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From 06/08/2022 to 07/07/2022

07/07/2022

02:35 PM feature request #10083 (Resolved): Add name relationship type "avoids homonym of"/"causes replacement name"
The relationship was added. We still need an update script or handling for the inverse label and for existing data. Andreas Müller
12:44 PM bug #10084: Adding a new specimen to character matrix fails
Katja Luther wrote in #note-4:
> Andreas Müller wrote in #note-3:
> > Generally the bug seems to be fixed and the t...
Katja Luther

07/06/2022

03:17 PM feature request #10081: Show name in source for sec ref of accepted taxon
Added a new tag for the separators surrounding the name used in source, this is extracted from the taggedTaxon and if... Katja Luther
10:11 AM task #3722: Using @OrderColumn does not work in trees
On PolytomousKeys:
* added a fresh PK
* added a new top level node (like always) results in a sortindex 1 for thi...
Andreas Müller
09:56 AM task #3722: Using @OrderColumn does not work in trees
Andreas Müller wrote in #note-18:
> Term trees/nodes also seem to work. Katja, can you please double check this?
...
Katja Luther
10:00 AM bug #10084 (Feedback): Adding a new specimen to character matrix fails
Andreas Müller
10:00 AM bug #10084: Adding a new specimen to character matrix fails
Katja Luther wrote in #note-4:
> Sometimes it needs a break, than a better solution could be found. I solved it with...
Andreas Müller
09:50 AM bug #10084 (Resolved): Adding a new specimen to character matrix fails
Andreas Müller wrote in #note-3:
> Generally the bug seems to be fixed and the ticket can be closed.
>
> Only the...
Katja Luther

07/05/2022

06:15 PM task #3722: Using @OrderColumn does not work in trees
Term trees/nodes also seem to work. Katja, can you please double check this? Andreas Müller
06:15 PM task #3722: Using @OrderColumn does not work in trees
SQL for testing persisted Polytomous Key Nodes:
~~~SQL
SELECT pkn.id, pkn.created, nodenumber, KEY_id, parent_id,...
Andreas Müller
06:08 PM task #8127: [Reminder] to check if Hibernate Null Value bug still exists
See also #3722#note-14 ff for comments relevant here. Andreas Müller
05:57 PM bug #10084 (Feedback): Adding a new specimen to character matrix fails
Generally the bug seems to be fixed and the ticket can be closed.
Only the handling of descriptionType in the code...
Andreas Müller
04:01 PM feature request #10081 (Resolved): Show name in source for sec ref of accepted taxon
Set the font-style for separator to normal, this is the way it is done for markers. Please review.
I also will have...
Katja Luther
01:43 PM feature request #10081 (Feedback): Show name in source for sec ref of accepted taxon
The current formatting shows brackets and "sub" in italics but only the name parts should be in italics.
This is b...
Andreas Müller
01:32 PM feature request #10081 (Resolved): Show name in source for sec ref of accepted taxon
Katja Luther
01:32 PM feature request #10081: Show name in source for sec ref of accepted taxon
with the correct init strategy the name in source is shown. for review : https://int.e-taxonomy.eu/dataportal/integra... Katja Luther
09:56 AM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
I discussed with WHK how far time information is needed in the phycobank dataportal. According to WHK it is (currentl... Andreas Müller

06/28/2022

05:52 PM bug #10080 (In Progress): Source Element sometimes does not appear after selecting a new designation status and after creating a new type designation
This is really strange behavior, the source element should be shown every time but in stable and nightly the source i... Katja Luther
12:59 PM bug #10080: Source Element sometimes does not appear after selecting a new designation status and after creating a new type designation
We need to check if this can be done fast. Andreas Müller
11:49 AM bug #10076 (Resolved): Exception when opening character matrix with classification as root node
This should be fixed, please review. Katja Luther
11:46 AM bug #10084 (Resolved): Adding a new specimen to character matrix fails
Please review. Katja Luther
11:43 AM bug #10084 (Closed): Adding a new specimen to character matrix fails
The following exception appears when trying to save the character matrix after adding a new specimen:
~~~
last ...
Katja Luther
09:23 AM feature request #10082: Improve formatting for pro parte misapplications
Example: https://europlusmed.org/cdm_dataportal/taxon/63fead7a-662a-4082-9503-c6ea994c2049 Andreas Müller

