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From 12/22/2020 to 01/20/2021

01/20/2021

08:06 PM bug #6164: cyprus: invalid data causing crash in modifier editor
test if this is still an open issue. Andreas Müller
07:55 PM feature request #3502: extensions not yet handled in compose_cdm_specimenOrObservation()
target version is missing! Put on current milestone like other specimen related issues? Andreas Müller
07:49 PM task #3485: object graph returned by REST services can be specified by initstrategy
target version is missing! Is this still an open issue? Andreas Müller
07:48 PM bug #3480: tagged text with square bracket confuses json
target version is missing. I put it to same milestone as related ticket. Please change if this is wrong. Andreas Müller
07:40 PM feature request #3030: Jenkins php jobs: setup for code analysis, mess detection etc..
target version is missing! Is it still an open issue? Andreas Müller
07:37 PM feature request #6016: ICN rules in cdm validation framework implemented
target version is missing! Is it still an open issue? Andreas Müller
07:35 PM feature request #6598: Migrate commands and handlers
target version is missing!
Can we assess in current milestone what still needs to be done to close this ticket. Th...
Andreas Müller
07:30 PM EDIT Platform Etablierung task #9377: Update of other documentation
target version is missing! Andreas Müller
07:27 PM feature request #8182: show blast search result
is this still an open issue? Should it be reviewed? Should open issues be moved to new ticket?
Is there an example...
Andreas Müller
07:25 PM bug #7829 (Closed): Improve deduplication of parsed names and references
This has been finished (with few exceptions) in #9085. Andreas Müller
07:10 PM feature request #6133 (Closed): Improve Rank Webservice
Created follow up #9406 for open issue, close this ticket Andreas Müller
07:09 PM feature request #9406: Open issue for Edaphobase rank web service
put to low priority as edaphobase is currently not active Andreas Müller
07:08 PM feature request #9406 (New): Open issue for Edaphobase rank web service
follow up for #6133
Open issue:
* representations are not mapped to a language
Andreas Müller
06:49 PM task #5085: Aggregate Distributions
This is a duplicate for some other tickets: #5176, #8679, #8677 and maybe someother.
Should be tested on FauEu Data ...
Andreas Müller
06:33 PM bug #7665 (Closed): ConcurrentModificationException when closing Editor
If at all it happens very seldom. We should open a new ticket with a new stacktrace if it happens again. Andreas Müller
06:23 PM bug #1119 (Duplicate): [PARSER] Duplicate inreferences created during parsing are NOT merged when...
This has been fully fixed in #9085 so close this ticket as duplicate Andreas Müller
06:04 PM bug #3737 (Closed): Protected caches for taxa and names behave inconsistent
The first issue is solved. The second was improved, however, it still sometimes works inconsistent meaning that the s... Andreas Müller
06:04 PM bug #9405 (In Progress): Fields set to irrelevant for cache should be set by state only
Andreas Müller
06:02 PM bug #9405 (Closed): Fields set to irrelevant for cache should be set by state only
follow up from #3737
Currently this is not yet the case as they are set during UI update by calling refresh only o...
Andreas Müller
05:52 PM feature request #6965 (Closed): Tropicos Import
open issues copied to #9404, close this Andreas Müller
05:51 PM feature request #9404 (New): Open issues for Tropicos Import
copied from #6965
* Tests genauer
* Progressmonitor
* "Analyse" vor Import
* Klären, welche Funktionen von ...
Andreas Müller
04:25 PM Revision d016b62b (cdmlib): ref 6308: result should be ok, if taxon can be deleted but not the name
Katja Luther
04:16 PM Revision 931ee538 (taxeditor): typo
Katja Luther
03:13 PM bug #7223 (Closed): ReferenceEditor: disable fields depending on the Reference type
Andreas Müller wrote:
> Personal Communication has no DOI neither in the interfaces nor in TaxEditor. If this is ava...
Andreas Kohlbecker
03:12 PM Revision 46f7b66d (cdmlib): ref #7223 proper definition of IPersonalCommunication in ReferencePro...
Andreas Kohlbecker
02:53 PM bug #7764 (Closed): Fix classification and synonym bug in taxon name freetext search
works as expected, see for example the http://caucasusflora.org/ where subtree limitation, classification and `doSyno... Andreas Kohlbecker
02:46 PM bug #7108 (Closed): supress unwanted sourcetypes in handle_annotations_and_sources()
Andreas Müller wrote:
> Works fine now and ticket can be closed.
>
> I only wonder if only a citation micro refer...
Andreas Kohlbecker
02:40 PM feature request #7720 (Closed): use new taxonRelationshipsDTO webservice for all taxon relations
cleanup TODO copied to #9403 and now closing this ticket Andreas Kohlbecker
02:38 PM bug #9403 (Closed): cleanup function cdm_related_taxon() from used paramerters and css class attr...
1.) remove unused parameters:
`$relsign = NULL, $reltype_representation = NULL, $doubtful=false, $doLinkTaxon = FA...
Andreas Kohlbecker
02:11 PM Revision c27b3a19 (cdmlib): ref #9290 castTo method for TypedEntityReference
Andreas Kohlbecker
02:03 PM feature request #7417 (Closed): Make pro parte and partial synonym relationships always visible i...
this is fully implemented and also covered by the tests on the synonymy of *Miconia cubacinerea* in the reference dat... Andreas Kohlbecker
01:53 PM bug #7745 (Closed): Subtree filter for dataportal services
Andreas Kohlbecker
01:51 PM bug #7745: Subtree filter for dataportal services
Andreas Kohlbecker wrote:
> For the polytomous keys the following webservices need to be filtered by the subTree to ...
Andreas Kohlbecker
01:51 PM task #9402 (New): Subtree filter for polytomousKey and polytomousKeyNode services
For the polytomous keys the following webservices need to be filtered by the subTree to avoid unpublished taxa showin... Andreas Kohlbecker
01:49 PM bug #7386 (Closed): TaxonNamePopEditor: com.vaadin.data.Property$ReadOnlyException on saving a ba...
Andreas Kohlbecker
01:44 PM bug #9401 (New): Name bulk editor: focus gets lost when list loading is going on
Allerdings habe ich ein Problem damit den Fokus im Bulkeditor dauerhaft auf einen Namen zu setzten. Solange der Bulke... Andreas Kohlbecker
01:39 PM Revision d7d6bc83 (cdm-vaadin): ref #9290 making TypeDesignationWorkingsetEditorIdSet --> TypeDes...
Andreas Kohlbecker
01:38 PM bug #9290 (Resolved): stop setting Registration.citation as citation for TypeDesignations in all ...
Hi Henning, could you please make some tests in the test-server to make sure the changes are not causing problems wit... Andreas Kohlbecker
01:32 PM Revision 0b71a670 (cdm-vaadin): ref #9290 making TypeDesignationWorkingsetEditorIdSet --> TypeDes...
Andreas Kohlbecker
12:43 PM Revision c63cad99 (cdmlib): fix #9391: fix test
Katja Luther
12:39 PM bug #9373: In specimen details view used within specimen tree editor titleCache field is not enab...
I can't reproduce this. When the titlecache is protected, the field is enabled and the button shows the open lock.
!...
Katja Luther
11:55 AM Revision eb2005b8 (cdmlib): ref 6308: check for namedeletion in taxonbase isDeletable and add war...
Katja Luther
11:54 AM feature request #6308 (Closed): Add configuration dialog for the deletion of synonyms in name editor
Andreas Müller wrote:
> The 2 warnings do not show up anymore so we can close this ticket.
> However, I am a bit as...
Katja Luther
11:34 AM bug #9398 (In Progress): ObjectNotFoundException when removing a synonym that is used as NameInSo...
Katja Luther
11:33 AM bug #9398: ObjectNotFoundException when removing a synonym that is used as NameInSource
I think the problem is that the name used as "name used in source" still have the information to be the name of the d... Katja Luther
11:03 AM Revision 4f7744bd (cdmlib): fix #9391: fix test
Katja Luther
10:46 AM Revision c530ad2e (taxeditor): ref #9393: remove possibility to delete parent in newTaxon wizard
Katja Luther
10:41 AM bug #9393 (Resolved): NPE when removing parent from TaxonNode editor
The newTaxon wizard does not allow deleting the parent taxon anymore. To create a orphan taxon the user should use th... Katja Luther
10:25 AM Revision cc9c04a4 (cdm-vaadin): ref #9290 cleaning up
Andreas Kohlbecker
09:43 AM Revision 91e53109 (cdm-vaadin): ref #9290 SpecimenTypeDesignationEditor now using designation ref...
Andreas Kohlbecker
09:38 AM bug #9391: If named area level does not exist remove the level information
please review Katja Luther
09:38 AM bug #9391 (Resolved): If named area level does not exist remove the level information
Applied in changeset commit:cdmlib|6d7fe5d574d1264196441524f674c24732b248a0. Katja Luther
09:38 AM Revision 6d7fe5d5 (cdmlib): fix #9391: if no level exist remove class name in label with level in...
Katja Luther
08:39 AM task #9400 (New): Check whether it is possible to set rights to reduce the work to descriptive da...
mail NK:
Deshalb schon mal die Frage: Gibt es separate Rechte ausschließlich für Arbeit mit Descriptive Data Sets,...
Katja Luther

