EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852024-03-25T15:12:35ZEDIT Project Management
Redmine bug #10487 (Resolved): Rename nameUseInSource to original spelling in CDM light name tablehttps://dev.e-taxonomy.eu/redmine/issues/104872024-03-25T15:12:35ZAndreas Müller
<p>WGB:</p>
<p>das erste verstehe ich immer noch nicht: Die nomenklatorische Referenz bezieht sich doch auf den Namen. Oder ist das das „Original spelling“? Dann sollten wir das Attribut auch so nennen, wenn wir die Doku updaten. <br>
Das wäre übrigens gut, wenn man das hätte, da man damit irgendwie die Indizierung von diesen Namen in Word erreichen könnte (die bisher nicht stattfindet, da der Name ja nicht ausgeschrieben wird). Dann sollten wir aber sowohl den _Fk als auch den Eintrag ausgeben.</p>
<p>Also </p>
<p>39 NameOriginalSpelling_Fk<br>
40 NameOriginalSpelling [der entsprechende Name mit Autor]<br>
41 AppendedPhrase</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 #10476 (Resolved): 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 #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 #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 #10357 (Resolved): CDMLight fix handling for names used as synonym and accepted taxahttps://dev.e-taxonomy.eu/redmine/issues/103572023-06-22T11:48:03ZKatja Luther
<p>mail ERS:</p>
<p>Hallo,</p>
<p>ich habe gerade versucht, für die Gattung Oncostema Raf. einen cdm-light Output aus Euro+Med Plantbase zu erstellen, da ich diesen an meine beiden Co-Autoren der Gattung schicken möchte.</p>
<p>Das Ergebnis ist anbei. Folgendes Problem tritt dabei auf:</p>
<p>Der Name Oncostema africanum (Borzi & Mattei) Speta taucht zweimal in Euro+Med Plantbase auf, einmal im bisher publizierten und auch im Portal sichtbaren Kew-Treatment als Synonym von Scilla peruviana L., und einmal als akzeptierter Name im unpublizierten, neuen Treatment von Raab-Straube & al.</p>
<p>In CDM light wollte ich mir eigentlich nur das neue Treatment anzeigen lassen (als Ausgangspunkt habe ich den Knoten Oncostema gewählt).</p>
<p>Was aber jetzt passiert, ist, dass im Word-Dokument auch die syn.sec. Kew Treatment angezeigt werden, nicht nur die syn.sec. Raab-Straube & al. (welche dagegen teilweise fehlen können, wenn es Überlappungen gibt). Mit dieser speziellen Situation kommt Euro+Med PlantBase also anscheinend nicht zurecht, da so eine datenbankstruktur nicht vorgesehen ist.</p>
<p>Um den Autoren also das eigentlich noch nicht publizierte Treatment schicken zu können, muss ich es also doch erstmal publizieren, damit ich die Mehrfachverwendung von Namen dann eliminieren kann, richtig?</p>
<hr>
<p>The problem comes from the handling of names used for more then one taxonbase.</p>
bug #9703 (Resolved): Improve handling of type designations with no status in TypeDesignationSetM...https://dev.e-taxonomy.eu/redmine/issues/97032021-07-08T16:46:01ZAndreas Müller
<p>Currently they are labeled as "Nametype: " wich is obviously not (always) correct.</p>
<p>Generally they should not get any status label and therefore should be put to the beginning as otherwise it is not fully clear from the formatting if they inherit the status from the previous record or if they have no status at all.</p>
bug #9551 (Resolved): Recognize "series" in article parsinghttps://dev.e-taxonomy.eu/redmine/issues/95512021-03-24T15:16:18ZAndreas Müller
<p>... maybe also books etc.</p>
bug #9461 (Resolved): Filter in vaadin distribution editor does not workhttps://dev.e-taxonomy.eu/redmine/issues/94612021-02-09T09:53:38ZAndreas Müller
<p>Previously the filter in the distribution editor did throw an exception (see <a class="issue tracker-4 status-8 priority-11 priority-default closed" title="bug: Filter in vaadin distribution editor throws exception (Worksforme)" href="https://dev.e-taxonomy.eu/redmine/issues/7254">#7254</a> and <a class="issue tracker-4 status-5 priority-10 priority-lowest closed" title="bug: Distribution editor: Taxon filter broken due to invalid HQL in TaxonNodeServiceImpl.getUuidAndTit... (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9457">#9457</a>). This is not the case anymore. However, the filter does not seem to work.</p>
<p>I tested on <a href="http://test.e-taxonomy.eu/cdmserver/flora_cuba/app/distribution">http://test.e-taxonomy.eu/cdmserver/flora_cuba/app/distribution</a> with area filter on Cuba, West Cuba and Central Cuba and filter "Ancistranthus harpo*" or only "Ac*" but nothing appeared in the "Taxonomy" box</p>
