EDIT

After setting Publish Flag to default and reopening:

login : admin
editor version : 5.8.0.201907180811
server : test.e-taxonomy.eu (edit-test) / rem_conf_am
schema version : 5.5.0.0.20190221
os : Windows Server 2012 R2 6.3 amd64
java : 1.8.0_121
java.lang.IllegalArgumentException: No enum constant eu.etaxonomy.cdm.model.metadata.PublishEnum.
    at java.lang.Enum.valueOf(Enum.java:238)
    at eu.etaxonomy.cdm.model.metadata.PublishEnum.valueOf(PublishEnum.java:1)
    at eu.etaxonomy.taxeditor.databaseAdmin.preferencePage.PublishFlagPreference.getValues(PublishFlagPreference.java:75)
    at eu.etaxonomy.taxeditor.preference.PublishFlagLocalPreference.createContents(PublishFlagLocalPreference.java:57)
    at org.eclipse.jface.preference.PreferencePage.createControl(PreferencePage.java:241)
    at eu.etaxonomy.taxeditor.preference.menu.CdmPreferencePage.createControl(CdmPreferencePage.java:65)
    at org.eclipse.jface.preference.PreferenceDialog.createPageControl(PreferenceDialog.java:1430)
    at org.eclipse.jface.preference.PreferenceDialog$9.run(PreferenceDialog.java:1197)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:50)
    at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:173)
    at org.eclipse.jface.preference.PreferenceDialog.showPage(PreferenceDialog.java:1189)
    at org.eclipse.jface.preference.PreferenceDialog$5.lambda$0(PreferenceDialog.java:656)
    at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
    at org.eclipse.jface.preference.PreferenceDialog$5.selectionChanged(PreferenceDialog.java:653)
    at org.eclipse.jface.viewers.StructuredViewer$3.run(StructuredViewer.java:878)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:50)
    at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:173)
    at org.eclipse.jface.viewers.StructuredViewer.firePostSelectionChanged(StructuredViewer.java:875)
    at org.eclipse.jface.viewers.StructuredViewer.setSelection(StructuredViewer.java:1729)
    at org.eclipse.jface.viewers.TreeViewer.setSelection(TreeViewer.java:1077)
    at org.eclipse.jface.preference.PreferenceDialog.selectSavedItem(PreferenceDialog.java:991)
    at org.eclipse.jface.preference.PreferenceDialog.lambda$0(PreferenceDialog.java:346)
    at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
    at org.eclipse.jface.preference.PreferenceDialog.createContents(PreferenceDialog.java:343)
    at org.eclipse.jface.window.Window.create(Window.java:426)
    at org.eclipse.jface.dialogs.Dialog.create(Dialog.java:1095)
    at eu.etaxonomy.taxeditor.workbench.handler.OpenAdminPreferencesHandler.execute(OpenAdminPreferencesHandler.java:123)
    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)
    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.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)

io.ABCD.config is stored in DB with value NULL even if nothing has changed, if this is default value, the default should not be stored

CRITICAL: if this value is set the navigator does not show any classifications after restart. We need to check why this is and fix it (it is the first page and this can happen accidentally).

Maybe these stacktraces are related:

java.lang.NullPointerException
    at eu.etaxonomy.taxeditor.preference.PreferencesUtil.getDBAbcdImportConfigurationPreference(PreferencesUtil.java:1447)
    at eu.etaxonomy.taxeditor.preference.PreferencesUtil.resetToDBPreferenceAbcdCOnfigurator(PreferencesUtil.java:1541)
    at eu.etaxonomy.taxeditor.preference.PreferencesUtil.updateAbcdImportConfigurationPreference(PreferencesUtil.java:1535)
    at eu.etaxonomy.taxeditor.preference.PreferencesUtil.updateDBPreferences(PreferencesUtil.java:1711)
    at eu.etaxonomy.taxeditor.databaseAdmin.preferencePage.AbcdImportPreference.performOk(AbcdImportPreference.java:367)
    at org.eclipse.jface.preference.PreferenceDialog$8.run(PreferenceDialog.java:905)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:50)
    at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:173)

java.lang.NullPointerException
    at eu.etaxonomy.taxeditor.ApplicationWorkbenchAdvisor$CdmStatusHandler.handle(ApplicationWorkbenchAdvisor.java:123)
    at org.eclipse.ui.internal.WorkbenchErrorHandlerProxy.handle(WorkbenchErrorHandlerProxy.java:31)
    at org.eclipse.ui.statushandlers.StatusManager.handle(StatusManager.java:204)
    at org.eclipse.ui.statushandlers.StatusManager.handle(StatusManager.java:246)
    at org.eclipse.ui.statushandlers.StatusManager.handle(StatusManager.java:257)

Andreas Müller wrote:

io.ABCD.config is stored in DB with value NULL even if nothing has changed, if this is default value, the default should not be stored

CRITICAL: if this value is set the navigator does not show any classifications after restart. We need to check why this is and fix it (it is the first page and this can happen accidentally).