01/19/2021

07:18 PM Revision 888558ae (taxeditor): simplify rank handling
Andreas Müller
06:56 PM Revision 68b29e1f (taxeditor): make getCollection method final and remove deprecated annotation
Andreas Müller
06:54 PM Revision 688220c6 (taxeditor): cleanup
Andreas Müller
04:18 PM Revision 508b8f01 (cdm-vaadin): ref #9290 NameTypeDesignationEditor now using designation referen...
Andreas Kohlbecker
04:01 PM feature request #6076 (Closed): Specimen biocase search should work on observations
this ticket was about the filter on preservedSpecimen in the biocase search, now all records can be found. Comparing ... Katja Luther
03:32 PM feature request #7345 (Resolved): [E+M] Common name references selectable in TaxEditor
this seems to be fixed, the preference is available and activate and deactivate the filtering for common name referen... Katja Luther
03:09 PM feature request #7810 (Closed): DB preference to make Specimen editors visible
Changed the title of this ticket because only the editor availability was implemented in 5.4, for the other issues a ... Katja Luther
03:09 PM feature request #9399 (New): DB preference to make all Specimen functionality/menu items invisible
the preference to hide all specimen related parts of the editor already exist (see #7810), but the implementation of ... Katja Luther
02:58 PM bug #9354: Sorting in distribution editor is broken
please review. Katja Luther
02:57 PM bug #9354 (Resolved): Sorting in distribution editor is broken
this is fixed now by sorting the list on server side. The sortMode is a method parameter. Katja Luther
09:08 AM bug #9354: Sorting in distribution editor is broken
Andreas Müller wrote:
> Generally the comparator should work the same way as the taxon navigator compartor. But th...
Katja Luther
02:56 PM feature request #8889 (In Progress): Remaining issues for distribution editor - continue
Katja Luther
02:55 PM Revision 5594bd68 (taxeditor): ref #8889: the dto list is already ordered for distribution editor...
Katja Luther
02:41 PM Revision bed37770 (cdmlib): ref #8889: sort taxonnodes for distribution editor on server side
Katja Luther
01:03 PM Revision b66bc2e5 (taxeditor): cleanup
Andreas Müller
12:47 PM bug #7386: TaxonNamePopEditor: com.vaadin.data.Property$ReadOnlyException on saving a basionym
can be set to closed Wolf-Henning Kusber
12:11 PM task #9300: Name Page: harmonize media specimen lectotype representations
Andreas Müller wrote:
> so should we change status to "in progress" as questions are solved?
the conclusion is on...
Andreas Kohlbecker
11:55 AM task #9300: Name Page: harmonize media specimen lectotype representations
so should we change status to "in progress" as questions are solved? Andreas Müller
11:49 AM task #9300: Name Page: harmonize media specimen lectotype representations
Wolf-Henning Kusber wrote:
> Nein, stimme nicht zu
after an extensive discussion we concluded the following inter...
Andreas Kohlbecker
10:42 AM task #9300: Name Page: harmonize media specimen lectotype representations
Nein, stimme nicht zu Wolf-Henning Kusber

