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From 06/24/2022 to 07/23/2022

07/23/2022

12:49 AM bug #9785 (Closed): Update script for missing measurment unit_ids (matrix)
I guess this worked. If we still find a database with non-updated data we should update manually. Andreas Müller
12:43 AM feature request #9906: Implement credits in dataportal
Model was adapte. Now we can implement in dataportal. Maybe we can do this during the performance sprint. Andreas Müller
12:41 AM feature request #9908 (Closed): Add timeperiod to credits
Implemented. Now we still need implementation in TaxEditor (#10098) and dataportal (#9906) Andreas Müller
12:39 AM feature request #10098 (Closed): Implement timePeriod for Credit in TaxEditor
see #9908 and #9906 for details Andreas Müller
12:37 AM feature request #10097 (Closed): Rename originalNameString to originalInfo
I guess this worked Andreas Müller
12:36 AM Revision df9935a6 (taxeditor): ref #10097 adapt originalNameString in taxeditor test
Andreas Müller
12:33 AM bug #9901 (Closed): Remove unique key Media_RightsInfo.rights_id
I guess this worked. I did not find any db with a uk-index only fk. Andreas Müller
12:27 AM bug #9830 (Closed): México Distrito Federal needs accent
Tested on integration_palmae Andreas Müller
12:10 AM Revision ee5a4c23 (taxeditor): ref #9908 adapt credits in taxeditor
Andreas Müller
12:09 AM Revision 50e674c4 (taxeditor): ref #10097 adapt originalNameString in taxeditor
Andreas Müller

