Activity

From 07/31/2022 to 08/29/2022

08/29/2022

06:34 PM bug #10132 (In Progress): Coding of special characters in Vaadin/PhycoBank (in docker instance only): The problem seems to occur only when using the docker installation. When running the CDM Server on the default BGBM i... Andreas Müller
12:52 PM bug #10132 (Closed): Coding of special characters in Vaadin/PhycoBank (in docker instance only): Copy a special character from a PDF, a MS Word file. Input of a special character by a user, using the keybord of a c... Wolf-Henning Kusber
12:26 PM feature request #10127: Add full reference information to sec. references in dataportal: NaK:
eine Fußnote fände ich besser, so dass alle Referenzen direkt auf der Taxon-Seite angezeigt würden. Beiden zu... Andreas Müller
11:25 AM bug #10131: Improve media specimen formatting for type designations: NaK (zu CDM-L Formatierung):
Guter Punkt, dort ist es auch halb-richtig in der Ausgabe, und die Reihenfolge ist an... Andreas Müller
10:46 AM bug #10131 (New): Improve media specimen formatting for type designations: NaK:
... In der Ausgabe fehlt aber die Seite auf der die Abbildung zu finden ist und der Autor wird abgekürzt ausg... Andreas Müller
11:22 AM bug #10128 (Feedback): Creating new user throws NPE for invalid user names: Is there a reason why you created your own regex and did not reuse the one in eu.etaxonomy.cdm.model.permission.User ... Andreas Müller
11:18 AM bug #10128: Creating new user throws NPE for invalid user names: yes Katja Luther
11:18 AM bug #10128: Creating new user throws NPE for invalid user names: Is this for review? Andreas Müller
11:11 AM bug #10128: Creating new user throws NPE for invalid user names: There were two things to fix, first the validator only checked for empty strings not for the not allowed characters. ... Katja Luther
11:09 AM bug #10128 (Resolved): Creating new user throws NPE for invalid user names: Applied in changeset commit:taxeditor|2c6ebebf07b709b6792ff9309b6dd6d39dbb5181. Katja Luther
11:16 AM bug #10130: Error Message in dataportal: Sorry, I didn't see that this is solved already. So probably we do not necessarily need an example on test, but we ma... Andreas Müller
11:05 AM bug #10130: Error Message in dataportal: On production it is https://caryophyllales.org/cactaceae/cdm_dataportal/reference/b5d153d4-97a7-4f3d-b1f1-a0765bdd3ed... Andreas Müller
10:26 AM bug #10130 (Resolved): Error Message in dataportal: This was a problem of the default value for the parameter, this should be in '' Katja Luther
10:04 AM bug #10130 (Feedback): Error Message in dataportal: Do we have an example in a test portal? Katja Luther
09:21 AM bug #10130 (Closed): Error Message in dataportal: Use of undefined constant span - assumed 'span' (this will throw an Error in a future version of PHP) Katja Luther
11:11 AM Revision c34fc45d (taxeditor): ref #10128: use better dialog message: Katja Luther
11:08 AM Revision 2c6ebebf (taxeditor): fix #10128: adapt validator for new username: Katja Luther
10:18 AM Revision 99b21ba9 (cdm-dataportal): ref #10130: the default value for parameter needs \': Katja Luther
10:03 AM Revision cfe47149 (cdm-dataportal): ref #10130: do not create empty annotations part: Katja Luther

08/27/2022

06:19 PM Revision c193fda8 (cdmlib-apps): ref #4670 fix further E+M problems in BerlinModelImport: Andreas Müller
04:32 PM Revision c5769cfd (cdmlib-apps): ref #4670 fix BerlinModelTaxonImport for non-EuroMed: Andreas Müller
04:31 PM Revision 9c000afd (cdmlib-apps): cleanup: Andreas Müller
04:29 PM Revision 7df5b145 (cdmlib-apps): ref #9359, ref #10072 replace log4j.properties by log4j.xml in app-import: Andreas Müller
02:49 PM Revision a8df3232 (cdmlib): cleanup: Andreas Müller
02:08 PM Revision 3bcf3e7b (cdmlib-apps): adapt app-import to latest changes: Andreas Müller
01:09 PM Revision d2973f10 (cdmlib-apps): ref #10092 changes to FloreGabonActivator: Andreas Müller
01:08 PM Revision 3bb3e6dd (cdmlib-apps): Adapt EfloraTaxonImport to Credit factory change: Andreas Müller
01:07 PM Revision bab269ce (cdmlib-apps): ref #9359, ref #10072 adapt app-import to log4j2 and cleanup: Andreas Müller
01:01 PM Revision 4ef7d1e0 (cdm-vaadin): ref #9359, ref #10072 final adaptations for upgrade to log4j2 in vaadin and cleanup: Andreas Müller
12:59 PM Revision 5c4b07f0 (cdmlib): ref #9359, ref #10072 final adaptations for upgrade to log4j2 in cdmlib: Andreas Müller
12:40 PM Revision 2a2a5802 (cdmlib): cleanup: Andreas Müller