01/18/2021

10:38 PM Revision 780809e8 (taxeditor): remove unused parent
Andreas Müller
10:38 PM Revision bc137806 (taxeditor): cleanup
Andreas Müller
07:11 PM Revision 17337b4f (taxeditor): fix generics compile error
Andreas Müller
05:27 PM Revision 17eaac4f (taxeditor): cleanup
Andreas Müller
05:24 PM Revision 9f1bb997 (taxeditor): ref #9354: improve sorting in distribution editor
Katja Luther
05:21 PM Revision 87855850 (cdmlib): ref #9354: add nodeDto to TaxonDistributionDTO
Katja Luther
04:11 PM Revision ad7201d3 (taxeditor): cleanup and generics for ICdmEntitySessionEnabled
Andreas Müller
03:54 PM bug #9354: Sorting in distribution editor is broken
Andreas Müller wrote:
> There are still open issues as the comparator does not follow the comparator contract and ha...
Katja Luther
09:35 AM bug #9354: Sorting in distribution editor is broken
I put this to critical as it is a requirement the E+M Bratislava team to edit disttribution data for CZ and SK which ... Andreas Müller
03:03 PM Revision 28ead5fc (taxeditor): cleanup
Andreas Müller
02:21 PM bug #9398 (In Progress): ObjectNotFoundException when removing a synonym that is used as NameInSo...
Either this is a problem on the order of operations during save. Or it is a general issue with merge where it could b... Andreas Müller
02:18 PM bug #9397 (Closed): Derivate tree view must show DerivedUnits even if the FieldUnit is missing
see also #7704 for the same problem in the specimen table Andreas Kohlbecker
02:05 PM Revision 26f72855 (cdmlib): fix #9395 DerivedUnit.collectFieldUnits() as DerivedUnit.collectRootU...
Andreas Kohlbecker
01:41 PM bug #9396 (New): nomenclatural status missing in typedesignations shown in synonymy
Example:
http://portal.cybertaxonomy.org/flora-cuba/cdm_dataportal/taxon/64e9f775-79fc-41cf-b154-225e8a4bc7d1
T...
Andreas Kohlbecker
01:08 PM feature request #6308 (Feedback): Add configuration dialog for the deletion of synonyms in name e...
The 2 warnings do not show up anymore so we can close this ticket.
However, I am a bit astonished that no warning ex...
Andreas Müller
12:31 PM Revision 1e863be8 (cdmlib): cleanup
Andreas Müller
12:21 PM bug #9395: DerivedUnit.collectFieldUnits() and findFieldUnitDTOByAssociatedTaxon() and findByAcce...
Hi, for your information:
to solve this ticket I renamed and extended DerivedUnit.collectFieldUnits() as DerivedUn...
Andreas Kohlbecker
12:17 PM bug #9395 (Resolved): DerivedUnit.collectFieldUnits() and findFieldUnitDTOByAssociatedTaxon() and...
Applied in changeset commit:cdmlib|485da8a92ae3a4c4c51e5631561d368de0915206. Andreas Kohlbecker
11:57 AM bug #9395 (Closed): DerivedUnit.collectFieldUnits() and findFieldUnitDTOByAssociatedTaxon() and f...
DerivedUnit.collectFieldUnits() needs to returns also DerivedUnits as root unit which do not have a FieldUnit. This i... Andreas Kohlbecker
12:17 PM Revision 485da8a9 (cdmlib): fix #9395 DerivedUnit.collectFieldUnits() as DerivedUnit.collectRootU...
Andreas Kohlbecker
11:37 AM feature request #7886 (Closed): Divide local preferences to db dependend local preferences
The open issue was moved to new ticket #9394.
This ticket can be closed.
Andreas Müller
11:36 AM bug #9394 (New): Local preferences can not be edited if no database connection exists
All database dependend preferences should be disabled in this case Andreas Müller
11:31 AM bug #7236 (Closed): Make available distribution status a database preference for TaxEditor distri...
This seems to be fixed. Open a new ticket if something does not work yet as expected. Andreas Müller
11:15 AM feature request #4363 (Resolved): Show more informative message for unsupported specimen structur...
Andreas Müller
11:11 AM bug #4362 (Closed): Some File->New dialogs do not work
Andreas Müller
11:10 AM bug #4362: Some File->New dialogs do not work
>Name cache fields behave strange as even with protected title cache they are not completely disabled.
This seems...
Andreas Müller
11:05 AM bug #9393 (In Progress): NPE when removing parent from TaxonNode editor
~~~
last remote method : http://test.e-taxonomy.eu:80/cdmserver/rem_conf_am/remoting/taxonnode.service
last remote ...
Andreas Müller
11:05 AM feature request #9392 (New): File -> new for specimen and taxa should be available again
With fixing #4362 specimen and taxa were removed, this should be reverted.
The creation of empty specimen should n...
Katja Luther
10:50 AM bug #6955 (Closed): NamedAreaSelection Dialog needs to be adapted to filtered getUuidAndTitleCach...
This is fixed. The open issue is moved to a follow up ticket: #9391 Andreas Müller
10:50 AM bug #9391 (Closed): If named area level does not exist remove the level information
from #6955:
in NamedArea selection dialog:
As #7144 is solved now, we should remove the showing of the class name...
Katja Luther
10:45 AM feature request #7121 (Closed): adapt remaining UuidAndTitleCache methods to use filter
As this is too long ago we close the ticket without linking to the revert. Andreas Müller
10:43 AM bug #7124 (Closed): Avoiding multiple repesentation exceptions by removing the conversation from ...
This seems to be fixed. Andreas Müller
10:38 AM feature request #6076 (Feedback): Specimen biocase search should work on observations
Katja Luther
10:37 AM feature request #6076 (Resolved): Specimen biocase search should work on observations
Katja Luther
10:34 AM feature request #6076 (Feedback): Specimen biocase search should work on observations
Andreas Müller
10:26 AM feature request #6315 (Closed): Implement setSecundumForSubtree in TaxEditor
Andreas Müller
10:25 AM feature request #6315: Implement setSecundumForSubtree in TaxEditor
Andreas Müller wrote:
> There is also a lot of space between label "New secundum reference" and the text box for the...
Andreas Müller
10:23 AM bug #9390 (Feedback): Remaining issues for set secundum dialog
follow up from #6315
there is too much space between label "If no reference is chosen ... " and the checkboxes. Al...
Andreas Müller
08:47 AM bug #9245: Creating derived units from existing derived unit is not possible in specimen tree editor
Keep it in 5.18 for check whether it is already fixed. Katja Luther

01/15/2021

04:00 PM bug #9379 (Closed): exclude disabled classifications from advanced taxon search form
Andreas Kohlbecker
03:59 PM bug #9379 (Resolved): exclude disabled classifications from advanced taxon search form
Applied in changeset commit:cdm-dataportal|5f5db6555726b52d86587db4c3834f8130d75011. Andreas Kohlbecker
03:59 PM Revision 5f5db655 (cdm-dataportal): fix #9379 excluding unselected classifications from search fo...
Andreas Kohlbecker
02:00 PM feature request #7599: treeView for specimen data in dataportal
Ahh, ich sehe gerade, dass in #9216 schon die finale Lösung hinterlegt ist. Andreas Kohlbecker
01:58 PM feature request #7599: treeView for specimen data in dataportal
Andreas Kohlbecker wrote:
