Activity
From 06/21/2022 to 07/20/2022
07/20/2022
- 02:16 PM task #10095 (In Progress): Synchronize dependency versions in CdmServer
- 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...
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.
~~... - 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... - 05:52 PM task #10094 (New): Reenabel anttask for 001-cdm.h2.sql creation
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
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... - 02:02 PM bug #10090 (Resolved): Many LIEs in cdmserver log for Team.getCollectorTitleCache()
- Applied in changeset commit:cdmlib|6c536aa028a283ed2041899ac33a13baa41bcaeb.
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...
- 09:43 AM task #10091 (Resolved): Add stacktrace to JSON repsonse
- Applied in changeset commit:cdmlib|0fffbab66709e2a4401a7fdc3ff4df8bc5fe1afe.
- 09:38 AM task #10091 (Closed): Add stacktrace to JSON repsonse
- ... for better error finding
07/13/2022
- 07:51 PM bug #10090: Many LIEs in cdmserver log for Team.getCollectorTitleCache()
- maybe related to #9949
- 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... - 12:34 AM bug #10089 (Resolved): Order TypeDesignationSetContainer by status type
- Applied in changeset commit:cdmlib|7af46cd80139907f3c80f4ee1ad644a0260c7b18.
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...
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...
- 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.
- 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 ...
- 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... - 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... - 11:42 AM feature request #10087 (Closed): Add taxon node source to status notes in cdmlight
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...
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...
- 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
- 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...
- 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
- 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... - 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.
- 10:53 PM task #3722 (Feedback): Using @OrderColumn does not work in trees
- 10:39 PM bug #10059 (Closed): Link for stored under and identification on specimen page does not work correctly
- Works as expected
- 09:33 PM bug #10076 (Closed): Exception when opening character matrix with classification as root node
- Works as expected.
- 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... - 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... - 02:26 PM feature request #10086: Taxonomic and geographic search for data portal
- ERS:
das typische Ergebnis einer Geo-Abfrage sieht so aus:
Man wählt ... - 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 ?)...
- 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?
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.
- 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...
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...
- 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... - 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?
... - 10:00 AM bug #10084 (Feedback): Adding a new specimen to character matrix fails
- 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... - 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...
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?
- 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,... - 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.
- 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... - 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... - 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... - 01:32 PM feature request #10081 (Resolved): Show name in source for sec ref of accepted taxon
- 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...
- 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...
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...
- 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.
- 11:49 AM bug #10076 (Resolved): Exception when opening character matrix with classification as root node
- This should be fixed, please review.
- 11:46 AM bug #10084 (Resolved): Adding a new specimen to character matrix fails
- Please review.
- 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 ... - 09:23 AM feature request #10082: Improve formatting for pro parte misapplications
- Example: https://europlusmed.org/cdm_dataportal/taxon/63fead7a-662a-4082-9503-c6ea994c2049
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... - 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... - 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... - 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...
- 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... - 11:55 AM feature request #10081: Show name in source for sec ref of accepted taxon
- ... and can you also please review my implementation.
- 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...
- 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...
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...
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.
- 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... - 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 ... - 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 ...
- 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 ... - 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... - 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...
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.
- 07:36 PM task #8127 (Resolved): [Reminder] to check if Hibernate Null Value bug still exists
- Probably solved but still needs code cleanup.
- 07:35 PM task #3722: Using @OrderColumn does not work in trees
- Please review.
- 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... - 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... - 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...
- 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.
- 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... - 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...
- 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... - 05:08 PM bug #10056 (Closed): Make Reference.Accessed deletable in TaxEditor
- Works as expected.
- 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:...
- 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... - 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... - 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...
- 02:53 PM bug #10079: Fix timezone problems after upgrading jadira.usertype, hibernate and/or mysql drivers
- This issue is closely related to #8343
- 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...
- 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, ... - 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...
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