Activity

From 07/21/2019 to 08/19/2019

08/19/2019

04:58 PM bug #8465 (Closed): Term nodes order in term trees is ignored in term tree editor: I would rather close this tickets because it was created only to handle the bug. All other issues will be adressed in... Patrick Plitzner
04:55 PM feature request #8235 (Resolved): Create separate menu for term tree editors for each term tree type: Applied in changeset commit:taxeditor|362b3a0c58e4b2b8620477ce38a80e2a3553bd36. Patrick Plitzner
04:15 PM feature request #8480 (Closed): Use DescriptionTypes for matrix descriptions: Patrick Plitzner
04:14 PM feature request #8480 (Resolved): Use DescriptionTypes for matrix descriptions: Applied in changeset commit:cdmlib|0b616910ec8af247ee13843c5058b22ac24efff0. Patrick Plitzner
04:11 PM feature request #8480 (Closed): Use DescriptionTypes for matrix descriptions: Patrick Plitzner
04:15 PM feature request #7957 (Closed): Add types for taxon description (as EnumSet): Adapted descriptive data set service to use DescriptionType. Tried aggregation and tested display in matrix editor. A... Patrick Plitzner
04:11 PM task #8479 (In Progress): [PESI][FE] Cdm-2-Cdm import for FauEu: Open issues:
* check if uuids are always kept for taxon nodes (sometimes addChild is used which probably creats co... Andreas Müller
03:21 PM feature request #8475: Adapt applicable state detail view elements to FeatureState: Added applicable detail elements to TermNode details view. Available features are filtered to only contain parent fea... Patrick Plitzner
03:19 PM feature request #8475 (Resolved): Adapt applicable state detail view elements to FeatureState: Patrick Plitzner
02:37 PM bug #8417: LazyInitializationException in TermDTO for media: not important for this release -> move to 5.10 Patrick Plitzner
02:33 PM feature request #8478 (New): Follow up ticket for update empty name in source handling in TaxEditor: We need a final implementation with a new wizard including the question if the name in sources should be taken from t... Katja Luther
01:27 PM feature request #8304: Name page redirects to according taxon depending on query parameter: Hi Andreas, I think we have discussed this issue sometime at phone. Do you remember the results? Are they somewhere i... Andreas Müller
10:16 AM feature request #3472: Update name in source data when changing an accepted taxon into a synonym: Ok, in generall this probably makes sense. Maybe I just wasn't used to it yet.
However, if this is the expected beha... Andreas Müller
09:40 AM feature request #3472: Update name in source data when changing an accepted taxon into a synonym: Andreas Müller wrote:
> Currently both methods do end in an unexpected state. After running the operation the old ta... Katja Luther

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~~
this is fixed 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 v... Andreas Müller
10:27 PM bug #8385: Open issues in DB preferences: ~~name.nomenclaturalStatus can not be removed by Reset Default~~
this is fixed. 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 selecte... 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 ba... 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 emp... 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 a synonym: 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 a synonym: 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 group in cdm light: 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, misapplications and hybrids: "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, misapplications and hybrids: 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, misapplications and hybrids: 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, misapplications and hybrids: 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 (Closed): Implement support for TermCollection.allowDuplicates 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 (Closed): 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 (Closed): 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 (Closed): Make TermCollection.orderRelevant usable for TermTrees: Dazu müsste es:
1. ~~editierbar sein~~
2. ~~Der TermTree müsste unterschiedlich sortiert angezeigt werden, je n... 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 (Closed): Transmission engine for distribution aggregation needs to be adapted to new DescriptionBase.types: 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 (Closed): 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 (Closed): 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 (In Progress): Open PolytomousKeyGenerator issues: * ~~adapt dependency handling to new FeatureState handling~~
* in general improve the handling of dependencies, mayb... Andreas Müller
11:35 AM task #8468 (Closed): 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 (Closed): 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 (Closed): 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 (Closed): 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 task #7099: Make CdmAuthority a persistable class: forgot to implement uniqueness. Moved to #8464 Andreas Müller
10:41 AM task #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

08/08/2019

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 (Closed): Adapt setPublishForSubtree to new parameters for pro parte, misapplications and hybrids: 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 pro parte synonyms: Applied in changeset commit:cdmlib|5fb16579cd1fbce2bfa19f12bebc0d4711b23b90. Andreas Müller
12:15 PM task #8445 (Closed): improve service description: a.mueller wrote:
„UTIS connects the web services of the Pan-European Species directories Infrastructure (EU-Nomen)... Andreas Kohlbecker

