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From 05/12/2022 to 06/10/2022

06/10/2022

02:55 PM task #10073 (New): Remove all docbkx related code/files from cdmlib
... and maybe others. They can be found at {parent}\src\docbkx\ and in parent-pom.
Probably also the changes folde...
Andreas Müller

06/09/2022

12:40 PM task #10072 (Closed): Upgrade fully to log4j2
We already upgraded to log4j2 in #9359.
~~However, the class eu.etaxonomy.cdm.opt.config.LoggingConfigurer is not ...
Andreas Müller

06/08/2022

10:57 AM bug #10071: TaxonNodeDtos should be created directly not from taxon objects
There were some follow up fixes, because the taxonnode dto created with SortableTaxonNodeQueryResult was not complete... Katja Luther

06/07/2022

01:19 PM bug #10033 (In Progress): For new FeatureTree only uuid is shown in dataportal
Katja Luther
01:19 PM bug #10033 (Resolved): For new FeatureTree only uuid is shown in dataportal
We need to adapt the taxeditor implementation, so that not the titlecache but the representation is used. Katja Luther
12:36 PM bug #10033: For new FeatureTree only uuid is shown in dataportal
Terms contain an termrepresentation object, this is empty for terms/termcollections created in taxeditor. As a first ... Katja Luther

06/02/2022

02:33 PM bug #10034 (Resolved): Flat feature tree throws exception
Now moving unsaved nodes is handled correctly. Please reviw. Katja Luther
09:41 AM bug #10071 (In Progress): TaxonNodeDtos should be created directly not from taxon objects
This is done for the search of the taxonnodes for a specific taxon and also for the search in a subtree. Katja Luther
08:50 AM bug #10071 (Closed): TaxonNodeDtos should be created directly not from taxon objects
The webservice getting the taxonnodeDtos for a taxon, first gets the taxon object and then creates the Dtos for the t... Katja Luther

06/01/2022

01:58 AM bug #10034 (In Progress): Flat feature tree throws exception
Andreas Müller wrote in #note-2:
> The problem does only seem to appear if you try to move a node before you save. I...
Andreas Müller
12:00 AM task #10009 (In Progress): Cleanup dependencies in TaxEditor
Andreas Müller

05/31/2022

02:43 PM bug #10034: Flat feature tree throws exception
Could not reproduce this problem with the actual nightly build.
Steps I tried to reproduce the problem:
* creat...
Katja Luther
01:12 PM feature request #10070 (New): Upgrade to hibernate 6+
Before start upgrade to hibernate 5.6.x if not yet done. There is still a problem with the TaxonGraphHibernateListene... Andreas Müller
12:44 PM bug #10056 (Resolved): Make Reference.Accessed deletable in TaxEditor
Added a delete button, please review. Katja Luther
11:57 AM bug #10059: Link for stored under and identification on specimen page does not work correctly
please review. Katja Luther
11:57 AM bug #10059: Link for stored under and identification on specimen page does not work correctly
The path to the name needs to be processed by url(), then the correct link is used. Katja Luther
11:56 AM bug #10059 (Resolved): Link for stored under and identification on specimen page does not work correctly
Applied in changeset commit:cdm-dataportal|c90f5440175074c6a350ad24fdaba0c0b6b9ae74. Katja Luther
10:22 AM bug #10059: Link for stored under and identification on specimen page does not work correctly
This problem occurs because there is an element data-cdm-render-path containing the actual render path and this is us... Katja Luther
08:28 AM task #10067 (In Progress): Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5
Andreas Müller
08:16 AM feature request #10069 (New): Upgrade hibernate search and lucene to hs6+ and lucene 8+
Lucene 6+ seems to require hs6+ as there is a strange dependency on org.apache.lucene.document.Field.Index and ...Fie... Andreas Müller

