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From 02/13/2019 to 03/14/2019

03/14/2019

06:26 PM bug #8179 (New): PopupEditorException
Type name editor, PopupEditorException
when saving a name type of a genus
in Workingset
http://api.phycobank.org...
Wolf-Henning Kusber
02:12 PM feature request #8178 (Rejected): Auto-create absence/presence character for every structure
Presence/Absence Property (PA)
* Jede Strukture muss in Kombination mit PA-Property einen Character bilden.
* Bei...
Patrick Plitzner
02:04 PM feature request #8121 (In Progress): Allow selecting structural/property modifiers when creating a character
Patrick Plitzner
01:56 PM feature request #6849 (In Progress): [DISCUSS] How to handle "kind of" term creation in TermEditor
Patrick Plitzner
12:11 PM feature request #6413 (Resolved): [DISCUSS] How to create type duplicates (e.g. isotypes) for a taxon name
The first implementation allows selection one of the already existing specimen type designation for creating the dupl... Patrick Plitzner

03/13/2019

12:52 PM feature request #8175: add name facts to cdm light export
the name facts are moved to their own table. Katja Luther
09:57 AM feature request #7428 (Resolved): Open issues for updating open data while subtree is updated
Applied in changeset commit:taxeditor|4fff2d21dfed4ae1ba6c5106e7d59cdf2e82548c. Katja Luther
09:36 AM bug #8176 (Resolved): WeaklyRelatedEntityCombobox is slow
test TaxonNamePopupEditor Genus field, replaced Synonym and Basionym also some ToManyRelatedEntitiesComboboxes and T... Andreas Kohlbecker

03/12/2019

05:57 PM bug #8176 (In Progress): WeaklyRelatedEntityCombobox is slow
Andreas Kohlbecker
02:15 PM bug #8176 (Closed): WeaklyRelatedEntityCombobox is slow
## on setting values
The WeaklyRelatedEntityCombobox needs to check if the value to set is at all contained in the...
Andreas Kohlbecker
02:22 PM report #8177 (Worksforme): Discuss: How to add originals of a type specimen
How to store? Wolf-Henning Kusber
01:07 PM bug #6627: Remaining cdm light issues
the name facts are implemented now, see #8175 Katja Luther
01:06 PM feature request #8175: add name facts to cdm light export
please review Katja Luther
01:06 PM feature request #8175 (Resolved): add name facts to cdm light export
Applied in changeset commit:cdmlib|852a1a9e5171370a8e3e6962b21837e38115cf9a. Katja Luther
01:04 PM feature request #8175 (Closed): add name facts to cdm light export
We decided to keep the name facts in cdm, so the name facts should be exported as well Katja Luther
12:53 PM bug #8099: Error saving name type designation editor due to problem in poupeditor context
can not reproduce Andreas Kohlbecker
12:03 PM bug #8111: User selection dialog for groups does not filter out existing users
please review Katja Luther
12:02 PM bug #8111 (Resolved): User selection dialog for groups does not filter out existing users
Applied in changeset commit:taxeditor|cbc83794de4303c54b45309ff151c70627e82e1a. Katja Luther
11:34 AM bug #8115: NPE when moving factual data
please review Katja Luther
11:33 AM bug #8115: NPE when moving factual data
the problem was the not persisted description, therefore the description needs to be passed to the service method. To... Katja Luther
11:26 AM bug #8115 (Resolved): NPE when moving factual data
Applied in changeset commit:taxeditor|803af83ee2911d193d6a95a3f73dee727ae77d45. Katja Luther
09:31 AM feature request #8136: Implement sources for type designations in TaxEditor
please review Katja Luther
09:30 AM feature request #8136 (Resolved): Implement sources for type designations in TaxEditor
Applied in changeset commit:taxeditor|9f40979f5e0d2fc55100acc5a7fabac00d48ce12. Katja Luther
08:36 AM bug #8105: better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
I did a brief research on the topic of hotfix branches:
1. git flow has the concept of ***support branches*** by whi...
Andreas Kohlbecker
08:11 AM task #8130: Check if related feature data is cleared when supported facts type is changed
For nomenclatural code there is a method checkForDeletableParts() where the deletable parts set to null.
But for ...
Katja Luther

03/11/2019

02:33 PM bug #8174: First test fails if term data is in loaded DataSet
This is the order how events are handled in unitils:
* [Unitils] beforeTestClass - TestClass1
* [Test] testBefore...
Andreas Müller
02:30 PM bug #8174 (New): First test fails if term data is in loaded DataSet
This is because the unitils/dbunit JpaModul starts the application context only during
~~~ java
beforeTestMethod...
Andreas Müller
01:53 PM bug #8170: javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource does not conform to the interface
I opened issue #8171 only for fixing the most severe problem quickly by storing the new connection in the cache field... Andreas Kohlbecker
01:41 PM bug #8170 (Feedback): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource does not conform to the interface
Is this still an open issue after #8171 is solved now?
I also do not fully understand the solution. In #8171 you s...
Andreas Müller
01:41 PM bug #8149: ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL
Related problem:
if e.g. "Phytotaxa" is tiped into the dopdown menue field, "Phytotaxa" is not selected, I have to s...
Wolf-Henning Kusber
01:10 PM feature request #6413 (In Progress): [DISCUSS] How to create type duplicates (e.g. isotypes) for a taxon name
Patrick Plitzner
12:59 PM feature request #8173 (In Progress): spring profile remoting enabled by default
Andreas Kohlbecker
12:55 PM feature request #8173 (Resolved): spring profile remoting enabled by default
Applied in changeset commit:cdmlib|5ab0f6455f6cb83bfba0bb5ad6aee6e210d8dd14. Andreas Kohlbecker
12:48 PM feature request #8173 (In Progress): spring profile remoting enabled by default
Andreas Kohlbecker
12:40 PM feature request #8173 (Closed): spring profile remoting enabled by default
the spring profile still needs to be enabled by passing `-Dspring.profiles.active=remoting` to cdm-remote instances.... Andreas Kohlbecker
12:57 PM feature request #8096 (Resolved): Implement CacheUpdater as long running task with correct progress monitoring
please review Katja Luther
12:54 PM bug #8171 (Resolved): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource fails to cache the connection which and leaves it unclosed
Applied in changeset commit:cdmlib|ddaf22cfc36cad56b677c8fecd8eb3e83db5cefb. Andreas Kohlbecker
12:13 PM bug #7874: TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters
fixed a small bug in updateCaches of Team.java which results in the result was always true. commit:cdmlib|694f0ef28f3... Katja Luther

03/08/2019

07:17 PM feature request #8172 (New): Discuss: Cite an image of the holotype
Probem: in Micoalgae, a type specimen can be designated, but nobody knows how the taxon looks like. E.g. Two differen... Wolf-Henning Kusber
05:17 PM bug #8132: phycobank cdm-server instance problems with db connections
Another situation in which a connection is being opened but not properly closed is occurring in the `DataSourceConfig... Andreas Kohlbecker
02:02 PM bug #8132: phycobank cdm-server instance problems with db connections
debugging the cdm-server to find connections that have been opened but which are not being closed properly (DebugC3P0... Andreas Kohlbecker
05:06 PM bug #8171 (Closed): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource fails to cache the connection which and leaves it unclosed
When the existing cached connection in the WrappedCdmDataSource is null a new connection will be created but is not s... Andreas Kohlbecker
04:59 PM bug #8170 (New): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource does not conform to the interface
the documentation of `javax.sql.DataSource.getConnection()` reads like *"**Attempts to establish** a connection with ... Andreas Kohlbecker

03/07/2019

03:26 PM bug #8169 (New): avoid factory.openSession() in DaoBase

In DaoBase using `factory.openSession()` is plain wrong, the HibernateTransactionManger should be used instead.
Andreas Kohlbecker
03:24 PM bug #7106 (In Progress): avoid factory.openSession() in CdmRepository
Andreas Kohlbecker
02:17 PM bug #7106: avoid factory.openSession() in CdmRepository
since February 25th there are only occurrences related to this issue in the log which affected the phycobank code.
W...
Andreas Kohlbecker
07:25 AM bug #7106: avoid factory.openSession() in CdmRepository
with the logging of the stacktrace it now becomes clear where the unmanaged sessions are being created:
~~~~
java...
Andreas Kohlbecker
12:37 PM bug #8132: phycobank cdm-server instance problems with db connections
The problem just occurred again. This time no one was using the Taxeditor since the instance has been started.
The...
Andreas Kohlbecker
11:21 AM task #8168 (New): Check if withdrawing of per entity permission is working correctly for inReferences
Andreas Kohlbecker
11:17 AM bug #8167 (Closed): Permission denied for Submitter when adding section to newly created journal

~~~
[phycobank] 2019-03-07 09:56:41,648 ERROR [qtp1510067370-69] [org.hibernate.internal.SessionImpl] - HHH000346:...
Andreas Kohlbecker
09:39 AM task #8118: Update MySQL drivers
Andreas Müller wrote:
> Some solution is setting on command line e.g. for Central European time (CET):
>
> mysql>...
Katja Luther

03/06/2019

08:57 PM task #8118: Update MySQL drivers
Some solution is setting on command line e.g. for Central European time (CET):
mysql> SET GLOBAL time_zone = '+1:0...
Andreas Müller
08:19 PM task #8118: Update MySQL drivers
Katja, I think you also had the problem localy. What did you do to fix it? Andreas Müller
08:11 PM task #8118: Update MySQL drivers
This is what I currently get when connecting to MySQL on PESIHPC:
~~~
Caused by: com.mysql.cj.exceptions.InvalidC...
Andreas Müller
08:06 PM task #8118: Update MySQL drivers
https://stackoverflow.com/questions/26515700/mysql-jdbc-driver-5-1-33-time-zone-issue Andreas Müller
05:00 PM bug #7106: avoid factory.openSession() in CdmRepository
In a locally running cdmserver started vi the eclipse launcher *cdm-server - start from war* multiple occurrences can... Andreas Kohlbecker
01:56 PM task #8166 (Closed): Adapt dataportal to term structure changes
the dataportal needs to be adapted to the changes applied in the context of #6794 Andreas Kohlbecker
01:05 PM task #8162: Move term related classes from model.common to model.term
Andreas Müller wrote:
> Other classes to move: Sources und IntextReferences, Rights, IReferencedEntity, ReferencedE...
Andreas Müller
01:03 PM task #8162: Move term related classes from model.common to model.term
Also move FeatureNode and FeatureTree to new term package as they become TermTreeNode and TermTree Andreas Müller
10:49 AM task #8130: Check if related feature data is cleared when supported facts type is changed
Katja, could you please check how we do these "model validations" in terms of e.g. nomenclatural code changes in Taxo... Andreas Müller
10:14 AM task #8130 (Feedback): Check if related feature data is cleared when supported facts type is changed
Andreas Müller wrote:
> We may want to implement hard or soft validation for this. Maybe also an update script to re...
Patrick Plitzner
10:07 AM task #8130 (In Progress): Check if related feature data is cleared when supported facts type is changed
Patrick Plitzner
10:44 AM feature request #8165 (New): enable logback jmx for cdm-server
having the logback jmx beans enabled would be a great help during debugging of the production server and other system... Andreas Kohlbecker
10:23 AM bug #5632: ClassNotFoundException for org.eclipse.jetty.servlet.listener.ELContextCleaner during taxeditor mvn integration-test
Moving the ticket back to decide what we want to do with it Patrick Plitzner
10:19 AM bug #5632: ClassNotFoundException for org.eclipse.jetty.servlet.listener.ELContextCleaner during taxeditor mvn integration-test
This exception is still thrown when the test is run.
This is the log of the last jenkins run: http://int.e-taxonom...
Patrick Plitzner
08:51 AM bug #8164 (New): ClassNotFoundException during deserialization for Reference
Andreas K.: "Ich habe in dem Produktions-Server-Log seit Oktober 10x
`org.springframework.web.util.NestedServletEx...
Patrick Plitzner

