Activity
From 02/24/2019 to 03/25/2019
03/25/2019
- 06:58 PM bug #8192: The curator must be able to unlock a published registration for edition
- Checked in Test-System with two names of Nupela, registered 2018-11-02.
TypeSpecimen: unlock and add a type: works... - 02:50 PM bug #8192 (Resolved): The curator must be able to unlock a published registration for edition
- done, please review
- 05:46 PM bug #8191: ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked
- I was able to include new journal names in Basionym references. I included sections in the name editor and was able t...
- 02:51 PM bug #8191 (Resolved): ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked
- please review
- 05:28 PM bug #8050 (In Progress): Create blocking registrations for un-registered names which are to be used in nomenclatural acts
- 04:45 PM bug #7962: PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more humane labels
- Please review
- 04:42 PM bug #7962 (Resolved): PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more humane labels
- Applied in changeset commit:cdm-vaadin|8745f04714df865f1780025b43b24b9eaa5a198a.
- 02:17 PM feature request #8033 (Duplicate): Add/Enable absent/present state for every character
- duplicates #8178
- 10:12 AM feature request #8153: Adapt cdmlib to FeatureNode/FeatureTree model changes
- By introducing the generics this is probably done. There is still some code which does not use/specify generics but t...
03/22/2019
- 07:58 PM bug #8075 (Resolved): multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations
- 07:49 PM bug #8075: multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations
- potentially fixed through the changes made for #8160, #7106
- 07:57 PM bug #8158 (Resolved): cascade="all-delete-orphan" problem when ....
- potentially fixed through the changes made for #8160, #7106
- 07:56 PM bug #7881 (Resolved): reference selection combobox broken after error in ...
- potentially fixed through the changes made for #8160, #7106
- 07:51 PM bug #8065 (Feedback): HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEditor type designation table
- potentially fixed through the changes made for #8160, #7106
- 07:20 PM bug #8149: ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL
- please review
- 07:18 PM bug #8149 (Resolved): ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL
- Applied in changeset commit:cdm-vaadin|27820075a6585b46648a6f1dcd4241a6b45596d8.
- 07:19 PM bug #8184: SpecimenTypedesignationEditor: add new specimen broken Chrome browser
- please review with Heba if this still occurs
- 07:18 PM bug #8184 (Resolved): SpecimenTypedesignationEditor: add new specimen broken Chrome browser
- Applied in changeset commit:cdm-vaadin|86f09e7b2e34f272b2f4769f5f7fb3729fea7ef7.
- 07:18 PM bug #8184: SpecimenTypedesignationEditor: add new specimen broken Chrome browser
- this seems to be a bug in the ListSelect which affects the Chrome browser
- 06:28 PM feature request #8180 (In Progress): Add property term "Presence/Absence" to CDM default terms
- 06:28 PM feature request #8153 (Feedback): Adapt cdmlib to FeatureNode/FeatureTree model changes
- is this still an open issue? If yes, can you give more inside?
- 06:13 PM bug #8183 (In Progress): Make Feature IndividualAssociation a generalization of Specimen and Observation
- 04:35 PM bug #8205 (New): SpecimenTypeDesignationsEditor: First selection of mediaReference gets lost
- Permanent bug:
Image Reference is selected for the first time -> selected but not gets lost when clicking in another... - 03:51 PM bug #8194 (Feedback): LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of a Name
- Even if the LazyInitializationException is avoided deletion of the section is impossible since it is still in use as ...
- 03:32 PM bug #8115: NPE when moving factual data
- I just tested it with cdmlib and taxeditor completely up-to-date. I tested on a copy of flora of greece this time to ...
- 02:06 PM bug #8115: NPE when moving factual data
- Did you test with the actual cdmlib version?
cdmlib was not build until this morning. - 01:46 PM bug #8115 (Feedback): NPE when moving factual data
- Now saving in step 4 works but the description with the description from which the element was moved away from disapp...
- 03:31 PM feature request #8204 (New): RegistrationWorkingsetEditor shows list of unused sections and allows for delting them
- the RegistrationUI does not allow deleting unused sections. The RegistrationWorkingsetEditor could show the list of u...
- 03:24 PM bug #8203 (New): Adapt specimen page title to record basis
- The current specimen page hast "Specimen" written in the title despite the actual record basis
Example: http://por... - 02:50 PM bug #8202 (Worksforme): Multiple representations exception when reusing image in image gallery
- In Flora of Greece I tried to move an image from taxon Anchusa aegyptiaca to Anchusella variegata.