07/22/2022

11:52 PM Revision b0675ba2 (cdmlib): adapt remote-webapp update path
Andreas Müller
11:52 PM Revision 4e2549d4 (cdmlib): adapt testH2 in remote-webapp
Andreas Müller
11:52 PM Revision 7cfdd498 (cdmlib): minor
Andreas Müller
11:52 PM Revision 5fbe7632 (cdmlib): ref #9785 fix SimpleSchemaUpdaterStep for error recovering
Andreas Müller
11:52 PM Revision 773534c5 (cdmlib): javadoc
Andreas Müller
11:52 PM Revision e16caaca (cdmlib): ref #10075, ref #9908 adapt test sql for OriginalSourceBase.accessed and Credits.timePeriod
Andreas Müller
11:52 PM Revision e6e7d41e (cdmlib): ref #10057 fix equalsShallowCompare in OriginalSourceBase
Andreas Müller
11:52 PM Revision 31598149 (cdmlib): ref #10057 fix isEmpty in OriginalSourceBase
Andreas Müller
11:51 PM Revision ce4dc9cf (cdmlib): update TestModelUpdater
Andreas Müller
11:51 PM Revision 5d5f629d (cdmlib): ref #9785 fix update script for measurement unit_ids
Andreas Müller
11:51 PM Revision 3720c2d4 (cdmlib): cleanup
Andreas Müller
11:51 PM Revision 9864b061 (cdmlib): ref #10097 add columnNameChanger for originalNameString to update script
Andreas Müller
11:51 PM Revision d05f8da0 (cdmlib): move CdmUpdater to new model version
Andreas Müller
11:51 PM Revision a80e5885 (cdmlib): ref #10057 add accessed field to OriginalSourceBase (cont., fullDataGenerator)
Andreas Müller
11:51 PM Revision 9d0815af (cdmlib): ref #9908 additional changes for Credit.timePeriod
Andreas Müller
11:51 PM Revision 2448aba7 (cdmlib): cleanup
Andreas Müller
11:51 PM Revision c4edd027 (cdmlib): ref #10057 add accessed field to OriginalSourceBase (cont., adapt clone, equals and isEmpty)
Andreas Müller
11:51 PM Revision 22847976 (cdmlib): ref #9908 add timePeriod to Credit
Andreas Müller
11:51 PM Revision 3783f232 (cdmlib): fix #9785 Update script for missing measurement unit_ids (matrix)
Andreas Müller
11:51 PM Revision 99637f24 (cdmlib): fix #9830 update México Distrito Federal label (add accent)
Andreas Müller
11:51 PM Revision b1e4eb3c (cdmlib): ref #9901 remove Media_RightsInfo.rights_id index
Andreas Müller
11:51 PM Revision c97ec7dd (cdmlib): ref #10097 adapt dataset.dtd (was incorrect before model change already)
Andreas Müller
11:50 PM Revision 89d135c6 (cdmlib): ref #10057 add accessed field to OriginalSourceBase
Andreas Müller
11:50 PM Revision 9c021029 (cdmlib): ref #10097 change originalNameString to originalInfo in cdmlib
Andreas Müller
11:50 PM Revision 8b57b93c (cdmlib): ref #10083 update script for blocking reverse label and schema updater for v5.32
Andreas Müller
11:38 PM Revision fceb01fb (taxeditor): adapt testH2 in taxEditor
Andreas Müller
11:38 PM Revision b2d2bb15 (cdm-vaadin): ref #10097 rename originalNameString to originalInfo in vaadin
Andreas Müller
11:37 PM Revision 5bbf59c3 (cdm-vaadin): adapt testH2 in vaadin
Andreas Müller
11:03 PM Revision e81d1360 (cdmlib): minor
Andreas Müller
10:47 PM Revision 0106eeef (cdm-vaadin): cleanup
Andreas Müller
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
04:37 PM Revision cdda449c (cdmlib): cleanup
Andreas Müller
02:50 PM Revision e3cea6b7 (cdmlib): fix log4j.xml
Andreas Müller
02:21 PM Revision 7a227ac8 (cdm-vaadin): cleanup
Andreas Müller
02:06 PM Revision f89ecd52 (cdm-vaadin): ref #10072 some adaptations for setLevel in vaadin
Andreas Müller
02:05 PM Revision 19920347 (cdm-dataportal): ref #10072 dome adaptations for setLevel in dataportal
Andreas Müller
02:05 PM Revision b4229a50 (cdmlib): cleanup and javadoc
Andreas Müller
02:04 PM Revision c8384ed5 (cdmlib): ref #10072 new methods for logging with deviating levels and reduce using of setLevel in production code
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
06:36 PM Revision 97ed1eda (cdm-server): ref #10055 add TODO in LoggingConfigurator
Andreas Müller
06:22 PM Revision ea3c5378 (cdm-dataportal): ref #10072, ref #9359 adapt log4j2 properties files in dataportal
Andreas Müller
06:05 PM Revision da72c9e9 (cdm-vaadin): cleanup and upgrade requiredMavenVersion
Andreas Müller
06:02 PM Revision 356c6915 (cdm-vaadin): ref 10072 remove LoggingConfigurer from vaadin
Andreas Müller
06:01 PM Revision 8bd9e993 (cdm-vaadin): ref 10072 remove log4j12 from vaadin and adapt log4j properties
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
05:46 PM Revision 282212d6 (taxeditor): ref 10072 remove log4j12 and apache-log4j-extras from taxeditor and adapt log4j properties
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
03:57 PM Revision dcb656c3 (cdmlib): ref #9359, ref 10095 try to remove xpp3 from cdmlib
Andreas Müller
03:56 PM Revision b0a7a43f (cdmlib): ref #9359 re-add javax.el-api as it is still needed hibernate-validation
Andreas Müller
03:34 PM Revision 67cc9bcd (cdm-server): test fixed length logging
Andreas Müller
03:19 PM Revision a67ce6e0 (cdm-server): test date and context logging
Andreas Müller
02:48 PM Revision 542ec6f1 (cdmlib): cleanup
Andreas Müller
02:48 PM Revision c36bdb95 (cdmlib): ref #10072, ref #9359, ref 10095 remove slf4j-nop from cdmlib
Andreas Müller
02:43 PM Revision 5d8ad42c (cdmlib): ref #10072 adapt integration test parameter name for log4j as it seems to be incorrect and switch from properties to log4j.xml there
Andreas Müller
02:41 PM Revision 116b3cae (cdmlib): ref #9359 javax.el-api from dependency management as it is not used anymore
Andreas Müller
02:40 PM Revision 1400461e (cdmlib): ref #10072, ref #9359 fully remove LoggingConfigurer as it is not adaptable to log4j2 and not used anymore (cont.)
Andreas Müller
02:10 PM Revision 8f45b947 (cdmlib): ref #10072, ref #9359 fully remove LoggingConfigurer as it is not adaptable to log4j2 and not used anymore
Andreas Müller
02:04 PM Revision ebfc034b (cdm-server): javadoc
Andreas Müller
02:04 PM Revision 78b0be7f (cdm-server): ref #9359, ref #10095 try to remove jakarta.el-api as apache-el is already on classpath in cdmserver
Andreas Müller
12:55 PM Revision 4309262f (cdm-server): ref #9359 replace javax.el-api by jakarata.el-api
Andreas Müller
12:54 PM Revision e985fe42 (cdm-server): cleanup
Andreas Müller
12:44 PM Revision feca66ca (cdm-server): ref #9359, ref #10072 add log4j2 to LoggingConfigurator in cdmserver
Andreas Müller
11:35 AM Revision a12dab80 (cdm-server): ref #9359, ref #10072, ref #10095 revert logging to logback classic for now and adapt correct handling for log4j in cdmserver
Andreas Müller
09:54 AM Revision 8c7f1b66 (cdmlib): ref #9359 upgrade to 3.0.6 for mariadb-java-client in cdmlib
Andreas Müller
09:54 AM Revision 95604162 (cdmlib): cleanup
Andreas Müller
09:51 AM Revision eb123a17 (cdm-server): ref #10095 remove old el-impl version from cdmserver
Andreas Müller
09:51 AM Revision d007e0a6 (cdm-server): cleanup
Andreas Müller
09:50 AM Revision b8c89622 (cdm-server): ref #9359, ref #10072, ref #10095 use log4j2 in cdmserver
Andreas Müller
12:42 AM Revision c269a0d9 (cdmlib): ref #10072 change log4j.properties to log4j.xml in remaining cdmlib modules
Andreas Müller

