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From: <rv...@us...> - 2010-02-15 16:05:25
|
Revision: 509
http://treebase.svn.sourceforge.net/treebase/?rev=509&view=rev
Author: rvos
Date: 2010-02-15 16:05:19 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
GUI change, the reviewer purl is too long
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-02-15 16:01:56 UTC (rev 508)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-02-15 16:05:19 UTC (rev 509)
@@ -18,7 +18,7 @@
<br/>
<a href="<c:out value="${submission.study.phyloWSPath.purl}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
- Reviewer access URL: <c:out value="${submission.study.phyloWSPath.purl}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html
+ Reviewer access URL: right-click and copy
</a>
<c:if test="${not empty citationsummary.study}">
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|
|
From: <rv...@us...> - 2010-02-15 16:02:03
|
Revision: 508
http://treebase.svn.sourceforge.net/treebase/?rev=508&view=rev
Author: rvos
Date: 2010-02-15 16:01:56 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Now explicitly displays purl for reviewer access.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-02-15 15:55:46 UTC (rev 507)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionSummaryView.jsp 2010-02-15 16:01:56 UTC (rev 508)
@@ -16,9 +16,9 @@
Contact Submitter
</a>
<br/>
-<a href="/treebase-web/phylows/<c:out value="${submission.study.phyloWSPath}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html">
+<a href="<c:out value="${submission.study.phyloWSPath.purl}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html">
<img class="iconButton" alt="link" src="<fmt:message key="icons.weblink"/>" />
- Reviewer access URL: right-click and copy me
+ Reviewer access URL: <c:out value="${submission.study.phyloWSPath.purl}"/>?x-access-code=<c:out value="${submission.study.namespacedGUID.hashedIDString}"/>&format=html
</a>
<c:if test="${not empty citationsummary.study}">
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From: <rv...@us...> - 2010-02-15 15:55:53
|
Revision: 507
http://treebase.svn.sourceforge.net/treebase/?rev=507&view=rev
Author: rvos
Date: 2010-02-15 15:55:46 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Loading properties file as ResourceStream instead.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-02-15 15:29:39 UTC (rev 506)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-02-15 15:55:46 UTC (rev 507)
@@ -439,7 +439,11 @@
Properties properties = new Properties();
String domainName = "";
try {
- properties.load( new FileInputStream("treebase.properties") );
+ properties.load(
+ TreebaseUtil.class
+ .getClassLoader()
+ .getResourceAsStream("treebase.properties"));
+ //properties.load( new FileInputStream("treebase.properties") );
LOGGER.info("properties loaded successfully");
domainName = properties.getProperty("treebase.purl.domain");
LOGGER.info("domain name: "+domainName);
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From: <rv...@us...> - 2010-02-15 15:29:48
|
Revision: 506
http://treebase.svn.sourceforge.net/treebase/?rev=506&view=rev
Author: rvos
Date: 2010-02-15 15:29:39 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Added logging messages.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java 2010-02-15 15:14:49 UTC (rev 505)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java 2010-02-15 15:29:39 UTC (rev 506)
@@ -3,11 +3,13 @@
import java.net.MalformedURLException;
import java.net.URL;
+import org.apache.log4j.Logger;
import org.cipres.treebase.domain.TBPersistable;
public class PhyloWSPath {
private NamespacedGUID mNamespacedGUID;
private Package mPackage;
+ private static final Logger LOGGER = Logger.getLogger(PhyloWSPath.class);
public StringBuilder getPath(StringBuilder sb) {
String[] packagePathFragments = mPackage.getName().split("\\.");
@@ -30,10 +32,12 @@
public URL getPurl () {
StringBuilder sb = new StringBuilder(TreebaseUtil.getPurlDomain());
sb = getPath(sb).append(mNamespacedGUID.toString());
+ LOGGER.info(sb);
URL url = null;
try {
url = new URL(sb.toString());
} catch (MalformedURLException e) {
+ LOGGER.warn("MalformedURLException: "+e.getMessage());
e.printStackTrace();
}
return url;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-02-15 15:14:49 UTC (rev 505)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-02-15 15:29:39 UTC (rev 506)
@@ -17,6 +17,7 @@
import java.util.Properties;
import java.util.TimeZone;
+import org.apache.log4j.Logger;
import org.cipres.treebase.domain.study.Citation;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.framework.ExecutionResult;
@@ -39,6 +40,7 @@
public static final String ANEMPTYSPACE = " ";
public static final String LINESEP = System.getProperty("line.separator");
public static final int citationMaxLength = 5000;
+ private static final Logger LOGGER = Logger.getLogger(TreebaseUtil.class);
private TreebaseUtil() {
super();
@@ -438,10 +440,14 @@
String domainName = "";
try {
properties.load( new FileInputStream("treebase.properties") );
+ LOGGER.info("properties loaded successfully");
domainName = properties.getProperty("treebase.purl.domain");
+ LOGGER.info("domain name: "+domainName);
} catch (FileNotFoundException e) {
+ LOGGER.warn("FileNotFoundException: " + e.getMessage());
e.printStackTrace();
} catch (IOException e) {
+ LOGGER.warn("IOException: "+e.getMessage());
e.printStackTrace();
}
return domainName;
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|