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 (Closed): 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 TermTree.termType,: 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 TermTree.termType,: 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 (Closed): 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 TermTree.termType,: 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 TermTree.termType,: 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 specimens in character matrix: 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 (Duplicate): 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 group in cdm light: Applied in changeset commit:cdmlib|e05bda1e6ca35dfb77dba833f34203525024a9cb. Katja Luther
10:27 AM feature request #8344 (Resolved): Cdm light export: add dummy line in simple 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 (Closed): Rename DeterminationEvent_Reference.setOfReferences_id: ~~~
[algaterra_new] 2019-07-30 15:49:23,008 INFO [qtp532445947-4997] [eu.etaxonomy.cdm.remote.controller.BaseControl... 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 (Closed): 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 (Closed): 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 (Closed): 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 (Closed): OccurrenceServiceImpl.findFieldUnitDTO() fails to merge derivation paths when a FieldUnit has two derivatives: 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 be solved in this milestone -> move to 5.10 Patrick Plitzner
01:52 PM feature request #8415 (Closed): use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to speed up type designation retrieval: Andreas Kohlbecker
01:52 PM feature request #8415 (Resolved): use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to speed up type designation retrieval: 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 (Rejected): 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 (Closed): 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 (In Progress): 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 op... 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 (Worksforme): Array to string conversion problem in render array produced for specimen page: At least the specimen page for (B B GT 0024094) in phycobank ( http://edit.test/d7/phycobank/cdm_dataportal/occurrenc... Andreas Kohlbecker
02:04 PM feature request #8415 (Closed): use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to speed up type designation retrieval: 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): additional requirements 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 (Closed): 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 (Closed): add nomenclatural code select to NameRelationField: see #8398 for details Andreas Kohlbecker
10:55 AM feature request #8408 (Closed): add nomenclatural code select to NomenclaturalStatusRow: 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 (Closed): 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
12:18 PM task #8363 (Worksforme): PESI SOAP service seems to return duplicate records: It turned out that the duplicates are not in the PESI response but that they an effect of an error in the downstram p... Andreas Kohlbecker
12:02 PM task #8363: PESI SOAP service seems to return duplicate records: I introduced this while I was working on the ticket overview page for Phycobank: https://dev.e-taxonomy.eu/redmine/pr... Andreas Kohlbecker
10:27 AM task #8363: PESI SOAP service seems to return duplicate records: Interesting that the UTIS project has a category utis ;-) Andreas Müller

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 yet well ordered. The sort order should follow the order of th... 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
04:15 PM bug #8400 (Closed): scientific names in Aphia client responses are missing authors citation: Andreas Kohlbecker
03:49 PM bug #8400 (Closed): scientific names in Aphia client responses are missing authors citation: Andreas Kohlbecker
04:14 PM bug #8401 (Closed): WoRMS client returns synonym for accepted name: Andreas Kohlbecker
04:14 PM bug #8401 (Resolved): WoRMS client returns synonym for accepted name: Applied in changeset commit:utis-core|b2cf9c25798fa510b3eda5b8d77630e1da1e9072. Andreas Kohlbecker
03:58 PM bug #8401 (Closed): WoRMS client returns synonym for accepted name: Andreas Kohlbecker
04:12 PM feature request #8355 (Closed): implement client adapter for phycobank: Andreas Kohlbecker
04:09 PM feature request #8360 (Worksforme): paging results of /classification/{taxonId}/children webservice: this has been solved in bug #6151 Andreas Kohlbecker
04:06 PM bug #6151 (Closed): implement pager for search service: 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 edition for NameRelationship and NomenclaturalStatus: see #7975#note-31 for details Andreas Kohlbecker
01:27 PM feature request #8398 (Closed): 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 task #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
03:19 PM feature request #8394 (New): org.cybertaxonomy.utis.tnr.msg.TaxonName add URL field: For phycobank and other name focused data providers it is crucial that the name url and identifier can be transported... 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}/typeDesignationsInHomotypicalGroup: Andreas Kohlbecker
08:05 AM bug #8393 (New): restarting utis-webapp causes OverlappingFileLockException: This happens after changing the last updated timestamp of the '/etc/jetty8/contexts/eubon-utis-1.3.xml'
~~~
java.... 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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