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From 09/25/2020 to 10/24/2020

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09:28 AM feature request #9246 (Duplicate): Additional fields in cdmLIght export
this ticket duplicates #9262 Andreas Müller

10/23/2020

06:00 PM bug #9263 (New): Unify case for type designation status
Current csv files use lower case for NameTypeDesignationStatus and upper case for SpecimenTypeDesignationStatus. This... Andreas Müller

10/22/2020

12:45 PM feature request #9262 (New): Several open issues for cdmlight export related to Cactaceae and oth...
Mail WGB 2020-10-22:
1. ~~Fehlerhafter Literatur-Output – zwei Autoren + et al. statt Erstautor + et al., siehe an...
Andreas Müller
12:15 PM bug #9260 (Closed): error in pages.inc calling compose_taxon_node_status()
Andreas Kohlbecker
12:15 PM bug #9261 (Closed): LazyInitializationException (LIE) in TaxonController.doGetTaxonNodes()
Andreas Kohlbecker
12:15 PM bug #9261 (Resolved): LazyInitializationException (LIE) in TaxonController.doGetTaxonNodes()
Applied in changeset commit:cdmlib|8728f23bae0e8758c46f09837af01070922d1d41. Andreas Kohlbecker
11:35 AM bug #9261 (Closed): LazyInitializationException (LIE) in TaxonController.doGetTaxonNodes()
http://api.cybertaxonomy.org/caryophyllales/portal/taxon/b6ec8d50-7f37-4a17-af01-b1fae138c749/taxonNodes.json fails w... Andreas Kohlbecker