> [Andreas Müller wrote:]
>
> wenn ich es richtig verstehe bezieht sich das auf die De...
Andreas Kohlbecker
01:34 PM Revision 20b503f3 (cdm-dataportal): ref #7599 showing link for present character data
Andreas Kohlbecker
01:31 PM bug #9386: orthographic variants should not be symmetrical
Hallo,
ich denke mittlerweile, dass wir zwei Beziehungen brauche wie schon von Andreas Müller vorgeschlagen:
>...
Andreas Kohlbecker
01:21 PM bug #9386: orthographic variants should not be symmetrical
[Eckhard wrote]
Hallo,
nach neuerlichem Lesen des At. 61 gebe ich dir recht, Walter: die gültige orthographisch...
Andreas Kohlbecker
12:29 PM bug #9386: orthographic variants should not be symmetrical
Ich möchte nochmal explizit auf die Probleme hinweisen, die sich datenverabeitungsseitig aus symmetrischen Beziehunge... Andreas Müller
12:17 PM bug #9386: orthographic variants should not be symmetrical
Wolf-Henning Kusber wrote:
> What is about data exports? Isn't it maybe more problematic if the relation symetrical ...
Andreas Müller
12:10 PM bug #9386: orthographic variants should not be symmetrical
Andreas Kohlbecker wrote:
> auch wenn diese Beziehung zwischen zwei Namen im Modell als ungerichtet definiert ist, b...
Andreas Müller
12:07 PM bug #9386: orthographic variants should not be symmetrical
Andreas Kohlbecker wrote:
> Ich würde dafür plädieren die Benennung der Relation beizubehalten, sie aber im Modell a...
Andreas Müller
11:54 AM bug #9386: orthographic variants should not be symmetrical
Andreas Kohlbecker wrote:
> auch wenn diese Beziehung zwischen zwei Namen im Modell als ungerichtet definiert ist, b...
Andreas Müller
11:23 AM bug #9386: orthographic variants should not be symmetrical
Das Datum sollte die meisten Fälle korrekt einsammeln. Wie Andreas sagt, sollte eine Richtung erkennbar sein. Ausnahm... Wolf-Henning Kusber
11:00 AM bug #9386: orthographic variants should not be symmetrical
Hallo,
auch wenn diese Beziehung zwischen zwei Namen im Modell als ungerichtet definiert ist, besteht dennoch eige...
Andreas Kohlbecker
10:46 AM bug #9386: orthographic variants should not be symmetrical
What is about data exports? Isn't it maybe more problematic if the relation symetrical in EDIT? Wolf-Henning Kusber
10:36 AM bug #9386: orthographic variants should not be symmetrical
> WGB:
>
> richtig, Art. 61.1 sagt, dass es nur eine gültige („valid“, nicht „correct“) Variante gibt, aber er spr...
Andreas Müller
09:50 AM bug #9386: orthographic variants should not be symmetrical
ERS:
ja, es kann nur eine korrekte orthographische Variante geben, und daher ist die Richtung nicht symmetrisch: s...
Andreas Müller
12:11 PM bug #9257 (Closed): revise filtering in OccurrenceServiceImpl.assembleFieldUnitDTO(FieldUnit fiel...
can be closed as open taks are copied to #9389 Andreas Kohlbecker
12:11 PM task #9389 (Closed): further improvement and revision of derivative filtering by type and Derived...
this is a follow-up ticket of #9257
see the comments in commit:aa52b6f0 for more details.
FieldUnitDTO.java:
...
Andreas Kohlbecker
11:07 AM Revision 4d95ead5 (cdm-dataportal): fixing deprecated use of join()
Andreas Kohlbecker
10:26 AM Revision 69a9dd7b (cdm-dataportal): fixing composition of invalid URLs for specific cases
Andreas Kohlbecker
10:25 AM bug #8874 (Resolved): move taxon is reverted when taxon is edited afterwards
this ticket was solved and assigned to you for review, sorry forgot to set to resolved. Katja Luther
10:12 AM bug #9356 (Resolved): Comparison method violates its general contract for SourceComparator and Ty...
adapted the comparator in cdmlib and removed hotfix workaround, please review. Katja Luther
10:11 AM Revision c018f269 (taxeditor): ref #9356: remove hotfix workaround
Katja Luther
10:00 AM Revision 8e507020 (cdmlib): ref #9356: adapt TypeDesignationComparator
Katja Luther
09:44 AM bug #9365: Reuse taxon does not work in new Taxon dialogue
please review Katja Luther
09:43 AM bug #9365 (Resolved): Reuse taxon does not work in new Taxon dialogue
Applied in changeset commit:taxeditor|de6b6edbe71e3f03039fbc6436ad7edba7651e3b. Katja Luther
09:43 AM Revision de6b6edb (taxeditor): fix #9365: fix reuse taxon in newTaxonNodeWizard
Katja Luther

01/14/2021

03:14 PM Revision c5c25011 (cdmlib): ref #9332 re-organizing source(es) in TypeDesignation init-strategy
Andreas Kohlbecker
03:06 PM Revision 600742ea (cdm-dataportal): whitespace
Andreas Kohlbecker
03:05 PM Revision f4c60bdf (cdm-dataportal): ref #9384 adapting test to modified createShortCitation method
Andreas Kohlbecker
01:27 PM feature request #9388 (New): show media specimen source in all pages
By now the `MediaSpecimen.media.souces.citation` is only shown in the registration page:
Registration page for
...
Andreas Kohlbecker
12:11 PM bug #7699: NPE when searching for specimen in bulk editor
There was the same issue while working with character matrix:
mail NK:
hm, es scheint aber doch noch ein Proble...
Katja Luther
11:55 AM bug #7699: NPE when searching for specimen in bulk editor
This way is would be more concise:
~~~java
boolean isCanceled = false;
while (true){
...
Andreas Kohlbecker
11:41 AM bug #7699: NPE when searching for specimen in bulk editor
Andreas Kohlbecker wrote:
> As far as I am understanding this problem it is the bulk editors which can be saves or c...
Katja Luther
11:43 AM Revision 6ce970f7 (taxeditor): ref #7699: wait for the thread to stop
Katja Luther
11:12 AM bug #7711 (Resolved): Bugs in media gallery
The issues mentioned above are solved except that deleting takes extremely long, I could not reproduce it anymore.
...
Katja Luther
11:07 AM Revision 0291fd25 (taxeditor): fix NPE in TextWithLabelElement
Katja Luther
10:16 AM bug #9386: orthographic variants should not be symmetrical
Wolf-Henning Kusber wrote:
> It is correct that there is only one correct spelling. In PhycoBank, we need to registe...
Andreas Müller
10:12 AM bug #9386: orthographic variants should not be symmetrical
WGB:
richtig, Art. 61.1 sagt, dass es nur eine gültige („valid“, nicht „correct“) Variante gibt, aber er spricht a...
Andreas Müller
10:10 AM Revision 5aa8ceb0 (cdmlib): ref #7711: delete last media in galery should not delete description
Katja Luther
08:50 AM bug #9387 (Closed): LazyInitializationException (LIE) in NameController.doGetTypeDesignationsInHo...
Andreas Kohlbecker
08:49 AM bug #9387 (Resolved): LazyInitializationException (LIE) in NameController.doGetTypeDesignationsIn...
Applied in changeset commit:cdmlib|f836859b0030a90cd789ea4e4fd1d24440293bcb. Andreas Kohlbecker
08:31 AM bug #9387 (Closed): LazyInitializationException (LIE) in NameController.doGetTypeDesignationsInHo...
doGetTypeDesignationsInHomotypicalGroup()GET: /cdmserver/greece_bupleurum_01_with_onthology/name/b0372cc9-cc9e-46c8-a... Andreas Kohlbecker
08:49 AM Revision f836859b (cdmlib): fix #9387 extending init strategy
Andreas Kohlbecker

