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From 07/20/2019 to 08/18/2019

08/16/2019

10:36 PM bug #8385: Open issues in DB preferences
Restore button does not yet work for Distribution Editor status and area selection preferences Andreas Müller
10:33 PM bug #8385: Open issues in DB preferences
Distribution editor status selection: changes are not visible in Preferences view after reopening the preferences vie... Andreas Müller
10:27 PM bug #8385: Open issues in DB preferences
name.nomenclaturalStatus can not be removed by Reset Default Andreas Müller
10:25 PM bug #8385: Open issues in DB preferences
some preferences are not deleted for NameDetailsView => deselect all and reopen preferences => 3 prefs stay selected Andreas Müller
10:21 PM bug #8385: Open issues in DB preferences
ABCD import is now implemented on both sides, but "allow override" does not yet exist for "ABCD import provider" Andreas Müller
10:19 PM bug #8385: Open issues in DB preferences
Andreas Müller wrote:
> When opening Peferences - Distribution Editor for the first time the drop downs for some fie...
Andreas Müller
10:12 PM bug #8385: Open issues in DB preferences
>Name details view can not be set to "default" (always chooses enabled after reopening)
Now it always sets it back...
Andreas Müller
10:09 PM bug #8385 (Feedback): Open issues in DB preferences
When opening Peferences - Distribution Editor for the first time the drop downs for some fields were completely empty... Andreas Müller
09:55 PM feature request #3472: Update name in source data when changing an accepted taxon into a synonym
Andreas Müller wrote:
> Please open a new ticket for the final implementation with a new wizard including the questi...
Andreas Müller
09:51 PM feature request #3472: Update name in source data when changing an accepted taxon into a synonym
The labels of the 2 menus should be equal except for the addition about the Name in Source. Is there a reason why you... Andreas Müller
09:44 PM feature request #3472: Update name in source data when changing an accepted taxon into a synonym
Please open a new ticket for the final implementation with a new wizard including the question if the name in sources... Andreas Müller
09:38 PM feature request #3472: Update name in source data when changing an accepted taxon into a synonym
The method with setting the name should be moved down in menu Andreas Müller
09:37 PM feature request #3472 (Feedback): Update name in source data when changing an accepted taxon into...
Currently both methods do end in an unexpected state. After running the operation the old taxon is dirty (and unsaved... Andreas Müller
09:40 AM feature request #3472 (Resolved): Update name in source data when changing an accepted taxon into...
this is implemented now.
The setting of the name in source is configurable, but in editor a new wizard would be ne...
Katja Luther
09:24 PM bug #8422 (Closed): Make PolytomousKeyGenerator work (correctly)
I close this ticket as there is a follow up ticket. Andreas Müller
09:22 PM feature request #8299 (Feedback): add typification column to scientific name and homotypical grou...
Testing is time consuming for me. Please ask Walter if it is as expected. Andreas Müller
09:20 PM feature request #8334 (Closed): Move sources for type designations to details view
Andreas Müller
09:17 PM bug #8444 (Closed): Show warning if misapplied names / pro parte synonyms are used more then once
Hmm, now the warning is also shown if the misapplication is referenced e.g. by an identification key which is not nec... Andreas Müller
09:05 PM feature request #8447: Adapt setPublishForSubtree to new parameters for pro parte, misapplication...
"Pro Parte Synonyme" as pro parte is latin and usually in small letters. However, I don't know if it is maybe better ... Andreas Müller
09:01 PM feature request #8447: Adapt setPublishForSubtree to new parameters for pro parte, misapplication...
I think we may move synonyms below taxa as they are the second biggest group. Misapplications and pro parte synonyms ... Andreas Müller
08:59 PM feature request #8447: Adapt setPublishForSubtree to new parameters for pro parte, misapplication...
Hybrids are not a set of independent taxa but more a filter on each group. So we should maybe move it down (directly ... Andreas Müller
08:57 PM feature request #8447 (Feedback): Adapt setPublishForSubtree to new parameters for pro parte, mis...
If only Misapplications and/or pro parte synonyms are selected the finish button is not enabled but should (at least ... Andreas Müller
08:43 PM feature request #8282: Implement placementDoubtful in TaxEditor
Also we should add the doubtful flag to the "Set flags" method in the taxon navigator right click menu. Andreas Müller
12:24 PM feature request #8282 (Feedback): Implement placementDoubtful in TaxEditor
The new field should be close to the taxon node information as it is from taxon node. Currently it is in the middle o... Andreas Müller
03:22 PM feature request #8477 (New): Implement support for TermCollection.isFlat in TaxEditor
Since #6794 it is possible to distinguish term collections which include duplicates (e.g. structure trees which inclu... Andreas Müller
03:09 PM feature request #8476 (New): Implement support for TermCollection.isFlat in TaxEditor
Often term collections are meant to be a flat list or set without hierarchical dependencies. For these collections th... Andreas Müller
03:08 PM feature request #8475 (New): Adapt applicable state detail view elements to FeatureState
Patrick Plitzner
02:58 PM bug #8465: Term nodes order in term trees is ignored in term tree editor
In general the ordering seems to work now. Andreas Müller
02:56 PM bug #8465 (Feedback): Term nodes order in term trees is ignored in term tree editor
As Term nodes should be not always ordered anymore (TermCollection.orderRelevant flag) we could implement this alread... Andreas Müller
02:45 PM feature request #8474 (New): Make TermCollection.orderRelevant usable for TermTrees

