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From 12/15/2020 to 01/13/2021

01/13/2021

06:29 PM bug #9386: orthographic variants should not be symmetrical
It is correct that there is only one correct spelling. In PhycoBank, we need to register the published name "as is" =... Wolf-Henning Kusber
06:12 PM bug #9386 (New): orthographic variants should not be symmetrical
According to the nomenclatural code there is always only 1 valid orthographic variant so the name relationship should... Andreas Müller
05:29 PM task #8455: Show specimen preferredStableURL as external link icon?
Screenshot for long URI in typification:
![](picture429-1.png)
Andreas Müller
05:16 PM task #8455: Show specimen preferredStableURL as external link icon?
Detail screenshot from the Derivate tree view (the derivate path view looks quite the same):
![](picture859-1.pn...
Andreas Kohlbecker
04:26 PM task #8455: Show specimen preferredStableURL as external link icon?
example for ugly linking: http://ws2.cybertaxonomy.org/dataportal/greece_bupleurum_01_with_onthology/?q=cdm_dataporta... Andreas Müller
05:26 PM bug #9384 (Closed): DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members
as we talk about bibliographic references here the ICN (or any other code) is not relevant here. It is the rule I hav... Andreas Müller
04:44 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members
The implementation is correct as far as the the implemented formatting rule for more than two authors is holding true... Andreas Kohlbecker
04:18 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members
The fix was not fully correct as it created teams like Name1, Name2 & al. but there should be always a maximum number... Andreas Müller
02:47 PM bug #7711 (In Progress): Bugs in media gallery
Katja Luther
12:08 PM bug #9369 (Resolved): Reference Detail is missing in MediaSpecimen details view
please review Katja Luther
12:07 PM bug #9372 (Resolved): in media details view unprotected title cache is not updated when underlying data is changed
this ios fixed, please review Katja Luther
11:41 AM bug #9371: Media bulk does not persist data anymore
please review Katja Luther
11:36 AM bug #9371 (Resolved): Media bulk does not persist data anymore
Applied in changeset commit:taxeditor|0ef0103a664888c0e398b9ab5f83b0c170c5a599. Katja Luther
09:58 AM task #9385 (New): Simplyfy boundingbox setting for user fixed map clipping
Problem:
The settings in `admin/config/cdm_dataportal/settings/geo` for the **Bounding box** needs to be complian...
Andreas Kohlbecker

01/12/2021

04:33 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members
please review
Tests for this method are missing and should be implemented asap. Please could you open a new ticke...
Andreas Kohlbecker
04:32 PM bug #9384 (Resolved): DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members
Applied in changeset commit:cdmlib|854244ff90c5ff67a0b30a3cee7f1d49e7623cc5. Andreas Kohlbecker
04:30 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members

Andreas Kohlbecker
04:29 PM bug #9384 (Closed): DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members
see https://api.phycobank.org/phycobank/registrationDTO.json?identifier=http://phycobank.org/102662
The Team "Mo...
Andreas Kohlbecker
03:19 PM bug #9383 (Closed): Adapt apache configuration to modified dataportal registration page URL pattern
Andreas Kohlbecker
02:57 PM bug #9383 (Closed): Adapt apache configuration to modified dataportal registration page URL pattern
the apache configuration of edit-community needs to be adapted to the changes made for #9220 Andreas Kohlbecker
11:55 AM bug #9174: After longer inactivity NPE for cache
Andreas Müller wrote:
> This is maybe the same as #7699
??
Andreas Müller
11:16 AM bug #9382 (Resolved): For nomenclatural source show taxonname in referencing objects view
Katja Luther
11:15 AM bug #9382 (Closed): For nomenclatural source show taxonname in referencing objects view
In referencing objects view the taxon name of a nomenclatural source is not shown, only 'sourced object not available' Katja Luther
09:34 AM feature request #9381 (New): Refresh button for character matrix
After adding new characters the matrix needs to be closed and reopened to get the changes. To optimize the workflow a... Katja Luther

