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From 11/07/2022 to 12/06/2022

12/06/2022

11:30 PM feature request #10133: Improve ontology state vocabularies
Analyzing the structure tree "structures 1.0" and the structure vocabularies shows that many of the structures in the... Andreas Müller
09:12 PM feature request #10196: Hybrid structure-state terms
AM:
Erstmal würde ich mir gerne nochmal ins Gedächtnis zurückrufen, inwiefern Terme beide Eigenschaften (State/Struk...
Andreas Müller
05:48 PM feature request #10196 (Closed): Hybrid structure-state terms
copied from #10133#note-1
some structures can also be used as states in a character matrix. We need to decide how ...
Andreas Müller
06:08 PM Revision 4e8bd680 (cdmlib): ref #2934, ref #4670 add moose-extensions
Andreas Müller
06:04 PM Revision 7eeaa9dc (cdmlib): cleanup
Andreas Müller
03:24 PM bug #10195: Character data should be ordered by character tree
Andreas Müller wrote in #note-7:
> Can you please check how far this is kind of a duplicate for #8657 or any other of...
Katja Luther
02:33 PM bug #10195: Character data should be ordered by character tree
Can you please check how far this is kind of a duplicate for #8657 or any other of the related tickets or how far the... Andreas Müller
02:47 PM Revision e5c6153b (taxeditor): cleanup
Andreas Müller
02:47 PM Revision 80271249 (taxeditor): javadoc
Andreas Müller
10:33 AM Revision d29a17c1 (cdm-dataportal): ref #10191: revert changes in method signature
Katja Luther
10:13 AM Revision 19255dc5 (cdm-dataportal): ref #10191: show label of fieldunit if not atmoised -continue
Katja Luther
09:05 AM bug #9629 (In Progress): Better handling of OptionalDataException
Reopen the ticket because it appeared again:
Hallo,
Caryophyllales_spp, beim Aufruf eines Synonyms aus der Suche:...
Katja Luther

12/05/2022

02:36 PM feature request #9584 (Resolved): specimen page: character data displayed in details section
Simple display of the character data added, new ticket created (#10195).
Please review this first implementation.
Katja Luther
02:28 PM feature request #9584: specimen page: character data displayed in details section
Actually to have the basic information about the existing character data in the portal I would commit the simple impl... Katja Luther
02:15 PM feature request #9584: specimen page: character data displayed in details section
There are implementations of the aggregated descriptions for the taxon page, but both representations missing informa... Katja Luther
01:22 PM feature request #9584: specimen page: character data displayed in details section
NoK:
ja, im Screenshot erscheinen die Characters in alphabetischer Reihenfolge des Character label. Die gewünschte...
Andreas Müller
12:20 PM feature request #9584: specimen page: character data displayed in details section
Actually I use the order used in the dto, need to check how this is created.
Andreas Müller wrote in #note-11:
> Nor...
Katja Luther
12:11 PM feature request #9584: specimen page: character data displayed in details section
Norbert, can you have a look on the last commit and give a comment if this is an acceptable layout?
Question from ...
Andreas Müller
11:07 AM feature request #9584 (In Progress): specimen page: character data displayed in details section
Displaying the character data in its own table would look like this:
![](Screenshot 2022-12-05 110556.png)
Katja Luther
02:35 PM bug #10195 (New): Character data should be ordered by character tree
The display of the character data in specimen details page and taxon page missing the information about the character... Katja Luther
02:30 PM Revision 52645dd4 (cdm-dataportal): ref #9584: show character data in specimen details page
Katja Luther
01:18 PM bug #10054: Changes on secundum reference are lost after changing status to basionym
Older mail from Maryam (2022-08-26) which is maybe related:
I received this email while saving the changes on sec....
Andreas Müller

12/02/2022

09:11 PM feature request #10194 (Resolved): Allow specimens as source for factual data
Andreas Müller
08:49 PM Revision f93763da (cdmlib): cleanup
Andreas Müller
02:47 PM bug #8132 (Worksforme): phycobank cdm-server instance problems with db connections
Andreas Müller
09:02 AM Revision bfffa47e (taxeditor): fix #4456: code cleaning
Katja Luther

