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Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

Browse source 
um, just mergin' in the remote changes before a push?
This commit is contained in:
brianjlowe 2012-11-27 12:59:16 -05:00
commit cd7fe20cac
28 changed files with 334 additions and 351 deletions
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9
webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ApplicationBean.java
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@ -49,15 +49,6 @@ public class ApplicationBean {
private String copyrightAnchor;
private String themeDir;
public static ApplicationBean getAppBean(ServletContext sc){
if( sc != null ){
Object obj = sc.getAttribute("applicationBean");
if( obj != null )
return (ApplicationBean)obj;
}
return new ApplicationBean();
}
public String toString() {
String output = "Application Bean Contents:\n";
output += " initialized from DB: [" + initialized + "]\n";

5
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/OntologyController.java
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@ -33,9 +33,6 @@ import edu.cornell.mannlib.vitro.webapp.web.ContentType;
public class OntologyController extends VitroHttpServlet{
private static final Log log = LogFactory.getLog(OntologyController.class.getName());
private String default_jsp = Controllers.BASIC_JSP;
private ApplicationBean appBean;
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException,IOException{
doGet(request, response);
@ -242,7 +239,7 @@ public class OntologyController extends VitroHttpServlet{
throws IOException, ServletException {
VitroRequest vreq = new VitroRequest(req);
ApplicationBean appBean = ApplicationBean.getAppBean(getServletContext());
ApplicationBean appBean = vreq.getAppBean();
//set title before we do the highlighting so we don't get markup in it.
req.setAttribute("title","not found");

4
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/VitroRequest.java
View file

@ -283,12 +283,8 @@ public class VitroRequest extends HttpServletRequestWrapper {
}
public ApplicationBean getAppBean(){
//return (ApplicationBean) getAttribute("appBean");
return getWebappDaoFactory().getApplicationDao().getApplicationBean();
}
public void setAppBean(ApplicationBean ab){
setAttribute("appBean",ab);
}
@SuppressWarnings("unchecked")
@Override

8
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/admin/StartupStatusController.java
View file

@ -7,7 +7,6 @@ import java.util.Map;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
@ -31,7 +30,7 @@ public class StartupStatusController extends FreemarkerHttpServlet {
body.put("title", "Startup Status");
body.put("status", StartupStatus.getBean(getServletContext()));
body.put("contextPath", getContextPath());
body.put("applicationName", getApplicationName());
body.put("applicationName", getApplicationName(vreq));
return new TemplateResponseValues("startupStatus-display.ftl", body);
}
@ -45,11 +44,10 @@ public class StartupStatusController extends FreemarkerHttpServlet {
}
}
private Object getApplicationName() {
private Object getApplicationName(VitroRequest vreq) {
String name = "";
try {
ApplicationBean app = ApplicationBean.getAppBean(getServletContext());
name = app.getApplicationName();
name = vreq.getAppBean().getApplicationName();
} catch (Exception e) {
// deal with problems below
}

6
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalysisContext.java
View file

@ -15,12 +15,6 @@ public interface IndividualRequestAnalysisContext {
*/
String getDefaultNamespace();
/**
* Is there a namespace for this prefix? If not, return an empty string, but
* never null.
*/
String getNamespaceForPrefix(String prefix);
/**
* Use the IndividualDao to get this individual.
*

21
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalysisContextImpl.java
View file

@ -15,8 +15,6 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.filestorage.model.FileInfo;
import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapperFactory;
/**
* Implement all of the fiddly-bits that we need for analyzing the request for
@ -45,25 +43,6 @@ public class IndividualRequestAnalysisContextImpl implements
return wadf.getDefaultNamespace();
}
@Override
public String getNamespaceForPrefix(String prefix) {
if (prefix == null) {
return "";
}
NamespaceMapper namespaceMapper = NamespaceMapperFactory
.getNamespaceMapper(ctx);
if (namespaceMapper == null) {
log.warn("No NamespaceMapper in ServletContext. Request URL was '"
+ vreq.getRequestURL() + "'");
return "";
}
String ns = namespaceMapper.getNamespaceForPrefix(prefix);
return (ns == null) ? "" : ns;
}
@Override
public Individual getIndividualByURI(String individualUri) {
if (individualUri == null) {