03/05/2019

05:39 PM task #8162: Move term related classes from model.common to model.term
Andreas Müller wrote:
> we should also adapt persistence layer
done
Andreas Müller
12:43 PM task #8162 (Resolved): Move term related classes from model.common to model.term
Applied in changeset commit:taxeditor|974d02d015234ec80816dfb47eaabde6688c2fa9. Andreas Müller
12:24 PM task #8162 (In Progress): Move term related classes from model.common to model.term
Andreas Müller
12:23 PM task #8162: Move term related classes from model.common to model.term
we should also adapt persistence layer Andreas Müller
12:12 PM task #8162 (Resolved): Move term related classes from model.common to model.term
Applied in changeset commit:taxeditor|b9dc6bb1d38897b06888836dd74d48684f73c5d5. Andreas Müller
10:52 AM task #8162: Move term related classes from model.common to model.term
Other classes to move: Sources und IntextReferences, Rights, IReferencedEntity, ReferencedEntityBase, Language? Andreas Müller
05:22 PM bug #8132: phycobank cdm-server instance problems with db connections
Results from the server log:
The problem occurred again. The jdbc connection which was being used by the tread `qt...
Andreas Kohlbecker
02:58 PM bug #8107 (Closed): NPE when throwing PopupEditorException in AbstractPopupEditor
issue is not reproducible - closing. Andreas Kohlbecker
11:49 AM feature request #8163 (Rejected): RegistrationService.setStatus() method implemented
This method need to be used by the RegistrationWorkingsetPresenter.saveRegistrationStatusChange() method in cdm-vaadi... Andreas Kohlbecker
11:21 AM bug #8161 (Rejected): *FilterablePagingProvider classes as transactional readonly spring beans
the *FilterablePagingProviders only are using service methods which are anyway annotated with `@Transactional(readOnl... Andreas Kohlbecker
11:21 AM bug #7945 (Rejected): TaxonNamePopupEditor: missing genus causes exception when updating name parts visibility
the *FilterablePagingProviders only are using service methods which are anyway annotated with `@Transactional(readOnl... Andreas Kohlbecker
11:14 AM bug #8075 (In Progress): multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations
Andreas Kohlbecker
10:55 AM bug #8158: cascade="all-delete-orphan" problem when ....
potentially duplicate of #8160 Andreas Kohlbecker

03/04/2019

03:19 PM task #8162 (Closed): Move term related classes from model.common to model.term
This means moving the following model classes:
* DefinedTerm
* DefinedTermBase
* OrderedTerm
* OrderedTermBase
...
Andreas Müller
03:06 PM bug #7881: reference selection combobox broken after error in ...
potentially duplicate of #8161 Andreas Kohlbecker
03:04 PM bug #7945: TaxonNamePopupEditor: missing genus causes exception when updating name parts visibility
potentially duplicate of #8161 Andreas Kohlbecker
03:00 PM bug #8065: HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEditor type designation table
potentially duplicate of #8160 Andreas Kohlbecker
02:07 PM bug #8160 (Resolved): CdmBeanItemContainerFactory as readonly service bean
Andreas Kohlbecker
12:43 PM bug #8160 (Closed): CdmBeanItemContainerFactory as readonly service bean
Turning the CdmBeanItemContainerFactory into a readonly service bean should solve the cascade="all-delete-orphan" pro... Andreas Kohlbecker
12:47 PM bug #8161 (Rejected): *FilterablePagingProvider classes as transactional readonly spring beans
Turing the TaxonNameStringFilterablePagingProvider into a readonly service bean should solve the cascade="all-delete-... Andreas Kohlbecker
11:52 AM task #4600 (New): Investigate and implement tests for security in cdm-vaadin
Andreas Kohlbecker
11:51 AM task #4600 (In Progress): Investigate and implement tests for security in cdm-vaadin
Andreas Kohlbecker
11:47 AM bug #7879: Book CacheStrategy does not show 'place published', 'publisher', 'editor'
Hi Andreas, I am passing this to you since it is a bug in the cache strategy and closely related to #1866 Andreas Kohlbecker
11:39 AM feature request #8124 (Resolved): Activate Name Facts in Taxeditor
please review Katja Luther
07:42 AM task #8159 (New): Replace LocalSelectionTransfer for DnD operations
Using LocalSelectionTransfer is in most cases too generic. It is better to define an own TransferData and assign the ... Patrick Plitzner