Dazu müsste es:
1. editierbar sein
2. Der TermTree müsste unterschiedlich sortiert angezeigt werden, je nach Zu...
Andreas Müller
01:22 PM bug #8473 (New): Migrate from GrantedAuthoritiesImpl to CdmAuthority and Role
First of all the handling of authorities needs to be migrated and tested to AuthorityBase (by AK). Once this is done ... Andreas Müller
01:14 PM bug #4884 (Closed): Update Reference_AUD.refType to allow NULL
I guess this works. Andreas Müller
12:41 PM feature request #8472 (New): Transmission engine for distribution aggregation needs to be adapted...
Currently it uses marker type "Computed" to mark the descriptions.
... also needs update script for existing descr...
Andreas Müller
12:38 PM feature request #7957: Add types for taxon description (as EnumSet)
This has been implemented now as an EnumSet for better performance.
Please review.
Andreas Müller
10:38 AM feature request #7957 (Resolved): Add types for taxon description (as EnumSet)
Applied in changeset commit:cdmlib|1962891319edeb12380aa69994467f674a96ce96. Andreas Müller
12:35 PM feature request #8471 (New): Computed descriptions should be disabled in TaxEditor
Taxon descriptions being computed (DescriptionBase.types contains COMPUTED or AGGREGATED) should be disabled for edit... Andreas Müller
12:16 PM feature request #8398: Add nomenclatural code edition to ruleConsidered
As this was your (phycobank) requirement I give it to you for review. Andreas Müller
12:15 PM feature request #8410: Add nomenclatural code edition to ruleConsidered in TaxEditor
Maybe we can do this in 5.10 latest so it is close to the model change.
I think we should add it to configuration ...
Andreas Müller
12:12 PM feature request #8404 (Closed): Add update step list within updaters
Seems to work as expected and is very nice. Andreas Müller
12:11 PM feature request #8442 (Closed): Add fields to handle external terms to DefinedTermBase or TermBase
So I close this ticket. Andreas Müller
12:10 PM feature request #8454: Only allow certain patterns as username and groupname
This should be fixed. Who ever wants please review. I tested creating a new user and a group in TaxEditor. For both w... Andreas Müller
12:04 PM feature request #8470 (New): Handle username constraints in user and group editing
Since #8454 a regex exist for usernames and groupnames.
For new usernames and groups the TaxEditor should validat...
Andreas Müller
11:47 AM feature request #8441: Add FeatureState class
Please review.
Maybe there are issues with orphan removal handling.
Andreas Müller
11:45 AM feature request #8441 (Resolved): Add FeatureState class
This is implemented, old implementation still exists in parallel. Should be removed with next update script.
SDD I...
Andreas Müller
11:41 AM feature request #8469 (New): Open PolytomousKeyGenerator issues
* adapt dependency handling to new FeatureState handling, in general improve the handling of dependencies, maybe work... Andreas Müller
11:35 AM task #8468 (New): Remove old InapplicableIf tables
Andreas Müller

08/15/2019

04:09 PM feature request #7597 (Closed): Aggregate and persist descriptions on taxon level
Closing this feature. No review needed as this is still experimental. Follow up ticket #8467 Patrick Plitzner
04:08 PM feature request #8467 (New): Save a "snapshot" of the SpecimenDescriptions used for aggregation
When aggregating SpecimenDescriptions to a TaxonDescriptions the SDs used should be cloned and associated as sources ... Patrick Plitzner
03:57 PM feature request #8464: Make AuthorityBases unique
This seems to be more difficult then I thought.
In general hibernate allows the ,uniqueConstraints=@UniqueConstra...
Andreas Müller
02:59 PM feature request #8441 (In Progress): Add FeatureState class
Andreas Müller
02:21 PM bug #8465 (Resolved): Term nodes order in term trees is ignored in term tree editor
Applied in changeset commit:taxeditor|74a9e9d7da34b3e2d6a895a7b091364125c6f648. Patrick Plitzner
12:19 PM bug #8465: Term nodes order in term trees is ignored in term tree editor
So, if the flag is switched on, the tree should be ordered by tree order, otherwise alphabetically (or by any other c... Andreas Müller
12:06 PM bug #8465: Term nodes order in term trees is ignored in term tree editor
Note: The new TermCollection base class has a flag now called "orderRelevant". This should in future decide if the or... Andreas Müller
10:32 AM bug #8465 (Feedback): Term nodes order in term trees is ignored in term tree editor
ich hatte gerade einen neuen Feature Term "Chemophenetics" für den Cichorieae Feature Tree geschaffen , den wollte ic... Patrick Plitzner
01:52 PM task #8466 (New): Delete FeatureTree tables
FeatureTree has been moved to TermCollection. The old tables have not yet been deleted to have the chance to find pos... Andreas Müller
12:39 PM feature request #8442: Add fields to handle external terms to DefinedTermBase or TermBase
Andreas Müller wrote:
> This should be fixed. Also added new field "importMethod" and extracted all data to an exter...
Patrick Plitzner
09:15 AM feature request #8334 (Resolved): Move sources for type designations to details view
Patrick Plitzner

08/14/2019

11:45 AM feature request #7957 (In Progress): Add types for taxon description (as EnumSet)
Patrick Plitzner
10:59 AM bug #7099: Make CdmAuthority a persistable class
forgot to implement uniqueness. Moved to #8464 Andreas Müller
10:41 AM bug #7099 (Resolved): Make CdmAuthority a persistable class
This is implemented for now. Old GrantedAuthorities still exist and are in use but we could easily switch to new ones... Andreas Müller
10:56 AM feature request #8464 (New): Make AuthorityBases unique
The old GrantedAuthorityImpl.authority was unique and NotNull. This was forgotten to implement when implementing CdmA... Andreas Müller
10:51 AM feature request #8442 (Resolved): Add fields to handle external terms to DefinedTermBase or TermBase
This should be fixed. Also added new field "importMethod" and extracted all data to an external embeddable class "Ext... Andreas Müller
10:48 AM feature request #3972 (Closed): Strictly validate username to not null and not empty
This should be fixed by fixing #8454 Andreas Müller
10:47 AM feature request #8454 (Resolved): Only allow certain patterns as username and groupname
This should be solved now and seems to work. Still needs testing in TaxEditor and maybe other surroundings. Andreas Müller
10:45 AM bug #8429 (Resolved): Rename DeterminationEvent_Reference.setOfReferences_id
This is fixed now by renaming the parameter in model from setOfReferences to references.
Making it a set of sourc...
Andreas Müller
10:45 AM feature request #8463 (New): Make DeterminationEvent.references sources
Currently the link to Reference but they should link to Source. DeterminationEvent should probably become a Sourceabl... Andreas Müller