16
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java
View file

@ -30,7 +30,6 @@ public class IndividualRequestAnalyzer {
private static Pattern RDF_REQUEST = Pattern.compile("^/individual/([^/]+)/\\1\\.(rdf|n3|ttl)$");
private static Pattern HTML_REQUEST = Pattern.compile("^/display/([^/]+)$");
private static Pattern LINKED_DATA_URL = Pattern.compile("^/individual/([^/]+)$");
private static Pattern NS_PREFIX_URL = Pattern.compile("^/individual/([^/]*)/([^/]+)$");
private final VitroRequest vreq;
private final IndividualRequestAnalysisContext analysisContext;
@ -164,7 +163,6 @@ public class IndividualRequestAnalyzer {
* /individual/localname/localname.rdf
* /individual/localname/localname.n3
* /individual/localname/localname.ttl
* /individual/nsprefix/localname
* </pre>
*
* @return null on failure.
@ -202,14 +200,6 @@ public class IndividualRequestAnalyzer {
return getIndividualByLocalname(rdfMatch.group(1));
}
// Does the URL look like a namespace prefix followed by a local
// name?
Matcher prefix_match = NS_PREFIX_URL.matcher(url);
if (prefix_match.matches() && prefix_match.groupCount() == 2) {
return getIndividualByPrefixAndLocalname(prefix_match.group(1),
prefix_match.group(2));
}
// Couldn't match it to anything.
return null;
} catch (Throwable e) {
@ -299,12 +289,6 @@ public class IndividualRequestAnalyzer {
return getIndividualByUri(uri);
}
private Individual getIndividualByPrefixAndLocalname(String prefix,
String localName) {
String ns = analysisContext.getNamespaceForPrefix(prefix);
return getIndividualByUri(ns + localName);
}
private Individual getIndividualByNetId(String netId) {
return analysisContext.getIndividualByNetId(netId);
}

67
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DateTimeValueFormGenerator.java
View file