12/01/2022

06:53 PM bug #8132 (Resolved): phycobank cdm-server instance problems with db connections
To me it seems that this problem did not occur anymore in the last years and we can close the ticket as worksforme.
...
Andreas Müller
06:42 PM bug #8170 (New): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource does not conform to the interface
Andreas Müller
06:31 PM feature request #10194: Allow specimens as source for factual data
WGB:
gibt es eigentlich eine Möglichkeit, Specimen sozusagen als Referenz (Voucher) für Faktendaten zu benutzen?
Da...
Andreas Müller
06:29 PM feature request #10194 (Closed): Allow specimens as source for factual data
... and maybe others.
Think can be handled model side with existing CdmLinkSource or as explicit attribute in Desc...
Andreas Müller
01:49 PM Revision 7fc954fe (taxeditor): revert unwanted changes
Katja Luther
12:21 PM Revision 60cfeb3d (taxeditor): remove unused initialize method to make it compile
Andreas Müller
11:58 AM Revision e1dddccc (taxeditor): cleanup
Andreas Müller
11:56 AM Revision b663b23c (taxeditor): adapt to new DescriptionElementFormatter package
Andreas Müller
11:20 AM Revision 89a92d2d (cdmlib-apps): cleanup
Andreas Müller
11:18 AM Revision d86c767b (cdm-vaadin): cleanup
Andreas Müller
11:17 AM Revision 361ca821 (cdm-vaadin): rename EllypsisFormatter interface in vaadin
Andreas Müller
11:14 AM Revision 1fabfba5 (cdmlib): rename EllypsisFormatter interface
Andreas Müller
11:12 AM Revision cb9fcd29 (cdmlib): rename abstract classes and some other cleanup
Andreas Müller
09:54 AM bug #10191 (Resolved): Error message on taxon specimen page for non-atomized specimens
Please review, as test you could use the same taxon on test: https://test.e-taxonomy.eu/dataportal/preview/cichorieae... Katja Luther
09:02 AM Revision 723cf0c5 (cdm-dataportal): ref #10191: show label of fieldunit if not atmoised
Katja Luther
12:19 AM bug #10193: OutOfMemory exception when exporting mexico flora
KL, I assigend the ticket to you as you may implement the workaround solution.
If this works we may discuss how to...
Andreas Müller
12:17 AM bug #10193 (New): OutOfMemory exception when exporting mexico flora
When running CDM-l export the OOME occurred after about 85% (see logfile at about line 39.467).
A bit earlier (li...
Andreas Müller

11/30/2022

08:25 PM Revision 058c22aa (cdmlib): cleanup
Andreas Müller
08:23 PM Revision e89c358b (cdmlib): cleanup
Andreas Müller
04:15 PM bug #10191: Error message on taxon specimen page for non-atomized specimens
This is caused by not atomised specimen, so the fields of the dto are not filled. We could use the summarylabel of th... Katja Luther
03:21 PM bug #10190 (Resolved): Invalid argument supplied for foreach() in order_fieldUnitDtos_by_date_and_type()
please review Katja Luther
03:21 PM bug #10190: Invalid argument supplied for foreach() in order_fieldUnitDtos_by_date_and_type()
The problem was caused by a NPE when the taxon/name of a determination was not set. Katja Luther
03:19 PM Revision 00d2d5ef (cdmlib): ref #10190: null check for taxonname and taxon in determination
Katja Luther
02:59 PM bug #10182: Portal does not show typespecimen for duplicated typedesignation
The Editor must guarantee that OcccurenceStatus.type is never null.
Additionally, we should add NotNull to Occurre...
Andreas Müller
10:52 AM Revision 604e7242 (taxeditor): add viewer generics to AbstractCdmEditorPart, remove deprecated ViewerSorter and some other cleanup
Andreas Müller
10:02 AM bug #10192 (Resolved): External Links do not work in E+M
I removed the javascript call and add the attribute to open the link in a new tab. Please review. Katja Luther
10:01 AM Revision 1ffd7502 (taxeditor): cleanup
Andreas Müller
09:55 AM bug #7699: NPE in CdmTransientEntityCacher.getCacheElement()
Now an explicit error is thrown with message "No cache available for cacheId = xxx" and some debug information.
For n...
Andreas Müller
08:51 AM bug #7699 (In Progress): NPE in CdmTransientEntityCacher.getCacheElement()
Andreas Müller
09:53 AM Revision 38db2a51 (cdm-dataportal): ref #10192: remove javascript call and add attribute to open external link in new tab
Katja Luther
09:48 AM Revision f1c74cff (cdmlib): ref #7699 add debugging to CdmTransientEntityCacher.getCache() (cont. II)
Andreas Müller
09:24 AM Revision b4aa8a57 (cdmlib): ref #7699 add debugging to CdmTransientEntityCacher.getCache() (cont.)
Andreas Müller
08:38 AM bug #9174 (Duplicate): After longer inactivity NPE for cache
This seems to be a duplicate for #7699 Andreas Müller
01:31 AM Revision 2014062e (cdmlib): ref #7699 add debugging to CdmTransientEntityCacher.getCache()
Andreas Müller
12:51 AM Revision 674b745b (taxeditor): ref #10186, ref #9174 add method logging to CachingHttpInvokerProxyFactoryBean
Andreas Müller
12:47 AM Revision 89374cca (taxeditor): cleanup
Andreas Müller