I did this by fir... - 02:39 PM task #8201 (In Progress): test all delete functionality in the RegistrationUI
- 02:35 PM bug #8200 (Closed): Changing title(cache) for factual data set not possible
- When trying to change the title of a factual data set in details view the old title is recreated during save.
Corr... - 02:32 PM bug #8197 (Resolved): Deleting Media from Image Gallery View does not make view dirty
- Applied in changeset commit:taxeditor|02bb31eada6b7edfb3c3d155bb13ad967428aa56.
- 02:22 PM bug #8197 (Closed): Deleting Media from Image Gallery View does not make view dirty
- ... therefore one may think that the media is deleted but it is not after reload. This is dangerous therefore high pr...
- 02:26 PM feature request #8199 (New): ReferencePage: show the relation of orthographic corrections to the corrected name
- in case of an orthographic correction both names which are related this way belong to the same publication.
In the... - 02:24 PM bug #8198 (Closed): Deleting an image gallery from image gallery view shows wrong configuration dialog
- It shows the same dialog like when deleting media, but the image gallery is something else. Image galleries should no...
- 02:16 PM feature request #8196 (Closed): display ortographic corrections in name relations as 'corrected name: <nameCache>'
- ortographic corrections are to be displayed as last entries in the name relations:
* corrected name: <nameCache> [... - 01:33 PM feature request #8195 (New): TaxonNamePopupEditor: offer Reference and RuleConsidered fields for replaced synonyms
- in contrast to earlier considerations for *Replaced Synonyms* it is also important to enter data into the Reference a...
- 09:08 AM bug #8190 (Resolved): Default FeatureTree throws exception
- I extended the type check to also allow subtypes in the term tree
03/21/2019
- 07:03 PM bug #8192: The curator must be able to unlock a published registration for edition
- use the lock and unlock icons from fontawesome:
https://fontawesome.com/icons/lock-open?style=solid
https://fon... - 06:32 PM bug #8192 (Closed): The curator must be able to unlock a published registration for edition
- The curator sometimes needs to modify the data for a registration after it has been published.
Currently it is req... - 07:01 PM bug #8194: LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of a Name
- Initializing the authorteam of the inReferences of the references loaded by the combobox should solve the problem.
- 06:59 PM bug #8194 (Closed): LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of a Name
Habe die Section des eines Namens die als nomenklatorische Referenz gesetzt war löschen wollen:
http://phycoba...- 06:46 PM feature request #8193 (Closed): TaxonNamePopupEditor: add select form element for Nomenclatural status
- Enable to add a nomenclatural status from a subset of status (see TaxEditor).
Exception invalid name in valitation =... - 06:26 PM bug #8191 (Closed): ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked
- By now when opening the ReferenceEditor for inReference of a TaxonName the user can not modify or set a new inreferen...
- 04:25 PM bug #8189 (Resolved): Allow configuration of 'user.home' via the spring environment
- close issue if the changes are not causing any problems.
- 12:15 PM bug #8189 (Closed): Allow configuration of 'user.home' via the spring environment
- By now it is only possible to configure the `${user.home}` via the system properties. That means the only option to s...
- 03:03 PM bug #8190 (In Progress): Default FeatureTree throws exception
- 01:30 PM bug #8190 (Closed): Default FeatureTree throws exception
- When there are Characters and Features in the data base and the default feature tree is created it will fetch all of ...
- 02:56 PM feature request #8058: Further issues for (local) preferences
- the common name language preference is added.
- 11:43 AM bug #8184: SpecimenTypedesignationEditor: add new specimen broken Chrome browser
- Specimen Editor: auch der erste Typus lässt sich nicht speichern (kritisch)
03/20/2019
- 04:41 PM feature request #7975: Implement a block to display name relations
- Validation:
![](picture156-1.png)
Replacement name:
Wie Validation behandeln,
Zudem wird
1. beim Widg... - 02:54 PM bug #8188 (In Progress): Allow configuring hibernate properties via properties file
- 02:54 PM bug #8188 (Closed): Allow configuring hibernate properties via properties file
- To allow for more flexible configuration of test environments it would be great if the hibernate properties which are...
- 11:10 AM feature request #8187 (New): Use Spring Environment instead of custom code in AbstractWebApplicationConfigurer
- the method `AbstractWebApplicationConfigurer.findProperty(String property, boolean required)` implements a similar st...
03/19/2019
- 07:31 PM feature request #7975: Implement a block to display name relations
- Examples correctly in PhycoBank as use case for output improvement:
Example Validation
https://www.phycobank.org... - 02:30 PM feature request #7428: Open issues for updating open data while subtree is updated
- please review.