03/01/2019

11:05 PM feature request #6794: Improve term structure
Current idea for a solution:
Collections:
* Common base class TermCollection(Base) for all Vocabularies and Graphs ...
Andreas Müller
04:05 PM bug #8132: phycobank cdm-server instance problems with db connections
It seems as if this problem is being cased by the CdmFilterablePagingProvider which might open an new Sesscion which ... Andreas Kohlbecker
02:46 PM bug #8132: phycobank cdm-server instance problems with db connections
this here https://stackoverflow.com/questions/34408362/c3p0-connection-pool-gives-connection-timeout-error-with-this-... Andreas Kohlbecker
01:58 PM bug #8132: phycobank cdm-server instance problems with db connections
Andreas Kohlbecker wrote:
> I set `testConnectionsOnCheckIn=true` temporarily via jmx in order to test if this helps...
Andreas Kohlbecker
11:13 AM task #615 (Closed): remove suns repository
the repository
~~~xml
<!-- sun repository -->
<repository>
<id>java.net</id>
<url>http:...
Andreas Kohlbecker
11:11 AM task #615 (Resolved): remove suns repository
Applied in changeset commit:cdmlib|d402220f823edfb01ec9385d20117d6afee9a77d. Andreas Kohlbecker
10:17 AM feature request #8150 (Resolved): Allow editing the representation label of characters in details view
Patrick Plitzner
07:17 AM bug #8158 (Closed): cascade="all-delete-orphan" problem when ....
I seem to remember that I did the following:
1. RegistrationWorkingsetEditor at http://api.phycobank.org/phycobank...
Andreas Kohlbecker

02/28/2019

09:54 PM feature request #8157 (New): Registration list view: sort registrations by the same order as in the dataportal
newer registrations should come first.
Oder by created when! (agreed)
Andreas Kohlbecker
09:50 PM feature request #8156: Registration items show type status in bold letters
should be easy to implement, thus i am setting the priority to high Andreas Kohlbecker
09:50 PM feature request #8156 (Closed): Registration items show type status in bold letters
The type status in registration items is not easy to see. Making the status bold would improve the readability. Andreas Kohlbecker
09:47 PM feature request #8155 (Feedback): SpecimenTypeDesignationEditor: allow choosing the typified name from the homotypical group for specific type status
Andreas Kohlbecker
09:47 PM feature request #8155: SpecimenTypeDesignationEditor: allow choosing the typified name from the homotypical group for specific type status
For how urgent do you consider this feature, Henning? I guess this situation will occur quite frequently? Andreas Kohlbecker
09:42 PM feature request #8155 (Feedback): SpecimenTypeDesignationEditor: allow choosing the typified name from the homotypical group for specific type status
In case of lecto-, epit- and neo-types the SpecimenTypeDesignationEditor should selecting the typified name from the ... Andreas Kohlbecker
05:30 PM bug #7514: Change direct and inverse symbol for pro parte synonym and misapplied name relationship types.
the test page http://int.e-taxonomy.eu/dataportal/integration/reference/cdm_dataportal/taxon/c6716cee-2039-4ba8-a239-... Andreas Kohlbecker
04:12 PM bug #8154 (Worksforme): NameController.doGetTaggedName fails due to [UPDATE] not permitted for 'anonymousUser' on Person
http://160.45.63.173:8081/phycobank/name/a2b01d35-fdcf-43fb-8376-f03f195c6e06/taggedName.json
fails every ~4 times...
Andreas Kohlbecker
03:05 PM bug #8152 (Duplicate): ReferencePopupEditor: inReference field allows to select references with type GEN but field validation fails in this case
Henning: References with type 'Generic' must not be in the list, filter only by matching type
So this is a duplica...
Andreas Kohlbecker
01:05 PM bug #8152 (Duplicate): ReferencePopupEditor: inReference field allows to select references with type GEN but field validation fails in this case
Heba reported an error which was due the Journal "Rickia" having the Referencetype 'Generic'
The reference could b...
Andreas Kohlbecker
01:30 PM feature request #8153 (Closed): Adapt cdmlib to FeatureNode/FeatureTree model changes
* Since the introduction of term trees with the last model change (5.6.0) `FeatureNode.getFeature()` is deprecated an... Patrick Plitzner
12:16 PM feature request #4611 (New): I18n for the TaxEditor menu
sorry, was a mistake Andreas Müller
12:12 PM feature request #4611 (Resolved): I18n for the TaxEditor menu
Andreas Müller
12:14 PM feature request #8124: Activate Name Facts in Taxeditor
Katja Luther wrote:
> when activating the name facts for the name displayed in the details view, the details view is...
Katja Luther
11:24 AM feature request #8124: Activate Name Facts in Taxeditor
when activating the name facts for the name displayed in the details view, the details view is the selectionProviding... Katja Luther
11:57 AM bug #7107: "Omit level" (TDWG Level2) in distribution hierarchy should not supress distributions source reference
OK Andreas Kohlbecker
11:52 AM bug #7107 (New): "Omit level" (TDWG Level2) in distribution hierarchy should not supress distributions source reference
Ich glaube nicht, dass das für E+M relevant ist, da wir in E+M ja das E+M Voc verwenden, welches keine Omit levels ha... Andreas Müller
11:37 AM bug #7107 (Feedback): "Omit level" (TDWG Level2) in distribution hierarchy should not supress distributions source reference
Hallo Andreas, ich denke das ist auch für Euro+Med releveant, oder?
Wenn ja, sollten wir das Tag hinzufügen und di...
Andreas Kohlbecker
11:57 AM feature request #4610: [DISCUSS] I18n for the EDIT platform
Please do not move unreviewed tickets to Reviewed milestone Andreas Müller
11:05 AM bug #8151 (Resolved): after creating a new synonym and pasting a name string the default string is not removed
the call of placeCursor() caused that the cursor was at the end of the "Klicken, um ..." string. Removing this method... Katja Luther
10:58 AM bug #8151 (Closed): after creating a new synonym and pasting a name string the default string is not removed
mail von S. v. M.:
Beim Reinkopieren eines neuen Synonyms blieb der Text “Klicken, um Namen hinzuzufügen” stehen.
...
Katja Luther
08:07 AM feature request #8146: Adapt taxeditor UI to structure and property term type
Add character to term menu with commit:2c98dda6165033a58c7df8c06b21518d380307b3 Patrick Plitzner

02/27/2019

03:52 PM bug #8132: phycobank cdm-server instance problems with db connections
I set `testConnectionsOnCheckIn=true` temporarily via jmx in order to test if this helps avoiding this connectivity p... Andreas Kohlbecker
03:30 PM feature request #8124: Activate Name Facts in Taxeditor
for the name bulk editor the name facts are activated now.
still missing is the activation if name is selected in ...
Katja Luther
02:24 PM feature request #8150 (Closed): Allow editing the representation label of characters in details view
Patrick Plitzner
01:56 PM feature request #8136 (In Progress): Implement sources for type designations in TaxEditor
Katja Luther
10:34 AM bug #8149 (Closed): ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL
In reference type = article
Drop down of Journals should only search for entries = journal (not for all references)
...
Wolf-Henning Kusber
10:19 AM bug #8148 (In Progress): Login Dialog cuts off information
Katja Luther
10:18 AM bug #8148 (Resolved): Login Dialog cuts off information
Applied in changeset commit:taxeditor|a08af9f9d2b8840b48fc63b647aca9ee0a34b68c. Katja Luther
09:38 AM bug #8148 (Closed): Login Dialog cuts off information
In the case of an exception and for the advanced section information is not correctly displayed.
![](picture896-1....
Patrick Plitzner
09:34 AM feature request #8147 (Resolved): Add "plural" to representation detail element
Fixed with commit:taxeditor|754fbf873ca0b63addc6842c089298fff76eb30d Patrick Plitzner
08:44 AM feature request #8147 (Closed): Add "plural" to representation detail element
Patrick Plitzner
08:37 AM feature request #8146 (Closed): Adapt taxeditor UI to structure and property term type
1. ~~Add term editor menu for each~~
1. ~~Restrict tree selection in CharacterEditor~~
1. ~~Restrict context menu,...
Patrick Plitzner

02/26/2019

04:55 PM feature request #3616: Show DescriptionElementBase.timeperiod in Dataportals
Improvements for formatting copied to #8145 Andreas Müller
02:37 PM feature request #3616: Show DescriptionElementBase.timeperiod in Dataportals
Andreas Müller wrote:
> Generally it looks fine.
>
> Only the formatting maybe needs discussion. It differs from...
Andreas Kohlbecker
02:26 PM feature request #3616 (Feedback): Show DescriptionElementBase.timeperiod in Dataportals
Generally it looks fine.
Only the formatting maybe needs discussion. It differs from the default formatting of ti...
Andreas Müller
01:00 PM feature request #3616 (Resolved): Show DescriptionElementBase.timeperiod in Dataportals
Implemented
please review, for the page used by the integration test, please see : http://int.e-taxonomy.eu/datapo...
Andreas Kohlbecker
03:09 PM feature request #8145 (New): Implement TimePeriod DTO with localized formatting