|
From: <rv...@us...> - 2010-02-15 15:15:10
|
Revision: 505
http://treebase.svn.sourceforge.net/treebase/?rev=505&view=rev
Author: rvos
Date: 2010-02-15 15:14:49 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Now uses purl as canonical url
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp 2010-02-15 15:06:59 UTC (rev 504)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp 2010-02-15 15:14:49 UTC (rev 505)
@@ -8,9 +8,7 @@
</head>
<body id="s-study"/>
-<c:set var="serverName" scope="request" value="<%= request.getServerName() %>"/>
-<c:set var="portNumber" scope="request" value="<%= request.getServerPort() %>"/>
-<c:set var="baseLink" scope="request" value='http://${serverName}:${portNumber}/treebase-web/phylows/${study.phyloWSPath}'/>
+<c:set var="baseLink" scope="request" value='${study.phyloWSPath.purl}'/>
<c:set var="currentSection" scope="request" value="Citation"/>
<c:set var="headerPrefix" scope="request" value="${currentSection} for"/>
<jsp:include page="nav.jsp"/>
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|
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From: <rv...@us...> - 2010-02-15 15:07:06
|
Revision: 504
http://treebase.svn.sourceforge.net/treebase/?rev=504&view=rev
Author: rvos
Date: 2010-02-15 15:06:59 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Changed getDomainName() to getPurlDomain(), changed the name of the property it looks up from treebase.domain.name to treebase.purl.domain
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-02-15 15:05:38 UTC (rev 503)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-02-15 15:06:59 UTC (rev 504)
@@ -433,12 +433,12 @@
*
* @return domain name
*/
- public static String getDomainName() {
+ public static String getPurlDomain() {
Properties properties = new Properties();
String domainName = "";
try {
properties.load( new FileInputStream("treebase.properties") );
- domainName = properties.getProperty("treebase.domain.name");
+ domainName = properties.getProperty("treebase.purl.domain");
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
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|
|
From: <rv...@us...> - 2010-02-15 15:06:07
|
Revision: 503
http://treebase.svn.sourceforge.net/treebase/?rev=503&view=rev
Author: rvos
Date: 2010-02-15 15:05:38 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Added getPurl() method.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java 2010-02-15 15:01:00 UTC (rev 502)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/PhyloWSPath.java 2010-02-15 15:05:38 UTC (rev 503)
@@ -1,5 +1,8 @@
package org.cipres.treebase;
+import java.net.MalformedURLException;
+import java.net.URL;
+
import org.cipres.treebase.domain.TBPersistable;
public class PhyloWSPath {
@@ -16,9 +19,27 @@
public String getPath() {
return getPath(new StringBuilder()).toString();
- }
+ }
/**
+ * This method constructs a permanent url based on the
+ * treebase.purl.domain property (as computed by TreebaseUtil.getPurlDomain()),
+ * the phylows path and the namespaced GUID for the object.
+ * @return the permanent url for the object
+ */
+ public URL getPurl () {
+ StringBuilder sb = new StringBuilder(TreebaseUtil.getPurlDomain());
+ sb = getPath(sb).append(mNamespacedGUID.toString());
+ URL url = null;
+ try {
+ url = new URL(sb.toString());
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+ return url;
+ }
+
+ /**
*
*/
public String toString() {
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|
From: <rv...@us...> - 2010-02-15 15:01:07
|
Revision: 502
http://treebase.svn.sourceforge.net/treebase/?rev=502&view=rev
Author: rvos
Date: 2010-02-15 15:01:00 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Changed treebase.domain.name to treebase.purl.domain
Modified Paths:
--------------
trunk/treebase-core/src/main/resources/treebase.properties
Modified: trunk/treebase-core/src/main/resources/treebase.properties
===================================================================
--- trunk/treebase-core/src/main/resources/treebase.properties 2010-02-15 13:52:32 UTC (rev 501)
+++ trunk/treebase-core/src/main/resources/treebase.properties 2010-02-15 15:01:00 UTC (rev 502)
@@ -1,3 +1,3 @@
#options are: NexusServiceMesquite | NexusServiceNCL
nexus.parser.impl=NexusServiceMesquite
-treebase.domain.name=treebase-dev.nescent.org:6666
+treebase.purl.domain=http://purl.org/phylo/treebase/phylows/
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From: <rv...@us...> - 2010-02-15 14:01:24
|
Revision: 497
http://treebase.svn.sourceforge.net/treebase/?rev=497&view=rev
Author: rvos
Date: 2010-02-15 12:29:51 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Added comment where genbank accession numbers should be serialized into nexml
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2010-02-12 07:21:53 UTC (rev 496)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2010-02-15 12:29:51 UTC (rev 497)
@@ -315,6 +315,11 @@
if ( tbSegment.getSpecimenLabel().getLongitude() != null ) {
((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLongitude", mDwCURI, tbSegment.getSpecimenLabel().getLongitude());
}
+ /*
+ if ( tbSegment.getSpecimenLabel().getGenBankAccession() != null ) {
+ ((Annotatable)xmlCell).addAnnotationValue(arg0, arg1, arg2)
+ }
+ */
}
}
charIndex++;
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From: SourceForge.net <no...@so...> - 2010-02-15 13:57:03
|