08/13/2019

12:02 PM bug #8462 (New): NoSuchElementException accessing Optional<RegistrationDTO> in RegistrationWorkin...
Reported by Henning on 04.08.19 19:17
**Fehler in PhycoBank, 102010, Treptacantha ballesterosii**
Beim Specie...
Andreas Kohlbecker
11:48 AM feature request #8461 (New): Change term URI of TDWG Term to identifier in additivity ontology
This should be done in bulk with a script Patrick Plitzner
11:20 AM feature request #8135 (Closed): Implement verbatim type information in TaxEditor
closing ticket -> translation will be handled in #8459 Patrick Plitzner
11:07 AM feature request #8460 (New): Show examples in text field
Some text field have labels that are not intuitive if you are not familiar with the EDIT platform. Having some inform... Patrick Plitzner
11:01 AM feature request #8459 (New): i18n for taxeditor details view
Patrick Plitzner

08/12/2019

11:41 PM task #8458: document FieldUnitDTOOccurrenceServiceImpl.findFieldUnitDTO()
As this has been worked on recently we should do it soon. Andreas Müller
05:39 PM task #8458 (New): document FieldUnitDTOOccurrenceServiceImpl.findFieldUnitDTO()
FieldUnitDTOOccurrenceServiceImpl.findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits, H... Andreas Kohlbecker
11:36 PM task #8456: FieldUnitDTO: remove newInstanceMethod
Passing this ticket to Katja or Patrick as I never worked on/with this class.
Note: syntax of the method name is a...
Andreas Müller
05:31 PM task #8456 (New): FieldUnitDTO: remove newInstanceMethod
copied from #8414
FieldUnitDTO providing a newInstance method. This has to be removed:
~~~
/**
* @pa...
Andreas Kohlbecker
05:44 PM bug #8448 (Closed): Maps settings > Bounding box inconsistent
works Andreas Kohlbecker
05:43 PM task #8414 (Closed): occurrence controller code cleaning and harmonization
all remaining tasks copied to new tickets Andreas Kohlbecker
05:36 PM task #8457 (Duplicate): FieldUnitDTO: remove taxonRelatedDerivedUnits
duplicates #8425 Andreas Kohlbecker
05:33 PM task #8457 (Duplicate): FieldUnitDTO: remove taxonRelatedDerivedUnits
copied from #8414
FieldUnitDTO.taxonRelatedDerivedUnits is an obsolete remain from an older implementation an ne...
Andreas Kohlbecker
05:08 PM task #8166 (Closed): Adapt dataportal to term structure changes
profile settings are working in the above test portals (palmweb has not been tested, since there is no cdm test insta... Andreas Kohlbecker
04:47 PM bug #8440 (Closed): specimen accession numbers link to specimen page
Wolf-Henning Kusber wrote:
>
> Warning in Test portal
> Notice: Array to string conversion in theme_item_list(...
Andreas Kohlbecker
04:46 PM task #8455 (New): Show specimen preferredStableURL as external link icon?
copied from #8440 , needs discussion. Andreas Kohlbecker
04:27 PM task #8449 (Closed): improve layout of registration page to clearly show the nomencaltural act
Andreas Kohlbecker
04:26 PM task #8436 (Closed): featureTree/* services should filter the termTrees by the TermType Feature
Andreas Kohlbecker
01:38 PM task #8406 (Feedback): specimens and occurrence code cleaning and harmonization
thank you for fixing this.
there are two commented code parts in this method:
~~~php
// $specimen_t...
Andreas Kohlbecker
11:27 AM task #8406: specimens and occurrence code cleaning and harmonization
the view for the search for the genetic accession number did not work anymore. I fixed it. Please have a look. Katja Luther
12:34 PM feature request #8411: base path for export/import path selection
the wizard shows the expanded view of the file system to the last selected diectory. So the last selected directory i... Katja Luther
12:25 PM bug #8446 (Closed): Allow setPublish for subtree to filter for hybrids
seems to work as expected Katja Luther
12:06 PM task #8437 (Resolved): ITermTreeService provides a list method which supports filtering by TermT...
Agreed ... and implemented in the way you pointed out. Andreas Kohlbecker
10:49 AM feature request #8447 (Resolved): Adapt setPublishForSubtree to new parameters for pro parte, mis...
please review Katja Luther

08/09/2019

02:36 PM bug #8444 (Resolved): Show warning if misapplied names / pro parte synonyms are used more then once
So I change ticket title for documentation Andreas Müller
11:59 AM bug #8444: Show warning if misapplied names / pro parte synonyms are used more then once
now the warning is implemented as well. Katja Luther
11:59 AM bug #8444 (Worksforme): Show warning if misapplied names / pro parte synonyms are used more then ...
ahh, yes, sorry, I didn't expect the taxon details to be in a subsection. But this makes sense. We can close this tic... Andreas Müller
11:19 AM bug #8444: Show warning if misapplied names / pro parte synonyms are used more then once
the publish flag is already implemented (maybe the taxon details are collapsed?).
Katja Luther
12:31 PM feature request #8282 (Resolved): Implement placementDoubtful in TaxEditor
this is implemented now, please review. Katja Luther
12:17 PM feature request #8282 (In Progress): Implement placementDoubtful in TaxEditor
Katja Luther
12:13 PM bug #7099 (In Progress): Make CdmAuthority a persistable class
Andreas Müller
10:36 AM feature request #8299: add typification column to scientific name and homotypical group in cdm light
please review Katja Luther
10:16 AM feature request #8454 (In Progress): Only allow certain patterns as username and groupname
Andreas Müller
09:20 AM feature request #8454 (Resolved): Only allow certain patterns as username and groupname
... to avoid unwanted characters like ;,ö*... Also avoid unvisible characters, whitespaces and linebrakes this way.
...
Andreas Müller

