParams.iterator();
@ -149,7 +155,16 @@ public class URLRewritingHttpServletResponse implements HttpServletResponse {
if ( (uri.getNamespace() != null) && (uri.getLocalName() != null) ) { if ( (uri.getNamespace() != null) && (uri.getLocalName() != null) ) {
String prefix = nsMap.getPrefixForNamespace(uri.getNamespace()); String prefix = nsMap.getPrefixForNamespace(uri.getNamespace());
String localName = uri.getLocalName(); String localName = uri.getLocalName();
if (prefix != null) { if (wadf.getDefaultNamespace().
equals(uri.getNamespace())
&& prefix == null) {
// make a URI that matches the URI
// of the resource to support
// linked data request
url.pathParts.add(localName);
// remove the ugly uri parameter
indexToRemove = qpIndex;
} else if (prefix != null) {
// add the pretty path parts // add the pretty path parts
url.pathParts.add(prefix); url.pathParts.add(prefix);
url.pathParts.add(localName); url.pathParts.add(localName);

52
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -24,6 +24,7 @@ import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.vocabulary.OWL; import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType; import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
/** /**
@ -35,6 +36,7 @@ public class ABoxUpdater {
private OntModel oldTboxModel; private OntModel oldTboxModel;
private OntModel newTboxModel; private OntModel newTboxModel;
private OntModel aboxModel; private OntModel aboxModel;
private OntModel newTBoxAnnotationsModel;
private OntologyChangeLogger logger; private OntologyChangeLogger logger;
private OntologyChangeRecord record; private OntologyChangeRecord record;
private OntClass OWL_THING = (ModelFactory private OntClass OWL_THING = (ModelFactory
@ -57,12 +59,14 @@ public class ABoxUpdater {
public ABoxUpdater(OntModel oldTboxModel, public ABoxUpdater(OntModel oldTboxModel,
OntModel newTboxModel, OntModel newTboxModel,
OntModel aboxModel, OntModel aboxModel,
OntModel newAnnotationsModel,
OntologyChangeLogger logger, OntologyChangeLogger logger,
OntologyChangeRecord record) { OntologyChangeRecord record) {
this.oldTboxModel = oldTboxModel; this.oldTboxModel = oldTboxModel;
this.newTboxModel = newTboxModel; this.newTboxModel = newTboxModel;
this.aboxModel = aboxModel; this.aboxModel = aboxModel;
this.newTBoxAnnotationsModel = newAnnotationsModel;
this.logger = logger; this.logger = logger;
this.record = record; this.record = record;
} }
@ -129,30 +133,58 @@ public class ABoxUpdater {
Resource newClass = ResourceFactory.createResource(change.getDestinationURI()); Resource newClass = ResourceFactory.createResource(change.getDestinationURI());
// Change class references in the subjects of statements // Change class references in the subjects of statements
// BJL 2010-04-09 : In future versions we need to keep track of
// the difference between true direct renamings and "use-insteads."
// For now, the best behavior is to remove any remaining statements
// where the old class is the subject, *unless* the statements
// is part of the new annotations file (see comment below) or the
// predicate is vitro:autolinkedToTab. In the latter case,
// the autolinking annotation should be rewritten using the
// new class name.
Property autoLinkedToTab = ResourceFactory.createProperty(VitroVocabulary.TAB_AUTOLINKEDTOTAB);
StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null); StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
int count = 0; int renameCount = 0;
int removeCount = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
count++;
Statement oldStatement = iter.next(); Statement oldStatement = iter.next();
if (newTBoxAnnotationsModel.contains(oldStatement)) {
continue;
// if this statement was loaded from the new annotations,
// don't attempt to remove it.
// This happens in cases where a class hasn't really
// been removed, but we just want to map any ABox
// data using it to use a different class instead.
}
if (autoLinkedToTab.equals(oldStatement.getPredicate())) {
renameCount++;
Statement newStatement = ResourceFactory.createStatement(newClass, oldStatement.getPredicate(), oldStatement.getObject()); Statement newStatement = ResourceFactory.createStatement(newClass, oldStatement.getPredicate(), oldStatement.getObject());
retractions.add(oldStatement);
additions.add(newStatement); additions.add(newStatement);
} else {
removeCount++;
retractions.add(oldStatement);
}
//logChange(oldStatement, false); //logChange(oldStatement, false);
//logChange(newStatement,true); //logChange(newStatement,true);
} }
//log summary of changes //log summary of changes
if (count > 0) { if (renameCount > 0) {
logger.log("Changed " + count + " subject reference" + ((count > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI()); logger.log("Changed " + renameCount + " subject reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI());
}
if (removeCount > 0) {
logger.log("Removed " + removeCount + " remaining subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class");
} }
// Change class references in the objects of statements // Change class references in the objects of rdf:type statements
iter = aboxModel.listStatements((Resource) null, (Property) null, oldClass); iter = aboxModel.listStatements((Resource) null, (Property) null, oldClass);
count = 0; renameCount = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
count++; renameCount++;
Statement oldStatement = iter.next(); Statement oldStatement = iter.next();
Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), oldStatement.getPredicate(), newClass); Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), oldStatement.getPredicate(), newClass);
retractions.add(oldStatement); retractions.add(oldStatement);
@ -163,8 +195,8 @@ public class ABoxUpdater {
} }
//log summary of changes //log summary of changes
if (count > 0) { if (renameCount > 0) {
logger.log("Changed " + count + " object reference" + ((count > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI()); logger.log("Changed " + renameCount + " object reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI());
} }
aboxModel.remove(retractions); aboxModel.remove(retractions);

