EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852021-03-25T15:03:11ZEDIT Project Management
Redmine feature request #9554 (New): option to suppress type designations in portal https://dev.e-taxonomy.eu/redmine/issues/95542021-03-25T15:03:11ZAndreas Kohlbecker
<p>in the <a href="http://portal.cybertaxonomy.org/flora-cuba/">http://portal.cybertaxonomy.org/flora-cuba/</a> typedesignations are just hidden per css. The related footnotes are still visible as these can not be suppressed this way.</p>
<p>The portal should offer an option to switch off the display of types. </p>
<p>TODO </p>
<ul>
<li>implement option</li>
<li>remove css from <a href="http://portal.cybertaxonomy.org/flora-cuba/">http://portal.cybertaxonomy.org/flora-cuba/</a> : </li>
</ul>
<pre><code class="css syntaxhl">
<span class="nc">.typeDesignations</span> <span class="p">{</span>
<span class="nl">display</span><span class="p">:</span> <span class="nb">none</span><span class="p">;</span>
<span class="p">}</span>
</code></pre> bug #9553 (New): Synonymy is missing in table of contenthttps://dev.e-taxonomy.eu/redmine/issues/95532021-03-25T14:50:19ZAndreas Kohlbecker
<p>Configuration: </p>
<ul>
<li>Tabless Taxon page</li>
<li>Synonym as separate tab</li>
</ul>
<p>==> the synonymy is missing in the TOC</p>
<p><a href="http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/4ee3e6f6-9bc8-441b-849e-95887b6e7a85">http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/4ee3e6f6-9bc8-441b-849e-95887b6e7a85</a></p>
bug #8570 (Closed): PolytomousKeyNode.otherNode missing in REST service responsehttps://dev.e-taxonomy.eu/redmine/issues/85702019-09-26T14:14:18ZAndreas Kohlbecker
<p><a href="http://api.cybertaxonomy.org/flora-cuba/polytomousKeyNode/11be28e1-00d6-4368-89d9-16782b7e5ac8.json">http://api.cybertaxonomy.org/flora-cuba/polytomousKeyNode/11be28e1-00d6-4368-89d9-16782b7e5ac8.json</a> </p>
<p>lacks the data for the <code>otherNode</code></p>
<p><a href="http://portal.cybertaxonomy.org/flora-de-la-republica-de-cuba/cdm_dataportal/polytomousKey/0337b535-09cc-473e-9099-3ea3d0b88843">http://portal.cybertaxonomy.org/flora-de-la-republica-de-cuba/cdm_dataportal/polytomousKey/0337b535-09cc-473e-9099-3ea3d0b88843</a></p>
bug #8500 (New): DistributionStatusUI: Error while detaching UI from sessionhttps://dev.e-taxonomy.eu/redmine/issues/85002019-08-29T08:54:05ZAndreas Kohlbecker
<pre>[flora-cuba] 2019-08-29 10:12:43,276 WARN [org.eclipse.jetty.server.session.HashSessionManager@5330da99Timer] [org.springframework.beans.factory.support.DisposableBeanAdapter] - Invocation of destroy method failed on bean with n
ame 'vaadinNavigator': org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'navigationUriFragmentManager': Scope 'vaadin-ui' is not active for the current thread; consider defining a scoped pro
xy for this bean if you intend to refer to it from a singleton; nested exception is java.lang.IllegalStateException: Current VaadinSession is not open
Aug 29, 2019 10:12:43 AM com.vaadin.ui.UI setSession
WARNING: Error while detaching UI from session
com.vaadin.event.ListenerMethod$MethodException: Invocation of method detach in eu.etaxonomy.cdm.vaadin.ui.DistributionStatusUI$$Lambda$180/630566897 failed.