@ -27,7 +27,7 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
implements EditConfigurationGenerator {
final static String vivoCore = "http://vivoweb.org/ontology/core#";
final static String toDateTimeValue = vivoCore + "dateTimeValue";
final String toDateTimeValue = vivoCore + "dateTimeValue";
final static String valueType = vivoCore + "DateTimeValue";
final static String dateTimeValue = vivoCore + "dateTime";
final static String dateTimePrecision = vivoCore + "dateTimePrecision";
@ -41,23 +41,23 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
initPropertyParameters(vreq, session, conf);
initObjectPropForm(conf, vreq);
conf.setTemplate("dateTimeValueForm.ftl");
conf.setTemplate(this.getTemplate());
conf.setVarNameForSubject("subject");
conf.setVarNameForPredicate("toDateTimeValue");
conf.setVarNameForObject("valueNode");
conf.setN3Optional(Arrays.asList(n3ForValue));
conf.setN3Optional(Arrays.asList(getN3ForValue()));
conf.addNewResource("valueNode", DEFAULT_NS_FOR_NEW_RESOURCE);
conf.addSparqlForExistingLiteral(
"dateTimeField-value", existingDateTimeValueQuery);
"dateTimeField-value", getExistingDateTimeValueQuery());
conf.addSparqlForExistingUris(
"dateTimeField-precision", existingPrecisionQuery);
conf.addSparqlForExistingUris("valueNode", existingNodeQuery);
"dateTimeField-precision", getExistingPrecisionQuery());
conf.addSparqlForExistingUris("valueNode", getExistingNodeQuery());
FieldVTwo dateTimeField = new FieldVTwo().setName("dateTimeField");
FieldVTwo dateTimeField = new FieldVTwo().setName(this.getDateTimeFieldName());
dateTimeField.setEditElement(new DateTimeWithPrecisionVTwo(dateTimeField,
VitroVocabulary.Precision.SECOND.uri(),
VitroVocabulary.Precision.NONE.uri()));
@ -67,34 +67,40 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
//Adding additional data, specifically edit mode
addFormSpecificData(conf, vreq);
//prepare
prepare(vreq, conf);
return conf;
}
prepare(vreq, conf);
return conf;
}
final static String n3ForValue =
"?subject <" + toDateTimeValue + "> ?valueNode . \n" +
//Writing these as methods instead of static strings allows the method getToDateTimeValuePredicate
//to be called after the class has been initialized - this is important for subclasses of this generator
//that rely on vreq for predicate
protected String getN3ForValue() {
return "?subject <" + this.getToDateTimeValuePredicate() + "> ?valueNode . \n" +
"?valueNode a <" + valueType + "> . \n" +
"?valueNode <" + dateTimeValue + "> ?dateTimeField-value . \n" +
"?valueNode <" + dateTimePrecision + "> ?dateTimeField-precision .";
"?valueNode <" + dateTimePrecision + "> ?dateTimeField-precision .";
}
final static String existingDateTimeValueQuery =
"SELECT ?existingDateTimeValue WHERE { \n" +
"?subject <" + toDateTimeValue + "> ?existingValueNode . \n" +
protected String getExistingDateTimeValueQuery () {
return "SELECT ?existingDateTimeValue WHERE { \n" +
"?subject <" + this.getToDateTimeValuePredicate() + "> ?existingValueNode . \n" +
"?existingValueNode a <" + valueType + "> . \n" +
"?existingValueNode <" + dateTimeValue + "> ?existingDateTimeValue }";
}
final static String existingPrecisionQuery =
"SELECT ?existingPrecision WHERE { \n" +
"?subject <" + toDateTimeValue + "> ?existingValueNode . \n" +
protected String getExistingPrecisionQuery() {
return "SELECT ?existingPrecision WHERE { \n" +
"?subject <" + this.getToDateTimeValuePredicate() + "> ?existingValueNode . \n" +
"?existingValueNode a <" + valueType + "> . \n" +
"?existingValueNode <" + dateTimePrecision + "> ?existingPrecision }";
final static String existingNodeQuery =
"SELECT ?existingNode WHERE { \n" +
"?subject <" + toDateTimeValue + "> ?existingNode . \n" +
}
protected String getExistingNodeQuery() {
return "SELECT ?existingNode WHERE { \n" +
"?subject <" + this.getToDateTimeValuePredicate() + "> ?existingNode . \n" +
"?existingNode a <" + valueType + "> }";
}
public static String getNodeVar() {
return "valueNode";
}
@ -103,6 +109,19 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
return "?" + getNodeVar();
}
//isolating the predicate in this fashion allows this class to be subclassed for other date time value
//properties
protected String getToDateTimeValuePredicate() {
return this.toDateTimeValue;
}
protected String getDateTimeFieldName() {
return "dateTimeField";
}
protected String getTemplate() {
return "dateTimeValueForm.ftl";
}
//Adding form specific data such as edit mode
public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
HashMap<String, Object> formSpecificData = new HashMap<String, Object>();

4
webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/serving/FileServingServlet.java
View file

@ -94,6 +94,10 @@ public class FileServingServlet extends VitroHttpServlet {
String actualFilename = findAndValidateFilename(fileInfo, path);
in = openImageInputStream(fileInfo, actualFilename);
} catch (FileServingException e) {
log.info("Failed to serve the file at '" + path + "' -- " + e.getMessage());
in = openMissingLinkImage(request);
mimeType = "image/png";
} catch (Exception e) {
log.warn("Failed to serve the file at '" + path + "' -- " + e.getMessage());
in = openMissingLinkImage(request);