for details see #3616#note-10 ff.
Once implemented we also need to adapt dataportal code to use the new timeperiod...
Andreas Müller
01:42 PM task #7356: setup selenium test suite for cdm-vaadin
Adding master thesis on Vaadin TestBench Andreas Kohlbecker
12:12 PM feature request #8144: Check if modifiers and modifyingText is handled correctly for description elements in data portals
since modifiers and modifyingText can not be added to the database easily I need to wait until the issue #3836 is com... Andreas Kohlbecker
11:10 AM task #8118: Update MySQL drivers
Andreas Müller wrote:
> Starting with MySQL JDBC Driver 5.1.33 serverTimezone needs to be explicitly defined in conn...
Andreas Kohlbecker

02/25/2019

10:08 PM feature request #3746: Implement time period scope for description elements in TaxEditor
Andreas Kohlbecker wrote:
> The output in the taxeditor can very ugly depending on the partial fields being used:
>...
Andreas Müller
05:28 PM feature request #3746: Implement time period scope for description elements in TaxEditor
The output in the taxeditor can very ugly depending on the partial fields being used:
* Timescope: start month: ...
Andreas Kohlbecker
10:01 PM feature request #3836: Implement modifiers and modifying text for Description Elements in TaxEditor
As we have decided to check for old unimplemented model issues in this version I add it to current milestone. But we ... Andreas Müller
08:54 PM bug #8140 (Resolved): Update list of type designation status which allow an explicit source
Applied in changeset commit:cdmlib|2a0a678b59b88779f6db98619be4d4510ea26f93. Andreas Müller
02:31 PM bug #8140 (Closed): Update list of type designation status which allow an explicit source
This list is currently returned by transient method TypeDesignationStatusBase.isLectotpye().
Currently it contains...
Andreas Müller
08:54 PM bug #7772: Rename TermBase_inverseRepresentation to DefinedTermBase_InverseRepresentation
Applied in changeset commit:cdmlib|3b49207de7d71fa2af4fcd8a6e7d913dc654d733. Andreas Müller
08:54 PM bug #7859: Increase size of CdmPreference.value
Applied in changeset commit:cdmlib|da556b1537505b615fe45afc8ea7f0d06c5d256b. Andreas Müller
08:28 PM task #8118 (Feedback): Update MySQL drivers
Starting with MySQL JDBC Driver 5.1.33 serverTimezone needs to be explicitly defined in connection string or one may ... Andreas Müller
06:22 PM bug #8143 (Resolved): It is possible to open multiple instances of the login dialog
Applied in changeset commit:taxeditor|e25ce35073e04836a1b382da50faf21ab605ae16. Patrick Plitzner
05:45 PM bug #8143 (Closed): It is possible to open multiple instances of the login dialog
With every click on General -> Login another login dialog is opened.
This could be potentially dangerous because t...
Patrick Plitzner
06:13 PM feature request #3747 (Closed): Check if time period is handled correctly for description elements in data portals
check for and modifiers and modifyingText copied to new ticket, closing this issue Andreas Kohlbecker
06:08 PM feature request #3747: Check if time period is handled correctly for description elements in data portals
since modifiers and modifyingText can not be added to the data easily I need to wait until the issue #3836 is complet... Andreas Kohlbecker
06:03 PM feature request #3747 (In Progress): Check if time period is handled correctly for description elements in data portals
The scope of this ticket includes modifiers and modifyingText ... reopening issue Andreas Kohlbecker
06:00 PM feature request #3747 (Closed): Check if time period is handled correctly for description elements in data portals
the output of timeperiod for DescriptionElements is missing so far in the Dataportal. So ticket #3616 becomes relevan... Andreas Kohlbecker
06:10 PM feature request #8144 (In Progress): Check if modifiers and modifyingText is handled correctly for description elements in data portals
not relevant for TextData as we expect that TextData will handle modifiers with its text (see #3836)
Andreas Kohlbecker
06:04 PM feature request #3616 (In Progress): Show DescriptionElementBase.timeperiod in Dataportals
Andreas Kohlbecker
05:45 PM feature request #8142 (Resolved): Representations have optional "plural" as additional field
Andreas Müller
05:32 PM feature request #8142 (Closed): Representations have optional "plural" as additional field
additional to label (required), description (optional, but recommended), abbrevLabel(optional)
https://wiki.bgbm.o...
Andreas Müller
04:00 PM bug #8105 (In Progress): better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
it turned out that it can happen that cherries need to be modified when picking them from hotfix to develop. This hap... Andreas Kohlbecker
03:48 PM bug #8132: phycobank cdm-server instance problems with db connections
Andreas Kohlbecker wrote:
> I added `autoReconnect=true` to the connection string of the phycobank datasource.
us...
Andreas Kohlbecker
03:21 PM bug #8132: phycobank cdm-server instance problems with db connections
I added `autoReconnect=true` to the connection string of the phycobank datasource. Andreas Kohlbecker
01:06 PM bug #8132: phycobank cdm-server instance problems with db connections
these connectivity problems should be prevented by c3p0 since the `idleConnectionTestPeriod` is set to `600` (10 minu... Andreas Kohlbecker
02:48 PM feature request #8017 (Resolved): TypeDesignations need sources additional to lectotypifcation sources
We may also want to rename the existing "citation" attribute. This will be doen within #6581 Andreas Müller
02:37 PM bug #8141 (New): explicitSource as additional attribute for TypeDesignationStatus
Some type designation status do allow an explicit source (see #8139). Currently the list of status are handled hardco... Andreas Müller
02:15 PM feature request #8139 (Resolved): [Rule] Validate lectotype sources
Andreas Müller
02:10 PM feature request #8139 (Resolved): [Rule] Validate lectotype sources
Lectotypes and some other type status allow an additional source which mentions in which source the lectotypification... Andreas Müller
02:04 PM feature request #6665 (New): Add "Add specimen duplicate" context menu item to specimen editor
Ok, maybe I closed this too fast. #6413 serves more as a master ticket and this is one step in solving it. Patrick Plitzner
02:01 PM feature request #6665 (Duplicate): Add "Add specimen duplicate" context menu item to specimen editor
Closed as duplicate because the issue description is fully copied to #6413
Also the discussion is done there
Patrick Plitzner

02/24/2019

01:33 PM feature request #7653 (Resolved): [DISCUSS] Delete NameFacts => Result: no
The public flag requirement from #7653#note-5 was moved to a new ticket #8138. I think we can close this ticket now ... Andreas Müller
12:47 PM feature request #7653: [DISCUSS] Delete NameFacts => Result: no
Unification of extensions and facts moved to new ticket #8133 Andreas Müller
01:30 PM feature request #8138 (Closed): [DISCUSS] Publish flag for facts and type designations
In #7653#note-5 there was the wish for an individual publish flag on type desginations (especially for text based typ... Andreas Müller
01:11 PM feature request #8137 (Feedback): Implement sources for type designations in data portal
For details see #8017.
Be aware that there are 2 different types of sources "lectotype"(hasDesignationSource) sour...
Andreas Müller
01:04 PM feature request #8136 (Closed): Implement sources for type designations in TaxEditor
For details see #8017.
Be aware that there are 2 different types of sources "lectotype" sources and general source...
Andreas Müller
12:58 PM feature request #8135 (Closed): Implement verbatim type information in TaxEditor
for details see #7470 and #7653
1. Implement a new detail element for verbatim type designations
2. Implement but...
Andreas Müller
12:53 PM feature request #8134 (Closed): Implement verbatim type information in dataportal
For details see also #7653#note-5.
Implementation of verbatim type information in cdm in #7470
Andreas Müller
12:41 PM feature request #8019: Add "Typification Notes", "Ortography" and "Etymology" to NameFeature vocabulary
Also "Ortography" and "Etymology" added. Andreas Müller
12:28 PM feature request #8133 (New): [DISCUSS] Combine Facts and Extensions
for a first discussion see #7653
Facts (DescriptionsElements) and Extensions are both meant for a generic extensio...
Andreas Müller

02/23/2019

01:01 AM bug #8024 (Duplicate): IndexOutOfBoundsException caused by RegistrationWorkingSet.getRegistrationDate()
seems to be duplicate for #7895 Andreas Müller
12:46 AM bug #7896: NPE, NullPointerException in RelationshipTermBase
There is not much information what data to use for reproducing error. However, I think dbb48641 should fix the proble... Andreas Müller
12:42 AM bug #7896 (Resolved): NPE, NullPointerException in RelationshipTermBase
Applied in changeset commit:cdmlib|dbb486417a2345628d068d0470c845b1cb3dee3a. Andreas Müller