at com.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:533)
at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:200)
at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:163)
at com.vaadin.server.AbstractClientConnector.fireEvent(AbstractClientConnector.java:1015)
at com.vaadin.server.AbstractClientConnector.detach(AbstractClientConnector.java:644)
at com.vaadin.ui.AbstractComponent.detach(AbstractComponent.java:701)
at com.vaadin.ui.UI.detach(UI.java:1307)
at com.vaadin.ui.UI.setSession(UI.java:462)
at com.vaadin.server.VaadinSession.removeUI(VaadinSession.java:873)
at com.vaadin.server.VaadinService$1$1.run(VaadinService.java:483)
at com.vaadin.ui.UI.accessSynchronously(UI.java:1392)
at com.vaadin.server.VaadinService$1.run(VaadinService.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.vaadin.server.VaadinService.runPendingAccessTasks(VaadinService.java:1859)
at com.vaadin.server.VaadinSession.unlock(VaadinSession.java:994)
at com.vaadin.server.VaadinService.ensureAccessQueuePurged(VaadinService.java:1822)
at com.vaadin.server.VaadinService.accessSession(VaadinService.java:1788)
at com.vaadin.server.VaadinSession.access(VaadinSession.java:1399)
at com.vaadin.server.VaadinService.fireSessionDestroy(VaadinService.java:460)
at com.vaadin.server.VaadinSession.valueUnbound(VaadinSession.java:324)
at org.eclipse.jetty.server.session.AbstractSession.unbindValue(AbstractSession.java:607)
at org.eclipse.jetty.server.session.MemSession.clearAttributes(MemSession.java:117)
at org.eclipse.jetty.server.session.AbstractSession.doInvalidate(AbstractSession.java:338)
at org.eclipse.jetty.server.session.HashedSession.doInvalidate(HashedSession.java:96)
at org.eclipse.jetty.server.session.AbstractSession.timeout(AbstractSession.java:317)
at org.eclipse.jetty.server.session.HashSessionManager.scavenge(HashSessionManager.java:358)
at org.eclipse.jetty.server.session.HashSessionManager$Scavenger.run(HashSessionManager.java:84)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'viewCache': Scope 'vaadin-ui' is not active for the current thread; consider defining a scoped proxy for this bean if you intend to refer to it from a singleton; nested exception is java.lang.IllegalStateException: Current VaadinSession is not open
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:355)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:220)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBean(DefaultListableBeanFactory.java:351)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBean(DefaultListableBeanFactory.java:332)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1066)
at com.vaadin.spring.internal.ViewScopeImpl$BeanFactoryContextViewCacheRetrievalStrategy.getViewCache(ViewScopeImpl.java:132)
at com.vaadin.spring.navigator.SpringViewProvider.getViewFromApplicationContext(SpringViewProvider.java:438)
at com.vaadin.spring.navigator.SpringViewProvider.getView(SpringViewProvider.java:405)
at eu.etaxonomy.cdm.vaadin.ui.DistributionStatusUI.lambda$init$8954eeae$1(DistributionStatusUI.java:91)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:510)
... 34 more
Caused by: java.lang.IllegalStateException: Current VaadinSession is not open
at com.vaadin.spring.internal.UIScopeImpl$VaadinSessionBeanStoreRetrievalStrategy.getVaadinSession(UIScopeImpl.java:132)
at com.vaadin.spring.internal.UIScopeImpl$VaadinSessionBeanStoreRetrievalStrategy.getUIStore(UIScopeImpl.java:139)
at com.vaadin.spring.internal.UIScopeImpl$VaadinSessionBeanStoreRetrievalStrategy.getBeanStore(UIScopeImpl.java:168)
at com.vaadin.spring.internal.UIScopeImpl.getBeanStore(UIScopeImpl.java:105)
at com.vaadin.spring.internal.UIScopeImpl.get(UIScopeImpl.java:81)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:340)
... 47 more
</pre> bug #7294 (Closed): keys block can not be disabled in tabless taxon pagehttps://dev.e-taxonomy.eu/redmine/issues/72942018-02-22T16:06:07ZAndreas Kohlbecker
<p>Außerdem sehe ich, dass bei der untabbed Darstellung im Checklisten-Portal z.B. <a href="http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/7b378cd6-68c3-4f07-b577-340f94c34f65">http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/7b378cd6-68c3-4f07-b577-340f94c34f65</a><br>
es nicht möglich ist die Schlüssel auszustellen, wenn sie existieren. Die Einstellung ist</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1179/picture8-1.png" alt="" /></p>
<p>Aber die Schlüssel werden trotzdem angezeigt.<br>
Das sollten wir zeitnah reparieren, da es sonst zu ungewollten Anzeigen auf dem Cuba Checklisten Portal kommt.</p>
bug #7293 (New): improve display of keys in tabless taxon page https://dev.e-taxonomy.eu/redmine/issues/72932018-02-22T16:03:30ZAndreas Kohlbecker