01/11/2021

10:13 PM feature request #9380 (New): It is not possible to show MediaRepresentation(Part) supplemental data
... as they can not be explicitly selected in the details view. This should be possible (e.g. for showing id and uuid) Andreas Müller
05:20 PM bug #8760: Presentation and linking of molecular data in specimen table too unclear
another example: http://caryophyllales.org/cactaceae/cdm_dataportal/taxon/d7bb858b-d8e0-4f9a-8a47-081d1cb740e9
Andreas Kohlbecker
02:37 PM bug #9379 (Closed): exclude disabled classifications from advanced taxon search form
Classifications which are disabled in the `admin/config/cdm_dataportal/settings` are to be excluded from the advanced... Andreas Kohlbecker
11:53 AM EDIT Platform Etablierung report #9378 (Closed): Meeting EDIT Platform documentation 2021-02-22
WebEx Meeting: https://fu-berlin.webex.com/fu-berlin/j.php?MTID=ma3d5a3cfabd30fbfdccb11e37122a1e4
## Teilnehmer:
...
Andreas Kohlbecker
11:45 AM EDIT Platform Etablierung task #8580 (Closed): Update documentation to latest revision of the Taxeditor
all Taxeditor documentation has been updates in Okt 2019, other activities are subject of #9377 Andreas Kohlbecker
11:44 AM task #9377 (In Progress): Update of other platform user documentation

Documents to check:
* Manual-EDIT-Platform-01-INSTALL.docx **DONE** in #8580
* Manual-EDIT-Platform-02-DEMO.doc...
Andreas Kohlbecker
11:41 AM EDIT Platform Etablierung task #9108 (Closed): Prepare Kurs Borsch
completed Andreas Kohlbecker
11:39 AM task #9376 (New): git checkout of datportal module fails with locally modified files
locally modified files prevent from updating the local git clone to the required version of the dataportal module.
...
Andreas Kohlbecker
11:09 AM feature request #9375 (Resolved): Alphabetical order for reference type drop down
Katja Luther
11:09 AM feature request #9375 (Closed): Alphabetical order for reference type drop down
mail AM:
weißt du, ob es einen Grund gibt, dass Section in der RefType Auswahl ganz oben steht, während alle ander...
Katja Luther
09:51 AM bug #9374 (Closed): ClassCastException when switching between media
When switching between media of one taxon following CCE is thrown:
~~~ text
last remote method : http://api.cyber...
Katja Luther

01/09/2021

11:24 AM feature request #5575 (In Progress): DNA Sample requires CacheStrategy
I added a very first version for DNASample cache strategy to avoid the -titleCache not availble- messages Andreas Müller
01:36 AM feature request #7612: CacheStrategy for MediaSpecimens
I implemented now a very basic version of the cache strategy to avoid -titleCache not yet implemented- messages Andreas Müller
01:34 AM feature request #7612 (In Progress): CacheStrategy for MediaSpecimens
To me it is a bit unclear what the suggestion is how the MediaSpecimen cache strategy should be implemented. Andreas Müller

01/08/2021

07:52 PM bug #9373 (Closed): In specimen details view used within specimen tree editor titleCache field is not enabled when it is protected
instead you first have to click on the protected button which does not change the button but the text field gets enabled Andreas Müller
07:49 PM bug #9371: Media bulk does not persist data anymore
See also related tickets when fixing this. Andreas Müller
07:38 PM bug #9371 (Closed): Media bulk does not persist data anymore
except for create and delete
I tested for title, description, uri, supplemental data = > nothing worked
This is...
Andreas Müller
07:48 PM bug #9372 (Closed): in media details view unprotected title cache is not updated when underlying data is changed
e.g. when only URI exists usually the title is the file name but changing the URI does not change the title field.
H...
Andreas Müller
07:32 PM feature request #9370 (New): Search in media bulk editor should include search on URI
there are multiple usecases for this Andreas Müller
07:17 PM bug #9369 (Closed): Reference Detail is missing in MediaSpecimen details view
but the detail often is important. In general we could also implement as like a (single) source but there is some mor... Andreas Müller
03:56 PM bug #9368 (Closed): NullPointerException (NPE) in ManifestComposer.representationPartsToImageContent()
~~~
15:51:31.562 [cichorieae] [qtp990416209-33917] INFO e.e.c.r.c.iiif.ManifestController - doGetMedia() GET: /cich...
Andreas Kohlbecker
02:51 PM task #9132: Update cyprus images to Scaler default API and add thumbnails
Hi Andreas,
ich bin ja gerade dabei #9132 auch für Cichorieae zu machen. Die Links habe ich bereits alle umgestel...
Andreas Müller
12:36 PM task #9132: Update cyprus images to Scaler default API and add thumbnails
Links in the Cichorieae database have all be updated to use the scaler API.
Only open issue is now to reload metad...
Andreas Müller