Bugs item #2903251, was opened at 2009-11-24 17:34 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2903251&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Rutger Vos (rvos) Summary: Exception when uploading nexus to a new submission Initial Comment: When I log in as a normal user (user: pieltest, password: pieltest) and I try to upload a nexus file to a new submission, I get the following error. bp Uncaught Exception Encountered java.lang.ExceptionInInitializerError at mesquite.Mesquite.main(Mesquite.java:2261) at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232) at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657) at ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-02-15 13:57 Message: File uploading now works as expected on 6666, which was configured following Jon A.'s directions, so it should also work on dev/stage/prod. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-17 13:54 Message: Mesquite now loads successfully. We're still getting Data Access Errors; something seems to be wrong with the way primary keys are incremented on postgres, but it's not a mesquite issue. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-17 13:54 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-10 16:26 Message: ALERT: (Mesquite): Please find the Mesquite manual file named "manual.html", which should be in the "docs/mesquite" directory. java.lang.NullPointerException at mesquite.lib.MesquiteFileDialog.<init>(MesquiteFileDialog.java:31) at mesquite.lib.MesquiteFile.checkFilePath(MesquiteFile.java:2015) at mesquite.Mesquite.findMesquiteDirectory(Mesquite.java:583) at mesquite.Mesquite.processSingleXMLPreference(Mesquite.java:802) at mesquite.lib.MesquiteModule.processPreferencesFromXML(MesquiteModule.java:745) at mesquite.lib.MesquiteModule.loadPreferences(MesquiteModule.java:704) at mesquite.Mesquite.init(Mesquite.java:184) at mesquite.Mesquite.<init>(Mesquite.java:2033) at mesquite.Mesquite.main(Mesquite.java:2088) at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232) at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:581) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.addNexusFilesJDBC(Unknown Source) at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:196) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Exception caught in Mesquite: null ALERT: (Mesquite): Mesquite cannot function: no file coordinator available (Following stack trace from object of class: class mesquite.lib.ProjectRead) java.lang.NullPointerException at mesquite.lib.ProjectRead.run(ProjectRead.java:212) at java.lang.Thread.run(Thread.java:636) at mesquite.lib.MesquiteThread.run(MesquiteThread.java:63) at mesquite.lib.ProjectReadThread.run(ProjectReadThread.java:55) ALERT: (Mesquite): File reading could not be completed because an exception or error occurred (i.e. a crash; class java.lang.NullPointerExcepti on). If you save any files, you might best use Save As... in case data were lost or file saving doesn't work properly. To report this as a bug , PLEASE send along the Mesquite_Log file from Mesquite_Support_Files. - ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-10 16:00 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2903251&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-02-15 13:55:06
|
Bugs item #2949853, was opened at 2010-02-11 18:26 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2949853&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: User cannot download his matrices within his own submission Initial Comment: For the user tb3, I uploaded a data matrix (matrix_id 4219), and then tried to download the "reconstructed" data like so: http://treebasedb-dev.nescent.org/treebase-web/user/downloadAMatrix.html?matrixid=4219 This generated an error because the code fails to enter the study_id in the matrix table. bp Uncaught Exception Encountered java.lang.NullPointerException at org.cipres.treebase.web.controllers.AbstractDownloadController.generateAFileDynamically(AbstractDownloadController.java:125) at org.cipres.treebase.web.controllers.DownloadAMatrixController.handleRequest(DownloadAMatrixController.java:79) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org/treebase-web/user/treeBlockList.html] itemToHighlight=[http%3A//treebasedb-dev.nescent.org/treebase-web/user/treeBlockList.html] JSESSIONID=[90FE0A6E3C5A36D5AA0576C554CB52D9] __utma=[53240375.1924499357.1236724314.1265838306.1265854340.45] __utmc=[53240375] __utmz=[53240375.1265602159.42.7.utmccn] ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-02-15 13:55 Message: Fixed as of revision 501 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2949853&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-02-15 13:54:46
|
Bugs item #2945440, was opened at 2010-02-03 19:24 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945440&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: User cannot download his trees within his own submission Initial Comment: A basic user (in this case, username "tb3" with password "tb3", and submission 9923) who uploads a tree to his submission, is blocked from downloading the "reconstructed" tree from within the submission interface. To replicate the problem, login to submission 9923, go to the tree blocks: http://treebasedb-dev.nescent.org:6666/treebase-web/user/treeBlockList.html Then click on the "download reconstructed tree" links, e.g.: http://treebasedb-dev.nescent.org:6666/treebase-web/user/downloadATreeBlock.html?treeblockid=9662 The result is "Access denied. Sorry! your action is not authorized." If you look inside the tree block and then try to download a reconstructed tree, you get a "Uncaught Exception Encountered" (see text below). These errors may be related to a recent fix that Rutger made to prevent "in progress" data from being accessed anonymously. The rules should be the following: 1. Anonymous users can only access data associated with studies that are considered "published" unless they use a /phylows/ url with a valid x-access-code parameter. Access as study with a valid x-access-code provides access to download links within that study throughout that session. 