<p>ich sehe gerade bei der Flora von Cuba (z.B. <a href="http://portal.cybertaxonomy.org/flora-de-la-republica-de-cuba/cdm_dataportal/taxon/7b378cd6-68c3-4f07-b577-340f94c34f65#keys">http://portal.cybertaxonomy.org/flora-de-la-republica-de-cuba/cdm_dataportal/taxon/7b378cd6-68c3-4f07-b577-340f94c34f65#keys</a> dass die Anzeige der Schlüssel bei ungetabbter Anzeige nicht sehr ansprechend ist:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1178/picture615-1.png" alt="" /></p>
bug #6523 (In Progress): Correct display of misspellings in synonymyhttps://dev.e-taxonomy.eu/redmine/issues/65232017-03-17T08:21:38ZAndreas Kohlbecker
<p>See <a class="issue tracker-4 status-2 priority-10 priority-lowest" title="bug: Correct display of misspellings in synonymy (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/6523#note-26">#6523#note-26</a> for possible solutions that need to be discussed</p>
<p>Note: this is not about origial spellings (they are handled elsewhere, e.g. <a class="issue tracker-5 status-5 priority-10 priority-lowest closed child" title="feature request: Implement correct implementation of original spelling in publications (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/3667">#3667</a>).</p>
<p>Old title and description:</p>
<p><strong>misspellings: display order of for- and to-taxon swapped</strong> </p>
<p>Es scheint so, dass bei misspellings (is misspelling for) NameRelationships diese falsch herum angezeigt werden. Hier sollte der fromName hinter dem non… stehen und der toName steht vorne. Bin mir gerade unsicher was der default ist bei der Richtung, hier stimmt es jedenfalls nicht, wie man bei</p>
<p>Rhynchospora eximia var. multiflora in Cuba sieht:</p>
<p><a href="http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/635f2251-4e39-42e9-9638-e6ba976308c5">http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/635f2251-4e39-42e9-9638-e6ba976308c5</a> </p>
<p>oder bei Nepenthes teysmanniana (<a href="http://caryophyllales.org/nepenthaceae/cdm_dataportal/taxon/c849a63b-e2be-473c-9a81-ec1e21da89d0/synonymy?highlite=05191549-83ec-490c-a0ad-ab1444ca7b01&acceptedFor=05191549-83ec-490c-a0ad-ab1444ca7b01#05191549-83ec-490c-a0ad-ab1444ca7b01):">http://caryophyllales.org/nepenthaceae/cdm_dataportal/taxon/c849a63b-e2be-473c-9a81-ec1e21da89d0/synonymy?highlite=05191549-83ec-490c-a0ad-ab1444ca7b01&acceptedFor=05191549-83ec-490c-a0ad-ab1444ca7b01#05191549-83ec-490c-a0ad-ab1444ca7b01):</a></p>
<pre> =Nepenthes teysmanniana Miq., Fl. Ned. Ind. 1(1): 1073. 1858 syn. sec. Martin Roy Cheek & Matthew H. P. Jebb, 2001
≡Nepenthes gracilis var. teysmanniana (Miq.) Beck in Wiener Ill. Gart.-Zeitung 20: 190. 1895 syn. sec. Martin Roy Cheek & Matthew H. P. Jebb, 2001
≡Nepenthes tupmanniana Bonstedt in Parey Blumeng. 1: 663. 1931 syn. sec. Martin Roy Cheek & Matthew H. P. Jebb, 2001 [non Nepenthes teysmanniana Miq. 1858]
Unknown type category: Sumatra, Sibolga by the coast, 2.1856, Teijsmann 530 p.p. (BO).
</pre> bug #6375 (Closed): footnotes on sensu references must not be prefixed with 'sensu'https://dev.e-taxonomy.eu/redmine/issues/63752017-01-24T08:30:55ZAndreas Kohlbecker
<p>Walter wrote:</p>
<p><a href="http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/c40f3ad5-e921-4d34-b8e4-f7235d3db73e">http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/c40f3ad5-e921-4d34-b8e4-f7235d3db73e</a></p>
<pre>"Dioscorea batatas" sensu Roig sensu J. Pérez & Raz1
1. sensu J. Pérez & Raz, Dioscoreaceae 22(1). 2017
</pre>
<p>In der Fußnote wird das „sec.“ (hier: „sensu“) wiederholt – da das ja nur eine Quelle ist, sollte das nicht so sein. </p>
feature request #5999 (Duplicate): Go directly to taxon page if only 1 result is returned for searchhttps://dev.e-taxonomy.eu/redmine/issues/59992016-07-21T12:31:22ZAndreas Müller
<p>WG: Kann man die (in diem Kontext) unnütze Zwischenseite überspringen, wenn nur ein Treffer da ist?</p>
<p>For lucene search this might be more difficult as the result is not necessarily exact but in percentage.</p>
<p>Maybe there exist a ticket already that I haven't found.</p>
feature request #5736 (Closed): Show sec reference for TaxonInteractionshttps://dev.e-taxonomy.eu/redmine/issues/57362016-04-22T13:55:08ZAndreas Müller
<p>It should should be possible to format the taxon shown for taxon interactions together with the sec. reference (same as for accepted taxa or synonyms).</p>
<p>Note: Once this is implemented the Cuba Checklist should be cleaned up (delete DescirptionSources from "families in other floras")</p>
<p>Blocks #5497</p>
feature request #5697 (Closed): Show name conserved against as [non xxx]https://dev.e-taxonomy.eu/redmine/issues/56972016-04-11T12:57:04ZAndreas Müller
<p>Currently only later homonyms, treated as later homonyms and is blocking name for are shown as [non xxx] in the dataportal.</p>