12:15 AM feature request #6316: display source references of media objects in media page
To me it looks like this is already implemented. I add to current milestone just to check. Either close+remove milest... Andreas Müller
12:08 AM feature request #5232: use TaxonBase.getTaggedTitle to get the sec reference in theme_cdm_taxonRelationships()
Shouldn't this be closed? See #note-26 Andreas Müller

02/22/2019

06:38 PM bug #8132 (Worksforme): phycobank cdm-server instance problems with db connections

the phycobank cdm-server instance which is running in a docker container got problems with the db connections
P...
Andreas Kohlbecker
06:28 PM bug #8119 (Rejected): Link a PhycoBank Id in a Proof to Portal
this is only a side effect of as problem with the server which fails to respond sometimes Andreas Kohlbecker
05:54 PM bug #8119: Link a PhycoBank Id in a Proof to Portal
the requires status message seems to be visible only for logged in users:
![](picture198-1.png)
Andreas Kohlbecker
06:18 PM feature request #8093 (Closed): harmonize registrationId links and make tesing easier
Andreas Kohlbecker
06:17 PM feature request #8093 (Resolved): harmonize registrationId links and make tesing easier
Applied in changeset commit:cdm-dataportal|977bba78560ff1387b601420f9c55409ac19fd92. Andreas Kohlbecker
06:09 PM bug #6380: typedesignations missing in homotypic group
Is this still a relevant issue once #7696 is fixed. As the later is on 5.6 I also moved **this** back. If we decide t... Andreas Müller
06:02 PM feature request #7696: use compact type representations in the synonymy as provided by the typedesignations/byTaxon/{taxon_uuid} service
This is related to the current milestone topic (typification) so I suggest to keep in current milestone. Also I think... Andreas Müller
05:59 PM feature request #7408: [E+M] Support for preferred common names in data portal
This is important for E+M and was promised for 5.5 already. Ok to keep in current milestone? Andreas Müller
05:51 PM bug #2074: network independend CdmUpdaterTest
yes this can be closed Andreas Müller
04:22 PM bug #2074 (Rejected): network independend CdmUpdaterTest
I am no longer using eu.etaxonomy.cdm.database.update.CdmUpdaterTest since cdm-remote supports the `force-scheamupdat... Andreas Kohlbecker
05:47 PM feature request #5807: Implement sub-distribution area inclusion in TaxonService.findTaxaAndNamesByFullText()
As this is E+M related I put it to highest. We may discuss who will finally fix it. I have to work on transmission en... Andreas Müller
04:45 PM feature request #5807 (New): Implement sub-distribution area inclusion in TaxonService.findTaxaAndNamesByFullText()
this is still not working:
http://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/search/results/taxo...
Andreas Kohlbecker
04:10 PM feature request #5807 (Feedback): Implement sub-distribution area inclusion in TaxonService.findTaxaAndNamesByFullText()
trying to reproduce this at the euro+med portal, since this taxon no longer is found in the caucasus portal:
http:...
Andreas Kohlbecker
05:37 PM feature request #7470 (Resolved): Verbatim type designation information
Andreas Müller
05:22 PM bug #5774: cdmserver misses to detect some errors in failed instances
I guess you are right. I was lowering the priority that much because the issue has not been reported for 2 years, but... Andreas Kohlbecker
04:03 PM bug #5774: cdmserver misses to detect some errors in failed instances
hmm, I consider this a very anoying and dagerous bug as one may not realize that some instances do work (we do not ha... Andreas Müller
05:15 PM bug #7087 (Worksforme): description/accumulateDistributions webservice can not be triggered
tested by using httpie and it works again, it seems this has been fixed meanwhile Andreas Kohlbecker
05:03 PM bug #7106 (Feedback): avoid factory.openSession() in CdmRepository
I am modifying the logging in mentioned case to allow us checking in the server logs if this case is actually happeni... Andreas Kohlbecker
04:34 PM feature request #8120 (Resolved): Add structural and property modifiers
Andreas Müller
10:05 AM feature request #8120 (In Progress): Add structural and property modifiers
Andreas Müller
09:28 AM feature request #8120 (Closed): Add structural and property modifiers
We need two specialized modifier types in the context of character creation:
* Structure modifier
* defining the...
Patrick Plitzner
04:18 PM bug #8131 (Rejected): reindexing fuction in dataportal setting reports fails
it was really the wrong credentials that i used Andreas Kohlbecker
04:09 PM bug #8131 (Rejected): reindexing fuction in dataportal setting reports fails
even with correct credentials "Error: Are your credentials correct?" is being reported Andreas Kohlbecker
03:52 PM bug #7938: cdmserver sub-processes (threads) with constant high cpu
this never occurred since 3 months, lowering priority Andreas Kohlbecker
03:41 PM bug #8105 (Closed): better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
Andreas Kohlbecker
03:31 PM bug #8099: Error saving name type designation editor due to problem in poupeditor context
Da gab es mehrere Korrekturen und Bearbeitungen [vielleicht ein Spezialproblem, das im normalen Betrieb nicht vorkomm... Wolf-Henning Kusber
10:01 AM bug #8099: Error saving name type designation editor due to problem in poupeditor context
AHH ich glaube jetzt habe ich es. Ein alter Dump der DB hat mir*Geitleriaceae Kilgore & J.R.Johans.* auf die Sprünge... Andreas Kohlbecker
01:34 PM task #8130: Check if related feature data is cleared when supported facts type is changed
We may want to implement hard or soft validation for this. Maybe also an update script to remove existing data (if it... Andreas Müller
01:16 PM task #8130 (In Progress): Check if related feature data is cleared when supported facts type is changed
For example:
1. Set a feature to support quantitative data and assign recommended measurement units, statistical m...
Patrick Plitzner
01:28 PM bug #7703 (New): Multiple names cannot be shown in TypeDesignationDetailElement for specimens
Patrick Plitzner
01:28 PM bug #7703: Multiple names cannot be shown in TypeDesignationDetailElement for specimens
Displaying the names is not the problem. What would take time is implementing the possibility of editing them. Right ... Patrick Plitzner
01:00 PM bug #7703: Multiple names cannot be shown in TypeDesignationDetailElement for specimens
Patrick Plitzner wrote:
> Before I try to fix this: Is this a frequent use case? Because you can also just create tw...
Andreas Müller
01:09 PM feature request #7741: Refresh supplemental data view title when editing terms
This is still an open issue. But I would rather fix this together with the other refresh tickets of #4135. It is more... Patrick Plitzner
12:36 PM feature request #7741: Refresh supplemental data view title when editing terms
Is this still an open issue or has it been fixed with the new term editor implementation?
If not yet fixed we shou...
Andreas Müller
12:31 PM bug #8129 (Closed): Load images asynchronously in media details view
Loading images takes often very long if full size images with e.g. ~10MB are involved. Currently the TaxEditor become... Andreas Müller
12:27 PM bug #5632: ClassNotFoundException for org.eclipse.jetty.servlet.listener.ELContextCleaner during taxeditor mvn integration-test
We recently talked about this issue. I just moved it to the release to check if it still happens and if there is an e... Patrick Plitzner
12:22 PM feature request #8011 (In Progress): Implement term search view
Patrick Plitzner
11:32 AM bug #8126: Mediarepresentations should not be shown in Referencing objects view
AM:
gibt es für das Problem, dass MediaRepresentations bei den referencing objects von Media angezeigt werden eige...
Andreas Müller
11:02 AM bug #8126 (New): Mediarepresentations should not be shown in Referencing objects view
MediaRepresentations belonging to the media object therefore they should not be shown in the referencing objects view... Katja Luther
11:29 AM feature request #7860: [Master] Remaining E+M editor issues
E+M should be highest priority Andreas Müller
11:25 AM feature request #8128 (In Progress): Add indicator for feature facts and/or vocabularies which description type they support
Andreas Müller
11:24 AM feature request #8128 (Duplicate): Add indicator for feature facts and/or vocabularies which description type they support
we need to distinguish if features and/or their vocabularies support taxon facts, specimen facts and/or name facts.
...
Andreas Müller
11:25 AM feature request #8124: Activate Name Facts in Taxeditor
Also consider #8128 for future implementations. Andreas Müller
11:19 AM feature request #8124: Activate Name Facts in Taxeditor
Can we also activate name facts in the same way as supplemental data are activated => if focus is explicitly on a nam... Andreas Müller
10:30 AM feature request #8124 (In Progress): Activate Name Facts in Taxeditor
Katja Luther
10:30 AM feature request #8124 (Closed): Activate Name Facts in Taxeditor
