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From 05/24/2022 to 06/22/2022

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
03:51 PM Revision 4f438db5 (cdm-dataportal): ref #10079 adapt tests to timezone handling
Andreas Müller
03:46 PM Revision 177a39cb (cdm-dataportal): ref #10079 add timezone to (registration) date
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
12:03 PM Revision 898ac44b (taxeditor): ref #10078: sort the terms at the beginning.
Katja Luther
11:37 AM Revision 0614271f (cdm-vaadin): cleanup and fix correct factory method usage
Andreas Müller
11:34 AM Revision be09d413 (cdmlib): cleanup
Andreas Müller
11:15 AM Revision d00d12fa (cdmlib): fix compile error for private MaterialOrMethodEvent constructor
Andreas Müller
11:12 AM Revision 2a7f40e5 (cdmlib): minor
Andreas Müller
10:57 AM Revision c5e9236a (cdmlib): ref #10067 update java-doc for and remove protected access to model constructors where possible in occurrence
Andreas Müller
09:44 AM Revision 08670423 (cdmlib): ref #7666 add test for pro parte MAN formatting
Andreas Müller
09:43 AM Revision a6d0a583 (cdmlib): cleanup
Andreas Müller

06/21/2022

12:04 PM Revision 51b5fd7a (cdmlib): ref #10067 update java-doc for and remove protected access to model constructors where possible
Andreas Müller
12:03 PM Revision 34ab2253 (cdmlib): cleanup
Andreas Müller

06/20/2022

02:46 PM Revision 81b378ac (cdmlib): ref #10076 fix HQL query (remove native)
Andreas Müller
02:43 PM Revision f47729f9 (utis-core): ref #9359 udpate enforcer plugin to 3.1.0. and log4j to 2.17.2 for utis-core
Andreas Müller
02:42 PM Revision 64e30c90 (cdm-webapp): ref #9359 udpate enforcer plugin to 3.1.0. for cdm-webapp
Andreas Müller
02:40 PM Revision bcaa3499 (cdm-vaadin): ref #9359 udpate enforcer plugin to 3.1.0. for vaadin
Andreas Müller
02:40 PM Revision 25ef1ef8 (cdmlib): ref #9359 udpate enforcer plugin to 3.1.0. for cdmlib
Andreas Müller
10:57 AM Revision eec20175 (taxeditor): ref #10033: vocabulary representation should be editable in taxeditor
Katja Luther
10:42 AM Revision a543b013 (taxeditor): TaxonRelationshipTypeInverseContainer should not inherit from DefinedTermBase and use InverseTermWrapper and RelationshipTypeCombo for NameRelType and TaxonRelType
Katja Luther

06/17/2022

08:54 PM Revision 9169740e (cdmlib): ref #10076 fix HQL query (remove native)
Andreas Müller
08:26 PM Revision 5778f462 (cdmlib): ref #10067 update java-doc for HibernateProxyHelper.deproxy (cont.)
Andreas Müller
08:20 PM Revision 3f11d79a (cdmlib): ref #10067 update java-doc for HibernateProxyHelper.deproxy
Andreas Müller
08:14 PM Revision 7d595ebb (taxeditor): ref #3722, ref #10067, ref #8127 remove childnodes nullcheck in ChecklistEditorInput
Andreas Müller
08:06 PM Revision 87d9741a (cdmlib): ref #10067 update java-doc for CdmBase.deproxy
Andreas Müller
08:05 PM Revision 3001e5ad (cdmlib): preliminary fix TaxEditor compile error due to non-protected DefinedTermBase constructor
Andreas Müller
07:46 PM Revision 5d6e72c2 (taxeditor): ref #10067, ref #3722 reenable and adapt readPolytomousKeyDataFromNodes() test
Andreas Müller
07:46 PM Revision f603e01a (taxeditor): fix order of expected and real value in test
Andreas Müller
07:46 PM Revision cbe3c7e4 (taxeditor): cleanup
Andreas Müller
05:26 PM Revision 77c9b8f8 (cdmlib): ref #3722, ref #8127, ref #10067 fully remove sortindex updating and collection null handling workaround from TaxonNode
Andreas Müller
05:23 PM Revision 93185e7b (cdmlib): adapt TaxonNodeService to private Representation constructor
Andreas Müller
04:56 PM Revision 608b3df3 (cdmlib): minor
Andreas Müller
04:54 PM Revision d56308b9 (cdmlib): cleanup and ref #10067 adapt some model constructors javadoc and privacy to bytebuddy
Andreas Müller
04:48 PM Revision 826a35b1 (cdmlib): move AvailableFor to term package
Andreas Müller
04:06 PM Revision 2d7694bf (cdmlib): cleanup
Andreas Müller
01:53 PM Revision 62c42797 (taxeditor): ref #5741: symbol and symbol2 field: add selection box and disable when selected
Katja Luther
09:59 AM Revision f99e2cae (cdmlib): ref #10067 add javassist to dependency management as it is also used by iiif-apis
Andreas Müller