08/08/2019

03:53 PM bug #8430 (Closed): maps zoom to wrong bbox with some layers
Seems to work correctly. I could not find a non-working portal. Also checked some production portals as this was rele... Andreas Müller
03:42 PM feature request #8135 (Feedback): Implement verbatim type information in TaxEditor
Works as expected. Minor issue: translation for button is missing. Can be closed afterwards. Andreas Müller
03:39 PM feature request #8334 (Feedback): Move sources for type designations to details view
Not designated (for SpecimenTypeDesignation) shows up below the sources, but should be above. Sources should be on bo... Andreas Müller
02:26 PM bug #8446: Allow setPublish for subtree to filter for hybrids
Kajta, can you please review functionality once implemented in TaxEditor? Andreas Müller
02:22 PM bug #8446 (Resolved): Allow setPublish for subtree to filter for hybrids
Applied in changeset commit:cdmlib|c44fd9bd6420a032ab1e04c3b92ee4c20f2aac93. Andreas Müller
01:42 PM task #8449: improve layout of registration page to clearly show the nomencaltural act
The layout is fully satisfying (for new names/types and types)
Order also checked for example for a type only:
...
Wolf-Henning Kusber
10:24 AM feature request #8453 (New): Improve performance of DescriptiveDataSet
A DescriptiveDataSet stores taxon and specimen descriptions and a set of taxon nodes. While taxon descriptions are di... Patrick Plitzner
09:38 AM bug #8440: specimen accession numbers link to specimen page
Tested for Registration page, name page, and specimen page.
Example: Gomphonella acsiae
Links are working.
W...
Wolf-Henning Kusber
09:22 AM task #8424: evaluate publish flags in the full derivative path
As far as I know the SpecimenOrObservation publish flag is not evaluated by webservices at all, yet (or only in very ... Andreas Müller
09:14 AM feature request #8452 (New): [DISCUSS] Should taxa hava an explicit taxon description for specimen?
Maybe it would be helpful to separate taxon descriptions with specimens and those with other description elements.
...
Patrick Plitzner
09:07 AM feature request #8451 (New): Link specimen to taxon via Drag and Drop
It would be a nice feature to be able to link a specimen to a taxon via drag&drop. This could be done from the specim... Patrick Plitzner
08:36 AM feature request #7589 (Closed): Performance, UX and stability patches for CharacterMatrix
Patrick Plitzner
08:36 AM feature request #7589: Performance, UX and stability patches for CharacterMatrix
Closing this ticket to avoid getting to big -> Opening new ticket with specific UX issues -> #8450 Patrick Plitzner
08:35 AM feature request #8450 (New): Character matrix UX
**Details View für Einzelwerte in Matrix**
wenn ich in der Matrix den Details View verwende (was sicher selten der F...
Patrick Plitzner

08/07/2019

10:00 PM task #8449 (Resolved): improve layout of registration page to clearly show the nomencaltural act
please review Andreas Kohlbecker
09:44 PM task #8449 (Closed): improve layout of registration page to clearly show the nomencaltural act
As discussed with Henning on Friday 2nd of August 2019, we decided for the following solution:
* the nomenclatural...
Andreas Kohlbecker
04:54 PM feature request #8403 (Rejected): name page: show types specimens as expandable derivate tree
Andreas Kohlbecker
04:54 PM feature request #8403 (Closed): name page: show types specimens as expandable derivate tree
Andreas Kohlbecker wrote:
> code need to be cleaned up
done!
Andreas Kohlbecker
04:50 PM bug #8440 (Resolved): specimen accession numbers link to specimen page
please review Andreas Kohlbecker
03:52 PM bug #8448 (Resolved): Maps settings > Bounding box inconsistent
Andreas Kohlbecker
03:37 PM bug #8448 (Closed): Maps settings > Bounding box inconsistent
according to the settings documentation the *Bounding box* needs to be entered in degree.
After fixing #8430 using...
Andreas Kohlbecker
01:44 PM feature request #8447 (Feedback): Adapt setPublishForSubtree to new parameters for pro parte, mis...
Also have in mind that the includeSharedTaxa parameter is valid for accepted taxa, misapplications and pro parte syno... Andreas Müller
01:42 PM bug #8446 (Closed): Allow setPublish for subtree to filter for hybrids
In E+M we do not want to set the publish flag to true for hybrids so we need a filter to do so. Alternatively we shou... Andreas Müller
01:39 PM feature request #7450 (Resolved): Allow setPublish for subtree to include misapplied names and pr...
Applied in changeset commit:cdmlib|5fb16579cd1fbce2bfa19f12bebc0d4711b23b90. Andreas Müller