2. Users who create a submission can alway access the data in that submission regardless of status, but they can only edit data if the submission is "in progress" 3. Admin and Associate Editors can both access and edit all data regardless of status. bp Uncaught Exception Encountered java.lang.NullPointerException at org.cipres.treebase.web.controllers.AbstractDownloadController.generateAFileDynamically(AbstractDownloadController.java:125) at org.cipres.treebase.web.controllers.DownloadATreeController.handleRequest(DownloadATreeController.java:76) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/treeBlockList.html] itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/submissionList.html] JSESSIONID=[A56E40E535C9BD4451883A467D1473F0] __utma=[53240375.1924499357.1236724314.1264137469.1264687265.41] __utmz=[53240375.1263756485.39.6.utmccn] ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2010-02-15 13:54 Message: Fixed as of revision 501 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945440&group_id=248804 |
|
From: <rv...@us...> - 2010-02-15 13:52:46
|
Revision: 501
http://treebase.svn.sourceforge.net/treebase/?rev=501&view=rev
Author: rvos
Date: 2010-02-15 13:52:32 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Obtaining the Study in a different way, this should address an NPE I've been having.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2010-02-15 13:32:51 UTC (rev 500)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2010-02-15 13:52:32 UTC (rev 501)
@@ -158,7 +158,8 @@
}
private boolean isSubmitter (long objectId,HttpServletRequest request) {
- Study study = getStudy(objectId,request);
+ Study study = ControllerUtil.findStudy(request, getStudyService());
+ //Study study = getStudy(objectId,request);
Submission submission = study.getSubmission();
TBPermission tbp = getSubmissionService().getPermission(request.getRemoteUser(), submission.getId());
if (tbp == TBPermission.WRITE || tbp == TBPermission.READ_ONLY || tbp == TBPermission.SUBMITTED_WRITE) {
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|
|
From: <rv...@us...> - 2010-02-15 13:32:57
|
Revision: 500
http://treebase.svn.sourceforge.net/treebase/?rev=500&view=rev
Author: rvos
Date: 2010-02-15 13:32:51 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Expanded bean configuration for downloaders: these need access to the submissionService to check whether a download can be permitted because the requester is a submitter (as opposed to a reviewer). This is needed to address issue 2949853
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-02-15 13:30:56 UTC (rev 499)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-02-15 13:32:51 UTC (rev 500)
@@ -109,7 +109,8 @@
<bean id="downloadAStudyController" class="org.cipres.treebase.web.controllers.DownloadAStudyController">
<property name="studyService"><ref bean="studyService"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
- <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<!-- Download A Tree -->
@@ -117,7 +118,8 @@
<property name="studyService"><ref bean="studyService"></ref></property>
<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
- <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<bean id="downloadATreeBlockController" class="org.cipres.treebase.web.controllers.DownloadATreeBlockController">
@@ -125,7 +127,8 @@
<property name="phyloTreeHome"><ref bean="phyloTreeHome"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
<property name="rdfaService"><ref bean="rdfaService"></ref></property>
- <property name="submissionHome"><ref bean="submissionHome"></ref></property>
+ <property name="submissionHome"><ref bean="submissionHome"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<!-- Download A Matrix -->
@@ -133,7 +136,8 @@
<property name="matrixService"><ref bean="matrixService"></ref></property>
<property name="studyService"><ref bean="studyService"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
- <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<!-- Download A NexusFile -->
@@ -142,7 +146,8 @@
<property name="studyService"><ref bean="studyService"></ref></property>
<property name="matrixService"><ref bean="matrixService"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
- <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<!-- Download An AnalysisStep's input and output as a NexusFile -->
@@ -152,14 +157,16 @@
<property name="analysisStepService"><ref bean="analysisStepService"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
<property name="rdfaService"><ref bean="rdfaService"></ref></property>
- <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="studyService"><ref bean="studyService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<!-- Download A NexusFile -->
<bean id="downloadANexusRCTFileController" class="org.cipres.treebase.web.controllers.DownloadANexusRCTFileController">
<property name="studyService"><ref bean="studyService"></ref></property>