01/13/2021

06:29 PM bug #9386: orthographic variants should not be symmetrical
It is correct that there is only one correct spelling. In PhycoBank, we need to register the published name "as is" =... Wolf-Henning Kusber
06:12 PM bug #9386 (New): orthographic variants should not be symmetrical
According to the nomenclatural code there is always only 1 valid orthographic variant so the name relationship should... Andreas Müller
05:29 PM task #8455: Show specimen preferredStableURL as external link icon?
Screenshot for long URI in typification:
![](picture429-1.png)
Andreas Müller
05:16 PM task #8455: Show specimen preferredStableURL as external link icon?
Detail screenshot from the Derivate tree view (the derivate path view looks quite the same):
![](picture859-1.pn...
Andreas Kohlbecker
04:26 PM task #8455: Show specimen preferredStableURL as external link icon?
example for ugly linking: http://ws2.cybertaxonomy.org/dataportal/greece_bupleurum_01_with_onthology/?q=cdm_dataporta... Andreas Müller
05:26 PM bug #9384 (Closed): DefaultReferenceCacheStrategy.createShortCitation() working not correctly for...
as we talk about bibliographic references here the ICN (or any other code) is not relevant here. It is the rule I hav... Andreas Müller
04:44 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams wi...
The implementation is correct as far as the the implemented formatting rule for more than two authors is holding true... Andreas Kohlbecker
04:18 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams wi...
The fix was not fully correct as it created teams like Name1, Name2 & al. but there should be always a maximum number... Andreas Müller
04:20 PM Revision 22b89169 (cdmlib): add javadoc comment
Andreas Müller
04:14 PM Revision 619db306 (cdmlib): fix #9384, ref #9279 fixed incorrect implementation of createShortCit...
Andreas Müller
04:12 PM Revision 8b822608 (cdmlib): cleanup
Andreas Müller
02:51 PM Revision 02879fb5 (taxeditor): fix state vocabulary menu parameter
Katja Luther
02:47 PM bug #7711 (In Progress): Bugs in media gallery
Katja Luther
12:08 PM bug #9369 (Resolved): Reference Detail is missing in MediaSpecimen details view
please review Katja Luther
12:07 PM Revision 66e893c0 (taxeditor): published in details more detailed label
Katja Luther
12:07 PM bug #9372 (Resolved): in media details view unprotected title cache is not updated when underlyin...
this ios fixed, please review Katja Luther
12:06 PM Revision 527b4867 (taxeditor): fix update of media details header and add published in details
Katja Luther
11:41 AM bug #9371: Media bulk does not persist data anymore
please review Katja Luther
11:36 AM bug #9371 (Resolved): Media bulk does not persist data anymore
Applied in changeset commit:taxeditor|0ef0103a664888c0e398b9ab5f83b0c170c5a599. Katja Luther
11:36 AM Revision 0ef0103a (taxeditor): fix #9371: fix save in media bulk editor
Katja Luther
09:58 AM task #9385 (New): Simplyfy boundingbox setting for user fixed map clipping
Problem:
The settings in `admin/config/cdm_dataportal/settings/geo` for the **Bounding box** needs to be complian...
Andreas Kohlbecker

01/12/2021

04:57 PM Revision 2a28e5d2 (cdmlib): TypedEntityReference: factory method with option to supress the label...
Andreas Kohlbecker
04:50 PM Revision bf3b398f (cdmlib): fixing inappropriate use of TypedEntityReference for creating tagged ...
Andreas Kohlbecker
04:33 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams wi...
please review
Tests for this method are missing and should be implemented asap. Please could you open a new ticke...
Andreas Kohlbecker
04:32 PM bug #9384 (Resolved): DefaultReferenceCacheStrategy.createShortCitation() working not correctly f...
Applied in changeset commit:cdmlib|854244ff90c5ff67a0b30a3cee7f1d49e7623cc5. Andreas Kohlbecker
04:30 PM bug #9384: DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams wi...