Maybe these stacktraces are related:

java.lang.NullPointerException
  at eu.etaxonomy.taxeditor.preference.PreferencesUtil.getDBAbcdImportConfigurationPreference(PreferencesUtil.java:1447)
  at eu.etaxonomy.taxeditor.preference.PreferencesUtil.resetToDBPreferenceAbcdCOnfigurator(PreferencesUtil.java:1541)
  at eu.etaxonomy.taxeditor.preference.PreferencesUtil.updateAbcdImportConfigurationPreference(PreferencesUtil.java:1535)
  at eu.etaxonomy.taxeditor.preference.PreferencesUtil.updateDBPreferences(PreferencesUtil.java:1711)
  at eu.etaxonomy.taxeditor.databaseAdmin.preferencePage.AbcdImportPreference.performOk(AbcdImportPreference.java:367)
  at org.eclipse.jface.preference.PreferenceDialog$8.run(PreferenceDialog.java:905)
  at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
  at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:50)
  at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:173)

java.lang.NullPointerException
  at eu.etaxonomy.taxeditor.ApplicationWorkbenchAdvisor$CdmStatusHandler.handle(ApplicationWorkbenchAdvisor.java:123)
  at org.eclipse.ui.internal.WorkbenchErrorHandlerProxy.handle(WorkbenchErrorHandlerProxy.java:31)
  at org.eclipse.ui.statushandlers.StatusManager.handle(StatusManager.java:204)
  at org.eclipse.ui.statushandlers.StatusManager.handle(StatusManager.java:246)
  at org.eclipse.ui.statushandlers.StatusManager.handle(StatusManager.java:257)

This is now fixed. It was an NPE because the ABCD config is stored as null in the DB Prefs. Wouldn't it be better to just delete the preference if the config is null. null means default in this case and default should be the same as deleting the preference.

Patrick Plitzner wrote:

Wouldn't it be better to just delete the preference if the config is null. null means default in this case and default should be the same as deleting the preference.

I just saw that this is already mentioned in the ticket description.

the above both fixes seem to work (though the last is only a workaround for a real fix (full delete of the preference))

Andreas Müller wrote:

When opening Peferences - Distribution Editor for the first time the drop downs for some fields were completely empty. Is this because maybe old values were stored that are not supported anymore? Do we need an update script for them? How does the TaxEditor handle such entries. Does it throw exceptions if it uses them or does it use the default value instead?

This even happend with freshly selected data. In Distribution Editor when selecting "IdInVoc" after reopening the drop down is empty.

this is fixed

ABCD import is now implemented on both sides, but "allow override" does not yet exist for "ABCD import provider"

this is fixed

some preferences are not deleted for NameDetailsView => deselect all and reopen preferences => 3 prefs stay selected

this is fixed

name.nomenclaturalStatus can not be removed by Reset Default
this is fixed.

Distribution editor status selection: changes are not visible in Preferences view after reopening the preferences view. I have not checked if they were correctly stored in the DB

this is fixed

Restore button does not yet work for Distribution Editor status and area selection preferences

this is fixed

Name Details View: when selecting "restore defaults" allow override is not set to default

this is fixed

"Show rank in Distribution Editor" should be relabled -> "Show rank column"

this is fixed

ABCD: Ignore Authorship ... -> Ignore authorship ...

fixed

Biocase Provider for associated DNA should be moved to "Biocase Provider"

this is not the same because this provider link belongs to the configurator

But still it would be nice to not allow to enter all providers may it be ABCD providers or DNA providers once at one place and then offer them where ever they are used as dropdown.

Also I do not understand why the biocase provider itself should not be part of the configurator while the DNA provider is part of it. Both is part of a specific import and therefore should be configurable when starting an import. Or do I misunderstand something here.

Note: to me it also seems like both should be usually a pair. For a given biocase provider I would expect that there is usually 1 DNA bank provider, so they could be selected as a pair.

Why does the nomenclatural code not provide a default? Is this wanted? Does ABCD not need a nomenclatural code? I remember ABCD distinguishes botanical, zoological, ... by itself so maybe this parameter is not needed and only comes from the super class? If so, we should remove it. If not, and if a null value is not explicitly handled without using a default instead we should define the usage of default here, I guess. But I don't know the import so well so maybe there is a reason for the current implementation.

