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From 06/23/2022 to 07/22/2022

07/22/2022

07:39 PM feature request #10097 (Resolved): Rename originalNameString to originalInfo
Resolved in cdmlib and probably also in dataportal and vaadin, but still needs adaptation in taxEditor Andreas Müller
03:34 PM feature request #10097: Rename originalNameString to originalInfo
Original Doumentation from DescriptionElementSource:
~~~
* The use of "originalNameString" within a DescriptionE...
Andreas Müller
03:21 PM feature request #10097 (Closed): Rename originalNameString to originalInfo
... as we agreed on storing all kind of original (verbatim) information in this field, not only taxon names. Andreas Müller
06:29 PM feature request #9908 (Resolved): Add timeperiod to credits
Class adapted and update script written. Andreas Müller
05:45 PM bug #9785 (Resolved): Update script for missing measurment unit_ids (matrix)
Update script written Andreas Müller
05:12 PM bug #9830 (Resolved): México Distrito Federal needs accent
update script added Andreas Müller
05:00 PM bug #9901 (Resolved): Remove unique key Media_RightsInfo.rights_id
Andreas Müller
04:56 PM feature request #10057 (In Progress): Add "accessed" field to OriginalSourceBase
Model change done (not yet tested). Still needs cache strategy update and TaxEditor adaptation. Also maybe in Phycoba... Andreas Müller

07/21/2022

07:08 PM bug #10044 (Closed): Maps in Flore Du Gabon are broken
I reimported all data (#10092) and (afterwards) moved all textdata based distribution to "Distribution (General)" and... Andreas Müller
07:02 PM task #10009 (Resolved): Cleanup dependencies in TaxEditor
Seems to work but still needs intensive testing and maybe some cleanup. Andreas Müller
06:58 PM task #10072: Upgrade fully to log4j2
Can you please review and maybe work on the **clean up** open issues a bit so we get clean code soon. Andreas Müller
04:06 PM task #10072 (Resolved): Upgrade fully to log4j2
More or less solved.
Open issues:
* ~~handl setLevel() better (see current workaround in cdmlib-commons LogUtils cl...
Andreas Müller
05:48 PM task #9205 (Resolved): Remove apache-log4j-extras from TaxEditor dependencies
This should be fixed with adapting TaxEditor to log4j2 and adapting the according log4j.properties
Please review.
Andreas Müller
04:53 PM bug #10090: Many LIEs in cdmserver log for Team.getCollectorTitleCache()
Should be fixed. Please review. Andreas Müller
04:52 PM task #10095 (Closed): Synchronize dependency versions in CdmServer
Andreas Müller
04:04 PM task #10095 (Resolved): Synchronize dependency versions in CdmServer
This is mostly done except for aopalliance which will be removed automatically when upgrading to spring 5.x Andreas Müller
04:51 PM feature request #10096 (Discussed): Add new TaxonNode status and make notes field more general
Andreas Müller
04:51 PM feature request #10096 (Closed): Add new TaxonNode status and make notes field more general
Add taxon node status
* Excluded geo., øg (geographically out of scope); specification of excluded status
* Exclu...
Andreas Müller

07/20/2022

02:16 PM task #10095 (In Progress): Synchronize dependency versions in CdmServer
Andreas Müller
02:16 PM task #10095 (Closed): Synchronize dependency versions in CdmServer
The CdmServer is a merge from cdmlib-remote-webapp and cdm-vaadin. Therefore it can happen that the same dependency a... Andreas Müller

07/19/2022

06:31 PM task #10094: Reenabel anttask for 001-cdm.h2.sql creation
This is on the log on the very beginning (after git fetch), however, it looks like it was there before already.
~~...
Andreas Müller
06:02 PM task #10094: Reenabel anttask for 001-cdm.h2.sql creation
It had to be switched due to errors during build in jenkins.
Log:
~~~
[ERROR] Failed to execute goal org.apach...
Andreas Müller
05:52 PM task #10094 (New): Reenabel anttask for 001-cdm.h2.sql creation
Andreas Müller

07/18/2022

10:10 PM feature request #10093 (New): Create print publication classification output using docx4j
https://www.baeldung.com/docx4j
https://javadoc.io/doc/org.docx4j/docx4j/latest/index.html
Andreas Müller

07/15/2022

03:33 PM bug #10090: Many LIEs in cdmserver log for Team.getCollectorTitleCache()
The reason was a missing property path for secsource authors.
The reason why it happened for **collectorTitleCache...
Andreas Müller
02:02 PM bug #10090 (Resolved): Many LIEs in cdmserver log for Team.getCollectorTitleCache()
Applied in changeset commit:cdmlib|6c536aa028a283ed2041899ac33a13baa41bcaeb. Andreas Müller

07/14/2022

06:26 PM task #10091 (Closed): Add stacktrace to JSON repsonse
This should be fixed. It is now possible to show the error message and the stacktrace of a failing webservice by addi... Andreas Müller
09:43 AM task #10091 (Resolved): Add stacktrace to JSON repsonse
Applied in changeset commit:cdmlib|0fffbab66709e2a4401a7fdc3ff4df8bc5fe1afe. Andreas Müller
09:38 AM task #10091 (Closed): Add stacktrace to JSON repsonse
... for better error finding Andreas Müller