07/20/2022

11:49 PM Revision 6d3e493d (cdmlib): ref #10072 change log4j.properties to log4j.xml in commons, model, persistence and services
Andreas Müller
07:30 PM Revision 1f913edc (cdm-vaadin): ref #9359 try to remove springmodules from vaadin
Andreas Müller
07:25 PM Revision f2c2c233 (cdmlib): cleanup
Andreas Müller
07:24 PM Revision 29192aec (cdmlib): ref #10072, ref #9359, ref #10095 remove commons-logging from xmlgraphics.fop
Andreas Müller
07:00 PM Revision 216ea5a9 (cdmlib): javadoc
Andreas Müller
06:59 PM Revision 9120a89a (cdmlib): ref #10072, ref #9359, ref #10095 remove commons-logging from unitils-core and commons-beanutils
Andreas Müller
06:58 PM Revision e1efda1a (cdmlib): ref #10072 use log4j for slf4j in cdmlib-commons already
Andreas Müller
06:50 PM Revision d1e4062e (cdmlib): ref #10072, ref #9359, ref #10095 replace commons-logging by jcl-over-slf4j (cont., move jcl-over-slf4j to cdmlib-commons)
Andreas Müller
06:45 PM Revision 0408c72c (cdm-vaadin): ref #10072 final adaption log4j12->log4j2 in vaadin
Andreas Müller
06:44 PM Revision aafc3f59 (cdm-vaadin): cleanup
Andreas Müller
06:42 PM Revision b5f21afa (cdmlib): ref #10072, ref #9359, ref #10095 replace commons-logging by jcl-over-slf4j and adapt some loggers to log4j
Andreas Müller
05:35 PM Revision c06457d0 (cdm-vaadin): ref #10095, ref #9359 adapt json version in vaadin to cdmlib json version
Andreas Müller
04:18 PM Revision 9fa4ac9a (cdmlib): cleanup
Andreas Müller
04:02 PM Revision dab2a7f4 (cdmlib): remove lifecycle mapping for cdmlib-cache
Andreas Müller
04:01 PM Revision 840b4522 (cdmlib): ref #10095, ref #9359 upgrade and synchronize fasterxml versions
Andreas Müller
04:01 PM Revision c2facd18 (cdmlib): cleanup and javadoc
Andreas Müller
04:00 PM Revision 3d585f9d (cdmlib): ref #10095, ref #9359 remove javax.activation-api, jaxb-api and xalan from classpath (replaced by jakarta versions)
Andreas Müller
02:40 PM Revision 8b7babf9 (cdmlib): ref #10095 add fixed version for jackson-datatype-jsr310
Andreas Müller
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
02:06 PM Revision 8b32a3ce (cdmlib): cleanup
Andreas Müller
02:06 PM Revision 2e47e11d (cdmlib): ref #9359 add version number for commons-pool to avoid multiple versions in cdmserver comming from remote-webapp and vaadin (though unclear why vaadin retrieves a higher version)
Andreas Müller
11:52 AM Revision d75171f5 (cdmlib): first test B
Escobari Vargas