Namefacts should be shown for names in bulk editor. (see discussion in #7653)
Therefore following is needed:
* ac...
Katja Luther
11:18 AM bug #6627: Remaining cdm light issues
Can you add the name facts to the TODO list? Is there an explicit ticket? Andreas Müller
10:25 AM bug #6627: Remaining cdm light issues
the name facts should be implemented in 5.6 Katja Luther
11:07 AM task #8127 (Discussed): [Reminder] to check if Hibernate Null Value bug still exists
see #5681 for details
https://hibernate.atlassian.net/browse/HHH-9751 (closed as duplicate, still open issue is ht...
Andreas Müller
11:03 AM feature request #7637: Handle intext references in CDM light
Andreas Müller wrote:
> Do we really want to keep in 5.6. We wanted to work on intext references in 5.7.
ups no, ...
Katja Luther
11:02 AM feature request #7637: Handle intext references in CDM light
Do we really want to keep in 5.6. We wanted to work on intext references in 5.7. Andreas Müller
11:00 AM task #7515: TypeDesignationStatusComparator to sort by vocabulary first and then by term order
We may also include the upcoming new term structure (using TermCollections) #6794. Andreas Müller
10:37 AM feature request #8089: improve abcd preference page
Does this not fit to our current milestone which includes preferences? Andreas Müller
10:33 AM bug #8125 (New): ClassCastException when adding person to newly created team
Hallo,
vermutlich ein ungünstiges Timing ...
Bulk Editor, neues Team, cache eingegeben -> Details view, Add Person,...
Katja Luther
10:26 AM feature request #8123 (Closed): Make available features a DB preference
... also distinguish taxon facts, specimen facts and name facts.
Adapt this also in the local preferences.
Stor...
Andreas Müller
10:20 AM bug #5278: Creating new taxon is slow in some cases
when creating a new taxonnode with a lot of siblings it takes some time because the sortindex is newly set for all si... Katja Luther
10:16 AM feature request #8046: Term lists in term manager should be positiv lists
Doesn't this belong much to the focus of our current milestone (terms, preferences, typification). So maybe we can ke... Andreas Müller
10:07 AM feature request #7810: DB preference to make Specimen editors visible
Because some major issues were implemented in 5.4. However, I think we should split the ticket for all remaining issu... Andreas Müller
09:01 AM feature request #7810: DB preference to make Specimen editors visible
Andreas Müller wrote:
> Patrick Plitzner wrote:
> > @all: Why is this ticket still open? What is left to do?
>
>...
Patrick Plitzner
10:01 AM bug #7689 (Worksforme): Mutliple representation exception when creating taxon nodes
I think this is fixed with the restructured taxonnode wizard (see #7680) Katja Luther
09:45 AM feature request #8096 (In Progress): Implement CacheUpdater as long running task with correct progress monitoring
Katja Luther
09:44 AM bug #8115 (In Progress): NPE when moving factual data
Katja Luther
09:35 AM feature request #8122 (New): Implement selection of modifier vocabulary for structures and properties
In the term editor for structure and property terms it should be possible to select one or more modifier vocabularies... Patrick Plitzner
09:32 AM feature request #8121 (Closed): Allow selecting structural/property modifiers when creating a character
When creating a character from a structure and a property the user can select from a predefined list of available mod... Patrick Plitzner

02/21/2019

05:18 PM feature request #7810: DB preference to make Specimen editors visible
Patrick Plitzner wrote:
> @all: Why is this ticket still open? What is left to do?
Isn't this quite obvious. See ...
Andreas Müller
04:41 PM feature request #7810: DB preference to make Specimen editors visible
Patrick Plitzner wrote:
> @Katja: Can you take a look at my last commit please commit:taxeditor|06ae687fc2061c691d70...
Katja Luther
04:04 PM feature request #7810: DB preference to make Specimen editors visible
@Katja: Can you take a look at my last commit please commit:taxeditor|06ae687fc2061c691d70c87b1da7e8b41b903385
@al...
Patrick Plitzner
05:10 PM task #8118: Update MySQL drivers
I read through the change sets, all are looking as expected.
As next step we should run a test against a maria db ...
Andreas Kohlbecker
03:28 PM task #8118 (Resolved): Update MySQL drivers
Andreas Müller
02:26 PM task #8118: Update MySQL drivers
compile error fixed Andreas Müller
02:04 PM task #8118 (In Progress): Update MySQL drivers
I added both drivers to cdmlib-db (b137f4e3) Andreas Müller
02:02 PM task #8118 (Feedback): Update MySQL drivers
We are using old JDBC drivers for MySQL. ALso we do not have drivers for MariaDB. Should be added. Andreas Müller
03:50 PM bug #8105: better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
note for developers added to the ticket description ..... Andreas Kohlbecker
03:40 PM bug #8105 (Resolved): better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
by this the git-hfx-cherry-check should be executed for all HFX_FINISH jobs, in case of errors the job will FAIL sinc... Andreas Kohlbecker
03:36 PM bug #8105: better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
and ... using git-hfx-cherry-check.sh in gitflow-finish.sh and maven-gitflow-HOTFIX-finish.sh
Andreas Kohlbecker
03:22 PM bug #8105: better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
Script to check for cherries in the HFX Finish jobs created: https://dev.e-taxonomy.eu/svn/trunk/server-scripts/jenki... Andreas Kohlbecker
03:22 PM bug #7703 (Feedback): Multiple names cannot be shown in TypeDesignationDetailElement for specimens
Before I try to fix this: Is this a frequent use case? Because you can also just create two TypeDesignation with diff... Patrick Plitzner
09:18 AM bug #7703: Multiple names cannot be shown in TypeDesignationDetailElement for specimens
This belongs content wise to our current milestone. Please decide if we should move it to 5.6 and who should work on it Andreas Müller
02:41 PM bug #8117: CdmFilterablePagingProviderFactory.taxonNamesWithoutOrthographicIncorrect() causes performance overhead
Correction: The sql query showing the problem is:
~~~sql
select
this_.id as id1_499_2_, this_.created as cr...
Andreas Kohlbecker
12:29 PM bug #8117: CdmFilterablePagingProviderFactory.taxonNamesWithoutOrthographicIncorrect() causes performance overhead
the most time is actually consumed by
![](picture588-1.png)
Do we need to update the mysql driver for some r...
Andreas Kohlbecker
12:24 PM bug #8117: CdmFilterablePagingProviderFactory.taxonNamesWithoutOrthographicIncorrect() causes performance overhead
The query created by the restriction performs not so bad (55ms):
~~~sql
select
this_.id as id1_499_2_, this_...
Andreas Kohlbecker
11:32 AM bug #8117 (New): CdmFilterablePagingProviderFactory.taxonNamesWithoutOrthographicIncorrect() causes performance overhead

in
CdmFilterablePagingProviderFactory.taxonNamesWithoutOrthophicIncorrect()
a restriction is being used whic...
Andreas Kohlbecker
02:28 PM bug #8119 (Rejected): Link a PhycoBank Id in a Proof to Portal
Proof (as of 21 Feb 2019), Phytotaxa:
Heterocapsa triquetra var. litoralis Er.Lindem., nom. corr. (Turland et al., 2...
Wolf-Henning Kusber
12:01 PM bug #8088: Open taxon node wizard issues
The hotfix tasks seem to work now. Andreas Müller
10:58 AM bug #8088 (Resolved): Open taxon node wizard issues
please review the hotfix tasks. Katja Luther
09:30 AM bug #8088: Open taxon node wizard issues
Hallo,
bekomme diese Fehlermeldung beim Anlegen eines neuen Taxons.
viele Grüße und schöne WE
Nadja
~~~ tex...
Katja Luther
11:37 AM bug #7772 (Resolved): Rename TermBase_inverseRepresentation to DefinedTermBase_InverseRepresentation
Renamed TermBase_inverseRepresentation to DefinedTermBase_InverseRepresentation and attribute term_id to definedTermB... Andreas Müller
11:28 AM bug #8116 (New): ProgressMonitorManager: logging instead of System.err
In the ProgressMonitorManager an ignored error is logged to `System.err.println`
All logging should go to the logg...
Andreas Kohlbecker
11:06 AM bug #8099 (Feedback): Error saving name type designation editor due to problem in poupeditor context
Andreas Kohlbecker
11:05 AM bug #8099: Error saving name type designation editor due to problem in poupeditor context
Hakllo Henning
ich verstehe Step 2,3 oben nicht, was hat du da genau gemacht?
Andreas
Andreas Kohlbecker
10:27 AM bug #6784 (Feedback): Right click menu in Specimen Editor appears after Details View refresh
When I tested, the context menu was rendered first and afterwards the details view. Could you try again? Maybe this i... Patrick Plitzner
09:49 AM bug #8115: NPE when moving factual data
Katja: I assign this to you because it has to do with the operations of the NameEditor which are executed during saving. Patrick Plitzner
09:35 AM bug #8115 (Closed): NPE when moving factual data
Steps to reproduce:
1. Create the following factual data ![](picture643-1.png)
1. Move the abstract element with ...
Patrick Plitzner