06/16/2022

11:05 PM Revision f5f8c7e7 (cdmlib): ref #10067, ref #10077 remove javassist as bytecode provider from cdmlib (fix pom)
Andreas Müller
10:56 PM Revision 5e6cc79c (cdmlib): minor
Andreas Müller
10:53 PM Revision fbc25777 (taxeditor): cleanup
Andreas Müller
10:46 PM Revision ea704d19 (cdm-vaadin): cleanup
Andreas Müller
10:31 PM Revision da5e6dc7 (cdmlib): cleanup
Andreas Müller
10:29 PM Revision ac512a79 (cdmlib): ref #10067, ref #10077 remove javassist as bytecode provider from cdmlib
Andreas Müller
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
09:47 PM Revision 9ee1ca44 (taxeditor): fix #10075 fix deserialization by overriding PreferredLoaderObjectInputStream from ehcache
Andreas Müller
08:48 PM Revision 15aa7a2c (cdmlib): cleanup
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
08:33 PM Revision 35d4b554 (cdmlib): move ehcache from model to service
Andreas Müller
08:30 PM Revision 317ec988 (cdmlib): cleanup
Andreas Müller
05:51 PM Revision f73ae1d9 (cdmlib): ref #10067 add bytecodeprovider handling to CdmApplicationController
Andreas Müller
05:50 PM Revision 107abc23 (cdmlib): cleanup
Andreas Müller
04:42 PM Revision 9fb87bef (cdmlib): ref #10076: fix taxonnodeDto creation for nodes without taxon and parent
Katja Luther
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

06/15/2022

01:06 PM Revision 3a976bf6 (taxeditor): cleanup
Andreas Müller
12:05 PM Revision 00ee5645 (taxeditor): ref #9359 upgrade maven-antrun-plugin to 3.1.0 in taxeditor
Andreas Müller
12:04 PM Revision 25436749 (taxeditor): cleanup
Andreas Müller

06/14/2022

10:52 PM Revision bedb5de8 (taxeditor): ref #9359 remove old Spring Source repositories from taxeditor cdmlib and local
Andreas Müller
10:48 PM Revision d336a791 (taxeditor): java-doc
Andreas Müller
04:21 PM Revision 3b1474a6 (taxeditor): ref #9359 add javax.annotation to import packages in MANIFEST.MFs
Andreas Müller
04:00 PM Revision 0561a2fc (taxeditor): cleanup
Andreas Müller
03:58 PM Revision df1cedb8 (taxeditor): ref #9359 add commons-collections4 to taxeditor dependencies
Andreas Müller
02:26 PM Revision fe32c5ea (taxeditor): remove store from required bundles in store MANIFEST.MF
Andreas Müller
12:31 PM Revision 907e7ec4 (cdmlib): use tuple class as return type
Katja Luther
09:46 AM Revision ac2536fb (cdmlib): fix hibernate problem with returntype and taxonnodeDto for missing publish flag
Katja Luther
12:03 AM Revision 328d91f0 (taxeditor): ref #9359 remove log4j12 exports from taxeditor.cdmlib MANIFEST.MF
Andreas Müller

06/13/2022

11:55 PM Revision 7872e2e8 (taxeditor): cleanup
Andreas Müller
11:06 PM Revision 926a7e65 (taxeditor): ref #9359 add taxeditor.local log4j2 to gitignore
Andreas Müller
11:03 PM Revision 23a596af (taxeditor): cleanup
Andreas Müller
11:03 PM Revision 62966b18 (taxeditor): fix remotingApplicationContext.xml
Andreas Müller
11:01 PM Revision 002dd8ef (taxeditor): remove whitespace from workbench MANIFEST.MF
Andreas Müller
02:21 PM Revision 4dcfee27 (cdm-dataportal): adapt test
Katja Luther
02:03 PM Revision d0b78a25 (cdm-dataportal): ref #9359 upgrade java dependencies in dataportal (except for selenium)
Andreas Müller
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
10:26 AM Revision c0497e2d (cdmlib): ref #10071: add statusNote to dto again
Katja Luther

