EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852024-03-18T14:48:57ZEDIT Project Management
Redmine bug #10482 (Resolved): Registrations with two or more types of the same type result in errorhttps://dev.e-taxonomy.eu/redmine/issues/104822024-03-18T14:48:57ZKatja Luther
<p>The registration page for names with more than one typedesignations of one type resulting in an error. </p>
bug #10481 (New): Vaadin type of the genus: selection truncatedhttps://dev.e-taxonomy.eu/redmine/issues/104812024-03-18T11:00:45ZWolf-Henning Kusber
<p>In the production system the following entries are missing:<br>
original designation<br>
monotypy<br>
automatic (not relevant for genus, but for ranks higher than genus and we decided to show all options for the genus, correct?)</p>
<p>In the selection:<br>
lectotype<br>
subsequent designation<br>
subsequent monotypy<br>
present designation<br>
not applicable</p>
<p>All options are shown in the test Vaadin (see):<br>
Genus: Monotypicgenus Kusber<br>
"Publication" Kusber, W.-H.: Generitype monotypic. – Zeitschrift für Tümpelkunde 11: 22-33</p>
bug #10480 (Resolved): Problems with name details view when ranks are limitedhttps://dev.e-taxonomy.eu/redmine/issues/104802024-03-15T11:45:48ZKatja Luther
<p>There are problems with the details view if the rank selection is reduced in the local preferences. This is fixed by loading the rank list during the connection to the data source.</p>
bug #10477 (In Progress): Table of contents shows only factual contenthttps://dev.e-taxonomy.eu/redmine/issues/104772024-03-13T07:21:21ZKatja Luther
<p>For pages without tabs the table of contents should show also the other chapters of the page like synonymy, specimen, keys, media, etc.</p>
bug #10476 (New): Sources with name in source are not correctly deduplicated in footnoteshttps://dev.e-taxonomy.eu/redmine/issues/104762024-02-20T11:38:29ZKatja Luther
<p>mail NaK:</p>
<p>Und manchmal wird die selbe Referenz zweimal in der Bibliographie angezeigt, hier z.B. <a href="https://caryophyllales.org/cdm_dataportal/taxon/382d5128-d409-4dac-be4b-a1a3df7fbcfc">https://caryophyllales.org/cdm_dataportal/taxon/382d5128-d409-4dac-be4b-a1a3df7fbcfc</a> unter C und D. Ist das noch ein Bug?</p>
<p>This problem appears because the html strings are compared and the cdm-render-path is not the same:</p>
<p>for example:</p>
<pre><span class="reference">A. A. Anderberg, B. Axelius, R. Lundin, A. Tehler, H.-E. Wantorp & A. Wiklund, Onosma orientale (L.) L. (Boraginaceae) collected in Cyprus in Kew Bull. 47. 1992<a href="/algaterra-new/cdm_dataportal/reference/dacf8897-0619-41ae-bc12-c320bb9d0d04">
<i class="superscript icon-interal-link-alt-solid"></i></a></span>
<span class="nameUsedInSource">(as <a href="http://dataportal.test/algaterra-new/cdm_dataportal/name/96dc242d-f2bd-4dab-a9e1-7b62e7db5621/null/null/">
<span class="cdm:TaxonName uuid:96dc242d-f2bd-4dab-a9e1-7b62e7db5621" data-cdm-ref="/name/96dc242d-f2bd-4dab-a9e1-7b62e7db5621"
data-cdm-render-path="1a28ed59-e15f-4001-b5c2-ea89f0012671">
<span class="name">
<span class="TaxonName">
<span class="name">Asparagus acutifolius</span>
<span class="authors"> L.</span></span></span>
<span class="reference"></span></span></span></a>)</span>
</pre>
<p>vs.</p>
<pre><span class="reference">A. A. Anderberg, B. Axelius, R. Lundin, A. Tehler, H.-E. Wantorp & A. Wiklund, Onosma orientale (L.) L. (Boraginaceae) collected in Cyprus in Kew Bull. 47. 1992<a href="/algaterra-new/cdm_dataportal/reference/dacf8897-0619-41ae-bc12-c320bb9d0d04">
<i class="superscript icon-interal-link-alt-solid"></i></a></span>
<span class="nameUsedInSource">(as <a href="http://dataportal.test/algaterra-new/cdm_dataportal/name/96dc242d-f2bd-4dab-a9e1-7b62e7db5621/null/null/">
<span class="cdm:TaxonName uuid:96dc242d-f2bd-4dab-a9e1-7b62e7db5621" data-cdm-ref="/name/96dc242d-f2bd-4dab-a9e1-7b62e7db5621"
data-cdm-render-path="fb16929f-bc9c-456f-9d40-dec987b36438" >
<span class="name"><span class="TaxonName">
<span class="name">Asparagus acutifolius</span>
<span class="authors"> L.</span></span></span>
<span class="reference"></span></span></span></a>)</span>