ABCD: Restore defaults does not seem to set allowOverride

io.ABCD.config is stored in DB with value NULL even if nothing has changed, if this is default value, the default should not be stored

This is still not fixed yet

Andreas Müller wrote:

Biocase Provider for associated DNA should be moved to "Biocase Provider"

this is not the same because this provider link belongs to the configurator

But still it would be nice to not allow to enter all providers may it be ABCD providers or DNA providers once at one place and then offer them where ever they are used as dropdown.

Also I do not understand why the biocase provider itself should not be part of the configurator while the DNA provider is part of it. Both is part of a specific import and therefore should be configurable when starting an import. Or do I misunderstand something here.

Note: to me it also seems like both should be usually a pair. For a given biocase provider I would expect that there is usually 1 DNA bank provider, so they could be selected as a pair.

In general we should distinguish clearly between the list of available providers (may it be ABCD providers or DNA providers) and the default or predefined single values for the import configuration which provider to use for ABCD and for DNA. This is currently still mixed up. (But might be a new ticket)

similar for BiocaseProvider: io.ABCD.providerList is stored with "Keine Provider verfügbar;" which seems to be incorrect as this is only a label for a non existing provider

This is fixed but still "Restore default" does not completely remove the preference (and even does not clear the existing list, what I would expect)

General: When choosing "No - allow override" for all 3 entries the values shown in local preferences are "Use Default(Yes)",Default(No)" and "Default(Yes)" but it should be all "Default(No)".

Also when choosing explicit "Yes" in local preferences for all 3 of them this is not stored in local prefs but after reopen it shows "Use Default XXX" again.

This might be the case elsewhere, too. For now I tested only for General page.

this is fixed

Nomenclatural status is not stored. Neither after reopening the pref dialog nor after restarting the TaxEditor the new values are recovered. Also they seem to be not stored in the CdmPreference table.

fixed

Same for ranks. They are not stored.

fixed

Andreas Müller wrote:

Same for ranks. They are not stored.

Hmm, maybe I made a mistake. This seems to work.

Name details view: "Restore Defaults" does not enable "Secundum enabled" and "Secundum Reference Details"

fixed

NDV: "Secundum Reference Details" -> "Secundum reference details"

NDV: NameCache of the name ... -> "Name cache of the name ..."

NDV: "Whole Authorship section" -> "Whole authorship section"

Andreas Müller wrote:

Name details view: "Restore Defaults" does not enable "Secundum enabled" and "Secundum Reference Details"

Same if checkbox for "Taxon of the name" is set to "true"

Publish Flage:

"Not Publish" -> "Don't Publish"
"Use Default (InheritFromParent)" -> kein Camel Case sondern wie bei "Inherit from Parent"

Eventuell überall klein schreiben außer am Anfang, aber vielleicht können wir das auch so lassen. Wie du willst.

fixed

Andreas Müller wrote:

General: When choosing "No - allow override" for all 3 entries the values shown in local preferences are "Use Default(Yes)",Default(No)" and "Default(Yes)" but it should be all "Default(No)".

Also when choosing explicit "Yes" in local preferences for all 3 of them this is not stored in local prefs but after reopen it shows "Use Default XXX" again.

This might be the case elsewhere, too. For now I tested only for General page.

Problem is similar for "Search Dialog". There the correct value is shown in local preferences but it should show "Use Default (%correct value%)". Currently it does not show the "Use default" even if no value was selected before.

fixed

Search dialog: "Search also for titlecache ..." -> "... title cache ..."

fixed

Andreas Müller wrote:

Andreas Müller wrote:

General: When choosing "No - allow override" for all 3 entries the values shown in local preferences are "Use Default(Yes)",Default(No)" and "Default(Yes)" but it should be all "Default(No)".

Also when choosing explicit "Yes" in local preferences for all 3 of them this is not stored in local prefs but after reopen it shows "Use Default XXX" again.

This might be the case elsewhere, too. For now I tested only for General page.

Problem is similar for "Search Dialog". There the correct value is shown in local preferences but it should show "Use Default (%correct value%)". Currently it does not show the "Use default" even if no value was selected before.

Same or similar for "Specimens"

fixed

Saving of "Publish Flag" does not always work. You may try different states including allow override adn "Restore Defaults". Sometime it seems to work, sometimes it does not. Not yet fully sure about the pattern.

fixed

Generally values recovered by "Restore default" often seem not to be persisted but old values are kept.

fixed

Andreas Müller wrote:

Is there a reason why allow override is always disabled for "Enable Distribution Editor"?