10/21/2020

10:02 AM bug #9260 (Closed): error in pages.inc calling compose_taxon_node_status()
http://caryophyllales.org/cdm_dataportal/taxon/b6ec8d50-7f37-4a17-af01-b1fae138c749
~~~
Recoverable fatal error: ...
Andreas Kohlbecker

10/20/2020

01:13 PM task #8081: Complete removal of redmine communication hub instances
all code has been removed now! see #7936 Andreas Kohlbecker
01:12 PM task #7315 (Rejected): remove workaround RedmineTransportAccessor
no longer needed, since the redmine message hub has been completely rejected Andreas Kohlbecker
01:10 PM bug #7936 (Closed): Consider complete removal of redmine communication hub code
Andreas Kohlbecker

10/19/2020

11:29 PM bug #9245: Creating derived units from existing derived unit is not possible in specimen tree editor
This ticket needs to be fixed urgently as it makes the specimen tree editor impossible to use Andreas Müller
05:04 PM bug #6757: AbcdImportWizard has all configurator flags set to false
Is this still an open issue? If yes we should fix it soon (probably a no-brainer), if not, we should close this ticke... Andreas Müller
02:05 PM task #9252 (Resolved): Harmonize SpecimenOrOberservationBase related DTOs
should be solved now, needs review Andreas Kohlbecker
09:56 AM task #9259 (Closed): reduce fields in TermBase json serializations
Andreas Kohlbecker
09:55 AM task #9259 (Resolved): reduce fields in TermBase json serializations
Applied in changeset commit:cdmlib|3ae4f12f20159b7e0ddb04c68f4bfc5fb17d5481. Andreas Kohlbecker
09:43 AM task #9259 (In Progress): reduce fields in TermBase json serializations
Andreas Kohlbecker
09:43 AM task #9259 (Closed): reduce fields in TermBase json serializations
The fields in json serializations produced by the TermBaseBeanProcessor can be reduced.
here an example of the cur...
Andreas Kohlbecker

10/16/2020

01:50 PM feature request #9258 (Closed): Use Partial for date in FieldUnitDTO
Andreas Kohlbecker
01:50 PM feature request #9258 (Resolved): Use Partial for date in FieldUnitDTO
Applied in changeset commit:cdmlib|e0089f681023c823ee9424dfe2ac550065414474. Andreas Kohlbecker
12:11 PM feature request #9258 (Closed): Use Partial for date in FieldUnitDTO
FieldUnitDTO contains the date as pure string this has at least two problems:
* FieldUnitDTOs can not be reliably ...
Andreas Kohlbecker
12:03 PM task #9253 (In Progress): revise OccurrenceServiceImpl.findFieldUnitDTO(..)
Andreas Kohlbecker
08:59 AM bug #8423 (Resolved): OccurrenceServiceImpl.findFieldUnitDTO() fails to merge derivation paths wh...
Andreas Kohlbecker
08:59 AM bug #8423 (Closed): OccurrenceServiceImpl.findFieldUnitDTO() fails to merge derivation paths when...
Andreas Kohlbecker

10/15/2020

09:30 PM bug #8423 (In Progress): OccurrenceServiceImpl.findFieldUnitDTO() fails to merge derivation paths...
Andreas Kohlbecker
03:38 PM task #9252: Harmonize SpecimenOrOberservationBase related DTOs
now only the term related tasks are left to do Andreas Kohlbecker
03:36 PM task #9252 (In Progress): Harmonize SpecimenOrOberservationBase related DTOs
Andreas Kohlbecker
12:51 PM bug #9257 (Feedback): revise filtering in OccurrenceServiceImpl.assembleFieldUnitDTO(FieldUnit fi...
Hi Katja & AM, the current implementation partially filters for DerivedUnits of the type `SpecimenOrObservationType.P... Andreas Kohlbecker
12:14 PM bug #9257 (Feedback): revise filtering in OccurrenceServiceImpl.assembleFieldUnitDTO(FieldUnit fi...
see FIXME comment in method Andreas Kohlbecker
12:17 PM bug #9256 (Resolved): CdmLightExport: NameTypeDesignation string misses parenthesis for authors
Katja Luther
11:58 AM bug #9256 (Resolved): CdmLightExport: NameTypeDesignation string misses parenthesis for authors
mail WB:
ein unangenehmer (und, glaube ich, neuer) Bug in HomotypicGroup.csv:
In der Spalte „TypeSpecimenString...
Katja Luther
12:12 PM bug #9254 (Closed): portal/occurrence/{uuid}/fieldUnitDTO.json fails with class cast exception
Andreas Kohlbecker
11:40 AM bug #9254 (Resolved): portal/occurrence/{uuid}/fieldUnitDTO.json fails with class cast exception
Applied in changeset commit:cdmlib|5a1fd3284147ad65dc6408afa94956df19fd07e1. Andreas Kohlbecker
11:39 AM bug #9254 (Closed): portal/occurrence/{uuid}/fieldUnitDTO.json fails with class cast exception
The request on portal/occurrence/{uuid}/fieldUnitDTO.json with the uuid of a FieldUnit fails with a ClassCast exception Andreas Kohlbecker
11:43 AM task #9255 (New): DerivateDataDTO implement support for TissueSample
see TODO comment in `public static DerivateDataDTO fromEntity()` at line 62. Andreas Kohlbecker
11:09 AM task #9253 (In Progress): revise OccurrenceServiceImpl.findFieldUnitDTO(..)
This intended function of `FieldUnitDTO OccurrenceServiceImpl.findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection... Andreas Kohlbecker

10/14/2020

02:03 PM task #9252 (Resolved): Harmonize SpecimenOrOberservationBase related DTOs
Problems with the current implementations:
* Naming:
* PreservedSpecimenDTO should be named DerivedUnitDTO
...
Andreas Kohlbecker

10/13/2020

06:04 PM bug #7606 (Duplicate): compact display of CDM Point data
closing as duplicate of #3978 Andreas Kohlbecker
06:02 PM task #3978 (Closed): Specimenview path: Compact representation of exactLocation
Andreas Kohlbecker
06:02 PM task #3978 (Resolved): Specimenview path: Compact representation of exactLocation
Andreas Kohlbecker
06:00 PM task #9251 (New): Specimenview path: better representation of RecordBasis
Copied from #3978
Hallo Andreas,
Bei der Specimenanzeige gäbe es glaube ich noch einige einfache Verbesserung...
Andreas Kohlbecker

10/12/2020

06:02 PM task #7917: Revise ReferenceSystemTerms
I checked the usage of ReferenceSystemTerms in the production dbs:
~~~
cdm_production_algaterra
-- WGS84
-...
Andreas Kohlbecker
04:48 PM task #7917: Revise ReferenceSystemTerms
Andreas Kohlbecker wrote:
> I discovered that adding 'gazetteer' was an explicit requirement which was handled in #2...
Andreas Kohlbecker
03:26 PM feature request #9249 (Closed): compact display of collection information
Andreas Kohlbecker
02:22 PM feature request #9249 (Closed): compact display of collection information
Andreas Kohlbecker
02:48 PM feature request #9250 (New): collection page implemented
also enable link rendering in `function render_collection($collection, $do_link = false )` by changing the default if... Andreas Kohlbecker
01:02 PM bug #9248 (New): ABCD import configuration is not fail save for creation of new classification
When licking on "do not create new classification for new taxa" but missing to define the classification for adding t... Katja Luther
09:35 AM bug #9247 (New): Link with taxon does not work correctly
mail WB:
ich habe die Caryophyllales_spp gerade aufgemacht und nach Hammada articulata gesucht und das Resultat ...
Katja Luther
09:24 AM feature request #9246 (Duplicate): Additional fields in cdmLIght export
mail WB:
Hallo,
wir sind ja dabei, mehrere Datenpaper vorzubereiten. Die Formate sind noch nicht ganz klar (hängt...
Katja Luther