</pre> bug #10475 (New): Removing names from homotypic group does not always workhttps://dev.e-taxonomy.eu/redmine/issues/104752024-02-17T12:19:23ZAndreas Müller
<p>This has been observed in Casearia where some names showed more types then expected. Research showed that these types came from names that where removed from taxonomy (or in 1 case moved to another taxon) in the meanwhile. However, the names did still bear type information which was therefore shown in print publication (other task: shouldn't the type module select only types from names shown in the synonymy or at least give a warning if such types/names exist?).</p>
<p>The following query gives a list of names which have a homotpyic group used at least in 2 taxa or in 1 taxon and a name not used in a taxon at all.</p>
<pre><code class="sql syntaxhl"><span class="k">SELECT</span> <span class="n">hid</span><span class="p">,</span> <span class="k">COUNT</span><span class="p">(</span><span class="n">accId</span><span class="p">)</span> <span class="n">naccId</span><span class="p">,</span> <span class="n">GROUP_CONCAT</span><span class="p">(</span><span class="n">accId</span><span class="p">),</span> <span class="n">GROUP_CONCAT</span><span class="p">(</span> <span class="n">fullName</span><span class="p">),</span> <span class="n">GROUP_CONCAT</span><span class="p">(</span><span class="n">nid</span><span class="p">)</span> <span class="n">nid</span>
<span class="k">FROM</span> <span class="p">(</span>
<span class="k">SELECT</span> <span class="n">n</span><span class="p">.</span><span class="n">homotypicalGroup_id</span> <span class="n">hid</span><span class="p">,</span> <span class="n">GROUP_CONCAT</span><span class="p">(</span><span class="n">n</span><span class="p">.</span><span class="n">titleCache</span><span class="p">)</span> <span class="n">fullname</span><span class="p">,</span> <span class="n">GROUP_CONCAT</span><span class="p">(</span><span class="n">n</span><span class="p">.</span><span class="n">id</span><span class="p">)</span> <span class="n">nid</span><span class="p">,</span>
<span class="k">CASE</span> <span class="k">WHEN</span> <span class="n">tb</span><span class="p">.</span><span class="n">DTYPE</span> <span class="o">=</span> <span class="s1">'TAXON'</span> <span class="k">THEN</span> <span class="n">tb</span><span class="p">.</span><span class="n">id</span> <span class="k">wHEN</span> <span class="n">tb</span><span class="p">.</span><span class="n">DTYPE</span> <span class="o">=</span> <span class="s1">'Synonym'</span> <span class="k">THEN</span> <span class="n">acc</span><span class="p">.</span><span class="n">id</span> <span class="k">ELSE</span> <span class="s1">'xxx'</span> <span class="k">END</span> <span class="n">accId</span>
<span class="k">FROM</span> <span class="n">TaxonName</span> <span class="n">n</span>
<span class="k">LEFT</span> <span class="k">JOIN</span> <span class="n">TaxonBase</span> <span class="n">tb</span> <span class="k">ON</span> <span class="n">tb</span><span class="p">.</span><span class="n">name_id</span> <span class="o">=</span> <span class="n">n</span><span class="p">.</span><span class="n">id</span>
<span class="k">LEFT</span> <span class="k">JOIN</span> <span class="n">TaxonBase</span> <span class="n">acc</span> <span class="k">ON</span> <span class="n">acc</span><span class="p">.</span><span class="n">id</span> <span class="o">=</span> <span class="n">tb</span><span class="p">.</span><span class="n">acceptedTaxon_id</span>
<span class="c1">-- WHERE n.homotypicalGroup_id = 814</span>
<span class="k">GROUP</span> <span class="k">BY</span> <span class="n">n</span><span class="p">.</span><span class="n">homotypicalGroup_id</span><span class="p">,</span> <span class="n">accId</span>
<span class="p">)</span> <span class="k">AS</span> <span class="n">tmp</span>
<span class="k">GROUP</span> <span class="k">BY</span> <span class="n">hid</span>
<span class="k">ORDER</span> <span class="k">BY</span> <span class="n">naccId</span> <span class="k">DESC</span><span class="p">,</span> <span class="n">hid</span><span class="p">,</span> <span class="n">fullName</span>