Bulkeditor and nameeditor are updated. - 01:36 PM bug #8115 (Resolved): NPE when moving factual data
- this problem is fixed.
- 01:29 PM bug #4545 (Resolved): Implement TeamOrPersonBaseSelectionDialog
- please review.
TeamOrPerson is used for example for TaxonNodeAgentRelations or for authors in references - 12:49 PM feature request #8185 (Feedback): Type layout
- Hi Andreas, the same kind of formatting has formerly also been requested by Walter.
I consider this a very good so... - 09:52 AM feature request #8186 (Duplicate): List view order
- ordering by registration numbers is hardly possible, see #7978.
Furthermore is this ticket a duplicate of #8157
03/18/2019
- 06:02 PM feature request #8186 (Duplicate): List view order
- List view in Vaadin should be arranged from new (high registration numbers) to old.
- 05:51 PM feature request #8185 (Feedback): Type layout
- Type (as is):
Holotype: (BM BM123)
should be:
Holotype: BM (BM123)
see for example: https://www.phycobank... - 05:45 PM bug #8184 (Closed): SpecimenTypedesignationEditor: add new specimen broken Chrome browser
- In Vaadin, type specimen editor a new line is created when a typ is selected.
This functions in FireFox. This does n... - 05:16 PM bug #8183 (In Progress): Make Feature IndividualAssociation a generalization of Specimen and Observation
- until now this has been handled in the static method Feature.INDIVIDUALS_ASSOCIATION() which is not the correct place...
- 03:55 PM bug #8115 (Feedback): NPE when moving factual data
- This setup now works because we have to save before dragging the abstract to the other description
There is howeve... - 02:07 PM task #7515: TypeDesignationStatusComparator to sort by vocabulary first and then by term order
- Andreas Kohlbecker wrote:
> The Taxeditor should be more resilient against unusual data.
>
> 1. Suggestion as d... - 01:33 PM feature request #7433: new service method to get specimen by genetic AccessionNumber
- this service method is implemented, but controller method is still missing
- 01:30 PM feature request #8182 (In Progress): show blast search result
- the json result of the blast search should be displayed and the accession number needs to be a link to the correspond...
- 01:20 PM bug #8148 (Resolved): Login Dialog cuts off information
- I put it to resolved to remind me reviewing.
Or are there still open issues? - 01:04 PM bug #8148: Login Dialog cuts off information
- I adapted the exception section and I could not reproduce the cutted advanced section (with the actual nightly). Coul...
- 11:55 AM feature request #5890 (New): Implement auto-suggest for data portal
03/15/2019
- 03:29 PM bug #8169: avoid factory.openSession() in DaoBase
- VersionableServiceBase.isDeletable misses the @Transactional(readOnly = true) annotation!
- 03:25 PM bug #8169: avoid factory.openSession() in DaoBase
- Here is a case found in the server log (occurred 6x in a couple of hours):
~~~
[phycobank] 2019-03-15 10:27:44,... - 11:44 AM feature request #8181 (New): Further features for bulk editors
- this is a ticket to collect all wanted features for bulkeditors:
Advanced search or column filter options:
* ... - 10:44 AM feature request #7755: Implement advanced detail page for occurrences
- mail from AM:
Hallo Katja,
ich bin im Zuge von FoG über die Specimenseite gestolpert. Sehr schön, dass da jetzt... - 09:21 AM feature request #8180 (Closed): Add property term "Presence/Absence" to CDM default terms
- When describing a specimen via Characters (almost) all structures may or may not exist. To be able to describe if a s...
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... - 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... - 02:04 PM feature request #8121 (In Progress): Allow selecting structural/property modifiers when creating a character
- 01:56 PM feature request #6849 (In Progress): [DISCUSS] How to handle "kind of" term creation in TermEditor
- 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...
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.
- 09:57 AM feature request #7428 (Resolved): Open issues for updating open data while subtree is updated
- Applied in changeset commit:taxeditor|4fff2d21dfed4ae1ba6c5106e7d59cdf2e82548c.
- 09:36 AM bug #8176 (Resolved): WeaklyRelatedEntityCombobox is slow
- test TaxonNamePopupEditor Genus field, replaced Synonym and Basionym also some ToManyRelatedEntitiesComboboxes and T...
03/12/2019
- 05:57 PM bug #8176 (In Progress): WeaklyRelatedEntityCombobox is slow
- 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... - 02:22 PM report #8177 (Worksforme): Discuss: How to add originals of a type specimen
- How to store?