15
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
View file

@ -96,13 +96,11 @@ public class OntologyUpdater {
settings.getNewTBoxModel(), settings.getNewTBoxModel(),
settings.getOldTBoxModel()); settings.getOldTBoxModel());
//updateTBox(changes); //process the TBox before the ABox
//preprocessChanges(changes); updateTBoxAnnotations();
updateABox(changes); updateABox(changes);
updateTBoxAnnotations();
} }
/** /**
@ -172,8 +170,12 @@ public class OntologyUpdater {
} }
} }
aboxModel.add(actualAdditions); aboxModel.add(actualAdditions);
if (actualAdditions.size() > 0) {
logger.log("Constructed " + actualAdditions.size() + " new " + logger.log("Constructed " + actualAdditions.size() + " new " +
"statements using SPARQL CONSTRUCT queries."); "statement"
+ ((actualAdditions.size() > 1) ? "s" : "") +
" using SPARQL CONSTRUCT queries.");
}
record.recordAdditions(actualAdditions); record.recordAdditions(actualAdditions);
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
@ -198,7 +200,8 @@ public class OntologyUpdater {
OntModel newTBoxModel = settings.getNewTBoxModel(); OntModel newTBoxModel = settings.getNewTBoxModel();
OntModel ABoxModel = settings.getOntModelSelector().getABoxModel(); OntModel ABoxModel = settings.getOntModelSelector().getABoxModel();
ABoxUpdater aboxUpdater = new ABoxUpdater( ABoxUpdater aboxUpdater = new ABoxUpdater(
oldTBoxModel, newTBoxModel, ABoxModel, logger, record); oldTBoxModel, newTBoxModel, ABoxModel,
settings.getNewTBoxAnnotationsModel(), logger, record);
aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges()); aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
aboxUpdater.processClassChanges(changes.getAtomicClassChanges()); aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
// run additional SPARQL CONSTRUCTS // run additional SPARQL CONSTRUCTS

4
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -54,9 +54,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
private final String ERROR_LOG_FILE = DATA_DIR + LOG_DIR + private final String ERROR_LOG_FILE = DATA_DIR + LOG_DIR +
"knowledgeBaseUpdate.error.log"; "knowledgeBaseUpdate.error.log";
private final String REMOVED_DATA_FILE = DATA_DIR + CHANGED_DATA_DIR + private final String REMOVED_DATA_FILE = DATA_DIR + CHANGED_DATA_DIR +
"removedData.rdf"; "removedData.n3";
private final String ADDED_DATA_FILE = DATA_DIR + CHANGED_DATA_DIR + private final String ADDED_DATA_FILE = DATA_DIR + CHANGED_DATA_DIR +
"addedData.rdf"; "addedData.n3";
private final String SPARQL_CONSTRUCTS_DIR = DATA_DIR + "sparqlConstructs/"; private final String SPARQL_CONSTRUCTS_DIR = DATA_DIR + "sparqlConstructs/";
private final String MISC_REPLACEMENTS_FILE = DATA_DIR + "miscReplacements.rdf"; private final String MISC_REPLACEMENTS_FILE = DATA_DIR + "miscReplacements.rdf";
private final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/"; private final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/";