02/20/2019

11:31 PM bug #7772 (In Progress): Rename TermBase_inverseRepresentation to DefinedTermBase_InverseRepresentation
Andreas Müller
07:13 PM bug #8114 (Duplicate): used author name cache in nomenclatural reference
For taxonomists/users it might be misleading when in the name editor the bibliographic authors are shown. In case of ... Wolf-Henning Kusber
03:45 PM feature request #7923 (New): Add context menu and drag'n'drop to CharacterEditor
Patrick Plitzner
03:45 PM bug #7112 (New): Ask for saving dirty editors when closing Taxeditor
Patrick Plitzner
03:45 PM feature request #6774 (New): Implement OWL export
Patrick Plitzner
02:29 PM bug #6205 (Duplicate): Move excluded nodes to the bottom of the list in TaxEditor navigator
this is already implmented in #6547 Katja Luther
12:19 PM bug #8113 (In Progress): Update TypeDesignationStatus labels
Andreas Müller
12:19 PM bug #8113 (Closed): Update TypeDesignationStatus labels
~~Currently SpecimentTypeDesig use upper case while NameTypeDesignations uses lower case.~~ => #9263. Also check corr... Andreas Müller
09:52 AM bug #8088: Open taxon node wizard issues
Ich habe versucht das Taxon eines Taxonnodes zu ändern und bekam den Fehler unten.
Gibt es dafür schon ein Ticket? K...
Katja Luther

02/19/2019

11:19 PM bug #8112: Refresh for Group doesn't work
This seems to be related to #2414 though #2414 is closed. Maybe behavior changed with remoting.
It is also relevan...
Andreas Müller
11:15 PM bug #8112 (New): Refresh for Group doesn't work
How to:
* Open User bulk editor and Group bulk editor and search for "*"
* In User bulk editor choose a user and ...
Andreas Müller
11:02 PM bug #8111 (Closed): User selection dialog for groups does not filter out existing users
... but shows all users by "*". Same holds for Group selection dialog for Users.
Andreas Müller
06:57 PM feature request #7912: Enhance checkbox tree viewer
Please always add the follow up tickets to the "related issues" section, too. Andreas Müller
05:46 PM bug #8097: Problem with inserting a section - inReference is "lost"
issue completed.
Please review.
Andreas Kohlbecker
05:46 PM bug #8097 (Resolved): Problem with inserting a section - inReference is "lost"
Applied in changeset commit:cdm-vaadin|2bcb1498b2db48c720edfcfcac25e733be35cfb8. Andreas Kohlbecker
05:07 PM bug #8097: Problem with inserting a section - inReference is "lost"
As first solution to this problem we decided on making the inReference field required for all iSection refernfence ty... Andreas Kohlbecker
04:48 PM bug #5699 (Closed): user profile settigs in cdm_dataportal module done wrong
Andreas Kohlbecker
04:48 PM bug #5699 (Resolved): user profile settigs in cdm_dataportal module done wrong
Applied in changeset commit:cdm-dataportal|bf31af5f546f2b686f6d05c1357ce41d4bf6d09c. Andreas Kohlbecker
04:46 PM bug #5699: user profile settigs in cdm_dataportal module done wrong
this feature isn't used in any of the portals can can be removed.
Andreas Kohlbecker
04:13 PM task #4564: [Post 3.4] Check if originalLabelInfo is handled correctly in CdmDataPortal
Havn't we decided to handle model change tickets in current release? Andreas Müller
04:08 PM bug #8104 (Closed): TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart
The revert looks reasonable Andreas Müller
11:31 AM bug #8104: TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart
Please can you have a quick look on the reversion of your commit? Andreas Kohlbecker
11:30 AM bug #8104 (Resolved): TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart
Applied in changeset commit:cdmlib|6b548bff807c53bdc4e3676d4b74b83b8f31be4f. Andreas Kohlbecker
04:04 PM feature request #7747: Enhance display for URI element
The space is reserved by the URI element for error messages when parsing the URI.
![](picture394-1.png)
I chang...
Patrick Plitzner
02:49 PM feature request #7695 (In Progress): web service providing compact TypeDesignation representation for homotypic groups and individual taxa
Andreas Müller
12:53 PM bug #8110 (New): Editing name in bulkeditor sets nameEditor dirty, but saving nameEditor after bulk editor reverts the changes
when editing a name which is open in name bulk editor and in name editor sets both editors dirty. But the changes are... Katja Luther
11:02 AM feature request #4922: GrantedAuthorities not reusable anymore
I have concerns about duplicating GAs as this will complicate first data inserters and managing of default GAs in gen... Andreas Kohlbecker
10:27 AM task #8109: Concept for linking from taxon entries to name pages
most important will be that it is configurable per project how and where all the different information is shown. Andreas Müller
09:29 AM task #8109 (New): Concept for linking from taxon entries to name pages
Taxon entries in the data portal do not allow to navigate to the according name page.
This will become important o...
Andreas Kohlbecker
10:14 AM feature request #7653 (In Progress): [DISCUSS] Delete NameFacts => Result: no
We decided to keep name facts to handle categories like "Notes on typification" or "Etymology".
We still need to ...
Andreas Müller
09:18 AM feature request #8108: Name page shows complete name information (I)
Hallo,

...

Allerdings ist die Frage schon interessant: Das wirkliche Potential Taxon fehlt halt in >99% der F...
Andreas Kohlbecker
09:17 AM feature request #8108: Name page shows complete name information (I)
Hallo,
will ja nicht pingelig sein, aber ein „Name used in Source“ ist ja im Prinzip ein Potential Taxon und kann ...
Andreas Kohlbecker
09:16 AM feature request #8108: Name page shows complete name information (I)
AM:
Wichtig wäre hier auch die Frage, wie man diese expliziten Namensinformationen auf einer normalen Taxonpage ve...
Andreas Kohlbecker
09:15 AM feature request #8108 (Closed): Name page shows complete name information (I)
Derzeit ist diese Seite mehr oder weniger nur ein Weiterleitungsmechanismus zu den zugehörigen Taxa.