07/19/2022

11:19 PM Revision f893a1ff (cdmlib): ref #10072 comment usage of log4j12 in LoggingConfigurer and cdmlib-io in general (last log4j12 in cdmlib)
Andreas Müller
11:18 PM Revision 8edfa814 (cdmlib): ref #10072 remove log4j12 from cdmlib-io except for LoggingConfigurer issue
Andreas Müller
11:16 PM Revision a27635bd (cdm-vaadin): ref #10072 adapt vaadin to log4j2 and cleanup
Andreas Müller
10:41 PM Revision 26b856f8 (taxeditor): cleanup
Andreas Müller
10:39 PM Revision 527ecb11 (taxeditor): adapt CdmServerUtils to changes in CdmApplicationUtils
Andreas Müller
10:30 PM Revision b9fab907 (cdmlib): move NoDuplicateNamesValidator to api.validation package to split service layer from other modules, see also last commit
Andreas Müller
10:29 PM Revision eb1e36b8 (cdmlib): cleanup
Andreas Müller
10:12 PM Revision cf29bfc1 (cdmlib): move CdmApplicationUtils to real persistence package to avoid multiple scanning with service layer
Andreas Müller
10:10 PM Revision 2b7a0e65 (cdmlib): cleanup
Andreas Müller
09:07 PM Revision 5d7fcb25 (cdm-dataportal): ref #10072 fix log4j-api version and remove commons.lang in dataportal
Andreas Müller
09:06 PM Revision 4279ed61 (cdmlib): ref #10072 remove log4j12 from remote
Andreas Müller
09:05 PM Revision cb7f0fab (cdmlib): cleanup
Andreas Müller
08:50 PM Revision 4c2ad250 (cdmlib): cleanup
Andreas Müller
08:40 PM Revision f64f32be (cdm-dataportal): ref #10072 adapt dataportal to log4j2
Andreas Müller
07:40 PM Revision cf0057ee (cdmlib): ref #10072 use log4j2 in slf4j
Andreas Müller
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
06:28 PM Revision 0cd73a67 (cdmlib): cleanup
Andreas Müller
06:27 PM Revision 766fb6fd (cdmlib): avoid cookie error log on cnn
Andreas Müller
05:57 PM Revision cebc5b3a (cdmlib): ref #10094 preliminary disable 001-cdm.h2.sql (maybe a java11 issue in jenkins) (cont.)
Andreas Müller
05:53 PM Revision 6eaa7820 (cdmlib): ref #10094 preliminary disable 001-cdm.h2.sql (maybe a java11 issue in jenkins)
Andreas Müller
05:29 PM Revision 811a65d8 (cdmlib): fix incorrect uuid in HomotypicGroupTaxonComparatorTest
Andreas Müller
05:28 PM Revision 90a35da7 (cdmlib): cleanup
Andreas Müller
05:16 PM Revision b09c0226 (cdmlib): cleanup and remove debugging in PolytomousKeyGeneratorTest
Andreas Müller
04:30 PM Revision ad18cde1 (cdmlib): further changes for debugging
Andreas Müller
03:41 PM Revision ddc2152f (cdmlib): add java version check to DdlCreator
Andreas Müller
03:01 PM Revision 08ea6978 (cdmlib): ref #10072 temporarily revert log4j.properties
Andreas Müller
02:25 PM Revision 24ea68aa (cdmlib): ref #10072 switch off security manager for DdlCreator
Andreas Müller
01:12 PM Revision 40c85eaa (cdmlib): cleanup
Andreas Müller

07/18/2022

10:11 PM Revision e72a6e61 (cdmlib): ref #10093 adding very first classes copied from cdmlight for docx4j output
Andreas Müller
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

07/17/2022

07:52 PM Revision 53bea31e (cdmlib): ref #10092 deproxy feature for FdG import
Andreas Müller
07:52 PM Revision 540b9682 (cdmlib): cleanup
Andreas Müller
07:06 PM Revision 2f53c10a (cdmlib): cleanup
Andreas Müller
10:34 AM Revision d9ff78b5 (cdmlib): ref #10072 temporarily rename log4j.xml
Andreas Müller