01/07/2021

01:16 PM bug #9367: E+M shapefile Baltikum subarea borders always visible
This may require to modify the SLD file for the euromed layer Andreas Kohlbecker
01:15 PM bug #9367 (New): E+M shapefile Baltikum subarea borders always visible
gerade fällt mir auf, dass die Arealgrenzen innerhalb des Baltikums seltsamerweise nicht angezeigt werden, wenn es do... Andreas Kohlbecker

01/06/2021

02:27 PM feature request #9114: Handle malformed URIs in user type
In #9111#note-1 AK suggests to also encode fragment and query parts. This has **not** been implemented in the origina... Andreas Müller
02:15 PM feature request #9114: Handle malformed URIs in user type
Katja, can you please check if you can find out what the httpinvoker problem is. I currently can't start the TaxEdito... Andreas Müller
12:08 PM feature request #9114 (In Progress): Handle malformed URIs in user type
I implemented a new class eu.etaxonomy.cdm.common.URI and use this in model but also at other places like import sour... Andreas Müller
02:20 PM feature request #9111 (Resolved): Handle Malformed URIs
I removed the related code again as #9114 is now more or less implemented and URI encoding is now done in cdmlib. Ple... Andreas Müller

01/04/2021

07:17 PM bug #9366: Specimen type designation with specimen having only collection name but not collection code does not show collection information
Please review Andreas Müller
07:14 PM bug #9366 (Resolved): Specimen type designation with specimen having only collection name but not collection code does not show collection information
Applied in changeset commit:cdmlib|99d3463856a840dd42c0532791b67b299b7b7fed. Andreas Müller
07:08 PM bug #9366 (Closed): Specimen type designation with specimen having only collection name but not collection code does not show collection information
e.g. Scorzonera kurtii Yıld. in Ot Sist. Bot. Dergisi 18(2): 15. 2012 in Cichorieae DB
The holotype collection inf...
Andreas Müller

12/22/2020

09:09 PM bug #9365 (Closed): Reuse taxon does not work in new Taxon dialogue
partly copied from #5114.
If reuse taxon is selected still a new taxon is created.
Also the secundum field shou...
Andreas Müller
08:52 PM feature request #4896 (Closed): Bulkeditor: deduplication of objects of different type
Generally this works. Open issue is handled in #9361 Andreas Müller
08:37 PM task #9364 (In Progress): Cleanup authors with multiple & and protected names and teams
Andreas Müller
07:29 PM task #9364: Cleanup authors with multiple & and protected names and teams
Protected Teams(nomenclaturalTitle):
AlgaTerra: >14000
Cichorieae: 8487
Cuba: 14
Campanula: 1171
Caryo_amarant...
Andreas Müller
03:56 PM task #9364: Cleanup authors with multiple & and protected names and teams
Protected Names (still without fulltitlecache and authorshipcache):
Bromeliaceae: 584
Cichorieae: 476
Cuba: 567
...
Andreas Müller
03:17 PM task #9364 (Closed): Cleanup authors with multiple & and protected names and teams
(high priority only to first issue as it is related to #2200)
In context of #2200 I already checked names with >1 ...
Andreas Müller
08:16 PM feature request #2200 (Closed): Handle multiple authors for names correctly when caching
This can be closed as it works now as expected. Open data issues are handled in #9364
The only directly related is...
Andreas Müller
09:59 AM bug #5163 (Closed): Converting persons to team members may result in "-empty team-"
The "empty team" issue has been solved. The handling of team members has been moved to follow up ticket #9363 as it i... Andreas Müller
09:56 AM feature request #9363 (New): Allow to parse the new team when converting person to team
copied from #5163
When converting a person to a team does not get team members by default. We could add a configur...
Andreas Müller
12:14 AM bug #2578 (Closed): Improve "move synonym"
Now we always move the full homotypical group to the other taxon, so this is fixed.
The check that the synonym is ...
Andreas Müller