06/27/2022

02:21 PM feature request #10083: Add name relationship type "avoids homonym of"/"causes replacement name"
Separate discussion WGB-AM:
...
AM
ja, das war semantisch nie einfach, was bei blocking name was ist bzw. be...
Andreas Müller
02:18 PM feature request #10083: Add name relationship type "avoids homonym of"/"causes replacement name"
AM:
diese Mail ist letztes Jahr leider bei mir liegen geblieben. Aus aktuellem Anlass würde ich sie gerne wieder a...
Andreas Müller
02:14 PM feature request #10083 (Discussed): Add name relationship type "avoids homonym of"/"causes replacement name"
ERS:
das Pendant zu „is blocking name for“ lautet „is new combination blocked by“. Es gibt aber auch den Fall, das...
Andreas Müller
01:51 PM feature request #10083 (Closed): Add name relationship type "avoids homonym of"/"causes replacement name"
Currently we have a name relationship type "is blocking name for" with a label "is new combination blocked by" for th... Andreas Müller
12:07 PM feature request #10082 (Closed): Improve formatting for pro parte misapplications
ERS:
... kann ich mich nicht mehr erinnern, ob wir uns schon auf eine einheitliche Darstellung des „p.p.“ geeinigt...
Andreas Müller
11:55 AM feature request #10081: Show name in source for sec ref of accepted taxon
... and can you also please review my implementation. Andreas Müller
11:54 AM feature request #10081 (In Progress): Show name in source for sec ref of accepted taxon
I implemented the cache strategy part. Katja, can you please take over and check what needs to be done for the portal... Andreas Müller
11:22 AM feature request #10081: Show name in source for sec ref of accepted taxon
AM:
Könntest du kurz ein Beispiel geben, wie das genau formattiert werden soll? Also ob mit eckiger(?) Klammer dru...
Andreas Müller

06/24/2022

12:22 PM feature request #10081 (Closed): Show name in source for sec ref of accepted taxon
WGB:
ich finde kein Setting, mit dem ich den Name in Source bei der sec. Ref. des [akzeptierten] Taxons ausgeben k...
Andreas Müller

06/23/2022

01:54 PM bug #10080 (In Progress): Source Element sometimes does not appear after selecting a new designation status and after creating a new type designation
When selecting the designation status holotype removes the source section of the typedesignation details view. Katja Luther
01:12 PM bug #9979: Flora Greece shows large images
Andreas Müller wrote in #note-6:
> Katja Luther wrote in #note-5:
> > This problem appears if the limit for the thumb...
Katja Luther
01:10 PM bug #9979: Flora Greece shows large images
Katja Luther wrote in #note-5:
> This problem appears if the limit for the thumbnail size is smaller as the size of ...
Andreas Müller
01:03 PM bug #9979: Flora Greece shows large images
This problem appears if the limit for the thumbnail size is smaller as the size of the smallest representation. Then ... Katja Luther
01:06 PM task #3722: Using @OrderColumn does not work in trees
Andreas Müller wrote in #note-15:
> Katja Luther wrote in #note-14:
> > For polytomouskey nodes there are still null ...
Katja Luther
12:20 PM task #3722: Using @OrderColumn does not work in trees
Katja Luther wrote in #note-14:
> For polytomouskey nodes there are still null values, after creating a new alternat...
Andreas Müller
10:45 AM task #3722: Using @OrderColumn does not work in trees
For polytomouskey nodes there are still null values, after creating a new alternativ and saving the rootnode contains... Katja Luther

06/22/2022

07:39 PM bug #9979: Flora Greece shows large images
As you currently work in this area I give this ticket to you for now. Andreas Müller
07:36 PM task #8127 (Resolved): [Reminder] to check if Hibernate Null Value bug still exists
Probably solved but still needs code cleanup. Andreas Müller
07:35 PM task #3722: Using @OrderColumn does not work in trees
Please review. Andreas Müller
07:27 PM bug #10034 (Feedback): Flat feature tree throws exception
The initial issue is fixed (or workarounded) correctly.
However, the labeling of the tree still behaves strange some...
Andreas Müller
07:11 PM bug #10078: Symbol and details view title of misapplied name type is not the same as shown in the type combo element
IMPORTANT:
Before closing the ticket we need to check existing data in production databases for incorrect relation...
Andreas Müller
05:05 PM bug #10078 (Feedback): Symbol and details view title of misapplied name type is not the same as shown in the type combo element
Seems to work correctly and code changes make sense. Can you still remove not needed commented code (and maybe also r... Andreas Müller
12:04 PM bug #10078 (Resolved): Symbol and details view title of misapplied name type is not the same as shown in the type combo element
This should be solved, please review. Katja Luther
11:34 AM bug #10078: Symbol and details view title of misapplied name type is not the same as shown in the type combo element
Andreas Müller wrote in #note-2:
> I do not understand the title of this ticket. The problem to me seems that the se...
Katja Luther
11:29 AM bug #10078: Symbol and details view title of misapplied name type is not the same as shown in the type combo element
I do not understand the title of this ticket. The problem to me seems that the selection in the dropdown is stored in... Andreas Müller
11:02 AM bug #10078 (Closed): Symbol and details view title of misapplied name type is not the same as shown in the type combo element
mail ERS:
Wenn man partial misapplication UND pro parte misapplication behalten will (den Unterschied habe ich per...
Katja Luther
05:08 PM bug #10056 (Closed): Make Reference.Accessed deletable in TaxEditor
Works as expected. Andreas Müller
03:54 PM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
For now, I implemented the date formatting in the way that timezone information is added using the "O" format (https:... Andreas Müller
03:43 PM bug #10079 (In Progress): Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
AM:
beim derzeitigen Upgrade unserer verwendeten Software Libraries fällt uns gerade wieder ein Thema auf die Füße...
Andreas Müller
03:19 PM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
Andreas Müller wrote in #note-4:
> The formatting seems to take place in name.inc, l.844 calling cdm_api.module.form...
Katja Luther
03:13 PM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
The formatting seems to take place in name.inc, l.844 calling cdm_api.module.format_datetime() l.449 which calls strt... Andreas Müller
02:53 PM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
This issue is closely related to #8343 Andreas Müller
02:52 PM bug #10079 (In Progress): Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
With #9359 and #10067 we upgraded hibernate and joda-time/jadira-usertype versions. Maybe also upgrading mysql-connec... Andreas Müller
03:01 PM bug #8343 (In Progress): potential timezone problem in application stack
IMPORTANT:
This task got a new flavour after upgrading some libraries (hibernate, jadira-usertype, mysql-connector, ...
Andreas Müller
02:58 PM bug #8343: potential timezone problem in application stack
Katja Luther wrote in #note-13:
> ... Actually there should be no timezone information in DATETIME??
Are we talki...
Andreas Müller