</code></pre>
<p>Be aware that names used in multiple taxa are also shown here , but can be recognized by duplicates in the nid column.</p>
<p>In Caryophyllales there are 690 such homotypic groups (including a larger number of names being used in >1 taxon for some reason, but still there are >>100 remaining cases).</p>
bug #10473 (Resolved): Problems in facts view for nameshttps://dev.e-taxonomy.eu/redmine/issues/104732024-02-16T07:20:49ZKatja Luther
<p>Hallo,<br>
wenn ich das Name Fact Fenster neu aufmache und das Kontext Menu wähle, dann bekomme ich unter New die ganze Liste der TAXON-fact categories gezeigt (s.u.)<br>
Wenn ich dann New factual dataset wähle, kommt die Null pointer exeption (weiter unten), aber der dataset wird angelegt. <br>
Auch wenn ich dann auf den Factual dataset rechts-klicke, bekomme ich die Taxon-Liste. <br>
Ich muss den Fokus dann neu auf den Scientific Name setzen, dann kann ich den Name Fact auswählen und eingeben.<br>
HG<br>
W</p>
<pre>
last remote service : https://api.cybertaxonomy.org:443/caryophyllales/remoting/common.service
last remote method : getDbSchemaVersion
last remote request client time : 2024-02-15T14:40:17.702
last remote request response header time : Thu, 15 Feb 2024 20:40:18 GMT
client error time : 2024-02-15T14:43:50.567
login : w.berendsohn
editor version : 5.42.0
server : api.cybertaxonomy.org (cybertaxonomy.org) / caryophyllales
schema version : 5.40.1.0.20230829
os : Windows 10 10.0 amd64
java : 1.8.0_401
org.eclipse.e4.core.di.InjectionException: java.lang.NullPointerException
at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:65)
at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:282)
at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:264)
at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:132)
at org.eclipse.e4.ui.workbench.renderers.swt.MenuManagerShowProcessor.processDynamicElements(MenuManagerShowProcessor.java:158)
at org.eclipse.e4.ui.workbench.renderers.swt.MenuManagerShowProcessor.menuAboutToHide(MenuManagerShowProcessor.java:113)
at org.eclipse.jface.internal.MenuManagerEventHelper.showEventPostHelper(MenuManagerEventHelper.java:92)
at org.eclipse.jface.action.MenuManager.handleAboutToShow(MenuManager.java:471)
at org.eclipse.jface.action.MenuManager.access$1(MenuManager.java:465)
at org.eclipse.jface.action.MenuManager$2.menuShown(MenuManager.java:497)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:256)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4418)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1079)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1103)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1084)
at org.eclipse.swt.widgets.Control.WM_INITMENUPOPUP(Control.java:5160)
at org.eclipse.swt.widgets.Control.windowProc(Control.java:4828)
at org.eclipse.swt.widgets.Canvas.windowProc(Canvas.java:359)
at org.eclipse.swt.widgets.Decorations.windowProc(Decorations.java:1656)
at org.eclipse.swt.widgets.Shell.windowProc(Shell.java:2199)
at org.eclipse.swt.widgets.Display.windowProc(Display.java:5110)
at org.eclipse.swt.internal.win32.OS.TrackPopupMenu(Native Method)
at org.eclipse.swt.widgets.Menu._setVisible(Menu.java:262)
at org.eclipse.swt.widgets.Display.runPopups(Display.java:4277)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3818)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$4.run(PartRenderingEngine.java:1121)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1022)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:150)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:693)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:610)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
at eu.etaxonomy.taxeditor.Application.start(Application.java:20)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:673)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:610)
at org.eclipse.equinox.launcher.Main.run(Main.java:1519)
Caused by: java.lang.NullPointerException
at eu.etaxonomy.taxeditor.editor.view.descriptive.e4.handler.DynamicFeatureMenuE4.aboutToShow(DynamicFeatureMenuE4.java:75)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55)