12/21/2020

11:39 PM bug #9362 (New): Convert Team to Person and vice versa saves immediately
When converting a team to a person or converting a person to a team the operation is immediately executed and not wai... Andreas Müller
11:32 PM feature request #4908 (Closed): adding convert Team to Person and Person to Team to the bulk editor
Open issues fixed or moved to new ticket. Andreas Müller
11:27 PM feature request #9361 (New): Give more specific information why person can not be converted to team
copied from #4908 and #4896 (says that current implementation is only a workaround as a suitable return type for isMe... Andreas Müller
10:46 PM feature request #4770 (Closed): Allow convert person to team
the open issue is fixed now. We can close the ticket Andreas Müller
01:36 PM feature request #4769 (Closed): Allow convert team to person
I used this intensively for deduplicating authors in cyprus DB and problems never occured. So I guess we can close th... Andreas Müller
01:26 PM bug #9360 (Feedback): Parsed hybrids can not be persisted
In Flora of Cyprus I tried to persist a hybrid formula (Aegilops biuncialis × geniculata) but got an NPE in TaxonName... Andreas Müller

12/18/2020

11:38 PM feature request #7894 (Closed): [CHECK] Import sourceNumber as Identifier for references
As ERS did not complain about missing numbers during the last 1.5 years I guess everything went well. Andreas Müller
11:37 PM feature request #7800 (Closed): Parse preliminary RefDetails
As the import did run and most of the above RefDetails were parsed I think we can close this ticket. However, there a... Andreas Müller
11:18 PM feature request #9204 (Closed): Update cdmlib and taxeditor dependencies
I close this ticket as related to v5.18 and open a new one for the remaining (and new) issues Andreas Müller
11:17 PM task #9359 (Closed): Update cdmlib, taxeditor, cdmserver etc. dependencies
A lot of version updates and updates to how dependencies are handled in TaxEditor has been done already in #9204.
...
Andreas Müller
11:13 PM task #9208 (Closed): Move cdmlib-print and cdmib-remote to taxeditor.printpublisher
I think we can close this ticket.
There is a very important follow up ticket #9351 (assigned to AK) that needs to ...
Andreas Müller
11:04 PM bug #9354 (Feedback): Sorting in distribution editor is broken
There are still open issues as the comparator does not follow the comparator contract and handling of names with rank... Andreas Müller
10:55 PM feature request #6076: Specimen biocase search should work on observations
What needs to be done to close this ticket?
Is it for review? If yes, how to review? Which search did not work? In T...
Andreas Müller
10:44 PM feature request #7262 (Closed): add progress monitor to csv print export and cdm light export
Looks like this is fixed (I did not check for CSV export as it is not so relevant anymore) Andreas Müller
10:34 PM bug #7013 (Closed): NonUniqueObjectException for setSecundumReferenceForSubtree
As far as I know and have tried this works now. Also the progress monitor seems to work again. Therefore I close the ... Andreas Müller
10:06 PM bug #7098 (Closed): reuse name does not work
The method has been fully refactored in the meanwhile so I guess the above question is not relevant anymore. Closing ... Andreas Müller
07:41 PM feature request #4867 (Feedback): Add menu item for subtree cloning
It seems that the menu entry was removed or does not work anymore, even with experimental features being switched on.... Andreas Müller
07:25 PM task #9228: Adaptations to allow editing Centaurea in Flora of Greece
After running the import it became clear that not reusing names is not a good idea as
* handling name relationship...
Andreas Müller
05:52 PM bug #9358: OptionalDataException during HTTP invoker call
