EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852020-04-07T13:38:18ZEDIT Project Management
Redmine bug #8943 (Closed): Term Preferences are not correctly handled in combo boxeshttps://dev.e-taxonomy.eu/redmine/issues/89432020-04-07T13:38:18ZKatja Luther
<p>mail WB:</p>
<p>Hallo,<br>
ich hatte mich da schon vor einiger Zeit dran versucht, war aber wieder abgekommen: Wie kann man die zur Verfügung stehenden Optionen beim nomenclatural status einstellen? Ich stelle mir das folgendermaßen vor:<br>
Unter Server-sided settings schalte ich die unsinnigen (z.B. „New combination“) und die nicht erwünschten (z.B. „Provisional“) aus, wie auch die zusätzlichen aus dem ICZN. <br>
Außerdem schalte ich auf „Allow overide“:</p>
<p>Dann gehe ich auf Local preferences – Nomenclatural status. <br>
(hier funktioniert übrigens – im Gegensatz zu den Server-sided Dialog – der Schieber rechts nicht)</p>
<p>Restore Defaults sollte dann die server-sided preferences ergeben. Das funktioniert auch. </p>
<p>Dann schalte ich hier auf Use local settings und wähle ein paar Sachen ab, damit ich die ganz gängigen (illeg., nud., inval.) in der Auswahl im Details View ohne zu scrollen bekomme: </p>
<p>Sicherheitshalber gehe ich ganz raus und starte den Editor neu</p>
<p>Aber alles ohne Effekt auf die Status-Auswahl. </p>
<p>Scheint nicht so wichtig, aber ich gebe das dauernd ein – und für alle gängigen Optionen muss man scrollen.</p>
<p>Herzlichen Gruß<br>
Walter</p>
<p>PS: Und „invalid“ ist immer noch doppelt:</p>
bug #8942 (Closed): Exception when try to get text of TextualTypeDesignation with language which ...https://dev.e-taxonomy.eu/redmine/issues/89422020-04-06T10:09:10ZKatja Luther
<pre>java.lang.NullPointerException
at eu.etaxonomy.cdm.model.name.TextualTypeDesignation.getText(TextualTypeDesignation.java:188)
at eu.etaxonomy.cdm.model.name.TextualTypeDesignation.getPreferredText(TextualTypeDesignation.java:219)
at eu.etaxonomy.cdm.io.cdmLight.CdmLightClassificationExport.handleName(CdmLightClassificationExport.java:1145)
at eu.etaxonomy.cdm.io.cdmLight.CdmLightClassificationExport.handleSynonym(CdmLightClassificationExport.java:853)
at eu.etaxonomy.cdm.io.cdmLight.CdmLightClassificationExport.handleTaxon(CdmLightClassificationExport.java:309)
at eu.etaxonomy.cdm.io.cdmLight.CdmLightClassificationExport.handleTaxonNode(CdmLightClassificationExport.java:280)
at eu.etaxonomy.cdm.io.cdmLight.CdmLightClassificationExport.doInvoke(CdmLightClassificationExport.java:154)
at eu.etaxonomy.cdm.io.cdmLight.CdmLightClassificationExport.doInvoke(CdmLightClassificationExport.java:1)
at eu.etaxonomy.cdm.io.common.CdmIoBase.invoke(CdmIoBase.java:107)
at eu.etaxonomy.cdm.io.common.CdmExportBase.invoke(CdmExportBase.java:1)
at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport.doExport(CdmApplicationAwareDefaultExport.java:230)
at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport.execute(CdmApplicationAwareDefaultExport.java:114)
at eu.etaxonomy.cdm.io.service.IOServiceImpl.export(IOServiceImpl.java:69)
at eu.etaxonomy.cdm.io.service.IOServiceImpl$2.doRun(IOServiceImpl.java:101)
at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:42)
</pre> bug #8940 (Closed): The export wizard does not remember last selected folderhttps://dev.e-taxonomy.eu/redmine/issues/89402020-04-06T08:47:14ZKatja Luther
<p>When opening the export wizard the last selected export folder was shown in the text field, this is not the case anymore.</p>
bug #8939 (Closed): Exception when opening Distribution Editor because of missing Preferencehttps://dev.e-taxonomy.eu/redmine/issues/89392020-04-06T07:48:43ZKatja Luther
<p>Dear Andreas,</p>
<p>I would like to report an error, when I try "Opening in..." "Distribution editor", I get the message:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1850/picture816-1.png" alt="picture816-1.png" /></p>
<p>and, if I click "ok", the sceen is like this:<br>
<img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1851/picture816-2.png" alt="picture816-2.png" /></p>
<p>The error details are as follows:</p>
<pre>last remote method : http://api.cybertaxonomy.org:80/flora-greece/remoting/vocabulary.service
last remote request client time : 2020-04-04T21:40:48.794
last remote request response header time : Sat, 04 Apr 2020 20:40:52 GMT
client error time : 2020-04-04T21:40:49.524
login : constantia
editor version : 5.13.1
server : api.cybertaxonomy.org (cybertaxonomy.org) / flora-greece
schema version : 5.12.0.0.20191202
os : Windows 7 6.1 amd64
java : 1.8.0_121
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.invokeUsingClass(InjectorImpl.java:288)
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.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:152)