06/10/2022

05:59 PM Revision 90a40d1d (cdmlib): ignore IpniServiceTest again
Andreas Müller
05:09 PM Revision 8866e92d (cdmlib): cleanup
Andreas Müller
05:00 PM Revision 05137c06 (cdmlib): update PresenceAbsenceTerm.csv, remove double whitespaces for invasive terms
Andreas Müller
04:59 PM Revision 33724181 (cdmlib): update lineendings
Andreas Müller
04:21 PM Revision b5f7b1f2 (cdmlib): cleanup
Andreas Müller
04:20 PM Revision f407d3fa (cdmlib): cleanup
Andreas Müller
04:17 PM Revision 01e98b70 (cdmlib): ref #10067, #10070 reassign javassist as bytecode provider in cdmlib
Andreas Müller
03:54 PM Revision 8757f365 (cdmlib): revert changes in taxonnodeDto.noteStatus
Katja Luther
03:51 PM Revision d7b4d78c (cdmlib): revert changes in taxonnodeDto.noteStatus
Katja Luther
03:39 PM Revision 5cf11d96 (cdm-vaadin): remove unnecessary component scan filters
Andreas Müller
03:06 PM Revision e9b0c758 (cdmlib): ref #10073 remove docbkx related files from gitattributes
Andreas Müller
03:06 PM Revision c5af637e (cdmlib): ref #9359 fully remove hsqldb to be supported by cdmlib, we only use h2 now (cont 2)
Andreas Müller
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
02:30 PM Revision 3b6301d5 (cdmlib): revert changes to get statusNote
Katja Luther
01:53 PM Revision d4f676c6 (cdmlib): adapt test data
Katja Luther
01:52 PM Revision 60474dec (cdmlib): remove the hsql files again
Katja Luther
01:30 PM Revision a69f97f1 (cdmlib): ref #10071: add statusNote to dto
Katja Luther
01:13 PM Revision 9139d0dd (cdm-vaadin): adapt spring xsd versions in all other applicationContexts
Andreas Müller
01:05 PM Revision 1521fa2e (cdmlib): revert some changes added accidently
Katja Luther
01:00 PM Revision 4df43dd4 (cdmlib): resolve the merge
Katja Luther
12:54 PM Revision cd3e6740 (cdmlib): white space problems
Katja Luther
12:54 PM Revision 6c541cef (cdmlib): adapt tests to added description
Katja Luther
12:36 PM Revision 40dd7cc6 (cdmlib): cleanup
Andreas Müller
12:26 PM Revision b1d8767d (cdmlib): ref #9359 fully remove hsqldb to be supported by cdmlib, we only use h2 now (cont)
Andreas Müller
12:22 PM Revision 6545b1d5 (cdmlib): ref #9359 fully remove hsqldb to be supported by cdmlib, we only use h2 now
Andreas Müller
12:16 PM Revision 475d237f (cdmlib): ref #9359 fully remove hsqldb to be supported by cdmlib, we only use h2 now
Andreas Müller
11:45 AM Revision db707134 (cdmlib): ref #10071: additional constructor and test added
Katja Luther
11:43 AM Revision 6e0c944e (cdmlib): ref #9359 temporarily neglect LoggingConfigurer
Andreas Müller
11:21 AM Revision 4f248b8f (cdm-vaadin): adapt spring xsd versions in applicationContext-service-integration.xml
Andreas Müller
11:06 AM Revision 2506b246 (cdmlib): cleanup
Andreas Müller
11:04 AM Revision 80d999e5 (cdmlib): remove h2-datasource.xml as it is not used anymore
Andreas Müller
10:56 AM Revision 2d405aee (cdmlib): remove applicationContext.xml from remote test base directory
Andreas Müller
10:45 AM Revision 56dd942a (cdmlib): remove all java and some licence/readme from gitattributes
Andreas Müller
10:10 AM Revision a23f2969 (cdm-vaadin): adapt spring xsd versions in cdm-vaadin-servlet.xml
Andreas Müller
08:09 AM Revision ac9cae76 (cdmlib): ref #10067 byteCodeProvider for HibernateConfiguration and factory methods
Andreas Müller