... 46 more
</pre> bug #10472 (In Progress): Improve simple search performance in dataportalhttps://dev.e-taxonomy.eu/redmine/issues/104722024-02-14T23:18:46ZAndreas Müller
<p>In the TaxEditor it is much faster. Need to check:</p>
<ul>
<li><del>if the same method is used</del> => no, different method, TaxEditor uses UuidAndTitleCache result</li>
<li>if thumbnails slow down (there is a ticket for this)</li>
<li>impact of common name search => very important, see <a href="#note-12">#note-12</a></li>
<li>if paging and/or ordering is an issue => only for common name search as the count(*) method takes the same time as the instance call and therefore doubles the time; in general paging works as long as pure names are not returned (which is currently not available in the dataportal). If the method is not used elsewhere we should remove this part of the code or otherwise split the code as merging pure names in the result will make paging much more complex </li>
<li>handling for concept relationships</li>
<li>...</li>
</ul>
<p>Also think about using lucene also for simple search.</p>
bug #10471 (New): Cloning typedesignation does not workhttps://dev.e-taxonomy.eu/redmine/issues/104712024-02-06T10:36:14ZKatja Luther
<p>mail MM:</p>
<p>I want to duplicate the type information for Limonium ×interjectum in Caryophyllales database. <br>
I added one isonyme using duplicate option but to add the second isotype I receive the below error. <br>
I tried multiple times and re-connected the software. But the error is occurring each time.</p>
<p>The type was designated before using the "add a type designation" option. <br>
I duplicated it using "create type duplicate" option, I added G as collection and isotype as type status. </p>
<p>For a user with admin permissions this problem does not appear!</p>
<pre>last remote service : https://api.cybertaxonomy.org:443/caryophyllales/remoting/name.service
last remote method : getDbSchemaVersion
last remote request client time : 2024-02-02T15:57:03.944
last remote request response header time : Fri, 02 Feb 2024 14:57:03 GMT
client error time : 2024-02-02T15:57:03.969
login : m.malekmohammadi
editor version : 5.42.0
server : api.cybertaxonomy.org (cybertaxonomy.org) / caryophyllales
schema version : 5.40.1.0.20230829
os : Windows 10 10.0 amd64
java : 1.8.0_121
java.lang.NullPointerException
at eu.etaxonomy.cdm.api.service.NameServiceImpl.cloneTypeDesignation(NameServiceImpl.java:245)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy821.cloneTypeDesignation(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.remoting.support.RemoteInvocationTraceInterceptor.invoke(RemoteInvocationTraceInterceptor.java:78)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy1356.cloneTypeDesignation(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:212)
at eu.etaxonomy.cdm.api.remoting.DebuggingRemoteInvocationExecutor.invoke(DebuggingRemoteInvocationExecutor.java:52)
at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78)
at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114)
at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:80)
at org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter.handle(HttpRequestHandlerAdapter.java:51)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder$NotAsyncServlet.service(ServletHolder.java:1395)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:755)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1617)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:317)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:215)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:214)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:177)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1604)