Andreas Kohlbecker
04:29 PM bug #9384 (Closed): DefaultReferenceCacheStrategy.createShortCitation() working not correctly for...
see https://api.phycobank.org/phycobank/registrationDTO.json?identifier=http://phycobank.org/102662
The Team "Mo...
Andreas Kohlbecker
04:32 PM Revision 5abafe6a (cdmlib): fixing NPE in RegistrationDTOController when identifier is not found
Andreas Kohlbecker
04:32 PM Revision 854244ff (cdmlib): fix #9384 fixing author team truncation
Andreas Kohlbecker
03:19 PM bug #9383 (Closed): Adapt apache configuration to modified dataportal registration page URL pattern
Andreas Kohlbecker
02:57 PM bug #9383 (Closed): Adapt apache configuration to modified dataportal registration page URL pattern
the apache configuration of edit-community needs to be adapted to the changes made for #9220 Andreas Kohlbecker
02:42 PM Revision 72a0a6e9 (taxeditor): fix link for webapp war
Katja Luther
12:02 PM bug #7699: NPE when searching for specimen in bulk editor
Andreas Müller wrote:
> AK: Why was the duplicate removed from this ticket in #note-23?
upps sorry this was a mis...
Andreas Müller
12:01 PM bug #7699: NPE when searching for specimen in bulk editor
AK: Why was the duplicate removed from this ticket in #note-23? Andreas Müller
11:55 AM bug #9174: After longer inactivity NPE for cache
Andreas Müller wrote:
> This is maybe the same as #7699
??
Andreas Müller
11:16 AM bug #9382 (Resolved): For nomenclatural source show taxonname in referencing objects view
Katja Luther
11:15 AM bug #9382 (Closed): For nomenclatural source show taxonname in referencing objects view
In referencing objects view the taxon name of a nomenclatural source is not shown, only 'sourced object not available' Katja Luther
09:34 AM feature request #9381 (New): Refresh button for character matrix
After adding new characters the matrix needs to be closed and reopened to get the changes. To optimize the workflow a... Katja Luther

01/11/2021

10:13 PM feature request #9380 (New): It is not possible to show MediaRepresentation(Part) supplemental data
... as they can not be explicitly selected in the details view. This should be possible (e.g. for showing id and uuid) Andreas Müller
05:20 PM bug #8760: Presentation and linking of molecular data in specimen table too unclear
another example: http://caryophyllales.org/cactaceae/cdm_dataportal/taxon/d7bb858b-d8e0-4f9a-8a47-081d1cb740e9
Andreas Kohlbecker
04:15 PM Revision d365bbda (taxeditor): use OrderIndexComparator for distributionEditor
Katja Luther
04:13 PM Revision 2ec77b4a (taxeditor): add compare package
Katja Luther
02:37 PM bug #9379 (Closed): exclude disabled classifications from advanced taxon search form
Classifications which are disabled in the `admin/config/cdm_dataportal/settings` are to be excluded from the advanced... Andreas Kohlbecker
11:53 AM EDIT Platform Etablierung report #9378 (Closed): Meeting EDIT Platform documentation 2021-02-22
WebEx Meeting: https://fu-berlin.webex.com/fu-berlin/j.php?MTID=ma3d5a3cfabd30fbfdccb11e37122a1e4
## Teilnehmer:
...
Andreas Kohlbecker
11:45 AM EDIT Platform Etablierung task #8580 (Closed): Update documentation to latest revision of the Taxeditor
all Taxeditor documentation has been updates in Okt 2019, other activities are subject of #9377 Andreas Kohlbecker
11:44 AM EDIT Platform Etablierung task #9377 (In Progress): Update of other documentation