at org.eclipse.core.commands.Command.executeWithChecks(Command.java:494)
at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:488)
at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210)
at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:433)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.handleWidgetSelection(AbstractContributionItem.java:454)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem$3.handleEvent(AbstractContributionItem.java:482)
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:24)
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)
Caused by: java.lang.NullPointerException
at eu.etaxonomy.taxeditor.preference.PreferencesUtil.getIntValue(PreferencesUtil.java:373)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.StatusDataCellEditor.<init>(StatusDataCellEditor.java:44)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.DistributionCellEditorDataConversionConfiguration.configureRegistry(DistributionCellEditorDataConversionConfiguration.java:76)
at org.eclipse.nebula.widgets.nattable.layer.AbstractLayer.configure(AbstractLayer.java:167)
at org.eclipse.nebula.widgets.nattable.layer.CompositeLayer.configure(CompositeLayer.java:126)
at org.eclipse.nebula.widgets.nattable.layer.CompositeLayer.configure(CompositeLayer.java:121)
at org.eclipse.nebula.widgets.nattable.NatTable.configure(NatTable.java:653)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.DistributionEditor.configureNatTable(DistributionEditor.java:353)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.DistributionEditor.createTable(DistributionEditor.java:366)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.DistributionEditorPart.init(DistributionEditorPart.java:150)
at eu.etaxonomy.taxeditor.editor.EditorUtil.openDistributionEditor(EditorUtil.java:121)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.handler.OpenChecklistEditorHandlerE4.open(OpenChecklistEditorHandlerE4.java:40)
at eu.etaxonomy.taxeditor.editor.view.checklist.e4.handler.OpenChecklistEditorHandlerE4.open(OpenChecklistEditorHandlerE4.java:1)
at eu.etaxonomy.taxeditor.handler.defaultHandler.e4.DefaultOpenSetBaseHandler.execute(DefaultOpenSetBaseHandler.java:62)
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.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55)
... 37 more
</pre>
<p>Best regards,<br>
Constantia</p>
bug #8938 (Closed): ProposalProvider in NameRelationshiptype combo does not work as expectedhttps://dev.e-taxonomy.eu/redmine/issues/89382020-04-06T07:13:11ZKatja Luther
<p>The ProposalProvider does not set the selection for the combo element, therefore the finish button is not enabled.</p>
bug #8927 (Closed): Fix isAdmin() method in LoginManagerhttps://dev.e-taxonomy.eu/redmine/issues/89272020-04-02T10:03:33ZKatja Luther
<p>The isAdmin() method uses only the name of the user to check whether the user is admin or not, but should use the role ROLE_ADMIN</p>
feature request #8926 (Closed): Remove 'expired' flags in users detailshttps://dev.e-taxonomy.eu/redmine/issues/89262020-04-02T09:01:38ZKatja Luther
<p>The fields 'Account Non Expired', 'Account locked', 'Credentials non Expired' are not used yet, so they should not be visible in the UI.</p>
bug #8925 (Closed): Users with ROLE_USER_MANAGER must be able to change any user passwordhttps://dev.e-taxonomy.eu/redmine/issues/89252020-04-02T08:53:50ZAndreas Kohlbecker
<p>For users with ROLE_USER_MANAGER the button in the User details view to change a users password must be generally enabled </p>
bug #8919 (Closed): Shorten label for "Reference Detail"https://dev.e-taxonomy.eu/redmine/issues/89192020-03-31T06:58:31ZAndreas Müller
<p>Use "Ref. Detail" instead. </p>
<p>In Details View for nom. ref.</p>
bug #8918 (Closed): Add "set as basionym" to accepted taxon https://dev.e-taxonomy.eu/redmine/issues/89182020-03-31T06:54:54ZAndreas Müller
<p>WGB:</p>
<p>eine kleine Verbesserungsmöglichkeit: Bei den Synonymen der heterotypischen Gruppen kann man im NameEditor (über Kontextmenü) eines als Basionym erklären. Das kann man auch mit einem Synonym des akzeptierten Namens machen, nicht aber mit dem akzeptierten Namen selbst. <br>
(Man kann natürlich die Namensrelation setzten, aber im Arbeitsfluss kostet das einfach zu viel Zeit)</p>
bug #8917 (Closed): NPE when opening Acacia in Name bulk editor (from search) https://dev.e-taxonomy.eu/redmine/issues/89172020-03-30T13:06:58ZAndreas Müller
<p>in FoG. </p>
<ul>
<li>Search for Acacia ( in FoG)</li>
<li>Open the pure name (orphaned name) via context menu -> bulk editor</li>
<li>=> exception</li>
</ul>
<p>(Directly opening the bulk editor and searching for Acacia* works)</p>