07/16/2022

11:45 PM Revision f905a388 (cdmlib): cleanup
Andreas Müller
11:22 PM Revision a4cab8c6 (cdmlib): ref #10092 adapt markup import to FdG requirements (fixing errors)
Andreas Müller
11:20 PM Revision 794be65e (cdmlib): cleanup
Andreas Müller
11:05 PM Revision 0e799f7c (cdmlib): ref #10072 change cdmlib-commons log4j.properties to log4j2 log4j.xml
Andreas Müller
08:34 PM Revision 0474ab0b (cdmlib-apps): ref #9359, ref #10072 adapt eflora to log4j2 logger and logmanager and some cleanup
Andreas Müller
02:12 PM Revision 22689a70 (cdmlib-apps): ref #10092 adapt FloreGabonActivator import largest volumes first and exclude feature tree and some logging issues
Andreas Müller
02:10 PM Revision 133817c6 (cdmlib-apps): ref #10092 adapt FdG sources to new location on PESIHPC
Andreas Müller
02:08 PM Revision 67da8787 (cdmlib-apps): cleanup
Andreas Müller

07/15/2022

03:51 PM Revision cfdb11fc (cdmlib): cleanup
Andreas Müller
03:51 PM Revision 643e100c (cdmlib): fix #10090 revert init strategy and catch LIE in getCollectorTitleCache()
Andreas Müller
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
02:02 PM Revision 6c536aa0 (cdmlib): fix #10090 add secsource reference author to the PolytomousKeyNode init strategy
Andreas Müller

07/14/2022

09:57 PM Revision f492f1d9 (cdm-dataportal): javadoc, cleanup and revert some debugging
Andreas Müller
09:42 PM Revision c28b130d (cdmlib): cleanup
Andreas Müller
07:56 PM Revision 7494f3b1 (cdmlib): cleanup
Andreas Müller
07:03 PM Revision c7ef3e53 (cdmlib): ref #10090 catch LIE in Team.getCollectorTitleCache
Andreas Müller
06:59 PM Revision ac7949f3 (cdmlib): cleanup
Andreas Müller
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
05:55 PM Revision c7f13f26 (cdm-dataportal): handle errors not as json for commands with expected json result
Andreas Müller
05:54 PM Revision cbed020f (cdm-dataportal): cleanup
Andreas Müller
05:54 PM Revision ccc02dc1 (cdm-dataportal): add debugging
Andreas Müller
02:17 PM Revision 650193a1 (cdmlib): ref #10091 show stacktrace only if debug parameter is added
Andreas Müller
10:07 AM Revision b559f0f9 (cdmlib): ref #10089 adapt json mapping to new TypeDesignationSet handling (cont.)
Andreas Müller
09:43 AM Revision ab1abcbe (cdmlib): cleanup
Andreas Müller
09:43 AM Revision 0fffbab6 (cdmlib): fix #10091 Add stacktrace to JSON repsonse
Andreas Müller
09:36 AM Revision fdbd1a3a (cdmlib): ref #10089 return JSONNull for null values in type designation value processor
Andreas Müller
09:35 AM Revision d54d6020 (cdmlib): cleanup
Andreas Müller
08:47 AM Revision 22b33a05 (cdmlib): cleanup
Andreas Müller
08:40 AM Revision 1e4c68b2 (cdmlib): ref #10089 handle null values for map and type designation value processor
Andreas Müller
12:45 AM Revision 2de2cf10 (cdm-vaadin): ref #10089 handle RegistrationDTO with TypedEntityReference again in vaadin
Andreas Müller
12:44 AM Revision 25b120ed (cdmlib): ref #10089 handle RegistrationDTO with TypedEntityReference again in cdmlib
Andreas Müller
12:41 AM Revision cf58d709 (cdm-dataportal): ref #10089 rename TypeDesignationWorkingSet in dataportal
Andreas Müller