06/09/2022

10:16 PM Revision 84808e22 (cdmlib): ref #9359 add exclusions to javax.mail and jena-tdl
Andreas Müller
09:39 PM Revision 222315aa (taxeditor): ref #9359 adapt taxeditor.local to log4j 2
Andreas Müller
07:32 PM Revision 661705c1 (taxeditor): ref #9359 fix Logger handling in some classes for which replace did not work (cont.)
Andreas Müller
07:25 PM Revision ba10d0e9 (taxeditor): ref #9359 fix Logger handling in some classes for which replace did not work
Andreas Müller
07:16 PM Revision 94de228d (taxeditor): minor
Andreas Müller
07:15 PM Revision 2bba4a19 (taxeditor): ref #9359 import log4j2 in some TaxEditor projects (fix)
Andreas Müller
07:12 PM Revision 9a6b2310 (taxeditor): ref #9359 import log4j2 in some TaxEditor projects
Andreas Müller
06:27 PM Revision d83fc07f (taxeditor): ref #9359 upgrade TaxEditor to log4j2 (adapt workbench to new package)(cont)
Andreas Müller
06:16 PM Revision db825808 (taxeditor): ref #9359 upgrade TaxEditor to log4j2 (add exported packages)
Andreas Müller
06:09 PM Revision e0ef5fb8 (taxeditor): ref #9359 upgrade TaxEditor to log4j2 (cont)
Andreas Müller
06:08 PM Revision 7de7dd91 (taxeditor): cleanup
Andreas Müller
03:34 PM Revision 50935afd (taxeditor): ref #9359 upgrade TaxEditor to log4j2 (adapt workbench to new package)
Andreas Müller
03:27 PM Revision f274f083 (taxeditor): ref #9359 upgrade TaxEditor to log4j2
Andreas Müller
02:45 PM Revision ec602490 (taxeditor): ref #9359 adapt log4j handling in TaxEditor (cont.)
Andreas Müller
01:56 PM Revision f97eecfd (taxeditor): ref #9359 adapt log4j handling in TaxEditor (cont.)
Andreas Müller
01:51 PM Revision b6f5d1a6 (cdmlib): ref #9359 add dependency management for error_prone_annotations
Andreas Müller
01:48 PM Revision 47f89b8f (taxeditor): ref #9359 adapt log4j handling in TaxEditor
Andreas Müller
01:37 PM Revision 15daf02c (taxeditor): ref #9359 update slf4j logging in TaxEditor
Andreas Müller
01:31 PM Revision 13307324 (cdmlib): minor
Andreas Müller
01:30 PM Revision 1feff2df (cdmlib): ref #9359 upgrade spring-security-oauth2 to latest version
Andreas Müller
01:25 PM Revision eadd0f35 (cdmlib): ref #9359 upgrade docx4j to latest version
Andreas Müller
01:23 PM Revision a820701f (cdmlib): ref #9359 upgrade plexus-utils to latest version
Andreas Müller
01:22 PM Revision e8694614 (cdmlib): ref #9359 upgrade Saxon-HE to latest version
Andreas Müller
01:21 PM Revision 94645f2d (cdmlib): ref #9359 replace slf4j-log4j12 by slf4j-reload4j
Andreas Müller
01:12 PM Revision 12c174d5 (cdmlib): ref #9359, ref #10072 some adaptations for log4j2
Andreas Müller
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
11:02 AM Revision 2b956f99 (cdmlib): #9359 update poi and xml-beans to latest version in cdmlib (cont.)
Andreas Müller
10:23 AM Revision c7d418c8 (cdmlib): ref #9359 upgrade docx4j to v8 and manage versions for plexus-classworlds and plexus-component-annotations
Andreas Müller
10:15 AM Revision 23de68fc (cdmlib): ref #9359 upgrade cdmlib to log4j 2
Andreas Müller

06/08/2022

03:02 PM Revision 427378b1 (cdmlib): #9359 update poi and xml-beans to latest version in cdmlib (cont.)
Andreas Müller
02:59 PM Revision f21c829a (cdmlib): #9359 update poi and xml-beans to latest version in cdmlib (cont.)
Andreas Müller
02:52 PM Revision c07f06a0 (cdmlib): #9359 update poi and xml-beans to latest version in cdmlib
Andreas Müller
02:39 PM Revision 9628a4a5 (taxeditor): #10009 add antlr again
Andreas Müller
01:55 PM Revision 7829b055 (cdmlib): ref #10067 change back bytecode provider to javassist in hibernate.cfg.xmls
Andreas Müller
01:53 PM Revision d8a4b95f (taxeditor): #10009 add lucene-core again
Andreas Müller
01:12 PM Revision 1c648453 (taxeditor): #10009 add hibernate-eners again
Andreas Müller
12:59 PM Revision 5a9cce4d (cdmlib): cleanup
Andreas Müller
12:59 PM Revision 3a1dbf7c (cdmlib): ref #10067 revert bytecode provider in hibernate.cfg.xmls
Andreas Müller
11:54 AM Revision 27dafab6 (cdmlib): minor
Katja Luther
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
10:28 AM Revision e3d5927a (cdm-dataportal): minor
Katja Luther
09:45 AM Revision 17e31533 (cdmlib): ref #10071: add node status to dto and implemented some tests
Katja Luther

06/07/2022

05:42 PM Revision 6103abfd (taxeditor): ref #9359 update surefire plugin to 3.0.0-M7 in taxeditor (cont.)
Andreas Müller
05:37 PM Revision b84468fb (cdmlib): fix NPEs in DTO creation
Katja Luther
03:08 PM Revision efa3824e (cdmlib): taxon node status needs to be added to the dto
Katja Luther
02:39 PM Revision 02a32271 (cdm-dataportal): adapt test
Katja Luther
01:19 PM bug #10033 (In Progress): For new FeatureTree only uuid is shown in dataportal
Katja Luther
01:19 PM bug #10033 (Resolved): For new FeatureTree only uuid is shown in dataportal
We need to adapt the taxeditor implementation, so that not the titlecache but the representation is used. Katja Luther
12:36 PM bug #10033: For new FeatureTree only uuid is shown in dataportal
Terms contain an termrepresentation object, this is empty for terms/termcollections created in taxeditor. As a first ... Katja Luther
12:33 PM Revision 5f4a411c (cdmlib): ref #10033: if term has no representation use titlecache in termrepresentation_L10n
Katja Luther
10:18 AM Revision f98660c3 (taxeditor): ref #9359 update surefire plugin to 3.0.0-M7 in taxeditor
Andreas Müller
09:52 AM Revision e629eadb (cdm-server): ref #9359 update surefire plugin to 3.0.0-M7 in cdm-server
Andreas Müller
09:50 AM Revision f05af282 (cdm-vaadin): ref #9359 update surefire plugin to 3.0.0-M7 in vaadin
Andreas Müller
09:49 AM Revision 7500a7a4 (cdmlib): ref #9359 update surefire plugin to 3.0.0-M7 in cdmlib
Andreas Müller