- 01:07 PM bug #6627: Remaining cdm light issues
- the name facts are implemented now, see #8175
- 01:06 PM feature request #8175: add name facts to cdm light export
- please review
- 01:06 PM feature request #8175 (Resolved): add name facts to cdm light export
- Applied in changeset commit:cdmlib|852a1a9e5171370a8e3e6962b21837e38115cf9a.
- 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
- 12:53 PM bug #8099: Error saving name type designation editor due to problem in poupeditor context
- can not reproduce
- 12:03 PM bug #8111: User selection dialog for groups does not filter out existing users
- please review
- 12:02 PM bug #8111 (Resolved): User selection dialog for groups does not filter out existing users
- Applied in changeset commit:taxeditor|cbc83794de4303c54b45309ff151c70627e82e1a.
- 11:34 AM bug #8115: NPE when moving factual data
- please review
- 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...
- 11:26 AM bug #8115 (Resolved): NPE when moving factual data
- Applied in changeset commit:taxeditor|803af83ee2911d193d6a95a3f73dee727ae77d45.
- 09:31 AM feature request #8136: Implement sources for type designations in TaxEditor
- please review
- 09:30 AM feature request #8136 (Resolved): Implement sources for type designations in TaxEditor
- Applied in changeset commit:taxeditor|9f40979f5e0d2fc55100acc5a7fabac00d48ce12.
- 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... - 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 ...
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... - 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... - 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...
- 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... - 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... - 01:10 PM feature request #6413 (In Progress): [DISCUSS] How to create type duplicates (e.g. isotypes) for a taxon name
- 12:59 PM feature request #8173 (In Progress): spring profile remoting enabled by default
- 12:55 PM feature request #8173 (Resolved): spring profile remoting enabled by default
- Applied in changeset commit:cdmlib|5ab0f6455f6cb83bfba0bb5ad6aee6e210d8dd14.
- 12:48 PM feature request #8173 (In Progress): spring profile remoting enabled by default
- 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....
- 12:57 PM feature request #8096 (Resolved): Implement CacheUpdater as long running task with correct progress monitoring
- please review
- 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.
- 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...
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...
- 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...
- 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...
- 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...
- 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 ...
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.
- 03:24 PM bug #7106 (In Progress): avoid factory.openSession() in CdmRepository
- 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... - 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... - 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... - 11:21 AM task #8168 (New): Check if withdrawing of per entity permission is working correctly for inReferences
- 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:...- 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>...
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... - 08:19 PM task #8118: Update MySQL drivers
- Katja, I think you also had the problem localy. What did you do to fix it?
- 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... - 08:06 PM task #8118: Update MySQL drivers
- https://stackoverflow.com/questions/26515700/mysql-jdbc-driver-5-1-33-time-zone-issue
- 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...
- 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
- 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... - 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
- 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...
- 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... - 10:07 AM task #8130 (In Progress): Check if related feature data is cleared when supported facts type is changed
- 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...
- 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
- 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... - 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...
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 - 12:43 PM task #8162 (Resolved): Move term related classes from model.common to model.term
- Applied in changeset commit:taxeditor|974d02d015234ec80816dfb47eaabde6688c2fa9.
- 12:24 PM task #8162 (In Progress): Move term related classes from model.common to model.term
- 12:23 PM task #8162: Move term related classes from model.common to model.term
- we should also adapt persistence layer
- 12:12 PM task #8162 (Resolved): Move term related classes from model.common to model.term
- Applied in changeset commit:taxeditor|b9dc6bb1d38897b06888836dd74d48684f73c5d5.
- 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?
- 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... - 02:58 PM bug #8107 (Closed): NPE when throwing PopupEditorException in AbstractPopupEditor
- issue is not reproducible - closing.
- 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...
- 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...
- 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...
- 11:14 AM bug #8075 (In Progress): multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations
- 10:55 AM bug #8158: cascade="all-delete-orphan" problem when ....
- potentially duplicate of #8160
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
... - 03:06 PM bug #7881: reference selection combobox broken after error in ...
- potentially duplicate of #8161
- 03:04 PM bug #7945: TaxonNamePopupEditor: missing genus causes exception when updating name parts visibility
- potentially duplicate of #8161
- 03:00 PM bug #8065: HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEditor type designation table
- potentially duplicate of #8160
- 02:07 PM bug #8160 (Resolved): CdmBeanItemContainerFactory as readonly service bean
- 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...
- 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-...
- 11:52 AM task #4600 (New): Investigate and implement tests for security in cdm-vaadin
- 11:51 AM task #4600 (In Progress): Investigate and implement tests for security in cdm-vaadin
- 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
- 11:39 AM feature request #8124 (Resolved): Activate Name Facts in Taxeditor
- please review
- 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 ...