10/09/2020

03:35 PM bug #9245 (New): Creating derived units from existing derived unit is not possible in specimen tr...
Trying to add a derived unit to an already existing derived unit is not possible because the menu entry "Add/Hinzufüg... Katja Luther
01:56 PM bug #7686 (Closed): Specimen title cache issues in data portal specimen table
to me it seems as if all issues are fixed now, except for the issue of the missing comma between two specimen type de... Andreas Kohlbecker
01:24 PM feature request #3307: optionally reduce complexity in specimen display
I think that we rather should work on a better and more concise layout than solving this with a settings option. Andreas Kohlbecker
01:19 PM feature request #2985 (Closed): Improve Specimen details display
remaining issues and suggestions from comment 23 copied to other issues.
So we can close this issue now.
Andreas Kohlbecker
12:47 PM feature request #9244 (New): Improve NamedArea page
copied from #2985#note-23
Show abbrev label, description, named area type, URI, valid period, and maybe also suppl...
Andreas Kohlbecker
11:27 AM feature request #8854 (Closed): Choose new base font size for the portal
all suggestions for further improvement have been copied to new tickets (#9242, #9243) and this issue here can thus b... Andreas Kohlbecker
11:24 AM task #9243 (New): zen_dataportal theme: Discuss reduced fontsize of headings
follow up to #8854
Walter wrote:
> Ansonsten fällt mir hier nur auf, dass die Überschriften (fact categories) e...
Andreas Kohlbecker
11:19 AM feature request #9242 (New): cdm_taxontree: strategy for better readability
follow up to #8854
walter wrote:
> caryophyllales_spp: Sieht gut aus, bis auf den Navigator – da wird’s dann zi...
Andreas Kohlbecker

10/08/2020

06:48 PM bug #9238 (Resolved): pure entities in DerivateDTO.derivates may cause LIEs
this should be fully solved now. Ticket can be closed as long as no further problems are popping up during the testing. Andreas Kohlbecker
06:40 PM bug #9238: pure entities in DerivateDTO.derivates may cause LIEs
The introduction of the SpecimenTypeDesignationDTO causes a couple problems since this dto is quite incomplete so far. Andreas Kohlbecker
06:38 PM bug #9238: pure entities in DerivateDTO.derivates may cause LIEs
this issue is problematic also in the context of other controller methods where DerivateDTO is being involved.
Ada...
Andreas Kohlbecker