06/16/2022

09:50 PM bug #10075: Fix deserialization exception for bytebuddy base hibernate SerializableProxy
Please review. Andreas Müller
09:50 PM bug #10075: Fix deserialization exception for bytebuddy base hibernate SerializableProxy
Fixed with a workaround by overriding the class net.sf.ehcache.util.PreferredLoaderObjectInputStream which does not c... Andreas Müller
09:47 PM bug #10075 (Resolved): Fix deserialization exception for bytebuddy base hibernate SerializableProxy
Applied in changeset commit:taxeditor|9ee1ca440a5bbe003ed1c34e8abcc9f76ec97533. Andreas Müller
04:50 PM bug #10075: Fix deserialization exception for bytebuddy base hibernate SerializableProxy
it happens in readObject0.readOrdinaryObject.readSerialData.defaultReadFields.readObject0.(TCArray)checkResolve(readA... Andreas Müller
02:51 PM bug #10075 (Closed): Fix deserialization exception for bytebuddy base hibernate SerializableProxy
... this is related to hibernate upgrade to v5.4 (#10067)
This happens when deserializing a org.hibernate.proxy.po...
Andreas Müller
08:34 PM task #10077 (New): upgrade ehcache to 3.x
Probably blocked by Spring upgrade to 5.x (#10216).
There is probably a duplicate #9207 which points out size, gro...
Andreas Müller
04:40 PM bug #10076: Exception when opening character matrix with classification as root node
This problem appears when the root node of the descriptive dataset is a classification, which has no parent node and ... Katja Luther
04:39 PM bug #10076 (Closed): Exception when opening character matrix with classification as root node
mail Konstantina Koutroumpa:
Dear Katja and Andreas,
I am getting an error when opening the character matrix in...
Katja Luther
11:20 AM bug #8343: potential timezone problem in application stack
Locally I added the timezone to the out put and for http://phycobank.org/100158 the timezone was CEST and for http:/... Katja Luther
09:14 AM bug #8343: potential timezone problem in application stack
Andreas Müller wrote in #note-9:
> Andreas Kohlbecker wrote in #note-8:
> > Andreas Müller wrote in #note-7:
> > > Is...
Katja Luther
08:36 AM feature request #10074 (New): Areas for common names should be a set
mail ERS:
Hallo,
bei der Eingabe von Common Names ist mir gerade aufgefallen, dass es die Möglichkeit geben sol...
Katja Luther

06/13/2022

10:46 AM bug #7635: ObjectNotFoundException during delete of synonym and name
Maybe this is a similar problem:
Hallo,
Caryophyllales_spp
Habe bei Sebsebia orthacantha, Synonym Kyphocarpa ort...
Katja Luther

06/10/2022

02:55 PM task #10073 (New): Remove all docbkx related code/files from cdmlib
... and maybe others. They can be found at {parent}\src\docbkx\ and in parent-pom.
Probably also the changes folde...
Andreas Müller

06/09/2022

12:40 PM task #10072 (Closed): Upgrade fully to log4j2
We already upgraded to log4j2 in #9359.
~~However, the class eu.etaxonomy.cdm.opt.config.LoggingConfigurer is not ...
Andreas Müller

06/08/2022

10:57 AM bug #10071: TaxonNodeDtos should be created directly not from taxon objects
There were some follow up fixes, because the taxonnode dto created with SortableTaxonNodeQueryResult was not complete... Katja Luther
 

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