<pre>last remote method : http://api.cybertaxonomy.org:80/flora-greece/remoting/common.service
last remote request client time : 2020-03-30T15:04:54.298
last remote request response header time : Mon, 30 Mar 2020 15:05:10 GMT
client error time : 2020-03-30T15:04:56.952
login : admin
editor version : 5.13.1
server : api.cybertaxonomy.org (cybertaxonomy.org) / flora-greece
schema version : 5.12.0.0.20191202
os : Windows 10 10.0 amd64
java : 1.8.0_241
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.invokeUsingClass(InjectorImpl.java:288)
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.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:152)
at org.eclipse.core.commands.Command.executeWithChecks(Command.java:494)
at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:488)
at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210)
at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:433)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.handleWidgetSelection(AbstractContributionItem.java:454)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem$3.handleEvent(AbstractContributionItem.java:482)
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:24)
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.bulkeditor.input.BulkEditorInputType.getInput(BulkEditorInputType.java:132)
at eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput.NewInstance(AbstractBulkEditorInput.java:96)
at eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput.NewInstance(AbstractBulkEditorInput.java:114)
at eu.etaxonomy.taxeditor.bulkeditor.handler.defaultHandler.OpenBulkEditorForIdentifiableEntityE4.open(OpenBulkEditorForIdentifiableEntityE4.java:36)
at eu.etaxonomy.taxeditor.handler.defaultHandler.e4.DefaultOpenHandlerBaseE4.execute(DefaultOpenHandlerBaseE4.java:47)
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)
... 37 more
</pre> bug #8914 (Closed): jetty 9.4.x returns error states as json which are parsed and processes by cd...https://dev.e-taxonomy.eu/redmine/issues/89142020-03-27T16:11:53ZAndreas Kohlbecker
<p>jetty 9.4.x returns error states as json which are parsed and processes by cdm_dataportal completely breaks with the assumption in many code parts that the parsed return object will be 'NULL' in case of errors.</p>
<p>example: <a href="http://160.45.63.173:8081/phycobank/occurrence/35cbbccc-aa88-4909-a18c-dab3b05d0555/taggedText.json">http://160.45.63.173:8081/phycobank/occurrence/35cbbccc-aa88-4909-a18c-dab3b05d0555/taggedText.json</a></p>
bug #8913 (Closed): InInVoc not showing up anymore in TermEditorhttps://dev.e-taxonomy.eu/redmine/issues/89132020-03-27T14:29:49ZAndreas Müller
<p>... even if local preference for Term Editor is set to "show vocabulary id"</p>
bug #8911 (Closed): LazyInitializationException (LIE) in portal/description/{uuid}https://dev.e-taxonomy.eu/redmine/issues/89112020-03-27T09:46:41ZAndreas Kohlbecker
<p><a href="http://api.cybertaxonomy.org/caryophyllales_spp/portal/description/f4fc4b11-90c7-4a02-b236-2d58f5891e6e.json">http://api.cybertaxonomy.org/caryophyllales_spp/portal/description/f4fc4b11-90c7-4a02-b236-2d58f5891e6e.json</a></p>
<pre>Caused by: org.hibernate.LazyInitializationException: could not initialize proxy - no Session
at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:148)
at org.hibernate.proxy.AbstractLazyInitializer.getImplementation(AbstractLazyInitializer.java:266)
at org.hibernate.proxy.pojo.javassist.JavassistLazyInitializer.invoke(JavassistLazyInitializer.java:68)
at eu.etaxonomy.cdm.model.agent.TeamOrPersonBase_$$_jvst5ab_6e.getNomenclaturalTitle(TeamOrPersonBase_$$_jvst5ab_6e.java)
at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getAuthorAndExAuthor(TaxonNameDefaultCacheStrategy.java:254)
at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getNonCacheAuthorshipCache(TaxonNameDefaultCacheStrategy.java:196)
at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getAuthorshipCache(TaxonNameDefaultCacheStrategy.java:170)
at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getTaggedTitle(TaxonNameDefaultCacheStrategy.java:411)
at eu.etaxonomy.cdm.model.name.TaxonName.getTaggedName(TaxonName.java:1477)
at eu.etaxonomy.cdm.remote.json.processor.bean.TaxonNameBeanProcessor.processBeanSecondStep(TaxonNameBeanProcessor.java:66)
at eu.etaxonomy.cdm.remote.json.processor.bean.TaxonNameBeanProcessor.processBeanSecondStep(TaxonNameBeanProcessor.java:25)
at eu.etaxonomy.cdm.remote.json.processor.bean.AbstractBeanProcessor.processBean(AbstractBeanProcessor.java:167)
at net.sf.json.JSONObject._fromBean(JSONObject.java:676)
... 107 more
</pre> bug #8910 (Closed): Correct handling of preference for determinationshttps://dev.e-taxonomy.eu/redmine/issues/89102020-03-27T09:06:23ZAndreas Müller