10/06/2020

05:25 PM bug #9240: nomenclatural status missing in name and registration page
Yes, it can be closed. The examples in PhycoBank are displayed perfectly. Wolf-Henning Kusber
05:01 PM bug #9240 (Resolved): nomenclatural status missing in name and registration page
default settings updated.
I think this ticket can be closed.
@Henning: Could you please review?
Andreas Kohlbecker
01:26 PM bug #9240 (In Progress): nomenclatural status missing in name and registration page
The
name render part for the nom status was missing in the default render template.
I added this to the phycob...
Andreas Kohlbecker
11:41 AM bug #9240 (Resolved): nomenclatural status missing in name and registration page
Navicula adminensis has status *nom. illeg* or *nom. superlf.*
https://www.phycobank.org/cdm_dataportal/name/26bd1...
Andreas Kohlbecker
02:42 PM feature request #9209: name page, registration page: show annotations for names and fieldunits
Example: http://phycobank.org/102598 Wolf-Henning Kusber
11:27 AM feature request #9209 (Closed): name page, registration page: show annotations for names and fiel...
please enter "Etymology: " as prefix to the annotation text.
Andreas Kohlbecker
01:41 PM bug #9241 (New): replace/adapt descriptionPart in render templated
after #6589 is fully solved the display of prologues in the data portal need to be adapted.
The render template de...
Andreas Kohlbecker

10/05/2020

01:42 PM feature request #9239 (New): When opening bulk editor via referencing objects view the selected r...
... so that the details view (and other views) are filled automatically Andreas Müller

10/02/2020

09:34 PM task #9231: Create statistics for Euro+Med
Zeitabhängigkeit:
~~~ sql
SELECT minYear, COUNT(*) AS n
FROM(
SELECT accId, accName.titleCache, MIN(Y) minY...
Andreas Müller
09:16 PM feature request #7685 (Closed): Add Selenium tests for specimen table in data portal
The test is fairly complete now.
Only tests for the indicator icons for DNA-sample and descriptive data are missin...
Andreas Kohlbecker
08:15 PM task #9187 (Duplicate): selenium test for specimen table view
duplicate of #7685 Andreas Kohlbecker
03:26 PM bug #9238 (Resolved): pure entities in DerivateDTO.derivates may cause LIEs
this request http://int.e-taxonomy.eu/cdmserver/integration_reference/portal/occurrence/89d36e79-3e80-4468-986e-411ca... Andreas Kohlbecker
12:15 PM bug #9234 (Closed): Error: Object of class stdClass could not be converted to string caused by co...
Andreas Kohlbecker
11:17 AM feature request #7599: treeView for specimen data in dataportal
[Andreas Müller wrote:]
Hallo,
wenn ich es richtig verstehe bezieht sich das auf die Derivate, die unterhalb vo...
Andreas Kohlbecker
11:17 AM feature request #7599: treeView for specimen data in dataportal
Naja, nicht ganz. Es geht auch im Tree View darum, dass in einem Derivat Baum, der aus einer Mischprobe entsteht, nic... Andreas Kohlbecker
11:15 AM feature request #7599: treeView for specimen data in dataportal
Ah ok,
das Ausblenden/Verstecken bezog sich nur auf die Compressed Table, richtig?
VG
A.
Andreas Kohlbecker
11:15 AM feature request #7599: treeView for specimen data in dataportal
[Katja wrote:]
Hallo Andreas,
die Origin derivate sollten schon angezeigt werden, auch wenn sie keine Assozia...
Andreas Kohlbecker
11:14 AM feature request #7599: treeView for specimen data in dataportal
Hallo Katja,
ich habe noch eine weitere Frage.
Soweit ich das verstanden habe gilt auch folgender Anforderung: ...
Andreas Kohlbecker
09:20 AM bug #9237 (New): FeatureTree SortIndex updater creates wrong sortindex
mail NK:
ich beobachte jetzt schon seit einer Weile, dass sich die Reihenfolge der Features, die ich im TaxEditor ...
Katja Luther

10/01/2020

06:18 PM feature request #9209 (Feedback): name page, registration page: show annotations for names and fi...
The annotations looks good, and the indicees are placed correctly. Some cache issues in references are remaining, but... Wolf-Henning Kusber
05:49 PM feature request #9209 (Resolved): name page, registration page: show annotations for names and fi...
Hi Henning,
please review on the test server:
http://test.e-taxonomy.eu/dataportal/preview/phycobank/cdm_datap...
Andreas Kohlbecker
06:17 PM bug #8340 (Rejected): is accepted for Footnotes missing and with wrong index
no need for any action on this issue since we decided to remove "is accepted" completely, see #8339 Andreas Kohlbecker
05:46 PM bug #9236: stopping an instance breaks the centralized logging
Further test showed that some service endpoints in fact are broken in the situation described above. Andreas Kohlbecker
05:38 PM bug #9236 (New): stopping an instance breaks the centralized logging
since switching to centralized logging through logback MDC (#7085) the logging gets broken when an cdm-webapp instanc... Andreas Kohlbecker
05:29 PM bug #6287 (Duplicate): Rolling cdmserver.log file only contains entries from startup phase
this has been solved by #7085
Closing as duplicate
Andreas Kohlbecker
04:58 PM bug #9235 (Closed): Footnote key for multiple cdm entities need to be rendered together
completed. Andreas Kohlbecker

09/29/2020

11:26 PM task #9231: Create statistics for Euro+Med
"Family" Query 4:
~~~ sql
-- E+M Families