11/29/2022

07:04 PM feature request #10156: Show field unit media in taxon image galleries
I guess this can not be handled in the current milestone, but maybe in the next one. Andreas Müller
12:48 PM bug #10192 (In Progress): External Links do not work in E+M
The problem comes from the call of "drupal_strip_dangerous_protocols("JavaScript:popupExternalLinks('url'))" inside l... Katja Luther

11/28/2022

01:23 PM task #10183 (Closed): Import Buxales via Cdm2Cdm
Andreas Müller
12:10 PM bug #10182 (In Progress): Portal does not show typespecimen for duplicated typedesignation
Andreas Müller
12:07 PM bug #10192 (Closed): External Links do not work in E+M
NaK:
die Externen Such-Links aus E+M funktionieren teilweise nicht, hinter dem Taxon-Namen bleibt immer ein Anführ...
Andreas Müller
12:04 PM bug #10186: Problems with session handling in taxeditor
Andreas Müller wrote in #note-7:
> A critical issue: In AbstractCdmEditorPartE4 line 182 it is checked if (new) sele...
Andreas Müller

11/27/2022

10:59 PM Revision 20d52c89 (taxeditor): ref #10186 fix incorrect delaySelection handling for multiselect and no active Editor
Andreas Müller
10:54 PM Revision df44f597 (taxeditor): cleanup
Andreas Müller
12:18 AM Revision dad85080 (taxeditor): ref #10186 fix incorrect delaySelection handling for equal previous selection (and remove some debugging)
Andreas Müller

11/25/2022

10:02 AM bug #10191 (Closed): Error message on taxon specimen page for non-atomized specimens
Message is: Uninitialized string offset: -1 in drupal_substr() (line 640 of /var/www/drupal-7-cdm-dataportal/web/incl... Katja Luther
09:59 AM bug #10190 (Closed): Invalid argument supplied for foreach() in order_fieldUnitDtos_by_date_and_type()
This exception appears for
https://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/ecb7a76e-694a-4706-b1ab-...
Katja Luther
12:06 AM Revision ed7192b6 (taxeditor): further rename taxonNameEditor -> taxonEditor (cont.)
Andreas Müller
12:05 AM Revision 92eade32 (taxeditor): cleanup
Andreas Müller
12:04 AM Revision d1e5306c (taxeditor): further rename taxonNameEditor -> taxonEditor
Andreas Müller