08/05/2019

02:01 PM bug #8444 (Closed): Show warning if misapplied names / pro parte synonyms are used more then once
... please also consider a "is used more then once" check for such relations Andreas Müller
12:42 PM bug #8443: a user with only rights on a subtree can edit taxa and names of another subtree
is this only an UI issue or is it also a cdmlib-security issue? Andreas Müller
12:14 PM bug #8443 (New): a user with only rights on a subtree can edit taxa and names of another subtree
the user with rights on a subtree is able to edit taxa outside the defined subtree. The only limitation is creation a... Katja Luther
10:58 AM task #8435: Reduce logging amount of exports and other long running tasks
Katja, can you work on this? Andreas Müller
10:55 AM task #8437: ITermTreeService provides a list method which supports filtering by TermTree.termType,
Andreas Kohlbecker wrote:
> Andreas Müller wrote:
> > Have you tested with termType = Character which is a subtype ...
Andreas Müller
10:37 AM task #8437: ITermTreeService provides a list method which supports filtering by TermTree.termType,
Andreas Müller wrote:
> Have you tested with termType = Character which is a subtype for Feature. I don't think the ...
Andreas Kohlbecker

08/02/2019

08:39 PM feature request #8442 (Closed): Add fields to handle external terms to DefinedTermBase or TermBase
Similar to those created for Reference (#6663).
The fields are
* last retrieved
* externalId
* externalLink
...
Andreas Müller
08:25 PM feature request #8441 (Resolved): Add FeatureState class
... for inapplicableIf and onlyApplicableIf states and add/change the relationships to TermNode Andreas Müller
08:22 PM bug #8429 (In Progress): Rename DeterminationEvent_Reference.setOfReferences_id
For now we do the column renaming with a model change.
DeterminationEvent_Reference.setOfReferences_id = reference...
Andreas Müller
05:53 PM feature request #8403 (In Progress): name page: show types specimens as expandable derivate tree
code need to be cleaned up Andreas Kohlbecker
05:52 PM feature request #8403 (Rejected): name page: show types specimens as expandable derivate tree
This feature request has been rejected in favor of #8440 Andreas Kohlbecker
05:51 PM bug #8440 (Closed): specimen accession numbers link to specimen page
The specimen accession numbers, aka specimen labels, should be clickable links to the specimen page.
This is neede...
Andreas Kohlbecker
05:29 PM task #8437: ITermTreeService provides a list method which supports filtering by TermTree.termType,
So we definetely should write tests before closing. Andreas Müller
05:27 PM task #8437 (Feedback): ITermTreeService provides a list method which supports filtering by TermT...
Have you tested with termType = Character which is a subtype for Feature. I don't think the "Restrictions" implementa... Andreas Müller
11:19 AM task #8437 (Resolved): ITermTreeService provides a list method which supports filtering by TermT...
please can you review my changes? Andreas Kohlbecker
05:11 PM feature request #8439 (New): Improve Layout of Registration in Name page and Search page
Improve Layout of Registration in Name page and Search page.
Example http://phycobank.org/100628
![](picture013-1....
Wolf-Henning Kusber
12:01 PM task #8438 (New): remove featureTree/* web services in August 2021 if they are unused
If the featureTree/* web services are no longer used since 2 years we can safely remove them.
Check the cdm-server...
Andreas Kohlbecker
11:56 AM task #8434 (Closed): Change FeatureTree contollers to TermTree controllers
Andreas Kohlbecker
11:55 AM task #8166 (Resolved): Adapt dataportal to term structure changes
check taxon profile settings in a couple of test portals:
* Cichorieae
* Corvidea
* Palmweb
* Cyprus
Andreas Kohlbecker
11:18 AM task #8436 (Resolved): featureTree/* services should filter the termTrees by the TermType Feature
Applied in changeset commit:cdmlib|0f5323457637b6f2214287eb3101c7db121540f5. Andreas Kohlbecker

08/01/2019

02:59 PM task #8437 (In Progress): ITermTreeService provides a list method which supports filtering by Te...
implemented but no tests yet, but maybe you can integrate into controller already Andreas Müller
12:26 PM task #8437 (Resolved): ITermTreeService provides a list method which supports filtering by TermT...
e.g.:
~~~java
public List<TermTree> list(TermType termType, Integer limit, Integer start, List<OrderHint> orde...
Andreas Kohlbecker
01:23 PM bug #8385 (In Progress): Open issues in DB preferences
Katja Luther
12:23 PM task #8436 (Closed): featureTree/* services should filter the termTrees by the TermType Feature
Die featureTree/* Service-Endpunkte sollte selbe Verhalten anzubieten wie zuvor (#8434). In diesem Fall sollte hinter... Andreas Kohlbecker
11:36 AM task #8435 (New): Reduce logging amount of exports and other long running tasks
One single CDMLight export of the euromed database produces 49173 lines of logging like :
~~~
[euromed] 2019-07-3...
Andreas Kohlbecker
09:08 AM feature request #7510 (Worksforme): Allow entering aggregated/statistical data for single specime...
Entering statistical information is possible if the Feature/Character is defined to allow that.
The data is then e...
Patrick Plitzner
08:28 AM task #8434 (Closed): Change FeatureTree contollers to TermTree controllers
The `FeatureTree` contollers need to be adapted to the changes which have been applied for #6794:
* rename Featur...
Andreas Kohlbecker