at eu.etaxonomy.cdm.servlet.DateHeaderFilter.doFilter(DateHeaderFilter.java:56)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1604)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1596)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:545)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:590)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1607)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1297)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:485)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1577)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1212)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at eu.etaxonomy.cdm.server.logging.InstanceLogWrapper.handle(InstanceLogWrapper.java:48)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:221)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
at org.eclipse.jetty.server.Server.handle(Server.java:500)
at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:547)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:270)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)
at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:336)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:313)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:171)
at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:129)
at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:388)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:806)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:938)
at java.lang.Thread.run(Thread.java:748)
at org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTraceIfPossible(RemoteInvocationUtils.java:45)
at org.springframework.remoting.support.RemoteInvocationResult.recreate(RemoteInvocationResult.java:149)
at org.springframework.remoting.support.RemoteInvocationBasedAccessor.recreateRemoteInvocationResult(RemoteInvocationBasedAccessor.java:85)
at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:158)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy137.cloneTypeDesignation(Unknown Source)
at eu.etaxonomy.taxeditor.ui.section.name.TypeDesignationSection$3.run(TypeDesignationSection.java:116)
at org.eclipse.jface.action.Action.runWithEvent(Action.java:473)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:565)
at org.eclipse.jface.action.ActionContributionItem.lambda$5(ActionContributionItem.java:436)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4418)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1079)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4236)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3824)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$4.run(PartRenderingEngine.java:1121)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1022)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:150)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:693)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:610)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
at eu.etaxonomy.taxeditor.Application.start(Application.java:20)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:673)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:610)
at org.eclipse.equinox.launcher.Main.run(Main.java:1519)
</pre> bug #10470 (New): Improve media metadata preference pagehttps://dev.e-taxonomy.eu/redmine/issues/104702024-02-02T15:26:43ZKatja Luther
<p>see <a href="https://dev.e-taxonomy.eu/redmine/issues/10440#note-42">https://dev.e-taxonomy.eu/redmine/issues/10440#note-42</a></p>
<p>and the handling if copyright information comes from media server and cdm.</p>
bug #10469 (New): Remember the sourceLinkBaseUrl https://dev.e-taxonomy.eu/redmine/issues/104692024-02-02T15:24:42ZKatja Luther
<p>see <a href="https://dev.e-taxonomy.eu/redmine/issues/10448#note-27">https://dev.e-taxonomy.eu/redmine/issues/10448#note-27</a></p>
bug #10468 (New): Image reference want to display a non-existing media specimen in PhycoBank user...https://dev.e-taxonomy.eu/redmine/issues/104682024-02-01T15:23:45ZWolf-Henning Kusber
<p>Display in Vaadin is correct:<br>
Lectotype for: Chlorosphaera antarctica Fritsch (<a href="http://phycobank.org/104339">http://phycobank.org/104339</a>)<br>
Southern Orkneys, Scotia Bay, beach lectotype: [icon] in Fritsch 1912: t. 10, fig. 2 designated by Chae & al. 2024</p>
<p>Under the registration:<br>
bug 1: designated by is missing<br>
bug 2: [icon] is missing<br>