06/03/2022

05:50 PM Revision bfb84c1f (taxeditor): ref #9359 revert ehcache in taxeditor
Andreas Müller
03:45 PM Revision cc5425b9 (cdmlib): ref #9359 revert ehcache
Andreas Müller
03:45 PM Revision f12f1234 (cdmlib): minor
Andreas Müller
03:45 PM Revision 2f048780 (cdmlib): ref #10067 try to use javassit as bytecode provider
Andreas Müller
03:31 PM Revision 37a35ef6 (taxeditor): cleanup
Andreas Müller
02:35 PM Revision 29ce7c87 (cdmlib): ref #10071: create taxonnodeDTOs, add classification uuid
Katja Luther

06/02/2022

02:33 PM bug #10034 (Resolved): Flat feature tree throws exception
Now moving unsaved nodes is handled correctly. Please reviw. Katja Luther
02:30 PM Revision 46fc1532 (taxeditor): ref #10034: better handling of messages
Katja Luther
09:41 AM bug #10071 (In Progress): TaxonNodeDtos should be created directly not from taxon objects
This is done for the search of the taxonnodes for a specific taxon and also for the search in a subtree. Katja Luther
08:50 AM bug #10071 (Closed): TaxonNodeDtos should be created directly not from taxon objects
The webservice getting the taxonnodeDtos for a taxon, first gets the taxon object and then creates the Dtos for the t... Katja Luther
09:34 AM Revision d9740b37 (cdmlib): ref #10071: create taxonnodeDTOs also for a subtree
Katja Luther
08:51 AM Revision 23b979d9 (cdmlib): ref #10071: create taxonnodeDTOs directly from taxon uuid
Katja Luther