bug #9223 (Resolved): make changes of nomenclatural references detectable again in TaxonGraphBefo...https://dev.e-taxonomy.eu/redmine/issues/92232020-09-11T15:53:13ZAndreas Kohlbecker
<p>due to the model modifications made for <a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: Make all microreferenced references OriginalSources (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6581">#6581</a> the <code>TaxonGraphHibernateListenerTest.testChangeNomRef()</code> fails since the exchange of the nomenclatural reference (now <code>nomenclaturalSource.citation</code> can no longer be detected.</p>
bug #9140 (Resolved): Deleting an image forgets moving operationhttps://dev.e-taxonomy.eu/redmine/issues/91402020-07-10T14:08:32ZAndreas Müller
<p>If I move an image in the taxon media view and then also delete an image and then save the movement is not stored but the image is moved back to it's old position during save.<br>
The same happens when first deleting the image and then move and then save. </p>
bug #9015 (Resolved): Comparator for Character Matrix creates strange resulthttps://dev.e-taxonomy.eu/redmine/issues/90152020-05-14T09:02:36ZKatja Luther
<p>When one higher taxon has computed (aggregated) description and another higher taxon has no aggregated description the order in character matrix is strange for the rankAndName order.</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1867/picture883-1.png" alt="picture883-1.png" /></p>
<p>after adding an aggregation to Acanthocereus the order is correct.</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1868/picture877-1.png" alt="picture877-1.png" /></p>
bug #8998 (Resolved): Terms created by abcd import should always be part of a vocabularyhttps://dev.e-taxonomy.eu/redmine/issues/89982020-05-05T09:49:49ZKatja Luther
<p>In abcd import dnaMarker are created if not existing, they are not added to a vocabulary, but should. The vocabulary needs to be created if not existing.</p>
bug #8901 (Resolved): Deleting an aggregated description from a descriptive matrix does not delet...https://dev.e-taxonomy.eu/redmine/issues/89012020-03-25T17:14:41ZAndreas Müller
<p>I removed aggregated taxon description via the matrix editor.<br>
This did not remove the descriptions from their according taxa. But at least if the description was created by aggegating the given dataset the description should be fully deleted from the DB not only removed from the dataset (but stay at the taxon).<br>
However, we should discuss details under which conditions fully removing is wanted and under which conditions only the link between the dataset and a description is wanted.</p>
<p>===</p>
<p>Also deleting an aggregated description should remove the cloned specimen descriptions which were created as sources for these descriptions. This is a bit complicated because we probably need to check if these descriptions are used elsewhere (or do we implement a strict rule that e.g. "Cloned" descriptions may be used only by exactly 1 referencing description?).</p>
<p>Note: Currently it is impossible to delete a cloned description via editor because it is referenced by the according dataset and by the specimen. Deleting from 1 of them creates an error saying that it is referenced by the other one. Needs discussion on how to attached cloned descriptions to the dataset.</p>
bug #8874 (Resolved): move taxon is reverted when taxon is edited afterwardshttps://dev.e-taxonomy.eu/redmine/issues/88742020-03-05T08:40:25ZKatja Luther
<p>mail W.B.:</p>
<p>ein merkwürdiger Bug – ist mir schon mehrfach aufgefallen, aber ich habe ihn nicht so recht dokumentiert. Caryophyllales_spp:<br>
Ich verschiebe ein als doubtful gekennzeichnetes Taxon (Alternanthera eupatorioides Remy) im Baum (über den Kontextdialog) – in diesem Fall aus der Gattung Alternanthera unter das Pseudotaxon _Amaranthaceae excluded. Dort öffne ich’s im Node-Dialog, markiere es als excluded und gebe meinen Kommentar ein.<br>
Wenn ich es jetzt wieder im Name Editor aufmache und dort etwas ändere (z.B. [früher aufgefallen] die doubtful flag entferne oder [jetzt] die sec.-Ref. ändere, dann wird das excluded flag entfernt und das Taxon springt zurück an seinen ursprünglichen Ort. Der Kommentar zu excluded ist noch da, aber das flag ist weg. <br>
Taxon wieder verschoben, Flag wieder gesetzt, Name Editor, Änderung (diesmal das doubtful-flag entfernt) – speichern – Alles gut. </p>