11/24/2022

11:08 PM Revision a7d6ad1f (taxeditor): cleanup
Andreas Müller
11:08 PM Revision 9c50b7b6 (taxeditor): ref #10189 split CdmApplicationController into repository and application part in taxeditor print publisher (only make compilable)
Andreas Müller
10:46 PM Revision eef673ec (cdm-vaadin): ref #10189 split CdmApplicationController into repository and application part in vaadin
Andreas Müller
06:20 PM Revision 9d02f251 (taxeditor): cleanup
Andreas Müller
06:19 PM Revision bac73844 (taxeditor): ref #10189 split CdmApplicationController into repository and application part in TaxEditor (cont.)
Andreas Müller
06:16 PM task #10189 (Resolved): Split CdmApplicationController into repository and application part
please review Andreas Müller
06:05 PM task #10189 (Closed): Split CdmApplicationController into repository and application part
The application part is only for local applications supporting transactions etc. while the repository part can be use... Andreas Müller
06:15 PM Revision 94a9209a (cdmlib-apps): ref #10189 split CdmApplicationController into repository and application part in app-import
Andreas Müller
06:13 PM Revision 058a92f1 (taxeditor): ref #10189 split CdmApplicationController into repository and application part in TaxEditor
Andreas Müller
06:06 PM Revision eb224aa5 (cdmlib): ref #10189 split CdmApplicationController into repository and application part in cdmlib
Andreas Müller
04:45 PM Revision 4cf52851 (taxeditor): cleanup
Andreas Müller
02:49 PM Revision 29dea790 (taxeditor): ref #10186 further remove ConversationHolder from TaxEditor code and some cleanup (cont.)
Andreas Müller
02:48 PM Revision 28651d0b (taxeditor): cleanup
Andreas Müller
02:48 PM Revision d02e900a (taxeditor): force usage of remoting everywhere
Andreas Müller
02:18 PM Revision 4c980025 (taxeditor): ref #10186 further remove ConversationHolder from TaxEditor code and some cleanup
Andreas Müller
01:03 PM Revision eb79d959 (taxeditor): rename some eu.*.Abstract*E4 classes
Andreas Müller
12:54 PM Revision 1f40607c (taxeditor): rename AbstractGroupedContainerE4 -> AbstractGroupedContainer and cleanup
Andreas Müller
12:44 PM Revision fff9f5d7 (taxeditor): rename AbstractCdmEditorPartE4 -> AbstractCdmEditorPart
Andreas Müller
12:44 PM Revision 03f01a13 (taxeditor): cleanup and rename createPartObject -> getPartObject
Andreas Müller
11:07 AM bug #10188 (New): Allow moving large subtrees
Currently it is not possible to move large subtrees in the TaxEditors due to memory issues during treeindex updating.... Andreas Müller

11/23/2022

01:11 PM Revision 2794c276 (taxeditor): ref 10138: use setDirty but do not change dirty flag of managedform
Katja Luther
12:35 PM Revision bd1aedf5 (taxeditor): ref 10138: revert changes to update taxon editor after changes in details view
Katja Luther
12:29 PM bug #10186: Problems with session handling in taxeditor
A critical issue: In AbstractCdmEditorPartE4 line 182 it is checked if (new) selection equals the previous selection.... Andreas Müller
09:33 AM Revision f65c4336 (taxeditor): revert changes in code cleaning commit
Katja Luther

11/22/2022

07:12 PM Revision 21d5361f (taxeditor): setFactsVisible and setMediaVisible again
Andreas Müller
07:11 PM Revision 5f709cc6 (taxeditor): cleanup
Andreas Müller
03:14 PM Revision bd122e26 (taxeditor): rename TaxonNameEditor to TaxonEditor and NameViewerE4 to NameViewer
Katja Luther
03:09 PM task #10187 (New): Use only 1 service call to initialize supplemental data
Currently for initializing supplemental data of e.g. a synonym in TaxEditor 7 services calls appear, 1 for each data ... Andreas Müller
01:57 PM Revision b135cc84 (taxeditor): handle default for TaxonEditorInput
Andreas Müller
01:57 PM Revision d7eb304b (taxeditor): cleanup
Andreas Müller
01:00 PM Revision e6469973 (taxeditor): cleanup and fix test
Andreas Müller
12:31 PM Revision 10ee1227 (taxeditor): cleanup
Andreas Müller
12:31 PM Revision 428d32bf (taxeditor): rename TaxonNameEditorTest -> TaxonEditorTest
Andreas Müller
12:25 PM Revision 0e7abe8a (cdmlib): cleanup
Andreas Müller
12:21 PM Revision bd4875e0 (cdmlib): cleanup
Andreas Müller
10:59 AM Revision 2faf3520 (cdmlib): cleanup
Andreas Müller