Lectotype: Southern Orkneys, Scotia Bay, beach Fritsch, F.E. 1912: Freshwater algae collected in the South Orkneys by Mr. B.R. Rudmose Brown, B.Sc. of the Scottish National Antarctic Expedition, 1902-04. – J. Linn. Soc. Bot. 40: 293-338: t. 10, fig. 2</p>
<p>Same information in PhycoBank protal (2024-02-01 under the species name):</p>
<p>Lectotype (designated by Chae, H., Choi, H.-G. & Kim, J.H.2): MediaSpecimen#7285 in Fritsch in J. Linn. Soc. Bot. 40. 1912: t. 10, fig. 2<br>
bug 2 [icon] is missing<br>
bug 3"MediaSpecimen#7285" is shown instead of the locus typicus</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2426/icon.PNG" alt="" /></p>
bug #10466 (Resolved): Open issues in logfileshttps://dev.e-taxonomy.eu/redmine/issues/104662024-02-01T00:19:01ZAndreas Müller
<p>copied from <a class="issue tracker-4 status-5 priority-10 priority-lowest closed" title="bug: LIE in logfiles for DefinedTermBase.includes (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10441">#10441</a> </p>
<pre>Caused by: org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: eu.etaxonomy.cdm.model.taxon.Taxon.descriptions, could not initialize proxy - no Session
at org.hibernate.collection.internal.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:606)
at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:218)
at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:585)
at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:149)
at org.hibernate.collection.internal.PersistentSet.iterator(PersistentSet.java:188)
at eu.etaxonomy.cdm.model.taxon.Taxon.getDefaultDescription(Taxon.java:459)
</pre>
<p>Also check for new issues in log files. Ask users to send them.</p>
bug #10465 (New): Changing reference of sec source should clear name in source and detailhttps://dev.e-taxonomy.eu/redmine/issues/104652024-01-29T14:33:10ZKatja Luther
<p>When changing or deleting reference of secundum source, the name in source and the detail should be removed.</p>
<p>This is the same for nomenclatural source. We should discuss this for other sources as well, but there the user would delete the whole source?</p>
bug #10457 (New): Print version of portal site sometimes shows links as texthttps://dev.e-taxonomy.eu/redmine/issues/104572024-01-19T12:12:29ZAndreas Müller
<p>observed in Firefox:</p>
<p>WGB:</p>
<p>Außerdem zeigte er einen Browser-Ausdruck für ein einzelnes Taxon, gemacht mit Firefox. Das sah für Revisionszwecke eigentlich recht gut aus, Karte und alles. Nur am Anfang, beim Contenido werden die Links mit ausgegeben:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2396/clipboard-202401191310-jpqlb.png" alt="" /></p>
<p>Das ist nicht so schön – habt Ihr eine Idee, wie man das (im Browser?) abstellen kann? Aus Opera kann ich ordentliche PDFs mit allem aber ohne diese Links generieren. </p>
<p>AM:</p>
<p>Hast du dafür den Link<br><br>
<img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2397/clipboard-202401191310-wfhvr.png" alt="" /><br>
verwendet? Katja, kannst du sehen, ob das Funktionalität von Drupal ist, oder AK das entwickelt hat und ob man irgendwie an den Code kommt?<br>
Erstmal finde ich es schwierig, zu erkennen, woran das liegen könnte. Einzigen Unterschiede zu anderen Links im HTML ist, dass diese Links nicht in einem intergriert sind:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2398/clipboard-202401191311-5wj5t.png" alt="" /></p>
<p>anders als z.B. die Fußnoten Links </p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2399/clipboard-202401191311-l40lj.png" alt="" /></p>
<p>Aber ich habe mal versucht das manuell im HTML zu ändern, das hat nichts gebracht.</p>
<p>AM:</p>
<p>ich sehe gerade, dass es nicht nur im Content-Bereich diese Probleme bei der Print-Darstellung gibt sondern z.B. auch hier </p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2400/clipboard-202401191311-orrq1.png" alt="" /></p>
<p>Quelle: <a href="https://test.e-taxonomy.eu/dataportal/preview/cichorieae/?q=cdm_dataportal/taxon/c4651898-743b-4ab2-837a-3146d2d3332d">https://test.e-taxonomy.eu/dataportal/preview/cichorieae/?q=cdm_dataportal/taxon/c4651898-743b-4ab2-837a-3146d2d3332d</a> </p>
<p>Da stimmt also grundsätzlich was nicht bzw. müsste anders konfiguriert werden.</p>