If it is true that this problem occurs client side we should catch the exception in a way that it becomes clear that ... Andreas Müller
04:28 PM bug #9358: OptionalDataException during HTTP invoker call
Same issue but slightly different stacktrace
~~~
last remote method : http://api.cybertaxonomy.org:80/euromed/rem...
Andreas Müller
04:27 PM bug #9358: OptionalDataException during HTTP invoker call
ERS: Das könnte sein. Ich habe auf meinem Rechner zuhause manchmal tatsächlich Kapazitätsprobleme - Ich werde das mal... Andreas Müller
04:20 PM bug #9358: OptionalDataException during HTTP invoker call
Lazy initializing distributions.
~~~
at org.hibernate.proxy.pojo.javassist.JavassistLazyInitializ...
Andreas Müller
04:11 PM bug #9358: OptionalDataException during HTTP invoker call
~~~
last remote method : http://api.cybertaxonomy.org:80/euromed/remoting/common.service
last remote request client...
Andreas Müller
04:11 PM bug #9358 (New): OptionalDataException during HTTP invoker call
Note: first issue to solve is catching the exception client side as explained in comment 6 => #9629
The bug in com...
Andreas Müller
11:25 AM bug #9142: The Agent search dialog shows duplicated entries
Andreas Müller wrote:
> Thats what I thought. It is actually not really a wrong implementation of the method but due...
Katja Luther
11:14 AM bug #9142 (Feedback): The Agent search dialog shows duplicated entries
Thats what I thought. It is actually not really a wrong implementation of the method but due to the above described s... Andreas Müller
10:54 AM bug #9142 (Resolved): The Agent search dialog shows duplicated entries
First I thought it was because the search method was called twice but the real cause was the wrong implementation of ... Katja Luther
11:11 AM bug #9264: Flag for toggle button for linking taxon with navigator looses/switch value without clicking the button
please review Katja Luther
10:59 AM bug #9264 (Resolved): Flag for toggle button for linking taxon with navigator looses/switch value without clicking the button
Applied in changeset commit:taxeditor|d3334540d33466758ed37e2c7648f74f99420f43. Katja Luther

12/17/2020

11:49 AM bug #9142 (Feedback): The Agent search dialog shows duplicated entries
Andreas Müller
11:39 AM bug #9142: The Agent search dialog shows duplicated entries
can you shortly explain what the problem was and why the commit fixes it? Andreas Müller
11:36 AM bug #9142: The Agent search dialog shows duplicated entries
Applied in changeset commit:taxeditor|359b77dda6efc328563cfd93e63aee841662b4e7. Katja Luther
11:30 AM bug #9142 (Resolved): The Agent search dialog shows duplicated entries
This should be fixed. Please review. Katja Luther
10:34 AM feature request #9337: Open issues for reimplementation of termtree editors
16. Add "Open in Vocabulary" to term tree editor context menu; this is generally needed the primary usecase is to all... Katja Luther
09:16 AM feature request #9337 (In Progress): Open issues for reimplementation of termtree editors
Katja Luther
10:10 AM feature request #8289 (Resolved): Add "Open in RefObj view" to term editor context menu
please review. Katja Luther
09:13 AM bug #9344: Datasets in Descriptive Dataset Navigator should be ordered
please review Katja Luther
09:13 AM bug #9344 (Resolved): Datasets in Descriptive Dataset Navigator should be ordered
Applied in changeset commit:taxeditor|b5f32b5d274ff26e8bf15ed9f42c61f028e79584. Katja Luther
08:48 AM bug #9353 (Resolved): Copy & Paste creates dirty data in term trees
Applied in changeset commit:taxeditor|27ca515332a1068e6f49ccff9a4466bce556a548. Katja Luther

12/15/2020

11:36 AM feature request #9338 (Resolved): Restructure term menus
Both menues have the same structure and also the handling of opening the editors are synchronized. Katja Luther
 

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