11/21/2022

03:03 PM Revision b9b6e1f4 (taxeditor): rename TaxonNameEditor and other classes and remove E4 - continue
Katja Luther
03:01 PM Revision c7bc3975 (taxeditor): rename TaxonNameEditor and other classes and remove E4 - continue
Katja Luther
02:54 PM Revision 98ca4627 (taxeditor): rename TaxonNameEditor and other classes and remove E4 - continue
Katja Luther
01:59 PM Revision 9b135851 (taxeditor): rename TaxonNameEditor and other classes and remove E$
Katja Luther
12:27 PM Revision 0a75fd54 (taxeditor): change logger
Katja Luther
11:53 AM Revision 0caafa75 (taxeditor): ref #10186 further remove ConversationHolder and cleanup
Andreas Müller
11:28 AM Revision eab688c3 (taxeditor): ref #10186: code cleaning
Katja Luther

11/18/2022

06:05 PM Revision 25c3d160 (taxeditor): ref #10186: remove conversation holder - continue
Katja Luther
05:59 PM Revision d3cfcce0 (taxeditor): ref #10186: remove datachangeBehaviour classes
Katja Luther
05:56 PM Revision 49d3c2dd (taxeditor): ref #10186: remove conversation holder
Katja Luther
02:22 PM bug #10186 (In Progress): Problems with session handling in taxeditor
Explaining the already cleaned up code:
SetSelection in setFocus of TaxonNameEditorE4 is not necessary and yields to...
Katja Luther
11:27 AM Revision 9d416700 (taxeditor): cleanup
Andreas Müller
11:25 AM Revision 154d4fe7 (taxeditor): ref #10186 remove ConversationHolder from many forms and some more cleanup (cont.)
Andreas Müller
10:57 AM Revision 8180822f (taxeditor): ref #10186 remove ConversationHolder from many forms and some more cleanup
Andreas Müller

11/17/2022

09:31 PM Revision 14b1eb40 (taxeditor): remove unused E4 temp code
Andreas Müller
09:31 PM Revision a0f770fe (taxeditor): cleanup
Andreas Müller
05:48 PM bug #10182: Portal does not show typespecimen for duplicated typedesignation
Katja Luther wrote in #note-2:
> The webservice failed because the derived unit had a occurrence status which had no...
Andreas Müller
03:27 PM bug #10182: Portal does not show typespecimen for duplicated typedesignation
The webservice failed because the derived unit had a occurrence status which had no type. Katja Luther
03:28 PM bug #10185 (Duplicate): Missing OccurrenceStatus Type creates NPE when creating DTO
Katja Luther
11:57 AM bug #10185 (Duplicate): Missing OccurrenceStatus Type creates NPE when creating DTO
If the Occurrence Status of a specimen does not have a type, the creation of the dto yields to a NPE and nothing is s... Katja Luther
02:41 PM Revision fa600854 (taxeditor): ref #10186: setSelection in setFocus is not necessary
Katja Luther
02:34 PM bug #10186 (Closed): Problems with session handling in taxeditor
This ticket should contain everything done/tested to fix the session handling problems in the editor, like unsaved ch... Katja Luther

11/16/2022

01:31 PM Revision fea04d02 (taxeditor): use cached terms also for uuid list
Katja Luther

11/15/2022

09:19 PM bug #5284 (Duplicate): [UML] Replace Scope by DefinedTerm in PolytomousKey UML
This is a duplicate for #9975 as it is automatically implemented there already. Andreas Müller
09:14 PM task #9975 (Feedback): Create new UML diagramms for the CDM
Diagrams currently available at https://cybertaxonomy.org/cdm-uml/v532/ Andreas Müller
07:36 PM task #8840: Display identifiers in the dataportal
This is also an issue for MCL and the MCL taxon id (#10050) Andreas Müller
03:52 PM feature request #10050 (In Progress): Add missing functionality for MCL CDM dataportal
Andreas Müller
01:19 PM Revision 0ed18126 (taxeditor): cleanup
Andreas Müller
11:07 AM bug #9358: OptionalDataException during HTTP invoker call
Looks like this problem does not appear so often anymore. Andreas Müller
11:06 AM bug #8620: Improve pro parte synonym search result for dataportal
Maybe we can fix this in the performance sprint. Andreas Müller