<property name="nexmlService"><ref bean="nexmlService"></ref></property>
- <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="rdfaService"><ref bean="rdfaService"></ref></property>
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
<!-- View Taxa -->
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|
From: <rv...@us...> - 2010-02-15 13:31:03
|
Revision: 499
http://treebase.svn.sourceforge.net/treebase/?rev=499&view=rev
Author: rvos
Date: 2010-02-15 13:30:56 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Added isSubmitter() method, which checks whether the current user has access to the download by virtue of being a submitter (as opposed to a reviewer), this is needed to address issue 2949853
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2010-02-15 13:28:43 UTC (rev 498)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java 2010-02-15 13:30:56 UTC (rev 499)
@@ -8,9 +8,12 @@
import javax.servlet.http.HttpServletResponse;
import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.admin.UserRole.TBPermission;
import org.cipres.treebase.domain.nexus.NexusService;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.StudyService;
+import org.cipres.treebase.domain.study.Submission;
+import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.web.util.ControllerUtil;
import org.cipres.treebase.web.util.WebUtil;
import org.springframework.web.servlet.mvc.Controller;
@@ -22,6 +25,7 @@
protected static final int FORMAT_RDF = 3;
private NexusService mNexmlService;
private NexusService mRdfaService;
+ private SubmissionService mSubmissionService;
private static String mNexmlContentType = "application/xml";
private static String mRdfContentType = "application/rdf+xml";
@@ -122,7 +126,7 @@
* @param downloadDirName
*/
protected void generateAFileDynamically(HttpServletRequest request, HttpServletResponse response, long objectId) {
- if ( ! ControllerUtil.isReviewerAccessGranted(request) && ! getStudy(objectId,request).isPublished() ) {
+ if ( ! isSubmitter(objectId,request) && ! ControllerUtil.isReviewerAccessGranted(request) && ! getStudy(objectId,request).isPublished() ) {
response.setStatus(HttpServletResponse.SC_SEE_OTHER);
response.setHeader("Location", "/treebase-web/accessviolation.html");
}
@@ -152,6 +156,18 @@
}
}
}
+
+ private boolean isSubmitter (long objectId,HttpServletRequest request) {
+ Study study = getStudy(objectId,request);
+ Submission submission = study.getSubmission();
+ TBPermission tbp = getSubmissionService().getPermission(request.getRemoteUser(), submission.getId());
+ if (tbp == TBPermission.WRITE || tbp == TBPermission.READ_ONLY || tbp == TBPermission.SUBMITTED_WRITE) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
/**
*
@@ -176,5 +192,13 @@
public void setRdfaService(NexusService rdfaService) {
mRdfaService = rdfaService;
}
+
+ public void setSubmissionService(SubmissionService submissionService) {
+ mSubmissionService = submissionService;
+ }
+
+ public SubmissionService getSubmissionService() {
+ return mSubmissionService;
+ }
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-02-15 13:28:51
|
Revision: 498
http://treebase.svn.sourceforge.net/treebase/?rev=498&view=rev
Author: rvos
Date: 2010-02-15 13:28:43 +0000 (Mon, 15 Feb 2010)
Log Message:
-----------
Removed unused import
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ControllerUtil.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ControllerUtil.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ControllerUtil.java 2010-02-15 12:29:51 UTC (rev 497)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ControllerUtil.java 2010-02-15 13:28:43 UTC (rev 498)
@@ -10,7 +10,6 @@
import org.apache.log4j.Logger;
import org.cipres.treebase.TreebaseIDString;
-import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.admin.User;
import org.cipres.treebase.domain.admin.UserService;
import org.cipres.treebase.domain.matrix.Matrix;
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|
From: <rv...@us...> - 2010-02-12 07:22:00
|
Revision: 496
http://treebase.svn.sourceforge.net/treebase/?rev=496&view=rev
Author: rvos
Date: 2010-02-12 07:21:53 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Added placeholder method for content-negotiation
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-02-12 04:41:13 UTC (rev 495)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2010-02-12 07:21:53 UTC (rev 496)
@@ -106,24 +106,25 @@
url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
} else {
String rawNamespacedGUID = pathComponents[pathComponents.length-1];
- if ( rawNamespacedGUID.startsWith("uBio:") ) {
+ if ( rawNamespacedGUID.startsWith("uBio:") ) { // XXX be polite, use real URL
url = uBioBaseUrl + rawNamespacedGUID.substring("uBio:".length());
}
- else if ( rawNamespacedGUID.startsWith("NCBI:") ) {
+ else if ( rawNamespacedGUID.startsWith("NCBI:") ) { // XXX be polite, use real URL
url = ncbiBaseUrl + rawNamespacedGUID.substring("NCBI:".length());
}
else {
NamespacedGUID namespacedGUID = new NamespacedGUID(rawNamespacedGUID);
TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
if ( hasWebPage(pathComponents) ) {
- if ( TreebaseUtil.isEmpty(req.getParameter(format)) ) {
+ String serializationFormat = createSerializationFormat(req);
+ if ( TreebaseUtil.isEmpty(serializationFormat) ) {
url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
}
- else if ( req.getParameter(format).equals("html") ) {
+ else if ( serializationFormat.equals("html") ) {