SELECT famName, rankName, STATUS, n
FROM
(
...
Andreas Müller
09:58 PM task #9231 (In Progress): Create statistics for Euro+Med
Query for 3:
~~~ sql
-- E+M Area statistics
SELECT areaSymbol, areaName, rankName, STATUS, n
FROM
(
SELEC...
Andreas Müller
04:51 PM feature request #9209: name page, registration page: show annotations for names and fieldunits
This is in principle solved but there are now potential layout problems due to the problem described in #9235.
We...
Andreas Kohlbecker
03:29 PM feature request #9209: name page, registration page: show annotations for names and fieldunits
Editorial note on the FieldUnit of the Holotype for *Paludistella asymmetrica* is already shown in the registration a... Andreas Kohlbecker
04:49 PM bug #9235 (Closed): Footnote key for multiple cdm entities need to be rendered together
Currently footnote keys are created per cdm entity. When footnote keys are created for name and taxon they need to be... Andreas Kohlbecker
04:38 PM bug #6821 (Worksforme): footnote keys without trailing dot character
Andreas Kohlbecker
12:22 PM bug #8567 (Worksforme): registration search results: cdm_compose_url(): missing pathParameter 0 f...
this has been fixed already in an other context Andreas Kohlbecker
12:19 PM feature request #8983: authors and team in combopox better distinguishable
elaualtion need to be done rather soon so that we know how to deal with his issue for the **Phycobank ready for submi... Andreas Kohlbecker
12:00 PM bug #8579 (Worksforme): Search in PhycoBank Portal with error
this has been fixed in the context of something else. Andreas Kohlbecker

09/28/2020

04:54 PM bug #9234 (Closed): Error: Object of class stdClass could not be converted to string caused by co...
casued by this code
~~~php
function compose_cdm_specimen_or_observation_tree_entry() {
...
...
Andreas Kohlbecker
02:44 PM bug #8547 (Resolved): Default type of a newly created inReference should depend on the type of th...
The default type of the newly created inReference depends of the reference now. Please review.
Updated the title.
Katja Luther
12:53 PM bug #8874: move taxon is reverted when taxon is edited afterwards
this should be fixed. please review. Katja Luther
11:45 AM bug #8846 (Worksforme): Correctly parsed nomenclatural reference uncorrectly saved when taxon has...
This seems to be fixed, could not reproduce this problem anymore. Katja Luther

09/25/2020

02:41 PM bug #4964 (Duplicate): footnotes for taxonRelationship sources and annotations should be rendered...
closing as duplicate of #8543 Andreas Kohlbecker
10:17 AM task #9189 (Resolved): Move datasource view to taxeditor.webapp
Katja Luther
10:03 AM task #9233 (In Progress): provide feedback mechanism for euro+med
Hallo,
ich habe mich daran gemacht ein Konzept für die Umsetzung der Feedbackfunktion zu entwickeln.
Wenn man d...
Andreas Kohlbecker
 

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