07/31/2019

04:03 PM feature request #8432 (In Progress): Improve "default" feature tree handling
Andreas Müller
12:58 PM feature request #8432 (In Progress): Improve "default" feature tree handling
Definitions:
* **default feature tree** = term tree of type feature which holds all features in the database in a...
Patrick Plitzner
03:41 PM feature request #8433 (New): Disallow user names with whitespace
Allow only certain letter like [a-z][A-Z]_. Other usernames are errorprone.
Same for group names.
Andreas Müller
03:20 PM bug #6523: Correct display of misspellings in synonymy
Walter:
Also, erstmal, „orthographic variant“ gibt es anscheinend nur in der Botanik s.l.
Folgende Aussagen im C...
Andreas Müller
03:06 PM task #8405 (Rejected): Adapt cdm-vaadin to term structure changes
I deed, there is nothing to do about this in the cdm-vaadin project. Andreas Kohlbecker
03:01 PM task #8406 (Resolved): specimens and occurrence code cleaning and harmonization
Hi Katja,
can you please have a look if everything is as it was intended?
Andreas Kohlbecker
02:58 PM bug #8395 (Closed): NullPointerException (NPE) in NameCatalogueController
This is fully solved. Andreas Kohlbecker
02:57 PM task #8414 (In Progress): occurrence controller code cleaning and harmonization
Andreas Kohlbecker
02:32 PM bug #8426 (Closed): IndexOutOfBoundsException during serialization of RegistrationWorkingSet
findFirst() will returns an Optional describing the first element of this stream, or an empty Optional if the stream ... Andreas Kohlbecker
01:56 PM bug #8431 (In Progress): missing status bar for cdm light export
Katja Luther
10:23 AM bug #8431 (In Progress): missing status bar for cdm light export
mail from AM:
beim Export von E+M via CDM light wird bei mir seltsamer Weise keine Statusbar angezeigt, die Prozen...
Katja Luther
10:33 AM feature request #8299 (Resolved): add typification column to scientific name and homotypical grou...
Applied in changeset commit:cdmlib|e05bda1e6ca35dfb77dba833f34203525024a9cb. Katja Luther
10:27 AM feature request #8344 (Resolved): cdm light export: add dummy line in simpla facts table
this is already implemented. Katja Luther
10:26 AM feature request #8322 (Resolved): add sortindex to cdm light export
yes it is already implemented, please review Katja Luther
09:04 AM bug #8430: maps zoom to wrong bbox with some layers
This should now be fixed for all situations. Could you please take a second look? Andreas Kohlbecker
08:45 AM bug #8430 (Resolved): maps zoom to wrong bbox with some layers
Applied in changeset commit:cdm-dataportal|779840f48519040a2ab59db5b7881ef0a265d6a8. Andreas Kohlbecker
08:43 AM bug #8430 (Closed): maps zoom to wrong bbox with some layers
This problem has been fixed for `POINT` maps (#8347) but is not yet fully solved for `AREA` maps.
`openlayers_map....
Andreas Kohlbecker

07/30/2019

09:53 PM bug #8429: Rename DeterminationEvent_Reference.setOfReferences_id
The reason is that the references are called setOfReferences while the getter is getReferences.
Simplest solution:...
Andreas Müller
05:25 PM bug #8429 (Resolved): Rename DeterminationEvent_Reference.setOfReferences_id
[algaterra_new] 2019-07-30 15:49:23,008 INFO [qtp532445947-4997] [eu.etaxonomy.cdm.remote.controller.BaseController] ... Andreas Kohlbecker
09:43 PM bug #8426: IndexOutOfBoundsException during serialization of RegistrationWorkingSet
isn't this very easy to fix? Therefore I put it to 5.9 (and also tried to fix in the meanwhile).
Open question: do...
Andreas Müller
09:40 PM bug #8426 (Resolved): IndexOutOfBoundsException during serialization of RegistrationWorkingSet
Applied in changeset commit:cdmlib|6b0f8cdfe1643a96638e02dbd924ffd0007785f8. Andreas Müller
05:09 PM bug #8426 (Closed): IndexOutOfBoundsException during serialization of RegistrationWorkingSet

IndexOutOfBoundsException during serialization of RegistrationWorkingSet:
~~~
[flora-central-africa] 2019-07-...
Andreas Kohlbecker
05:19 PM bug #8428 (New): NPE in ClassificationServiceImpl.loadTreeBranchToTaxon()

~~~
[euromed] 2019-07-30 16:07:08,780 INFO [qtp532445947-5019] [eu.etaxonomy.cdm.remote.controller.ClassificationP...
Andreas Kohlbecker
05:11 PM bug #8427 (New): LazyInitializationException in NameController.doGetTaggedFullTitle()
found in production server log:
* /cichorieae/name/ddf9cc53-cdfc-45d5-98f9-1e5ef9a8e4df/taggedFullTitle
* /cichor...
Andreas Kohlbecker
03:27 PM feature request #8403: name page: show types specimens as expandable derivate tree
please see http://test.e-taxonomy.eu/dataportal/preview/phycobank/cdm_dataportal/name/f5048e6e-303a-41f6-933b-84c678e... Andreas Kohlbecker
11:35 AM feature request #8403 (Resolved): name page: show types specimens as expandable derivate tree
Andreas Kohlbecker
03:16 PM task #8425 (New): FieldUnitDTO: remove taxonRelatedDerivedUnits
FieldUnitDTO has the field `taxonRelatedDerivedUnits`. This can be removed, this is a relict of a first approach to ... Andreas Kohlbecker
03:12 PM task #8424 (New): evaluate publish flags in the full derivative path
eu.etaxonomy.cdm.remote.controller.OccurrenceController.doGetOccurencesDTO(@PathVariable(value="uuid") UUID uuid, Htt... Andreas Kohlbecker
03:01 PM bug #8423 (New): OccurrenceServiceImpl.findFieldUnitDTO() fails to merge derivation paths when a ...
OccurrenceServiceImpl.findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits, HashMap<UUID,... Andreas Kohlbecker
02:53 PM bug #8422 (In Progress): Make PolytomousKeyGenerator work (correctly)
Andreas Müller
02:53 PM bug #8422 (Closed): Make PolytomousKeyGenerator work (correctly)
Andreas Müller
02:25 PM task #8406 (In Progress): specimens and occurrence code cleaning and harmonization
Andreas Kohlbecker
02:15 PM bug #8385: Open issues in DB preferences
Passing the ticket back to Katja. We may have a look on it together, though. Patrick Plitzner
02:14 PM feature request #8238: Allow interoperability between term trees
Does not have to solved in this milestone -> move to 5.10 Patrick Plitzner
01:52 PM feature request #8415 (Closed): use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to s...
Andreas Kohlbecker
01:52 PM feature request #8415 (Resolved): use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to...
Applied in changeset commit:cdm-dataportal|dfbc27b033a2eda86d74b57a4d14189f7d6e5cd0. Andreas Kohlbecker
01:48 PM feature request #8390 (Closed): implement /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup
Andreas Kohlbecker
01:07 PM task #8414: occurrence controller code cleaning and harmonization
http://test.e-taxonomy.eu/dataportal/preview/algaterra-new/cdm_dataportal/taxon/c3350592-db9d-44cb-80ed-29bfb685e3a0/... Katja Luther
11:35 AM bug #8421 (New): icons in compose_specimen_table_top_down() are not visible
in `compose_specimen_table_top_down()` font awesome icons are added to the render array, but these are not getting di... Andreas Kohlbecker
11:28 AM task #8420 (New): improve admin settings for specimens representations
* The kind of representation of specimens lists needs to be selectable via a set of radio buttons.
* should the sett...
Andreas Kohlbecker
11:25 AM task #8419 (New): harmonization of the different specimen representations
* There are different kinds of "views" for specimens lists
* some of them provide a pager others do not
* do ...
Andreas Kohlbecker
11:21 AM task #8418 (Closed): specimens and occurrence links must not have a target=_blank attribute
Andreas Kohlbecker
11:01 AM task #8418 (Closed): specimens and occurrence links must not have a target=_blank attribute
Even is this was frequently requested by users using the target attribute is in general considered an UX anti-pattern... Andreas Kohlbecker
10:14 AM bug #8417 (New): LazyInitializationException in TermDTO for media
Im TaxonRelationshipsDTOTest, der ein einfacher UnitTest ist kommt es zu Problemen wegen der media die neuerdings an ... Patrick Plitzner
09:20 AM feature request #8412 (In Progress): Remaining issues for cdm light export (II)
Katja Luther