url = domain + createUrl(tbID.getTypePrefix(),tbID.getId(),req);
}
else {
- url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),req.getParameter(format));
+ url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),serializationFormat);
}
}
else {
@@ -145,6 +146,16 @@
return null;
}
+ /**
+ * This is a placeholder method that might parse accept headers for content-negotiation
+ * one day
+ * @param request
+ * @return
+ */
+ private String createSerializationFormat(HttpServletRequest request) {
+ return request.getParameter(format);
+ }
+
private String createSearchUrl(String path,HttpServletRequest request) {
StringBuilder sb = new StringBuilder();
sb
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From: <rv...@us...> - 2010-02-12 04:41:20
|
Revision: 495
http://treebase.svn.sourceforge.net/treebase/?rev=495&view=rev
Author: rvos
Date: 2010-02-12 04:41:13 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Removed commented-out, redundant code
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2010-02-12 04:37:30 UTC (rev 494)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2010-02-12 04:41:13 UTC (rev 495)
@@ -23,7 +23,6 @@
public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
-// private DomainHome mDomainHome;
private TaxonLabelHome mTaxonLabelHome;
@Override
@@ -35,12 +34,6 @@
protected DomainHome getDomainHome() {
return null; // do not need persistence service.
}
-
- /*
- public void setDomainHome(DomainHome domainHome) {
- mDomainHome = domainHome;
- }
- */
public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
ProgressionListener listener) {
@@ -66,30 +59,10 @@
}
public String serialize(NexusDataSet nexusDataSet) {
- /*
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
- return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
- */
return serialize(nexusDataSet,null);
}
public String serialize(Study study) {
- /*
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
- return ndc.fromTreeBaseToXml(study).getXmlString();
- */
return serialize(study,null);
}
@@ -120,38 +93,12 @@
}
public String serialize(NexusDataSet nexusDataSet, Properties properties) {
- /*
- String baseURI = null;
- if ( null != properties ) {
- baseURI = properties.getProperty("nexml.uri.base");
- }
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document,baseURI);
- */
- NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(null, properties);
+ NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, properties);
return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
}
public String serialize(Study study, Properties properties) {
- /*
- String baseURI = null;
- if ( null != properties ) {
- baseURI = properties.getProperty("nexml.uri.base");
- }
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document,baseURI);
- */
- NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(study, properties);
+ NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
return ndc.fromTreeBaseToXml(study).getXmlString();
}
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|
From: <rv...@us...> - 2010-02-12 04:37:37
|
Revision: 494
http://treebase.svn.sourceforge.net/treebase/?rev=494&view=rev
Author: rvos
Date: 2010-02-12 04:37:30 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Added DwC:DecimalLatitude and DwC:DecimalLongitude annotations
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2010-02-12 04:35:22 UTC (rev 493)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2010-02-12 04:37:30 UTC (rev 494)
@@ -2,6 +2,7 @@
import java.util.ArrayList;
import java.util.List;
+import java.util.Set;
import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
@@ -22,6 +23,7 @@
import org.cipres.treebase.domain.matrix.MatrixElement;
import org.cipres.treebase.domain.matrix.MatrixRow;
import org.cipres.treebase.domain.matrix.PhyloChar;
+import org.cipres.treebase.domain.matrix.RowSegment;
import org.cipres.treebase.domain.matrix.StandardMatrix;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -292,11 +294,12 @@
DiscreteMatrix tbMatrix) {
OTUs xmlOTUs = xmlMatrix.getOTUs();
List<org.nexml.model.Character> characterList = xmlMatrix.getCharacters();
- for ( MatrixRow row : tbMatrix.getRowsReadOnly() ) {
- OTU xmlOTU = getOTUById(xmlOTUs, row.getTaxonLabel().getId());
+ for ( MatrixRow tbRow : tbMatrix.getRowsReadOnly() ) {
+ Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
+ OTU xmlOTU = getOTUById(xmlOTUs, tbRow.getTaxonLabel().getId());
int charIndex = 0;
if ( characterList.size() <= MAX_GRANULAR_NCHAR && xmlOTUs.getAllOTUs().size() <= MAX_GRANULAR_NTAX ) {
- for ( MatrixElement tbCell : row.getElements() ) {
+ for ( MatrixElement tbCell : tbRow.getElements() ) {
org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
DiscreteCharState tbState = ((DiscreteMatrixElement)tbCell).getCharState();
@@ -304,11 +307,21 @@
CharacterState xmlState = xmlCharacter.getCharacterStateSet().lookupCharacterStateBySymbol(tbSymbolString);
xmlCell.setValue(xmlState);
attachTreeBaseID((Annotatable)xmlCell,tbCell,DiscreteMatrixElement.class);
+ for ( RowSegment tbSegment : tbSegments ) {
+ if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
+ if ( tbSegment.getSpecimenLabel().getLatitude() != null ) {
+ ((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLatitude", mDwCURI, tbSegment.getSpecimenLabel().getLatitude());
+ }
+ if ( tbSegment.getSpecimenLabel().getLongitude() != null ) {
+ ((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLongitude", mDwCURI, tbSegment.getSpecimenLabel().getLongitude());
+ }
+ }
+ }