06/01/2022

10:57 PM Revision 5cef85cb (taxeditor): #10009 add xml-apisand commons-pool and remove others from bin.includes
Andreas Müller
08:09 PM Revision e0a68352 (taxeditor): #10009 adapt c3p0 version number
Andreas Müller
05:26 PM Revision cd817281 (taxeditor): #10009 add c3p0 and other DB drivers
Andreas Müller
04:06 PM Revision b00a278f (cdmlib): ref #10067 add bytebuddy check to ProxyUtils
Andreas Müller
04:05 PM Revision 90d49e1d (cdmlib): cleanup
Andreas Müller
02:40 PM Revision 909ec7f3 (taxeditor): #9359, #10009 adding jackson-annotations and jboss-transaction-api_1.2_spec required for login and transactions
Andreas Müller
01:49 PM Revision 1c2181be (cdmlib): create taxonnodeDto directly with taxonUuid - continue
Katja Luther
01:47 PM Revision 1a9f6e9d (cdmlib): create taxonnodeDto directly with taxonUuid
Katja Luther
01:46 PM Revision 76701f6e (taxeditor): #9359, #10009 remove slf4j-log4j12
Andreas Müller
01:40 PM Revision 77fcaa65 (taxeditor): #9359, #10009 remove bean-utils from taxeditor.cdmlib (still exists in molecular.lib)
Andreas Müller
01:33 PM Revision 2e5e28a6 (taxeditor): #9359, #10009 update slf4j-log4j12 version in case we still need it
Andreas Müller
01:28 PM Revision 8f7929b5 (taxeditor): ref #10067, #10009 remove hibernate-jpa-2.1-api
Andreas Müller
01:23 PM Revision 112f74db (taxeditor): #10009 preliminary remove usertype.core
Andreas Müller
01:23 PM Revision 7c4f7d92 (taxeditor): move byte-buddy
Andreas Müller
01:20 PM Revision 2e76ec21 (cdmlib): ref #10067, ref #3722 add parent.childNodes to taxonNode property path to allow sortindex computation
* should be preliminary Andreas Müller
01:08 PM Revision b121cf83 (taxeditor): #10009 remove commons-collections4
Andreas Müller
12:54 PM Revision 7f99924f (cdmlib): ref #9359 removed duplicated manage version of jcl-over-slf4j in cdmlib
Andreas Müller
12:53 PM Revision 55c15c2d (cdmlib): ref #10067 remove direct dependencies to javassist and hibernate-jpa-2.1 from cdmlib-persistence
Andreas Müller
12:30 PM Revision 87a6f8ae (taxeditor): cleanup
Andreas Müller
12:27 PM Revision 6dbe2e69 (taxeditor): ref #10067, #9359, #10009 ignore CdmEntitySessionAwareTest.readPolytomousKeyDataFromNodes preliminary to allow full build
Andreas Müller
11:55 AM Revision 29655c12 (cdmlib): ref #10067 add byte-buddy dependency management
Andreas Müller
11:52 AM Revision f4a1eae4 (taxeditor): ref #10067, #10009 add byte-buddy (replaces javassist in hibernate)
Andreas Müller
11:51 AM Revision 82fc1145 (taxeditor): ref #10067, #10009 remove javassist (not used by hibernate anymore)
Andreas Müller
11:32 AM Revision db27d783 (taxeditor): #10009 remove spring-security-remoting again as it was not the reason
Andreas Müller
11:30 AM Revision bdf38d94 (taxeditor): ref #10067 adapt AbstractPersistentCollection serialVersionUID
Andreas Müller
11:25 AM Revision 8bd58569 (taxeditor): #10009 add spring-security-remoting again to try to solve serialVersionUID issue
Andreas Müller
11:06 AM Revision 06a1c881 (taxeditor): #10009 remove empty lines from bin.includes
Andreas Müller
10:53 AM Revision adc61987 (taxeditor): ref #10067, #9359, #10009 adapt taxeditor to new jakarta validation package
Andreas Müller
10:39 AM Revision 88d6cebc (taxeditor): ref #10067, #9359, #10009 remove not used entries in bin.includes and fix copying of jadira usertypes
Andreas Müller
10:29 AM Revision 0f6841be (taxeditor): ref #10067, #9359, #10009 adapt dependencies in taxeditor to latest versions in cdmlib and remove all dependencies not needed directly or for export
* this version will not work yet Andreas Müller
10:29 AM Revision 5056c949 (taxeditor): use static method in Conditions as suggested
Andreas Müller
10:29 AM Revision 9da105d2 (taxeditor): cleanup
Andreas Müller
10:25 AM Revision 2629c0c7 (cdmlib): ref #9359 manage version of jcl-over-slf4j in cdmlib
Andreas Müller
10:20 AM Revision af8867dd (cdmlib): ref #9359 upgrade xmlgraphics-fop and -commons to latest version in cdmlib
Andreas Müller
10:10 AM Revision 84a352cb (cdmlib): ref #9359 upgrade slf4j-xxx, commons-imaging, xercesImpl, hibernate-commons-annotations, javassist and jakarta.validation-api to latest version in cdmlib
Andreas Müller
09:09 AM Revision 428e9ed2 (taxeditor): ref #10034: check dirty nodes at the beginning of move operation.
Katja Luther
01:58 AM bug #10034 (In Progress): Flat feature tree throws exception
Andreas Müller wrote in #note-2:
> The problem does only seem to appear if you try to move a node before you save. I...
Andreas Müller
12:53 AM Revision a7a4b973 (cdmlib): cleanup
Andreas Müller
12:00 AM task #10009 (In Progress): Cleanup dependencies in TaxEditor
Andreas Müller