Die besser a...
Andreas Kohlbecker

02/18/2019

10:34 PM feature request #8017 (In Progress): TypeDesignations need sources additional to lectotypifcation sources
Andreas Müller
06:05 PM bug #8107 (Feedback): NPE when throwing PopupEditorException in AbstractPopupEditor
Andreas Kohlbecker
06:05 PM bug #8107: NPE when throwing PopupEditorException in AbstractPopupEditor
[Henning:]
> Hier waren Gattungsnamen vor dem Import nicht verfügbar, daher wurde das Pflichtfeld Gattungsname nic...
Andreas Kohlbecker
05:01 PM bug #8107 (In Progress): NPE when throwing PopupEditorException in AbstractPopupEditor
The NPE occurred during while creating the PopupEditorException to be thrown in turn of an other exception which has ... Andreas Kohlbecker
04:51 PM bug #8107 (Closed): NPE when throwing PopupEditorException in AbstractPopupEditor
Heba reported an NPE which occurred while saving a name popup editor:
Problem beim Speichern um 10:08 Uhr.
http:/...
Andreas Kohlbecker
04:11 PM feature request #8106 (Closed): improve image gallery settings labeling
done! Andreas Kohlbecker
04:11 PM feature request #8106 (Resolved): improve image gallery settings labeling
Applied in changeset commit:cdm-dataportal|5358baffb125a13d97910717acfcca8e978d63f5. Andreas Kohlbecker
04:03 PM feature request #8106 (Closed): improve image gallery settings labeling
requested by AM:
Vielleicht könnte man bei der Configuration den Text noch etwas anpassen, so dass klar ist was pa...
Andreas Kohlbecker
12:22 PM bug #8105 (In Progress): better hotfix branch strategy in git flow to avoid commits in master which are missing in develop
During the release of the taxeditor 5.5.0 it turned out, that the `master`branch has received commits from the `hotfi... Andreas Kohlbecker
11:42 AM task #7811: Import higher classifications
I give this back for review Andreas Müller
09:51 AM bug #8104 (Closed): TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart
**The TaxonName property `lastNamePart` has erroneously been changed during the refactoring for #7238 to `familyNam... Andreas Kohlbecker

02/15/2019

04:57 PM bug #8101 (New): cdm-server docker container uses wrong timezone
The docker container uses UTC but should be in the same timezone as the host system.
~~~~
edit-production ~ # dat...
Andreas Kohlbecker
04:40 PM bug #8098 (Duplicate): Cache update for Portal view
I can no longer reproduce this problem, the reference looks ok now.
I thus will close this issue as duplicate of #...
Andreas Kohlbecker
04:02 PM bug #8098: Cache update for Portal view
seems to be a result from update problem in documented in #8100 Wolf-Henning Kusber
03:24 PM bug #8098 (Duplicate): Cache update for Portal view
Documentation (release version):
ID 100486 was prepared as shown in the screen shot.
Under curation the journal "...
Wolf-Henning Kusber
04:37 PM bug #8100: Cache update in UI
It seems as if the updating of in-reference Article is not causing the contained reference section to be updated. Andreas Kohlbecker
04:30 PM bug #8100: Cache update in UI
in the article just the journal was missing Wolf-Henning Kusber
04:30 PM bug #8100: Cache update in UI
Did not update the in-reference Wolf-Henning Kusber
04:29 PM bug #8100: Cache update in UI
Did you update the inreference "Fottea"? The Article was not touched? Andreas Kohlbecker
04:00 PM bug #8100 (New): Cache update in UI
If a reference has been not correct when preparing novelties
And the reference was updated,
the uncorrected referen...
Wolf-Henning Kusber
03:51 PM bug #8099 (Closed): Error saving name type designation editor due to problem in poupeditor context
Documentation:
Step 1: open Name type of "Geitleriaceae"
Step 2: type name was wrong, select unregistered genus nam...
Wolf-Henning Kusber
02:33 PM bug #8097 (Closed): Problem with inserting a section - inReference is "lost"
IAPT Entry:
BACILLARIOPHYCEAE
Astartiella bahusiensis (Grunov) Witk., Lange-Bert. & Metzeltin
in Biblioth. Diato...
Wolf-Henning Kusber
12:55 PM task #7811: Import higher classifications
Euastrum exists with 2 authors. Arbitrarily Euastrum Ralfs, Brit. Desmid.: 49, 78. 1848 has been taken for import of ... Andreas Müller
12:24 PM task #7811: Import higher classifications
Wolf-Henning Kusber wrote:
> Navicula Grunow is an old import error to be deleted
>
> Navicula Bory is the only r...
Andreas Müller
12:21 PM task #7811: Import higher classifications
Wolf-Henning Kusber wrote:
> Arachnophyllum exists 2x in ae5e4774-9657-4910-812c-937e2ebe5647. Once as child of Dele...
Andreas Müller
12:20 PM task #7811: Import higher classifications
Wolf-Henning Kusber wrote:
> Gymnocystodinium exists 2x in 174d5905-9b28-406d-8e15-98958123b4ae: with parent Gymnodi...
Andreas Müller
11:40 AM task #7811: Import higher classifications
Navicula Grunow is an old import error to be deleted
Navicula Bory is the only right one
Wolf-Henning Kusber
11:37 AM task #7811: Import higher classifications
Navicula exists 2x as accepted taxon in Phycobank, with 2 different authors. During import of 03c791d0-2da4-42d0-8bc6... Andreas Müller
11:13 AM task #7811: Import higher classifications
Arachnophyllum exists 2x in ae5e4774-9657-4910-812c-937e2ebe5647. Once as child of Delesserioideae, 2nd time as child... Wolf-Henning Kusber
11:07 AM task #7811: Import higher classifications
Gymnocystodinium exists 2x in 174d5905-9b28-406d-8e15-98958123b4ae: with parent Gymnodiniaceae and child Gymnodinium ... Wolf-Henning Kusber
11:01 AM task #7811: Import higher classifications
Wolf-Henning Kusber wrote:
> #9
> Eolimna exists twice in 03c791d0-2da4-42d0-8bc6-15a2154ad241.
> To be deleted: O...
Andreas Müller
10:54 AM task #7811: Import higher classifications
Arachnophyllum exists 2x in ae5e4774-9657-4910-812c-937e2ebe5647. Once as child of Delesserioideae, 2nd time as child... Andreas Müller
10:50 AM task #7811: Import higher classifications
Gymnocystodinium exists 2x in 174d5905-9b28-406d-8e15-98958123b4ae: with parent Gymnodiniaceae and child Gymnodinium ... Andreas Müller
10:17 AM task #7811: Import higher classifications
#9
Eolimna exists twice in 03c791d0-2da4-42d0-8bc6-15a2154ad241.
To be deleted: Once as direct child of Naviculales...
Wolf-Henning Kusber
09:35 AM task #7811: Import higher classifications
Ordo of Polypodochrysis in 03c791d0-2da4-42d0-8bc6-15a2154ad241 (Pinguioch **r** ysidales)
differs from above Ordo...
Andreas Müller
09:28 AM task #7811: Import higher classifications
Eolimna exists twice in 03c791d0-2da4-42d0-8bc6-15a2154ad241. Once as direct child of Naviculales (line 754), other t... Andreas Müller
09:23 AM task #7811: Import higher classifications
Also there is a new column subfam. As rank columns are hardcoded in import code all new columns need to be explicitly... Andreas Müller
12:02 PM bug #8088: Open taxon node wizard issues
Something went wrong in previous ticket #7794. The taxon itself should be selectable for both "New" and "Edit" mode. ... Andreas Müller

02/14/2019

04:20 PM task #8091: Discuss Referencetype PrintSeries with respect to user needs of PhycoBank and taxonomic projects
yes please Andreas Kohlbecker
10:45 AM task #8091 (In Progress): Discuss Referencetype PrintSeries with respect to user needs of PhycoBank and taxonomic projects
Andreas Müller
10:45 AM task #8091: Discuss Referencetype PrintSeries with respect to user needs of PhycoBank and taxonomic projects
ok, that I have a look on this first? Andreas Müller
10:46 AM task #7918 (Closed): Revision of reference type specific properties
As remaining issues are now in #8091 we can close this ticket. Andreas Müller
10:42 AM bug #7998 (Closed): Store newly created Characters in selected vocabulary
I think we can close this ticket now. Andreas Müller
08:56 AM feature request #8030 (Closed): Cache updater service methods externalized and base class specific
review completed, no issues found Andreas Kohlbecker
08:55 AM bug #7874 (Closed): TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters
looks like fixed by 100% Andreas Kohlbecker

02/13/2019

06:52 PM bug #7874 (Resolved): TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters
This should be fully fixed now with fixing #8030 Andreas Müller
01:45 PM bug #7874: TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters
You are right! Sorry for this bug in the assertion. Please correct it to :
~~~java
assertEquals(
"Expecting n...
Andreas Kohlbecker
01:03 PM bug #7874: TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters
I do not understand this line in user tests:
~~~
assertEquals("Expecting nomenclaturalTitle to be set sin...
Andreas Müller
06:51 PM feature request #8096 (Closed): Implement CacheUpdater as long running task with correct progress monitoring
Andreas Müller
06:41 PM feature request #8030 (Resolved): Cache updater service methods externalized and base class specific
I think this is fixed now. Please review. Andreas Müller
01:19 PM feature request #8030 (In Progress): Cache updater service methods externalized and base class specific
Andreas Müller
 

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