Documents to check:
* Manual-EDIT-Platform-01-INSTALL.docx **DONE** in #8580
* Manual-EDIT-Platform-02-DEMO.doc...
Andreas Kohlbecker
11:41 AM EDIT Platform Etablierung task #9108 (Closed): Prepare Kurs Borsch
completed Andreas Kohlbecker
11:39 AM EDIT Platform Etablierung task #9376 (New): git checkout of datportal module fails with locally modified files
locally modified files prevent from updating the local git clone to the required version of the dataportal module.
...
Andreas Kohlbecker
11:28 AM Revision 90d80081 (taxeditor): setText in TextWithLabelElement should use trim()
Katja Luther
11:09 AM feature request #9375 (Resolved): Alphabetical order for reference type drop down
Katja Luther
11:09 AM feature request #9375 (Closed): Alphabetical order for reference type drop down
mail AM:
weißt du, ob es einen Grund gibt, dass Section in der RefType Auswahl ganz oben steht, während alle ander...
Katja Luther
11:07 AM Revision e6e3f311 (taxeditor): alphabetical order for refType combo
Katja Luther
09:51 AM bug #9374 (Closed): ClassCastException when switching between media
When switching between media of one taxon following CCE is thrown:
~~~ text
last remote method : http://api.cyber...
Katja Luther

01/10/2021

11:05 AM Revision 0ccecb37 (cdmlib-apps): ref #1447 latest changes to PesiFindIdenticalNamesActivator and...
Andreas Müller
11:02 AM Revision cd156f0a (cdmlib-apps): latest changes to PesiTaxonExport
Andreas Müller
11:01 AM Revision 8b256be0 (cdmlib-apps): ref #6591 adapt PESI import to new original spellings handling
Andreas Müller
10:56 AM Revision c1a8faa1 (cdmlib): ref #6591 adapt PESI import to new original spellings handling
Andreas Müller
10:54 AM Revision b36706c7 (cdmlib): cleanup
Andreas Müller

01/09/2021

04:17 PM Revision 45c2e0b4 (cdmlib-apps): ref #1447 latest changes to PesiCommandLineMerge and PesiMergeOb...
Andreas Müller
04:11 PM Revision 600a00cd (cdmlib): cleanup
Andreas Müller
11:24 AM feature request #5575 (In Progress): DNA Sample requires CacheStrategy
I added a very first version for DNASample cache strategy to avoid the -titleCache not availble- messages Andreas Müller
11:22 AM Revision 26008f31 (cdmlib): ref #5573, ref #7612 adapt MediaSpecimenDefaultCacheStrategy to Occur...
Andreas Müller
11:21 AM Revision a30452ad (cdmlib): ref #5575 add first version of DnaSample cache strategy
Andreas Müller
01:36 AM feature request #7612: CacheStrategy for MediaSpecimens
I implemented now a very basic version of the cache strategy to avoid -titleCache not yet implemented- messages Andreas Müller
01:34 AM feature request #7612 (In Progress): CacheStrategy for MediaSpecimens
To me it is a bit unclear what the suggestion is how the MediaSpecimen cache strategy should be implemented. Andreas Müller
01:30 AM Revision 197a9558 (cdmlib): ref #7612 a first (preliminary) version of MediaSpecimenDefaultCacheS...
Andreas Müller
01:03 AM Revision 4dbcb616 (cdmlib): cleanup and use TermTestBase for model tests
Andreas Müller

01/08/2021

10:30 PM Revision fb6b774e (cdmlib): cleanup
Andreas Müller
07:52 PM bug #9373 (New): In specimen details view used within specimen tree editor titleCache field is no...
instead you first have to click on the protected button which does not change the button but the text field gets enabled Andreas Müller
07:49 PM bug #9371: Media bulk does not persist data anymore
See also related tickets when fixing this. Andreas Müller
07:38 PM bug #9371 (Closed): Media bulk does not persist data anymore
except for create and delete
I tested for title, description, uri, supplemental data = > nothing worked
This is...
Andreas Müller
07:48 PM bug #9372 (Closed): in media details view unprotected title cache is not updated when underlying ...
e.g. when only URI exists usually the title is the file name but changing the URI does not change the title field.
H...
Andreas Müller
07:32 PM feature request #9370 (New): Search in media bulk editor should include search on URI
there are multiple usecases for this Andreas Müller
07:17 PM bug #9369 (Closed): Reference Detail is missing in MediaSpecimen details view
but the detail often is important. In general we could also implement as like a (single) source but there is some mor... Andreas Müller
03:56 PM bug #9368 (New): NullPointerException (NPE) in ManifestComposer.representationPartsToImageContent()
~~~
15:51:31.562 [cichorieae] [qtp990416209-33917] INFO e.e.c.r.c.iiif.ManifestController - doGetMedia() GET: /cich...
Andreas Kohlbecker
02:51 PM task #9132: Update cyprus images to Scaler default API and add thumbnails
Hi Andreas,
ich bin ja gerade dabei #9132 auch für Cichorieae zu machen. Die Links habe ich bereits alle umgestel...
Andreas Müller
12:36 PM task #9132: Update cyprus images to Scaler default API and add thumbnails
Links in the Cichorieae database have all be updated to use the scaler API.
Only open issue is now to reload metad...
Andreas Müller

01/07/2021

01:16 PM bug #9367: E+M shapefile Baltikum subarea borders always visible
This may require to modify the SLD file for the euromed layer Andreas Kohlbecker
01:15 PM bug #9367 (New): E+M shapefile Baltikum subarea borders always visible
gerade fällt mir auf, dass die Arealgrenzen innerhalb des Baltikums seltsamerweise nicht angezeigt werden, wenn es do... Andreas Kohlbecker

01/06/2021

02:27 PM feature request #9114: Handle malformed URIs in user type
In #9111#note-1 AK suggests to also encode fragment and query parts. This has **not** been implemented in the origina... Andreas Müller
02:15 PM feature request #9114: Handle malformed URIs in user type
Katja, can you please check if you can find out what the httpinvoker problem is. I currently can't start the TaxEdito... Andreas Müller
12:08 PM feature request #9114 (In Progress): Handle malformed URIs in user type
I implemented a new class eu.etaxonomy.cdm.common.URI and use this in model but also at other places like import sour... Andreas Müller
02:20 PM feature request #9111 (Resolved): Handle Malformed URIs
I removed the related code again as #9114 is now more or less implemented and URI encoding is now done in cdmlib. Ple... Andreas Müller
02:18 PM Revision 9916da4a (taxeditor): ref #9111, ref #9114 remove TaxEditor specific URI encoding code a...
Andreas Müller
01:07 PM Revision 84aa450d (cdmlib): uncomment RdfViewTest.testNameInformationRdf as it seems to work curr...
Andreas Müller
01:01 PM Revision 9691cba9 (cdmlib): cleanup
Andreas Müller
01:00 PM Revision c22065e1 (cdmlib): ref #9114 fix RdfViewTest
Andreas Müller
11:00 AM Revision 5402f2a6 (cdmlib): cleanup
Andreas Müller
11:00 AM Revision 4ad992ed (cdmlib): ref #9114 further adapt jsonConfigurations and add new constructor to...
Andreas Müller
10:50 AM Revision 3154d43f (taxeditor): ref #9114 further adapt some classes to URI wrapper in taxeditor
Andreas Müller
10:49 AM Revision adb769b4 (taxeditor): cleanup
Andreas Müller
10:18 AM Revision f9c3f295 (cdmlib): ref #9114 adapt json mapping to new URI wrapper
Andreas Müller
10:17 AM Revision 6b33224a (cdmlib): ref #9114 adapt javadoc for new URI wrapper user type
Andreas Müller
10:17 AM Revision 7ab5b913 (cdmlib): cleanup
Andreas Müller
01:35 AM Revision 4d87641f (cdmlib): ref #9114 add toFile() to URI to wrapper
Andreas Müller
01:30 AM Revision 5acb8103 (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor (cont.)
Andreas Müller
01:29 AM Revision 2ab21f97 (taxeditor): cleanup
Andreas Müller