05/31/2022

11:43 PM Revision e20f99e1 (taxeditor): ref #10067 add remoting specific parts to AbstractLazyInitializer again in taxeditor
Andreas Müller
11:30 PM Revision 58696c35 (taxeditor): ref #10067 adapt AbstractLazyInitializer to new hibernate version in taxeditor
Andreas Müller
11:28 PM Revision 59695a56 (taxeditor): cleanup
Andreas Müller
11:27 PM Revision 2760b7b4 (taxeditor): ref #10067 adapt AbstractPersistentCollection to new hibernate version in taxeditor
Andreas Müller
10:55 PM Revision cbadc5e7 (cdmlib): ref #9359 javadoc
Andreas Müller
10:53 PM Revision 99c1e469 (cdmlib): ref #9359 downgrade jboss-logging version to 3.4.3 as 3.5.0 requires java11 in cdmlib
Andreas Müller
10:40 PM Revision 57863fba (cdmlib): ref #9359 add dependency management for jboss-logging-processor in cdmlib
Andreas Müller
10:35 PM Revision 9805efb5 (cdmlib): ref #9359 revert removing jboss-logging-annotations in cdmlib
Andreas Müller
10:21 PM Revision 28218fda (cdmlib): ref #9359 upgrade jboss-logging to latest version and remove jboss-logging-annotations in cdmlib
Andreas Müller
09:47 PM Revision fe29288a (taxeditor): cleanup
Andreas Müller
09:36 PM Revision 383098c0 (taxeditor): cleanup
Andreas Müller
09:25 PM Revision d7670e34 (cdmlib): ref #9359 javadoc
Andreas Müller
09:25 PM Revision b86b1f35 (cdmlib): ref #9359 upgrade net.sf.ehcache/ehcache and org.json/json to latest version in cdmlib
Andreas Müller
06:12 PM Revision 159e7b25 (taxeditor): cleanup
Andreas Müller
03:38 PM Revision 73054571 (cdm-vaadin): ref #10067 adapt vaadin to new preference lookup handling
Andreas Müller
03:36 PM Revision 29f43e42 (cdm-vaadin): cleanup
Andreas Müller
03:32 PM Revision 0053a70e (taxeditor): minor
Andreas Müller
03:28 PM Revision c46c3b29 (cdmlib): ref #9359 upgrade xtream version 1.4.14->1.4.19 and remove xmlpull
Andreas Müller
03:17 PM Revision 88dee2f2 (cdmlib): ref #9359 downgrade xmlpull:xmlpull to 1.1.3.1 as 1.2.0 is only available in the JBoss repo which is currently switched off
Andreas Müller
03:16 PM Revision c240e90c (cdmlib): update metadata in parent pom
Andreas Müller
03:02 PM Revision d7905be5 (taxeditor): cleanup
Andreas Müller
03:00 PM Revision c1537fe2 (taxeditor): ref #10067 fix cacheStrategy compile issue in taxeditor
Andreas Müller
02:43 PM bug #10034: Flat feature tree throws exception
Could not reproduce this problem with the actual nightly build.
Steps I tried to reproduce the problem:
* creat...
Katja Luther
02:12 PM Revision 519bff7b (cdmlib): ref #10067 replace deprecated hibernate validation NotEmpty by JPA version
Andreas Müller
01:51 PM Revision 533864b4 (taxeditor): ref #9359 cleanup gitignore
Andreas Müller
01:51 PM Revision cea8edf6 (taxeditor): ref #9359 update joda-time and mysql-connector-java to latest version in taxeditor
Andreas Müller
01:51 PM Revision a10b0a4e (taxeditor): ref #9359 update itextpdf to latest version in taxeditor
Andreas Müller
01:51 PM Revision 9e7380cc (taxeditor): ref #9359 update postgresql version to 42.3.6 in taxeditor (cont.)
Andreas Müller
01:51 PM Revision 9f485921 (taxeditor): ref #9359 update taxeditor to latest jackson version
Andreas Müller
01:51 PM Revision 502edc8a (taxeditor): ref #9359 update postgresql version to 42.3.6 in taxeditor
Andreas Müller
01:19 PM Revision a4de9dec (cdmlib): cleanup
Andreas Müller
01:12 PM feature request #10070 (New): Upgrade to hibernate 6+
Before start upgrade to hibernate 5.6.x if not yet done. There is still a problem with the TaxonGraphHibernateListene... Andreas Müller
01:08 PM Revision c3190812 (cdmlib): cleanup some base DAOs (rename, remove @Repository, ...)
Andreas Müller
12:44 PM bug #10056 (Resolved): Make Reference.Accessed deletable in TaxEditor
Added a delete button, please review. Katja Luther
12:43 PM Revision ec8df5bb (taxeditor): ref #10056: add delete button to date element
Katja Luther
12:14 PM Revision 0d59864d (cdmlib): cleanup
Andreas Müller
11:57 AM bug #10059: Link for stored under and identification on specimen page does not work correctly
please review. Katja Luther
11:57 AM bug #10059: Link for stored under and identification on specimen page does not work correctly
The path to the name needs to be processed by url(), then the correct link is used. Katja Luther
11:56 AM bug #10059 (Resolved): Link for stored under and identification on specimen page does not work correctly
Applied in changeset commit:cdm-dataportal|c90f5440175074c6a350ad24fdaba0c0b6b9ae74. Katja Luther
10:22 AM bug #10059: Link for stored under and identification on specimen page does not work correctly
This problem occurs because there is an element data-cdm-render-path containing the actual render path and this is us... Katja Luther
11:57 AM Revision 89c7717e (cdmlib): cleanup
Andreas Müller
11:56 AM Revision 9fd2eb7e (cdmlib): ref #9359 update joda-time, mariadb-java-client and mysql-connector-java to latest version in cdmlib
Andreas Müller
11:56 AM Revision c90f5440 (cdm-dataportal): fix #10059: the url needs to be processed with url()
Katja Luther
11:36 AM Revision ce43a73f (cdmlib): ref #9359 update itextpdf to latest version in cdmlib
Andreas Müller
11:31 AM Revision 92c60bc1 (cdmlib): ref #9359 update jackson and guava to latest version in cdmlib
Andreas Müller
11:12 AM Revision 8c468c66 (cdmlib): ref #10067 adapt getAllPersistedClasses() to new hibernate metadata handling
Andreas Müller
10:43 AM Revision 10634f7c (cdm-dataportal): ref #10059: remove render path
Katja Luther
10:16 AM Revision b220af7c (cdmlib): ref #9359 remove JBoss and apache incubating repository
Andreas Müller
10:13 AM Revision f9e2340e (cdmlib): ref #9359, #10067 upgrade pom to hibernate 5.4.33,hibernate-validator 6.2.3 and hibernate-search 5.11.10
Andreas Müller
08:28 AM task #10067 (In Progress): Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5
Andreas Müller
08:16 AM feature request #10069 (New): Upgrade hibernate search and lucene to hs6+ and lucene 8+
Lucene 6+ seems to require hs6+ as there is a strange dependency on org.apache.lucene.document.Field.Index and ...Fie... Andreas Müller
02:54 AM Revision f5a9c13f (cdmlib): ref #9359, #10067 add lucene-sandbox
Andreas Müller
02:52 AM Revision a95fbfcc (cdmlib): ref #9359, #10067 prepare Lucene6+ double queries
Andreas Müller
02:47 AM Revision 6155fd74 (cdmlib): ref #9359, #10067 remove SortFieldOptions
Andreas Müller
02:46 AM Revision 77f0d8ee (cdmlib): ref #9359, #10067 remove most index boosts
Andreas Müller