11/14/2022

03:34 PM bug #8381: Closing the details view throws widget is disposed exception
Is this still an open issue? If yes it is probably fast to fix? Andreas Müller

11/11/2022

04:48 PM Revision 15ac03a5 (cdmlib-apps): ref #10048 add source to distributions and handle MCL-number as identifier
Andreas Müller
02:41 PM Revision c9b9c655 (cdmlib-apps): ref #10048 add MCL destination
Andreas Müller
02:40 PM Revision e111b15c (cdmlib-apps): ref #10048 cleanup and rename presenceAbsence terms for MCL
Andreas Müller
02:38 PM Revision c4032e64 (cdmlib-apps): ref #10048 distribution import for MCL
Andreas Müller
02:37 PM Revision d249946f (cdmlib): ref #10048 some term and voc uuids for MCL import and usage of Distribution
Andreas Müller
02:35 PM Revision e360bed5 (cdmlib): ref #10048 make PresenceAbsenceTerm uuids public for MCL import
Andreas Müller
01:41 PM Revision 7e2e67a0 (cdmlib-apps): cleanup
Andreas Müller
01:39 PM Revision adad498c (cdmlib): cleanup
Andreas Müller
01:37 PM Revision db4d3543 (cdmlib): ref #10048 use OrderedTermVocabulary in getNamedAreaLevel
Andreas Müller

11/10/2022

06:21 PM Revision 61ea5c2d (cdmlib-apps): ref #2934 some adaptations for Moose import
Andreas Müller
03:54 PM Revision 8fe0cb9f (cdmlib-apps): cleanup
Andreas Müller
03:50 PM Revision c5ed5599 (cdmlib-apps): ref #10048 exclude name facts for MCL
Andreas Müller
03:49 PM Revision 6fc1d869 (cdmlib-apps): ref #10048 handle differing nomStatusFks for MCL
Andreas Müller
03:48 PM Revision 72296cbb (cdmlib): cleanup
Andreas Müller
03:48 PM Revision e3524064 (cdmlib): ref #10048, ref # 10170 add static method for nom. & orth. cons.
Andreas Müller
03:47 PM Revision 014ae691 (cdmlib): ref #10048 handle differing nomStatusFks for MCL
Andreas Müller
02:59 PM Revision 2ebf0e13 (cdmlib-apps): ref #10048 add MclActivator and normalize users
Andreas Müller
02:57 PM Revision 2517f189 (cdmlib-apps): cleanup
Andreas Müller
01:52 PM task #10183 (Resolved): Import Buxales via Cdm2Cdm
Andreas Müller
01:42 PM task #10183 (Closed): Import Buxales via Cdm2Cdm
From Flora Cuba to new Buxales DB
Open issue:
* ~~UUIDs are still the same as in Flora Cuba which is not correc...
Andreas Müller
01:50 PM Revision ed7e5b0d (cdmlib): ref #10183 deduplicate terms for findByUuidWithoutFlush
Andreas Müller
01:48 PM Revision 35e07b85 (cdmlib): ref #10183 adapt Cdm2CdmImportBase to latest model changes and correct type designation handling
Andreas Müller
01:46 PM Revision ba1622fa (cdmlib): cleanup
Andreas Müller
01:44 PM Revision 316d0e5e (cdmlib-apps): ref #10183 add BuxalesExportActivator
Andreas Müller

11/09/2022

11:40 AM bug #10182: Portal does not show typespecimen for duplicated typedesignation
The webservice to get the specimen_dto of the typespecimen returns false. Katja Luther
11:39 AM bug #10182 (Closed): Portal does not show typespecimen for duplicated typedesignation
mail NadjaK:
wenn ich einen Typus über „Create type duplicate“ dupliziere, wird das im Portal nicht angezeigt.
...
Katja Luther

11/08/2022

10:47 AM bug #10181 (New): Search images do not show thumbnails
Observed for flora of cyprus.
E.g. search for Althenia filiformis shows large images
![](clipboard-202211081039...
Andreas Müller
 

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