charIndex++;
}
}
else {
- String seq = row.buildElementAsString();
+ String seq = tbRow.buildElementAsString();
if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
StringBuilder sb = new StringBuilder();
for ( int i = 0; i < seq.length(); i++ ) {
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|
|
From: <rv...@us...> - 2010-02-12 04:35:30
|
Revision: 493
http://treebase.svn.sourceforge.net/treebase/?rev=493&view=rev
Author: rvos
Date: 2010-02-12 04:35:22 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Added DarwinCore namespace
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2010-02-11 16:37:07 UTC (rev 492)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2010-02-12 04:35:22 UTC (rev 493)
@@ -24,7 +24,9 @@
protected static URI mDCURI;
protected static URI mPrismURI;
protected static URI mTBTermsURI;
- protected URI mBaseURI;
+ protected static URI mDwCURI;
+ protected URI mBaseURI;
+ private static String mDwCString = "http://rs.tdwg.org/dwc/terms/";
private static String mTBTermsString = "http://treebase.org/terms#";
private static String mDCURIString = "http://purl.org/dc/terms/";
private static String mPrismURIString = "http://prismstandard.org/namespaces/1.2/basic/";
@@ -43,6 +45,7 @@
mDCURI = new URI(mDCURIString);
mPrismURI = new URI(mPrismURIString);
mTBTermsURI = new URI(mTBTermsString);
+ mDwCURI = new URI(mDwCString);
if ( null != baseURI ) {
mBaseURI = new URI(baseURI);
}
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|
From: SourceForge.net <no...@so...> - 2010-02-12 03:01:05
|
Bugs item #2950258, was opened at 2010-02-11 22:01 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2950258&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Row Segment Spreasheet covered by menu Initial Comment: Two things: (1) the row segment upload spreadsheet is covered by the menu div which prevents access to popups. (2) the row segment upload spreadsheet is missing the little help icon. For (1): Using Safari, when I upload an edited Row Segment Template, I first download a blank template from here: http://treebasedb-dev.nescent.org/treebase-web/user/uploadRowSegmentData.html And then upload a finished spreadsheet here: http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html The result (attached image) shows a spreadsheet where the menu system is hovering over (and blocking access to) several important popups. This can be avoided if the window width is decreased below 944 pixels, but it's not at all obvious to the user that shrinking the window is the solution to the problem. Instead, I think it would be better to hide the menu for this page (or shift the spreadsheet down so that is is not covered by the menu). Then for (2) we just need to add a help icon so that I can enter instructions for the user on the row segment upload spreadsheet. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2950258&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-02-11 18:57:59
|
Bugs item #2949882, was opened at 2010-02-11 13:57 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2949882&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: List of default algorithms needs updating Initial Comment: When a submitter creates an analysis step, e.g.: http://treebasedb-dev.nescent.org/treebase-web/user/analysisStepForm.html?analysis_id=4922 and then clicks the "Edit analysis step details" pencil button, he is able to pick from a popup list of default choices for the "Algorithm". The current choices are: maximum likelihood parsimony distance other algorithm These choices should be changed to the following: bayesian inference maximum likelihood minimum evolution neighbor joining parsimony UPGMA other algorithm I could not find a place in the database to modify this list, so I'm assuming that this is hard-coded somewhere. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2949882&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-02-11 18:26:05
|
Bugs item #2949853, was opened at 2010-02-11 13:26 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2949853&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: User cannot download his matrices within his own submission Initial Comment: For the user tb3, I uploaded a data matrix (matrix_id 4219), and then tried to download the "reconstructed" data like so: http://treebasedb-dev.nescent.org/treebase-web/user/downloadAMatrix.html?matrixid=4219 This generated an error because the code fails to enter the study_id in the matrix table. bp Uncaught Exception Encountered java.lang.NullPointerException at org.cipres.treebase.web.controllers.AbstractDownloadController.generateAFileDynamically(AbstractDownloadController.java:125) at org.cipres.treebase.web.controllers.DownloadAMatrixController.handleRequest(DownloadAMatrixController.java:79) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org/treebase-web/user/treeBlockList.html] itemToHighlight=[http%3A//treebasedb-dev.nescent.org/treebase-web/user/treeBlockList.html] JSESSIONID=[90FE0A6E3C5A36D5AA0576C554CB52D9] __utma=[53240375.1924499357.1236724314.1265838306.1265854340.45] __utmc=[53240375] __utmz=[53240375.1265602159.42.7.utmccn] ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2949853&group_id=248804 |
|
From: <vga...@us...> - 2010-02-11 16:37:13
|
Revision: 492
http://treebase.svn.sourceforge.net/treebase/?rev=492&view=rev
Author: vgapeyev
Date: 2010-02-11 16:37:07 +0000 (Thu, 11 Feb 2010)
Log Message:
-----------
Documenting the remaining use of hibernate_sequence.