05/30/2022

11:56 PM Revision 273ff5e1 (cdmlib): cleanup
Andreas Müller
10:59 PM bug #5477 (Resolved): lucene index not updated in all cases after Taxon.addMisappliedName
Was not fully fixed yet. Problem reoccurred after upgrading to hibernate-search 5.7.3. "ContainedIn" was still missin... Andreas Müller
10:56 PM Revision 44e77359 (cdmlib): ref #7487 fix fulltext search for proparten MAN and partial MAN+synonyms
Andreas Müller
10:51 PM Revision 74b8cb5c (cdmlib): cleanup
Andreas Müller
10:47 PM bug #7487 (Resolved): Full text misapplied name search with area filter uses fixed relation type uuid
Solved by adding also proparte and partial MAN and partial synonym relationship type subqueries. Also related to fina... Andreas Müller
10:01 PM Revision e0a87ccd (cdmlib): ref #7487 adapt test
Andreas Müller
09:59 PM Revision 384235ed (cdmlib): ref #10067, ref #5477 add containedIn to relatedFrom and relatedTo to adapt to hibernate search 5.7.3
Andreas Müller
09:56 PM Revision 127e8d62 (cdmlib): cleanup
Andreas Müller
01:55 PM Revision de68a697 (cdmlib): minor
Andreas Müller
11:54 AM bug #10068 (Closed): Changing focus to accepted taxon does not work
After opening a the name editor with focus on a synonym, the change of focus to the accepted taxon does not work, res... Katja Luther
11:27 AM bug #10060: Exception when adding kind-of-unit information to a field unit
Katja Luther wrote in #note-1:
> I think we should not allow to set a kind of unit for a field unit, so I would remo...
Katja Luther
09:18 AM bug #10060 (In Progress): Exception when adding kind-of-unit information to a field unit
I think we should not allow to set a kind of unit for a field unit, so I would remove the possibility to edit the kin... Katja Luther
10:20 AM Revision be473233 (cdmlib): cleanup
Andreas Müller

05/25/2022

03:05 PM Revision 40fc8ef7 (cdmlib): ref #9359 update postgresql version to 42.3.6 in cdmlib
Andreas Müller
01:39 PM Revision 0eeb74cb (cdmlib): ref #10067 update to hibernate 5.3 (cont.)
Andreas Müller
01:38 PM Revision 8b4d3b05 (cdmlib): ref #10067 update to hibernate-search 5.9
Andreas Müller
01:37 PM Revision 1a2ac5f4 (cdmlib): ref #10067 update to hibernate 5.3
Andreas Müller
12:56 PM Revision 009442e0 (cdmlib): cleanup
Andreas Müller
10:49 AM task #3722 (Resolved): Using @OrderColumn does not work in trees
Probably solved, still needs intensive testing and code cleanup. Andreas Müller
10:39 AM Revision bfab2edd (cdmlib): cleanup
Andreas Müller
10:39 AM Revision 857528e8 (cdmlib): ref #10067 improve handling of CdmPreferenceLookup (now ...Cache) to allow running with >1 entity managers (e.g. during maven tests)
Andreas Müller
10:29 AM feature request #7861 (In Progress): TaxonGraphHibernateListener: inject the ITaxonGraphDao into TaxonGraphBeforeTransactionCompleteProcess
A somehow similar solution was implemented in 8c6b6172722d to adapt the TaxonGraphBeforeTransactionCompleteProcess to... Andreas Müller
10:23 AM feature request #7648: Create taxonrelation to genus or species when subordinate names are created
Andreas Kohlbecker wrote in #note-10:
> "Session is closed!"-problem is solved now.
This fix was only a workaroun...
Andreas Müller

05/24/2022

07:44 PM Revision 56edf3ba (cdmlib): ref #10067, ref #3722, ref #8127 adapt handling of sortIndex after upgrade to hibernate5.2
Andreas Müller
07:06 PM Revision 665d2a60 (cdmlib): cleanup
Andreas Müller
08:58 AM Revision adabc933 (cdmlib): cleanup
Andreas Müller
 

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