07/13/2022

11:28 PM Revision 54143f9a (cdmlib): ref #10089 adapt json mapping to new TypeDesignationSet handling
Andreas Müller
11:27 PM Revision f0b8034c (cdmlib): cleanup
Andreas Müller
08:02 PM Revision 2efce339 (cdmlib): ref #10090, ref #10089 try to avoid LIE in TypeDesignationSet
Andreas Müller
08:01 PM Revision d6353c79 (cdmlib): cleanup
Andreas Müller
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
06:49 PM Revision 85f4724b (cdm-dataportal): add some debugging for finding drush exception (cont.)
Andreas Müller
05:56 PM Revision a3b7c3d9 (cdm-dataportal): add some debugging for finding drush exception
Andreas Müller
05:41 PM Revision a0d044d3 (cdm-dataportal): cleanup
Andreas Müller
12:44 AM Revision 046d6228 (cdmlib): fix #10089 final fixes for TypeDesignationSet formatting ordered by type status (cont.)
Andreas Müller
12:36 AM Revision 230f5b70 (cdm-vaadin): rename RegistrationTypeDesignationStatusComparator
Andreas Müller
12:34 AM bug #10089 (Resolved): Order TypeDesignationSetContainer by status type
Applied in changeset commit:cdmlib|7af46cd80139907f3c80f4ee1ad644a0260c7b18. Andreas Müller
12:34 AM Revision 7af46cd8 (cdmlib): fix #10089 final fixes for TypeDesignationSet formatting ordered by type status
Andreas Müller
12:05 AM Revision 98768399 (cdmlib): cleanup and support for orderedBy and factory methods for TypeDesignationSetContainer
Andreas Müller

07/12/2022

11:49 PM Revision f104a204 (cdmlib): cleanup
Andreas Müller
11:03 PM Revision fc477304 (cdm-vaadin): cleanup
Andreas Müller
11:02 PM Revision 7aa81094 (cdm-vaadin): cleanup and rename RegistrationValidationException to TypeDesignationSetException in vaadin
Andreas Müller
10:50 PM Revision 45356f85 (cdmlib): ref #10089 implement TypeDesignationSetContainer ordered by status not field unit
Andreas Müller
10:42 PM Revision 8e73bb3d (cdmlib): cleanup
Andreas Müller
10:40 PM Revision 9a5a2693 (cdmlib): cleanup and rename RegistrationValidationException to TypeDesignationSetException (cont.)
Andreas Müller
10:03 PM Revision c4a57e04 (cdmlib): cleanup and rename RegistrationValidationException to TypeDesignationSetException
Andreas Müller
09:16 PM Revision 48c8ef25 (cdmlib): minor
Andreas Müller
09:14 PM Revision 50778c94 (cdmlib): ref #10089 rename TypeDesignationSetManager to TypeDesignationSetContainer in cdmlib
Andreas Müller
08:54 PM Revision d9a042e5 (cdm-vaadin): ref #10089 rename TypeDesignationWorkingSet to TypeDesignationSet in vaadin
Andreas Müller
08:52 PM Revision 262c0177 (cdmlib): ref #10089 rename TypeDesignationWorkingSet to TypeDesignationSet in cdmlib
Andreas Müller
08:15 PM Revision d7160e6b (cdm-vaadin): ref #10089 remove TypedEntityReference from TypeDesignationWorkingSet in vaadin
Andreas Müller
08:13 PM Revision 3fb08830 (cdmlib): ref #10089 remove TypedEntityReference from TypeDesignationWorkingSet
Andreas Müller
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
07:54 PM Revision 4ce0e91d (cdm-vaadin): cleanup
Andreas Müller
06:25 PM Revision 61d1e335 (cdm-vaadin): replace LinkedHashMap by Map where possible in vaadin
Andreas Müller
06:24 PM Revision 7667f093 (cdm-vaadin): cleanup
Andreas Müller
06:22 PM Revision 8d7c7784 (cdmlib): make TypeDesignationWorkingSet a decorator and not inherit directly from LinkedHashMap
Andreas Müller
05:59 PM Revision edc8c14e (cdmlib): replace LinkedHashMap by Map where possible
Andreas Müller
05:58 PM Revision 1ddf0695 (cdmlib): cleanup
Andreas Müller

07/11/2022

08:41 PM Revision 7de1e8a5 (cdmlib): ref #10087 make placement source and placement source FK explicit columns and refactor test (also ref #10081 )
Andreas Müller
08:39 PM Revision b1fafec1 (cdmlib): ref #10087 make placement source and placement source FK explicit columns and refactor test (also ref #10081 )
Andreas Müller
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
06:42 PM Revision 9e545c61 (cdmlib): ref #10081 add secundum name used in source to cdmlight
Andreas Müller
06:41 PM Revision 9e5bde9c (cdmlib): cleanup
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
01:03 PM Revision a9f7b763 (cdmlib): ref #10087 add taxon node source to status notes in cdmlight
Andreas Müller
01:02 PM Revision 09da8d56 (cdmlib): cleanup
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