07/29/2019

02:13 PM bug #8416 (New): Array to string conversion problem in render array prodiced for specimen page
At leas the specimen page for (B B GT 0024094) in phycobank ( http://edit.test/d7/phycobank/cdm_dataportal/occurrence... Andreas Kohlbecker
02:04 PM feature request #8415 (Closed): use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to s...
copied from #6380.
This webservice should be used to speed up `type_designations_for_synonymy_group($synonymy_grou...
Andreas Kohlbecker
01:59 PM task #8414 (Closed): occurrence controller code cleaning and harmonization
eu.etaxonomy.cdm.remote.controller.OccurrenceController.doGetOccurencesDTO(@PathVariable(value="uuid") UUID uuid, Htt... Andreas Kohlbecker
12:36 PM feature request #8413 (New): Abcd import with file containing list of unit ids
For a bulk import it is necessary to have the possibility to import all specimen of a list of unit IDs Katja Luther
10:36 AM bug #6627 (Resolved): Remaining cdm light issues
created a new "remaining issues" ticket and close this one Katja Luther
10:35 AM feature request #8412 (In Progress): Remaining issues for cdm light export (II)
* Instance name and instance ID
* Discuss whether we should handle the citation facts separate to the other simple...
Katja Luther
10:29 AM feature request #8411 (New): base path for export/import path selection
mail from w.b.
Hallo,
ein nice to have, wohl vor allem für Leute die nicht ständig in einer Datenbank arbeiten, ...
Katja Luther