50
webapp/src/edu/cornell/mannlib/vitro/webapp/filters/StartupStatusDisplayFilter.java
View file

@ -21,6 +21,8 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang.StringUtils;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import freemarker.cache.WebappTemplateLoader;
import freemarker.template.Configuration;
@ -67,36 +69,36 @@ public class StartupStatusDisplayFilter implements Filter {
statusAlreadyDisplayed = true;
}
private void displayStartupStatus(ServletRequest req, ServletResponse resp) throws IOException,
ServletException {
HttpServletResponse hResp = (HttpServletResponse) resp;
private void displayStartupStatus(ServletRequest req, ServletResponse resp)
throws IOException, ServletException {
HttpServletResponse hresp = (HttpServletResponse) resp;
HttpServletRequest hreq = (HttpServletRequest) req;
try {
Map<String, Object> bodyMap = new HashMap<String, Object>();
bodyMap.put("status", ss);
bodyMap.put("showLink", !isFatal());
bodyMap.put("contextPath", getContextPath());
bodyMap.put("applicationName", getApplicationName());
HttpServletRequest httpreq = (HttpServletRequest) req;
String url = "";
String path = httpreq.getRequestURI();
if( path != null ){
url = path;
}
String query = httpreq.getQueryString();
if( !StringUtils.isEmpty( query )){
url = url + "?" + query;
}
bodyMap.put("url", url );
bodyMap.put("applicationName", getApplicationName());
hResp.setContentType("text/html;charset=UTF-8");
hResp.setStatus(SC_INTERNAL_SERVER_ERROR);
String url = "";
String path = hreq.getRequestURI();
if (path != null) {
url = path;
}
String query = hreq.getQueryString();
if (!StringUtils.isEmpty(query)) {
url = url + "?" + query;
}
bodyMap.put("url", url);
hresp.setContentType("text/html;charset=UTF-8");
hresp.setStatus(SC_INTERNAL_SERVER_ERROR);
Template tpl = loadFreemarkerTemplate();
tpl.process(bodyMap, hResp.getWriter());
tpl.process(bodyMap, hresp.getWriter());
} catch (TemplateException e) {
throw new ServletException("Problem with Freemarker Template", e);
}
@ -114,7 +116,9 @@ public class StartupStatusDisplayFilter implements Filter {
private Object getApplicationName() {
String name = "";
try {
ApplicationBean app = ApplicationBean.getAppBean(ctx);
WebappDaoFactory wadf = (WebappDaoFactory) ctx
.getAttribute("webappDaoFactory");
ApplicationBean app = wadf.getApplicationDao().getApplicationBean();
name = app.getApplicationName();
} catch (Exception e) {
// deal with problems below

13
webapp/src/edu/cornell/mannlib/vitro/webapp/filters/VitroRequestPrep.java
View file

@ -38,7 +38,6 @@ import edu.cornell.mannlib.vitro.webapp.auth.identifier.RequestIdentifiers;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
import edu.cornell.mannlib.vitro.webapp.auth.policy.ServletPolicyList;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@ -82,19 +81,10 @@ public class VitroRequestPrep implements Filter {
};
private ServletContext _context;
private ApplicationBean _appbean;
@Override
public void init(FilterConfig filterConfig) throws ServletException {
_context = filterConfig.getServletContext();
Object o = _context.getAttribute("applicationBean");
if (o instanceof ApplicationBean) {
_appbean = (ApplicationBean) o;
} else {
_appbean = new ApplicationBean();
}
log.debug("VitroRequestPrep: AppBean theme " + _appbean.getThemeDir());
}
@Override
@ -132,9 +122,6 @@ public class VitroRequestPrep implements Filter {
VitroRequest vreq = new VitroRequest(req);
//-- setup appBean --//
vreq.setAppBean(_appbean);
//-- setup DAO factory --//
WebappDaoFactory wdf = getWebappDaoFactory(vreq);
//TODO: get accept-language from request and set as preferred languages