07/13/2022

07:51 PM bug #10090: Many LIEs in cdmserver log for Team.getCollectorTitleCache()
maybe related to #9949 Andreas Müller
07:49 PM bug #10090 (Closed): Many LIEs in cdmserver log for Team.getCollectorTitleCache()
from int cdmserver (startup.log)
~~~
Caused by: org.hibernate.LazyInitializationException: failed to lazily initi...
Andreas Müller
12:34 AM bug #10089 (Resolved): Order TypeDesignationSetContainer by status type
Applied in changeset commit:cdmlib|7af46cd80139907f3c80f4ee1ad644a0260c7b18. Andreas Müller

07/12/2022

08:13 PM bug #10089 (Closed): Order TypeDesignationSetContainer by status type
Currently it is first ordered by base entity (e.g. field unit) alphabetically and only within TypeDesignationWorkingS... Andreas Müller

07/11/2022

06:48 PM feature request #10081: Show name in source for sec ref of accepted taxon
I also implemented for CDM light (commit:9e545c61). This was still missing as CDM light does not use the TaxonDefault... Andreas Müller
03:03 PM feature request #10088 (New): Implement bibliography parser
Pensoft uses:
For the parser you can check https://anystyle.io/. It works pretty well in most cases.
Andreas Müller
01:05 PM feature request #10087 (Resolved): Add taxon node source to status notes in cdmlight
This is implemented, however, we still need to discuss if this is really the correct solution or if we better should ... Andreas Müller
12:55 PM feature request #10087: Add taxon node source to status notes in cdmlight
AM:
Ganz sicher bin ich mir aber nicht, ob das semantisch immer 100% richtig ist. Die Placement Source ist ja eine g...
Andreas Müller
11:43 AM feature request #10087: Add taxon node source to status notes in cdmlight
WGB:
Hallo,
mir ist aufgefallen, dass in Taxon.csv zwar die „Status notes“ (aus dem Taxon Node Dialog) ausgegeben...
Andreas Müller
11:42 AM feature request #10087 (Closed): Add taxon node source to status notes in cdmlight
Andreas Müller

07/10/2022

10:37 AM task #10064: Upgrade cybertaxonomy.org to Drupal9
Editing text on https://cybertaxonomy.org/setups/group/server_requirements does not work. The text seems to be store... Andreas Müller

07/08/2022

11:21 PM task #10064: Upgrade cybertaxonomy.org to Drupal9
On https://cybertaxonomy.org/node/4/edit I tried to change the link for "Taxonomic Editor (TaxEditor)" from "http://w... Andreas Müller
11:06 PM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
Remaining issues should be solved in next milestone Andreas Müller
11:05 PM bug #8343 (Closed): potential timezone problem in application stack
I think this ticket can be closed. The timezone problem is now solved with correct availability of timezone informati... Andreas Müller
10:58 PM feature request #10081: Show name in source for sec ref of accepted taxon
Tests and improved handling of secundum part is handled in #10085 Andreas Müller
10:33 PM feature request #10081 (Feedback): Show name in source for sec ref of accepted taxon
Generally works but there is an unwanted whitespace after the closing bracket.
See https://test.e-taxonomy.eu/dat...
Andreas Müller
10:54 PM bug #10075 (Closed): Fix deserialization exception for bytebuddy base hibernate SerializableProxy
I think we can close this ticket as the problem did not show up anymore. Andreas Müller
10:53 PM task #3722 (Feedback): Using @OrderColumn does not work in trees
Andreas Müller
10:39 PM bug #10059 (Closed): Link for stored under and identification on specimen page does not work correctly
Works as expected Andreas Müller
09:33 PM bug #10076 (Closed): Exception when opening character matrix with classification as root node
Works as expected. Andreas Müller
04:32 PM feature request #10083: Add name relationship type "avoids homonym of"/"causes replacement name"
Update script is written and checked on integration.
Dataportal and cdmlight(?) still need to be updated.
Relationsh...
Andreas Müller
04:20 PM feature request #10083: Add name relationship type "avoids homonym of"/"causes replacement name"
~~~
SELECT r.id relId, n1.titleCache n1, t.titleCache rel, n2.titleCache n2, n1.nameCache n1short, n2.nameCache n2sho...
Andreas Müller
02:26 PM feature request #10086: Taxonomic and geographic search for data portal
ERS:
das typische Ergebnis einer Geo-Abfrage sieht so aus:
![](clipboard-202207081421-julug.png)

Man wählt ...
Andreas Müller
02:22 PM feature request #10086 (New): Taxonomic and geographic search for data portal
Geo search already works but the taxonomic filter is still missing. This is a filter on any higher taxon (>= genus ?)... Andreas Müller
02:15 PM task #8865 (In Progress): more external-links to be implemented
Eckhard, can you please check if there is still some issue open from this ticket or if it can be closed? Andreas Müller

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
 

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