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 ... - 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 ...
- 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-...
- 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... - 11:13 AM task #615 (Closed): remove suns repository
- the repository
~~~xml
<!-- sun repository -->
<repository>
<id>java.net</id>
<url>http:... - 11:11 AM task #615 (Resolved): remove suns repository
- Applied in changeset commit:cdmlib|d402220f823edfb01ec9385d20117d6afee9a77d.
- 10:17 AM feature request #8150 (Resolved): Allow editing the representation label of characters in details view
- 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...
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) - 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
- 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.
- 09:47 PM feature request #8155 (Feedback): SpecimenTypeDesignationEditor: allow choosing the typified name from the homotypical group for specific type status
- 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?
- 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 ...
- 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-...
- 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... - 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... - 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... - 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...
- 12:16 PM feature request #4611 (New): I18n for the TaxEditor menu
- sorry, was a mistake
- 12:12 PM feature request #4611 (Resolved): I18n for the TaxEditor menu
- 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... - 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...
- 11:57 AM bug #7107: "Omit level" (TDWG Level2) in distribution hierarchy should not supress distributions source reference
- OK
- 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...
- 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... - 11:57 AM feature request #4610: [DISCUSS] I18n for the EDIT platform
- Please do not move unreviewed tickets to Reviewed milestone
- 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...
- 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.
... - 08:07 AM feature request #8146: Adapt taxeditor UI to structure and property term type
- Add character to term menu with commit:2c98dda6165033a58c7df8c06b21518d380307b3
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...
- 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 ... - 02:24 PM feature request #8150 (Closed): Allow editing the representation label of characters in details view
- 01:56 PM feature request #8136 (In Progress): Implement sources for type designations in TaxEditor
- 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)
... - 10:19 AM bug #8148 (In Progress): Login Dialog cuts off information
- 10:18 AM bug #8148 (Resolved): Login Dialog cuts off information
- Applied in changeset commit:taxeditor|a08af9f9d2b8840b48fc63b647aca9ee0a34b68c.
- 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.... - 09:34 AM feature request #8147 (Resolved): Add "plural" to representation detail element
- Fixed with commit:taxeditor|754fbf873ca0b63addc6842c089298fff76eb30d
- 08:44 AM feature request #8147 (Closed): Add "plural" to representation detail element
- 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,...
02/26/2019
- 04:55 PM feature request #3616: Show DescriptionElementBase.timeperiod in Dataportals
- Improvements for formatting copied to #8145
- 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... - 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... - 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... - 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... - 01:42 PM task #7356: setup selenium test suite for cdm-vaadin
- Adding master thesis on Vaadin TestBench
- 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...
- 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...
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:
>... - 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: ... - 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 ...
- 08:54 PM bug #8140 (Resolved): Update list of type designation status which allow an explicit source
- Applied in changeset commit:cdmlib|2a0a678b59b88779f6db98619be4d4510ea26f93.
- 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... - 08:54 PM bug #7772: Rename TermBase_inverseRepresentation to DefinedTermBase_InverseRepresentation
- Applied in changeset commit:cdmlib|3b49207de7d71fa2af4fcd8a6e7d913dc654d733.
- 08:54 PM bug #7859: Increase size of CdmPreference.value
- Applied in changeset commit:cdmlib|da556b1537505b615fe45afc8ea7f0d06c5d256b.
- 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 ...
- 06:22 PM bug #8143 (Resolved): It is possible to open multiple instances of the login dialog
- Applied in changeset commit:taxeditor|e25ce35073e04836a1b382da50faf21ab605ae16.
- 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... - 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
- 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...
- 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
- 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...
- 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)
- 06:04 PM feature request #3616 (In Progress): Show DescriptionElementBase.timeperiod in Dataportals
- 05:45 PM feature request #8142 (Resolved): Representations have optional "plural" as additional field
- 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... - 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...
- 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... - 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.
- 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...
- 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
- 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...
- 02:15 PM feature request #8139 (Resolved): [Rule] Validate lectotype sources
- 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...
- 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.
- 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
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 ...
- 12:47 PM feature request #7653: [DISCUSS] Delete NameFacts => Result: no
- Unification of extensions and facts moved to new ticket #8133
- 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...
- 01:11 PM feature request #8137 (Closed): 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... - 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... - 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... - 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 - 12:41 PM feature request #8019: Add "Typification Notes", "Ortography" and "Etymology" to NameFeature vocabulary
- Also "Ortography" and "Etymology" added.
- 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...
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