<p>[non xxx] may also be required for name relationship xxx conserved against yyy. The relationship should be shown if xxx is part of the synonymy. So it is the same direction as for later homonyms and the opposite direction as for "is blocking name for". </p>
<p>Maybe it is even better to implement it in both directions as the other way round it has more or less the meaning of "is blocked by".</p>
<p>As an example check Cuba Checklist:</p>
<p>Bulbostylis pauciflora (Liebm.) C. B. Clarke, nom. cons. [ non Bulbostylis pauciflora (Kunth) DC., nom. rej.]</p>
<p>This implementation should be optional (administratable by the admin) as other portals may want other solutions, e.g. annotations as described in <a class="issue tracker-6 status-5 priority-11 priority-default closed parent" title="task: display of name relationships in synonymy broken (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/4177">#4177</a>).</p>
<p>This solution requires that the related names (or at least one of the names) have/has the status nom. cons. or nom. rej. attached. Otherwise it can be misunderstood as "is blocked by" relation with opposite meaning</p>
feature request #5683 (Closed): loading animation for open layers map viewerhttps://dev.e-taxonomy.eu/redmine/issues/56832016-04-05T10:43:09ZAndreas Kohlbecker
<p>A loading animation should be shown as long a not all layers are fully loaded.</p>
<p>It should be possible to hide/close the animation.</p>
<p>see <a href="http://lists.osgeo.org/pipermail/openlayers-users/2012-April/024858.html">http://lists.osgeo.org/pipermail/openlayers-users/2012-April/024858.html</a> for an example</p>
<p>There is also a LoadingPanel Control which could be used:</p>
<p><a href="http://trac.osgeo.org/openlayers/wiki/Addins/LoadingPanel">http://trac.osgeo.org/openlayers/wiki/Addins/LoadingPanel</a></p>
bug #5676 (Closed): Sensu does not show up if no author exists for secundum referencehttps://dev.e-taxonomy.eu/redmine/issues/56762016-04-01T15:07:17ZAndreas Müller
<p>If a secundum reference used in a misapplied name does not have an author no sensu information is shown on the dataportal.</p>
<p>By default it should show instead the title cache (this is how the taxon title cache strategy does it).</p>
<p>Also I wonder if it is wanted behavior, that the publication date is usually not shown for the sensu reference even if given.</p>
<p>I tried this with Cyperus unifolius which is a misapplied name for Cyperus filiformis in the Cuba Checklist. I preliminary removed the author FC-S(which is actually not the correct author string, later replaced by Alain [hno.]).</p>
feature request #5647 (Closed): Aggregate misapplied names with multiple sensu referenceshttps://dev.e-taxonomy.eu/redmine/issues/56472016-03-14T12:12:15ZAndreas Müller
<p>Sometimes we do have multiple sensu references for a misapplied name as multiple sources use the name in the wrong way.</p>
<p>This kind of messes up the synonymy if we repeat the name for each sensu.</p>
<p>Instead we could check if misapplied names in the synonymy are exactly equal except for the sensu and instead create a sensu reference like sensu A, B, C & D.</p>
<p>An example is Ossaea glomerata which is a misapplied name for Miconia cubacinerea Judd & Majure in Cuba Checklist: <a href="http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/6bbb3f75-ac3c-40f8-b91d-01069d5173c9">http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/6bbb3f75-ac3c-40f8-b91d-01069d5173c9</a> (we do now have 2 misapplied names, one for sec A&S which has an author, and for Flora de Cuba which has no author)</p>
<p>Note: Deduplication is already implemented somehow, currently sensu information is as annotation</p>
bug #5492 (Closed): Doubtful synonyms and misapplied names to be displayed correctlyhttps://dev.e-taxonomy.eu/redmine/issues/54922016-01-22T16:01:22ZAndreas Müller
<p>Currently synonyms and misapplied names with taxon status doubtful do not show the doubtful marker (question mark in front) and do not showTaxonBase.namePhrase at all.</p>
<p>Example from Cuba Checklist <a href="http://portal.cybertaxonomy.org/flora-cuba:">http://portal.cybertaxonomy.org/flora-cuba:</a> </p>
<ul>
<li><p>"Oncidium carthaginense" which is a misapplied name for Trichocentrum undulatum in Flora of Cuba <a href="http://portal.cybertaxonomy.org/flora-cuba">http://portal.cybertaxonomy.org/flora-cuba</a> . Should be </p>
<ul>
<li>? "Oncidium carthaginense" auct.</li>
</ul></li>
<li><p>Pharbitis calycosa A. Rich. should be ?Pharbitis calycosa A. Rich.</p></li>
</ul>
<p>see also <a class="issue tracker-4 status-5 priority-10 priority-lowest closed child" title="bug: Implement name phrase correctly for misapplied names (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/5491">#5491</a>, #5753</p>