I cannot reproduce this. But will have a look.

Andreas Müller wrote:

General: When choosing "No - allow override" for all 3 entries the values shown in local preferences are "Use Default(Yes)",Default(No)" and "Default(Yes)" but it should be all "Default(No)".

This might be the case elsewhere, too. For now I tested only for General page.

This is not yet fixed for all such cases. I tested for Publish Flag and Distribution Editor preferences and the default values were not taken from the DB prefs. It works correct for the "General" page.

Please carefully check ALL pages for this issue.

Katja Luther wrote:

Andreas Müller wrote:

Is there a reason why allow override is always disabled for "Enable Distribution Editor"?

I cannot reproduce this. But will have a look.

is fixed

Andreas Müller wrote:

Saving of "Publish Flag" does not always work. You may try different states including allow override adn "Restore Defaults". Sometime it seems to work, sometimes it does not. Not yet fully sure about the pattern.

This is still open. Currently I can't save the state at all. Always "default" is shown after reopening.

Andreas Müller wrote:

Andreas Müller wrote:

General: When choosing "No - allow override" for all 3 entries the values shown in local preferences are "Use Default(Yes)",Default(No)" and "Default(Yes)" but it should be all "Default(No)".

This might be the case elsewhere, too. For now I tested only for General page.

This is not yet fixed for all such cases. I tested for Publish Flag and Distribution Editor preferences and the default values were not taken from the DB prefs. It works correct for the "General" page.

Please carefully check ALL pages for this issue.

this should be fixed now

Andreas Müller wrote:

Andreas Müller wrote:

Saving of "Publish Flag" does not always work. You may try different states including allow override adn "Restore Defaults". Sometime it seems to work, sometimes it does not. Not yet fully sure about the pattern.

This is still open. Currently I can't save the state at all. Always "default" is shown after reopening.

this is fixed with the last commit as well.

Andreas Müller wrote:

Generally values recovered by "Restore default" often seem not to be persisted but old values are kept.

Still does not work for Name details view. Only if pressing "Apply" it works. OK does not delete the record.
I have not tested other pages. Please check all pages if it works.

Andreas Müller wrote:

Andreas Müller wrote:

Generally values recovered by "Restore default" often seem not to be persisted but old values are kept.

Still does not work for Name details view. Only if pressing "Apply" it works. OK does not delete the record.
I have not tested other pages. Please check all pages if it works.

sorry, I missed to call setApply(true), this is fixed.

Names.NomenclaturalStatus restores default only after clicking 2x "Restore Default". Or more exact, clicking the first time seem to restore only the state before opening the preferences while the second time the value is really set to the default value.

Distribution editor status and area selection: restore default deletes the values correctly but when opening the selection dialogs still the old values are shown.

Andreas Müller wrote:

Distribution editor status and area selection: restore default deletes the values correctly but when opening the selection dialogs still the old values are shown.

you need to click on apply or ok

Distribution editor: Restore default removes the entry "distribution.status.term" from the above table (and completely removes all values from DB).

When reopening the entry in the table is shown again. This is inconsistent.

The main problem is that the table does not show the actual value, but only subject and predicate. So I can't see what value was restored.

Also it is not clear why this first line always seems to appear even if no preference was set yet.

Katja Luther wrote:

Andreas Müller wrote:

Distribution editor status and area selection: restore default deletes the values correctly but when opening the selection dialogs still the old values are shown.

you need to click on apply or ok

why? This is not what I would expect.
Hmm, now I see that the dialog values are also stored if I click on Cancel. This is also not what I would expect. But it is consistent with the above issue.
Generally we need to change this. But I guess it is more difficult so we probably better open a new ticket.

Andreas Müller wrote:

Distribution editor: Restore default removes the entry "distribution.status.term" from the above table (and completely removes all values from DB).

When reopening the entry in the table is shown again. This is inconsistent.

The main problem is that the table does not show the actual value, but only subject and predicate. So I can't see what value was restored.

Also it is not clear why this first line always seems to appear even if no preference was set yet.

now the default preference is not shown in the table anymore

In local preferences Publish Flag for "Use Default" the Camel Case is used, not the current correct label. E.g. (NotPublished) instead of "(Don't publish)"

Andreas Müller wrote:

In local preferences Publish Flag for "Use Default" the Camel Case is used, not the current correct label. E.g. (NotPublished) instead of "(Don't publish)"

is fixed, but for the next release.