01/05/2021

12:34 AM Revision 7b06bd8f (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor (cont.)
Andreas Müller
12:33 AM Revision 53e60781 (taxeditor): cleanup
Andreas Müller
09:49 PM Revision 15c5de38 (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor (cont.)
Andreas Müller
09:49 PM Revision 00b46185 (taxeditor): cleanup
Andreas Müller
09:37 PM Revision 5dfe9f9b (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor (cont.)
Andreas Müller
09:27 PM Revision 38556872 (taxeditor): cleanup
Andreas Müller
09:26 PM Revision f5a55599 (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor (cont.)
Andreas Müller
09:07 PM Revision 5b2e9e6b (cdmlib): ref #9114 add compareTo to URI wrapper
Andreas Müller
09:02 PM Revision 96378f2b (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor (cont.)
Andreas Müller
09:02 PM Revision 66eb9f49 (taxeditor): cleanup
Andreas Müller
08:34 PM Revision c7a6e70f (taxeditor): cleanup
Andreas Müller
08:34 PM Revision bf3cb991 (taxeditor): ref #9114 adapt some classes with URI to wrapper in taxeditor
Andreas Müller
08:16 PM Revision dd94c99b (cdmlib-apps): ref #9114 adapt URI to wrapper in cdmlib-app (cont.)
Andreas Müller
08:13 PM Revision 7cc5a1d7 (cdm-vaadin): cleanup
Andreas Müller
08:13 PM Revision 4cd4de2d (cdm-vaadin): ref #9114 adapt URIs to URI wrapper in vaadin
Andreas Müller
08:08 PM Revision 999006a7 (cdmlib): ref #9114 preliminary ignore RdfViewTest
Andreas Müller
08:07 PM Revision f588e53b (cdmlib): cleanup
Andreas Müller
08:05 PM Revision de8249cf (cdmlib): ref #9114 add URI Wrapper and replace all java.net.URI occurrences by...
Andreas Müller
07:45 PM Revision 20a31445 (cdmlib-apps): Adapt CentaureaCloneActivator to moved clone method
Andreas Müller
07:45 PM Revision 26790e9b (cdmlib-apps): ref #9114 adapt URI to wrapper in cdmlib-app
Andreas Müller
07:23 PM Revision b920f5c2 (cdmlib-apps): cleanup
Andreas Müller
05:45 PM Revision 2720ea2c (cdmlib): cleanup
Andreas Müller

01/04/2021

07:38 PM Revision 5da100f1 (cdmlib): ref #9366 fix test in TypeDesignationSetManagerTest
Andreas Müller
07:17 PM bug #9366: Specimen type designation with specimen having only collection name but not collection...
Please review Andreas Müller
07:14 PM bug #9366 (Resolved): Specimen type designation with specimen having only collection name but not...
Applied in changeset commit:cdmlib|99d3463856a840dd42c0532791b67b299b7b7fed. Andreas Müller
07:08 PM bug #9366 (Closed): Specimen type designation with specimen having only collection name but not c...
e.g. Scorzonera kurtii Yıld. in Ot Sist. Bot. Dergisi 18(2): 15. 2012 in Cichorieae DB
The holotype collection inf...
Andreas Müller
07:14 PM Revision 99d34638 (cdmlib): fix #9366 add collection name to specimen titleCache if collection co...
Andreas Müller
07:13 PM Revision 960711fc (cdmlib): cleanup
Andreas Müller

12/22/2020

09:09 PM bug #9365 (Closed): Reuse taxon does not work in new Taxon dialogue
partly copied from #5114.
If reuse taxon is selected still a new taxon is created.
Also the secundum field shou...
Andreas Müller
08:52 PM feature request #4896 (Closed): Bulkeditor: deduplication of objects of different type
Generally this works. Open issue is handled in #9361 Andreas Müller
08:37 PM task #9364 (In Progress): Cleanup authors with multiple & and protected names and teams
Andreas Müller
07:29 PM task #9364: Cleanup authors with multiple & and protected names and teams
Protected Teams(nomenclaturalTitle):
AlgaTerra: >14000
Cichorieae: 8487
Cuba: 14
Campanula: 1171
Caryo_amarant...
Andreas Müller
03:56 PM task #9364: Cleanup authors with multiple & and protected names and teams
Protected Names (still without fulltitlecache and authorshipcache):
Bromeliaceae: 584
Cichorieae: 476
Cuba: 567
...
Andreas Müller
03:17 PM task #9364 (In Progress): Cleanup authors with multiple & and protected names and teams
(high priority only to first issue as it is related to #2200)
In context of #2200 I already checked names with >1 ...
Andreas Müller
08:16 PM feature request #2200 (Closed): Handle multiple authors for names correctly when caching
This can be closed as it works now as expected. Open data issues are handled in #9364
The only directly related is...
Andreas Müller
10:51 AM Revision dc310f85 (cdmlib): ref #4770, ref #4908, ref #5163 remove commented line as it seems to ...
Andreas Müller
10:10 AM Revision f8fa7762 (cdmlib): ref #4770, ref #4908, ref #5163 try to remove explicit setting of pro...
Andreas Müller
09:59 AM bug #5163 (Closed): Converting persons to team members may result in "-empty team-"
The "empty team" issue has been solved. The handling of team members has been moved to follow up ticket #9363 as it i... Andreas Müller
09:56 AM feature request #9363 (New): Allow to parse the new team when converting person to team
copied from #5163
When converting a person to a team does not get team members by default. We could add a configur...
Andreas Müller
09:48 AM Revision 6057b354 (cdmlib): ref #4770, ref #4908, ref #5163 some finetuning on convertPerson2Team
Andreas Müller

12/21/2020

12:14 AM bug #2578 (Closed): Improve "move synonym"
Now we always move the full homotypical group to the other taxon, so this is fixed.
The check that the synonym is ...
Andreas Müller
12:07 AM Revision 304fcfc8 (cdmlib): ref #4770, ref #4908, ref #5163 assert that team has protected nomenc...
Andreas Müller
 

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