05/30/2022

10:59 PM bug #5477 (Resolved): lucene index not updated in all cases after Taxon.addMisappliedName
Was not fully fixed yet. Problem reoccurred after upgrading to hibernate-search 5.7.3. "ContainedIn" was still missin... Andreas Müller
10:47 PM bug #7487 (Resolved): Full text misapplied name search with area filter uses fixed relation type uuid
Solved by adding also proparte and partial MAN and partial synonym relationship type subqueries. Also related to fina... Andreas Müller
11:54 AM bug #10068 (Closed): Changing focus to accepted taxon does not work
After opening a the name editor with focus on a synonym, the change of focus to the accepted taxon does not work, res... Katja Luther
11:27 AM bug #10060: Exception when adding kind-of-unit information to a field unit
Katja Luther wrote in #note-1:
> I think we should not allow to set a kind of unit for a field unit, so I would remo...
Katja Luther
09:18 AM bug #10060 (In Progress): Exception when adding kind-of-unit information to a field unit
I think we should not allow to set a kind of unit for a field unit, so I would remove the possibility to edit the kin... Katja Luther

05/25/2022

10:49 AM task #3722 (Resolved): Using @OrderColumn does not work in trees
Probably solved, still needs intensive testing and code cleanup. Andreas Müller
10:29 AM feature request #7861 (In Progress): TaxonGraphHibernateListener: inject the ITaxonGraphDao into TaxonGraphBeforeTransactionCompleteProcess
A somehow similar solution was implemented in 8c6b6172722d to adapt the TaxonGraphBeforeTransactionCompleteProcess to... Andreas Müller
10:23 AM feature request #7648: Create taxonrelation to genus or species when subordinate names are created
Andreas Kohlbecker wrote in #note-10:
> "Session is closed!"-problem is solved now.
This fix was only a workaroun...
Andreas Müller

05/23/2022

03:56 PM task #3722 (In Progress): Using @OrderColumn does not work in trees
Andreas Müller
10:57 AM task #3722: Using @OrderColumn does not work in trees
sortIndex needs to be handled newly in hibernate5.2 so we can try to handle this ticket, too. Andreas Müller
03:55 PM task #8127 (In Progress): [Reminder] to check if Hibernate Null Value bug still exists
Andreas Müller
03:55 PM task #8127: [Reminder] to check if Hibernate Null Value bug still exists
HHH_9751_Util is closed in the meanwhile (https://hibernate.atlassian.net/browse/HHH-9751) and we probably can remove... Andreas Müller
01:04 PM bug #10012 (Closed): Fix failing SpecimensTreeViewTest for dataportals after debian11 migration
Tests are ok again, so we can close this ticket. Katja Luther
10:03 AM bug #10012: Fix failing SpecimensTreeViewTest for dataportals after debian11 migration
php5 needed to be disabled and php7.4 enabled. This is done and pages with jstor image viewer as url are displayed co... Katja Luther
10:34 AM task #10067: Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5
mvn clean install –fail-never (or just –fn)
https://maven.apache.org/surefire/maven-surefire-plugin/examples/single-...
Andreas Müller

05/20/2022

06:03 PM task #10067 (Closed): Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5
https://stackoverflow.com/questions/50207195/how-to-upgrade-hibernate-from-version-4-3-to-5-2-for-migration-to-jdk-10... Andreas Müller
02:50 PM task #10064 (Resolved): Upgrade cybertaxonomy.org to Drupal9
cybertaxonomy.org is updated to 9.3 and using core-recommended (see https://github.com/drupal/core-recommended), the ... Katja Luther

05/18/2022

11:05 AM feature request #10066 (New): Secundum reference should be clickable
The secundum reference should be clickable to open the details of the reference. Katja Luther

05/17/2022

11:46 AM task #10064 (In Progress): Upgrade cybertaxonomy.org to Drupal9
Updated to 8.9, now the update to drupal 9 should work.
-> To check whether everything is compatible with drupal 9, ...
Katja Luther

05/16/2022

05:21 PM bug #10007: fix reindex jobs on jobber
There are/were multiple problems.
TRIGGER-cdmserver-reindex:
1. No groovy was installed at all on the server
...
Andreas Müller
08:45 AM task #10064: Upgrade cybertaxonomy.org to Drupal9
see https://www.drupal.org/docs/upgrading-drupal/how-to-prepare-your-drupal-7-or-8-site-for-drupal-9/upgrading-a-drup... Katja Luther