07/26/2019

05:53 PM feature request #8410 (New): Add nomenclatural code edition to ruleConsidered in TaxEditor
for nomenclatural status, name relation (and hybrid relation once it exists).
Make the field only available if rul...
Andreas Müller
03:14 PM feature request #8334 (Resolved): Move sources for type designations to details view
Patrick Plitzner
02:51 PM feature request #8135 (Resolved): Implement verbatim type information in TaxEditor
Patrick Plitzner
02:38 PM bug #8365: DerivedUnitFacadeCacheStrategy should remove collection codes from accession numbers
Andreas Müller wrote:
> To me there seems to be a misunderstanding. My understanding of #8365#note-8 is that is fine...
Andreas Müller
02:19 PM bug #8365: DerivedUnitFacadeCacheStrategy should remove collection codes from accession numbers
One last question: is the original task of the ticket to deduplicate collection code if necessary now implemented in ... Andreas Müller
02:13 PM bug #8365: DerivedUnitFacadeCacheStrategy should remove collection codes from accession numbers
To me there seems to be a misunderstanding. My understanding of #8365#note-8 is that is fine to have brackets for typ... Andreas Müller
01:58 PM bug #8365: DerivedUnitFacadeCacheStrategy should remove collection codes from accession numbers
Andreas Kohlbecker wrote:
> Users frequently enter the collection code with the accession number which can cause to ...
Andreas Müller
01:50 PM feature request #8180 (In Progress): Add property term "Presence/Absence" to CDM default terms
As the current solution works for additivity maybe we should postpone creating the two new terms until the above ques... Andreas Müller
01:46 PM feature request #8180: Add property term "Presence/Absence" to CDM default terms
Query for above request:
~~~sql
SELECT REPLACE (uri, 'https://terms.tdwg.org/wiki/ft:','')
FROM DefinedTermBase...
Andreas Müller
01:31 PM feature request #8180: Add property term "Presence/Absence" to CDM default terms
Hallo,
ich sehe gerade das folgende Terme doppelt vorkommen in der Ontologie:
"REPLACE (uri, 'https://terms.tdw...
Andreas Müller
11:07 AM task #8166: Adapt dataportal to term structure changes
Yes, we should at least do a string search for "FeatureTree". Also a string search on "FeatureNode". Andreas Müller
09:27 AM task #8166 (New): Adapt dataportal to term structure changes
I am reopening this issue since the data portal code even if being fully functional might need to be adapted to the ... Andreas Kohlbecker
08:53 AM task #8166 (Worksforme): Adapt dataportal to term structure changes
Andreas Müller wrote:
> Are there any changes needed? Currently it looks like most things work (except maybe for the...
Andreas Kohlbecker
11:06 AM feature request #8238 (In Progress): Allow interoperability between term trees
Patrick Plitzner
10:57 AM feature request #8409 (New): add nomenclatural code select to NomenclaturalStatusRow
see #8398 for details Andreas Kohlbecker
10:55 AM feature request #8408 (New): add nomenclatural code select to NameRelationField
see #8398 for details Andreas Kohlbecker

07/25/2019

11:13 PM task #8405: Adapt cdm-vaadin to term structure changes
Are there any changes needed? Vaadin compiles and does not really make use of TermTree(former FeatureTree) so it is m... Andreas Müller
10:16 AM task #8405 (Rejected): Adapt cdm-vaadin to term structure changes
the vaadin editor needs to be adapted to the changes applied in the context of #6794 Andreas Kohlbecker
11:10 PM task #8166: Adapt dataportal to term structure changes
Are there any changes needed? Currently it looks like most things work (except maybe for the Specimen page, is this c... Andreas Müller
02:54 PM task #8336 (Duplicate): Unignore FeatureTest
Andreas Müller
02:50 PM bug #8407 (New): Fix "FeatureTest"
Fix "FeatureTest" (or may now TermTreeTest) which checks the correkt behavior for exporting (and importing?) TermTree... Andreas Müller
01:16 PM task #8406 (Feedback): specimens and occurrence code cleaning and harmonization
## cdmlib-remote
issues copied to #8414
## data portal
* There are different kinds of "views" on specimens l...
Andreas Kohlbecker
10:13 AM bug #8395 (Resolved): NullPointerException (NPE) in NameCatalogueController
Applied in changeset commit:cdmlib|dd4347b628d5737e2682c8d95fcb0e1aff9e7ad7. Andreas Kohlbecker

07/24/2019

07:50 PM feature request #8404 (Resolved): Add update step list within updaters
Andreas Müller
04:23 PM feature request #8404 (Closed): Add update step list within updaters
currently it is needed to add the step externaly to the step list which leads to errors and requires unnecessary code Andreas Müller
07:50 PM feature request #8281 (Resolved): Doubtful flag for TaxonNode
still need to update E+M data Andreas Müller
07:49 PM bug #4884 (Resolved): Update Reference_AUD.refType to allow NULL
Andreas Müller
07:48 PM feature request #8398 (Resolved): Add nomenclatural code edition to ruleConsidered
Applied in changeset commit:cdmlib|3b49c84a0287d1f78acb49ff1270a38c679cfd3a. Andreas Müller
02:56 PM feature request #8402 (Closed): ordering typedesignations in name and taxon page
Andreas Kohlbecker
02:56 PM feature request #8402 (Resolved): ordering typedesignations in name and taxon page
Applied in changeset commit:cdm-dataportal|fb939fdc818762b23215321ff183be8700e88161. Andreas Kohlbecker

07/23/2019

06:03 PM feature request #8403 (Rejected): name page: show types specimens as expandable derivate tree
In the name page, type specimens used in type designations should be expandable like in the taxon page Andreas Kohlbecker
05:58 PM feature request #8402 (Closed): ordering typedesignations in name and taxon page
The typedesignation in the name and taxon page are not jet well orderd. The sort order should follow the order of the... Andreas Kohlbecker
04:39 PM bug #6523: Correct display of misspellings in synonymy
Guten Morgen,

ich bin hinsichtlich einer endgültigen Lösung leidenschaftslos und kann nicht mit eigenen Vorschläg...
Andreas Kohlbecker
03:33 PM feature request #7975: Implement a block to display name relations
Andreas Kohlbecker wrote:
> In the developer standup today we almost already decided for adding an enumeration field...
Andreas Kohlbecker
03:31 PM bug #8399 (New): show nomenclatural code reference for NameRelationship and NomenclaturalStatus
see #7975#note-31 for details Andreas Kohlbecker
01:27 PM feature request #8398 (Resolved): Add nomenclatural code edition to ruleConsidered
copied from #7975#note-31 :
"... adding an enumeration field to NameRelationship and to NomenclaturalStatus to al...
Andreas Müller
01:20 PM feature request #6794 (In Progress): Improve term structure
Andreas Müller
11:27 AM feature request #8396 (New): make "not in classification warning" configurable

once completed remove
~~~css
.messages--warning {
display: none;
}
~~~
from phycobank portal
Andreas Kohlbecker
11:24 AM report #8392: Types in PhycoBank
the type status in the name page should be bold but
~~~css
.node-cdm-name .typeDesignations .status {
font-wei...
Andreas Kohlbecker

07/22/2019

03:23 PM bug #8395 (Closed): NullPointerException (NPE) in NameCatalogueController
This NPE problem currently breaks searching for "Planothidium" in phycobank via UTIS
~~~
Caused by: java.lang.Nu...
Andreas Kohlbecker
02:42 PM feature request #8180 (Feedback): Add property term "Presence/Absence" to CDM default terms
Patrick Plitzner
08:28 AM feature request #8390 (In Progress): implement /portal/name/{uuuid}/typeDesignationsInHomotypical...
Andreas Kohlbecker
07:48 AM bug #8340 (New): is accepted for Footnotes missing and with wrong index
I think there is nothing to do about this ticket as long #8339 is not decided by 100%. Andreas Kohlbecker
 

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