11:58 PM Revision 0bb5c8a2 (cdmlib): ref #10067 cleanup CdmModelCacher
Andreas Müller
11:01 PM Revision 5864d558 (cdmlib): ref #6696 write model cache to target and use compile phase
Andreas Müller
11:00 PM Revision 2b7260c4 (cdmlib): add ehcache to cdmlib-cache
Andreas Müller
09:57 PM Revision 49eb471d (cdmlib): cleanup
Andreas Müller
09:43 PM Revision 22aa850d (cdmlib): ref #6696 change maven phase for CdmModelCache creation and move cdmlib-cache modul up behind cdmlib-service
Andreas Müller
08:49 PM Revision 1a1e2ca4 (cdmlib): ref #6696 create CdmModelCache during maven and remove cached model from git
Andreas Müller
05:54 PM Revision c0ed5d8e (cdmlib): ref #10067 save new cache model created with hibernate version 5.4
Andreas Müller
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
10:57 AM Revision 017bce1e (cdmlib): ref #10083 add AVOIDS_HOMONYM_OF name relationship
Andreas Müller
10:57 AM Revision d1ea8316 (cdmlib): cleanup
Andreas Müller

07/06/2022

04:12 PM Revision 36a4dfbd (cdmlib): ref #10081: add secNameInSourceSeparator to separator
Katja Luther
03:19 PM Revision a1998e47 (cdm-dataportal): ref #10081: remove the font-style for separator again
Katja Luther
03:18 PM Revision 143a6271 (cdmlib): ref #10081: add tag secNameInSourceSeparator and use it in cacheStrategy
Katja Luther
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
03:03 PM Revision ff162af3 (cdm-dataportal): ref #10081: adapt nameInSource handling in portal
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
09:49 AM Revision f134a838 (cdmlib): ref #10084: add type comparison to hql again
Katja Luther

07/05/2022

11:24 PM Revision 4d1f9d42 (taxeditor): cleanup
Andreas Müller
11:19 PM Revision 5e838349 (taxeditor): cleanup
Andreas Müller
11:14 PM Revision 599c91e5 (taxeditor): cleanup
Andreas Müller
10:56 PM Revision 9a6e5099 (cdmlib): cleanup
Andreas Müller
10:55 PM Revision 758086db (taxeditor): Preferenzen->Präferenzen
Andreas Müller
10:55 PM Revision 3f5ed758 (taxeditor): cleanup
Andreas Müller
10:20 PM Revision 35105144 (cdmlib): ref #10067, ref #3722, ref #8127 remove remaining sortindex handling from polytomous key node
Andreas Müller
10:19 PM Revision 4b8da4a0 (cdmlib): cleanup
Andreas Müller
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
03:57 PM Revision c377a0d9 (cdm-dataportal): ref #10081: add separator font-style
Katja Luther
01:52 PM Revision 3b4b9e2f (taxeditor): ref #10067, ref #3722, ref #8127 remove null value handling from PolytomousKeyGraphContentProvider in taxEditor
Andreas Müller
01:28 PM Revision 5c45a99a (cdmlib): ref #10067, ref #3722, ref #8127 remove all manual sortindex and null value handling from polytomous key (node)
Andreas Müller
01:25 PM Revision 0694bb3d (cdmlib): ref #10067, ref #8127 remove remaining null value handling from taxon node
Andreas Müller
01:24 PM Revision 3dc1adc5 (cdmlib): ref #10067, ref #3722, ref #8127 remove all manual sortindex and null value handling from term node
Andreas Müller
01:19 PM Revision ab85ad67 (cdmlib): ref #10067, ref #8127 remove "removeAllNull" (HHH_9751_Util) from DescriptionBase
Andreas Müller
11:16 AM Revision 059a8e53 (taxeditor): ref #8818: remove predicate from distribution status table in preferences
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
09:46 AM Revision edb488c8 (taxeditor): test
Katja Luther