05/13/2022

12:07 PM task #10006: Check backups fully work after upgrades to debian 11
**edit-backup:**
The monthly for edit-community seems to be made every week instead every month.
Last monthlies are...
Andreas Müller
11:42 AM feature request #10003 (Closed): Implement specimen status in Data portal
Seems to work as expected and can be closed. Andreas Müller

05/12/2022

10:51 PM task #9991: Move content for users and admins from site.xml's to cybertaxonomy.org/drupal
This was blocked by problems with D8 version. So we may want to wait until D9 is installed (#10064) Andreas Müller
10:44 PM task #9994 (Closed): Tasks from documentation meeting 3/22
For all tasks from https://wiki.bgbm.org/bdinotes/index.php/BDI_332 tickets have been created. So we can close this t... Andreas Müller
10:41 PM task #10064 (Resolved): Upgrade cybertaxonomy.org to Drupal9
... as support for Drupal8 already ended this is an urgent issue.
#9994: "Drupal8 needs to be upgraded to D9/10"
Andreas Müller
10:36 PM task #10063 (New): Move online tutorials to single place
"we put all online tutorials a single place, preferable at https://cybertaxonomy.org/download/manual/ or https://cybe... Andreas Müller
10:28 PM feature request #10062 (New): Migrate TaxEditor word documentation to markdown
Word documents Manual-EDIT-Platform-01-XXX.pdf, -02 and -03 should be fully migrated to markdown for testing if every... Andreas Müller
10:24 PM bug #10061 (New): Current in-TaxEditor documentation needs to be removed
... (and replaced by up-to-date docmentation if possible, pdf?, html?)
see meeting 2022-03-18 (https://wiki.bgbm.o...
Andreas Müller
06:12 PM task #10015 (Duplicate): Cleanup EDIT server pages on BDI notes
Close this as duplicate as #10042 has a bit larger focus. Andreas Müller
06:09 PM task #10015 (In Progress): Cleanup EDIT server pages on BDI notes
I created an Retire and Archive section on the main page. Andreas Müller
06:05 PM discussion #7917 (In Progress): Revise ReferenceSystemTerms
Andreas Müller
05:55 PM bug #9007: Enable i18n support for media description UI
There seems to be a related open issue with the details view for the MediaSpecimen in the specimen tree editor.
* i...
Andreas Müller
05:54 PM bug #9007 (Feedback): Enable i18n support for media description UI
This to me seems to be fixed. Can you please verify and close the ticket if possible.
Andreas Müller
05:13 PM feature request #3756: Missing data and layout improvements for MediaSpecimen in data portal
I checked the MediaSpecimen and changed the ticket in the way that it becomes an implementation ticket. Andreas Müller
02:55 PM feature request #3756: Missing data and layout improvements for MediaSpecimen in data portal
Many things happened since this ticket was created. We need to check if there are still open issues. Andreas Müller
02:33 PM bug #10060 (In Progress): Exception when adding kind-of-unit information to a field unit
When trying to edit the "kind of unit" field of a field unit in specimen-tree-editor details view the following error... Andreas Müller
02:12 PM feature request #6866: Improve specimen page
Move back to original milestone. Andreas Müller
02:09 PM feature request #6866 (Closed): Improve specimen page
This can be closed. Open issues were moved to follow-up ticket #10058 (missing attributes) and related ticket #9879 (... Andreas Müller
12:19 PM bug #10059 (Closed): Link for stored under and identification on specimen page does not work correctly
**Stored under** links to e.g. https://portal.cybertaxonomy.org/salvador/cdm_dataportal/occurrence/cdm_dataportal/nam... Andreas Müller
12:17 PM feature request #10058 (New): Further improve specimen page (factual data, extensions,
follow up for #6866
In #6866 data has been atomized and structured already. However, there are datatypes missing. ...
Andreas Müller
11:27 AM feature request #3307 (Worksforme): optionally reduce complexity in specimen display
I guess this is fixed more or less with current implementations of 3 representations for specimens and the possibilit... Andreas Müller
 

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