Modified Paths:
--------------
trunk/treebase-core/db/TODO.txt
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java
Modified: trunk/treebase-core/db/TODO.txt
===================================================================
--- trunk/treebase-core/db/TODO.txt 2010-02-11 16:35:29 UTC (rev 491)
+++ trunk/treebase-core/db/TODO.txt 2010-02-11 16:37:07 UTC (rev 492)
@@ -4,8 +4,6 @@
* Drop geospot_id_sequence -- there is no corresponding sequence
-* Drop hibernate_sequence
-
* Correct PK name in stepmatrixelement and create stepmatrixelement_id_sequence
* Create indexes, as suggested by Bill 2010-02-03 (and maybe later)
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java 2010-02-11 16:35:29 UTC (rev 491)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java 2010-02-11 16:37:07 UTC (rev 492)
@@ -202,6 +202,7 @@
@CollectionId(columns = @Column(name = "COLLECTION_ID", nullable = false), type = @Type(type = "long"), generator = "sequence")
// @Cascade(org.hibernate.annotations.CascadeType.DELETE_ORPHAN)
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "studyCache")
+ //VG 2010-02-11 This property causes, in DB, values for SUB_TREEBLOCK.COLLECTION_ID being drawn from hibernate_sequence.
protected Collection<TreeBlock> getSubmittedTreeBlocks() {
return mSubmittedTreeBlocks;
}
@@ -224,6 +225,7 @@
@CollectionId(columns = @Column(name = "COLLECTION_ID", nullable = false), type = @Type(type = "long"), generator = "sequence")
// @Cascade(org.hibernate.annotations.CascadeType.DELETE_ORPHAN)
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "studyCache")
+ //VG 2010-02-11 This property causes, in DB, values for SUB_MATRIX.COLLECTION_ID being drawn from hibernate_sequence.
protected Collection<Matrix> getSubmittedMatrices() {
return mSubmittedMatrices;
}
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|
|
From: <vga...@us...> - 2010-02-11 16:35:36
|
Revision: 491
http://treebase.svn.sourceforge.net/treebase/?rev=491&view=rev
Author: vgapeyev
Date: 2010-02-11 16:35:29 +0000 (Thu, 11 Feb 2010)
Log Message:
-----------
Modifying DB2-specific SQL to work under Pg
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2010-02-11 06:51:56 UTC (rev 490)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2010-02-11 16:35:29 UTC (rev 491)
@@ -165,8 +165,10 @@
// insert new phylochar.
// Note: this is db2 specific code (faster), see EnvrionmentTest.testGetGeneratedKey()
// for generic jdbc code.
- String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?))";
-
+ //--String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?))";
+ //VG 2010-02-10 Replacing above DB2 sql with this PostreSQL:
+ String queryBuf = "INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?) returning phylochar_id";
+
PreparedStatement ps = pCon.prepareStatement(queryBuf);
for (MatrixColumnJDBC columnJDBC : columns) {
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2010-02-11 06:51:56 UTC (rev 490)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2010-02-11 16:35:29 UTC (rev 491)
@@ -334,8 +334,10 @@
try {
// insert new discrete phylochar.
//Note: this is db2 specific code (faster), see EnvrionmentTest.testGetGeneratedKey() for generic jdbc code.
- String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) VALUES('D', default, 0, ?))";
-
+ //VG-- String queryBuf = "select phylochar_id from final table(INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) VALUES('D', default, 0, ?))";
+ //VG 2010-02-10 Replacing above DB2 sql with this PostreSQL:
+ String queryBuf = "INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) VALUES('D', default, 0, ?) RETURNING phylochar_id";
+
PreparedStatement ps = pCon.prepareStatement(queryBuf);
// String stateStr = "INSERT INTO DISCRETECHARSTATE(DISCRETECHARSTATE_ID, VERSION,
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