07/04/2022

10:35 PM Revision 84f11f2b (cdmlib): revert remove strange IkeyPlusImport properties files in io/src/test/resources/main
Andreas Müller
10:12 PM Revision bb03b5f4 (cdmlib): cleanup and remove strange IkeyPlusImport properties files in io/src/test/resources/main
Andreas Müller
10:02 PM Revision 53fc098d (taxeditor): improve logging for exception in AbstractPersistentCollection.remoteInitialize()
Andreas Müller
09:43 PM Revision f13320e2 (cdmlib): fix CCE in IOServiceImpl for URI based imports
Andreas Müller
09:43 PM Revision 27f9f715 (cdmlib): cleanup and javadoc
Andreas Müller
03:43 PM Revision 4c68380d (cdmlib-apps): ref #9359 remove hsqldb StringComparator from ErmsTaxonImport
Andreas Müller
03:43 PM Revision 5bb9c7d1 (cdmlib-apps): update e-Flora and pesi to 5.32.0-SNAPSHOT
Andreas Müller
03:35 PM Revision e11ce0a9 (cdmlib-apps): cleanup
Andreas Müller
03:35 PM Revision 4b88f183 (cdmlib-apps): adapt BerlinModelImport to new cacheStrategy getter
Andreas Müller
03:34 PM Revision b10eeaf7 (cdmlib-apps): update app-import to 5.32.0-SNAPSHOT
Andreas Müller
03:30 PM Revision 8c64898f (cdmlib): ref #9359 update log4j to 2.18.0 in cdmlib
Andreas Müller
03:29 PM Revision 7af8b889 (utis-webapp): ref #9359 update log4j to 2.18.0 in utis-webapp
Andreas Müller
03:27 PM Revision f2234658 (cdm-dataportal): ref #9359 update log4j to 2.18.0 in dataportal
Andreas Müller
03:04 PM Revision c7e9d1ed (cdmlib): add nomenclatural author of nameInSource to init strategy
Katja Luther
12:29 PM Revision 904397ee (taxeditor): remove debug messages
Katja Luther
12:19 PM Revision bc55416e (cdmlib): ref #10081: add nameUsedInSource to initStrategy
Katja Luther
10:22 AM Revision 4287668c (taxeditor): add debugging for source section
Katja Luther
09:52 AM Revision ea87ffcb (taxeditor): add debugging for source section
Katja Luther
09:25 AM Revision 083eabed (taxeditor): minor
Katja Luther

07/01/2022

11:26 AM Revision f29ead53 (taxeditor): ref #10080: add messages
Katja Luther

06/29/2022

06:31 PM Revision 00931afd (cdmlib): cleanup
Andreas Müller
06:14 PM Revision 2c1a59f9 (taxeditor): adapt TaxEditor to WordTermExportConfigurator
Andreas Müller
06:14 PM Revision c7f0af52 (taxeditor): cleanup
Andreas Müller
04:27 PM Revision 5552c0c6 (cdmlib): rename WordTermExport
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
11:44 AM Revision bce2d0e5 (cdmlib): fix 10084: fix problem with missing taxonuuid in dto
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
11:52 AM Revision 5f41e9a8 (cdmlib): ref #10081 add nameUsedIn sec source to accepted taxon cache strategy
Andreas Müller

06/24/2022

05:04 PM Revision 009c376e (cdmlib): code cleaning
Katja Luther
05:04 PM Revision e11d6984 (cdmlib): code cleaning
Katja Luther
03:13 PM Revision 7fd76b2b (cdmlib): ref #10067, ref #3722, ref #8127 preliminary add sortIndex field again to avoid problem with model cache in TaxEditor (cont. fix JAXB issue)
Andreas Müller
03:02 PM Revision c3d56a52 (cdmlib): cleanup
Andreas Müller
02:42 PM Revision 172c0b19 (cdmlib): ref #10067, ref #3722, ref #8127 preliminary add sortIndex field again to avoid problem with model cache in TaxEditor
Andreas Müller
01:19 PM Revision 3b96b3e5 (cdmlib): cleanup
Andreas Müller
01:19 PM Revision e1fe2afa (cdmlib): ref #10067, ref #3722, ref #8127 fully remove TaxonNode sortindex code from TaxonNode and CdmLight
Andreas Müller
01:09 PM Revision bcc64240 (cdmlib): cleanup
Andreas Müller
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
 

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