08/26/2022

10:58 PM bug #10129: Allow to create MediaSpecimen when creating specimen for a type designation: If not fast to implement please remove tag and move to other milestone. Andreas Müller
10:57 PM bug #10129 (New): Allow to create MediaSpecimen when creating specimen for a type designation: When creating a new specimen (unit) for a type designation one may currently only create a PreservedSpecimen. This sh... Andreas Müller
03:52 PM bug #10114: Problem with parser for author string with whitespace between initials: ERS:
ich hatte jetzt die Autoreninitialen vorläufig als D.C. ohne Leerzeichen eingetragen. Es genügt, das Leerzeic... Andreas Müller
03:45 PM task #7987: [DISUCSS] Do we need an editor in Reference linking to TeamOrPersonBase: AM:
Ich habe die in der Priorität nochmal nach oben geschoben, da das wirklich ein dringendes Thema ist.
Wobei di... Andreas Müller
03:42 PM bug #10128 (Closed): Creating new user throws NPE for invalid user names: ... instead the name should be validated before saving and if still an invalid name is saved the error should be cach... Andreas Müller
02:38 PM feature request #10127 (Closed): Add full reference information to sec. references in dataportal: Sec-references use the short form (author + year) in the dataportal (and other outputs). We should allow to add a foo... Andreas Müller
01:10 PM task #10009: Cleanup dependencies in TaxEditor: Online search and import works as expected, but importing from a file does not work anymore. I don't know whether thi... Katja Luther
12:02 PM task #10064: Upgrade cybertaxonomy.org to Drupal9: Please have a look whether everything works now. I checked adding an image and editing the text, also the layout is t... Katja Luther
11:51 AM task #10064 (Resolved): Upgrade cybertaxonomy.org to Drupal9: Andreas Müller wrote in #note-18:
> Also the old drupal databases should be archived?
All old drupal directories ... Katja Luther
09:58 AM task #10064: Upgrade cybertaxonomy.org to Drupal9: Andreas Müller wrote in #note-17:
> Uploading an image while editing content (in basic html mode) did not work. I alw... Katja Luther
09:47 AM bug #10126 (New): Refresh original source element after changing from dynamic reference to not dynamic reference or other way round: copied from #10057:
Also first implementation in TaxEditor implemented, see commit:29de040015b98 . However, the acce... Katja Luther
09:45 AM feature request #10057 (Closed): Add "accessed" field to OriginalSourceBase: Andreas Müller wrote in #note-7:
> This is implemented now in model and first implementations for OriginalSourceForm... Katja Luther

08/22/2022

03:07 PM bug #10116 (Closed): Create a new name denied for users: Blocker (2, role user)
Not able to create a new name in a given reference (submitted by curator or admin)
Title: ... Wolf-Henning Kusber
03:05 PM bug #10115 (Duplicate): Create new reference denied for users: Role User:
Blocker (1, role user): not able to create a new reference
Title: Create new reference denied
Backgro... Wolf-Henning Kusber
03:04 PM feature request #10096: Add new TaxonNode status and make notes field more general: Newly set status are not shown in the navigator (tested for 'taxon included in parent taxon with doubts' and 'unplace... Katja Luther
02:55 PM feature request #10096: Add new TaxonNode status and make notes field more general: When adding taxonnode status and status note, but this seems to be a problem with the note.
~~~
last remote method ... Katja Luther
02:50 PM bug #10114: Problem with parser for author string with whitespace between initials: ERS:
danke für das Ticket. Dabei ist zu beachten, dass dieser Fehler durchaus nicht immer auftritt, sondern sogar ... Andreas Müller
02:44 PM Revision 2b06f876 (taxeditor): revert remove of hibernate search in gitignore: Katja Luther
02:13 PM Revision b698cbb5 (taxeditor): revert remove of hibernate search in pom: Katja Luther
12:21 PM Revision 76a052cc (taxeditor): revert remove of hibernate search: Katja Luther
12:09 PM task #9975: Create new UML diagramms for the CDM: Can you still format the above comment as real table (see https://www.redmine.org/projects/redmine/wiki/RedmineTextFo... Andreas Müller

08/19/2022

01:59 PM Revision 349f2c7c (taxeditor): ref #10080: always remove not_designated checkbox and create new: Katja Luther
12:53 PM bug #10080: Source Element sometimes does not appear after selecting a new designation status and after creating a new type designation: Andreas Müller wrote in #note-5:
> Has this been reported by a user? If yes please add as watcher.
I can not reme... Katja Luther
12:52 PM bug #10080: Source Element sometimes does not appear after selecting a new designation status and after creating a new type designation: Andreas Müller wrote in #note-4:
> I got an NPE when changing to no status:
>
> ~~~
> last remote method : https... Katja Luther
12:43 PM feature request #10098: Implement timePeriod for Credit in TaxEditor: Timeperiod is implemented, please review. Katja Luther
12:42 PM feature request #10098 (Resolved): Implement timePeriod for Credit in TaxEditor: Applied in changeset commit:taxeditor|35c569e4b0ff1545d0d3a37d8736b4b70334441e. Katja Luther
12:42 PM Revision 35c569e4 (taxeditor): fix #10098: add timeperiod to creditelement: Katja Luther
12:35 PM Revision ce3cc213 (taxeditor): fix bug with list of last references: Katja Luther
11:50 AM feature request #10081 (Closed): Show name in source for sec ref of accepted taxon: The whitespace is removed, so I close this ticket Katja Luther
11:47 AM Revision fe8ca5d8 (cdm-dataportal): ref #10081: add secNameInSourceSeparator to separator list: Katja Luther

08/18/2022

12:43 PM bug #10108: Description for MediaSpecimen not shown even if it exists (i18n): Adding the description is implemented now, we should discuss whether it should be collapsable. Katja Luther
12:38 PM bug #10107 (Resolved): i18n bug when editing media not having a default language title: This should be fixed,please review Katja Luther
12:37 PM Revision bff0ad69 (taxeditor): ref #10107, #6228: fix default language handling: Katja Luther
11:53 AM Revision 32071906 (taxeditor): ref #10107, #6228: add remove button to MultiLanguageTextElement and fix default text: Katja Luther
11:51 AM bug #6228 (In Progress): Fix behavior of multi-language editing: Katja Luther
11:51 AM bug #6228: Fix behavior of multi-language editing: The issue that only two languages are saved is solved in the meanwhile, the missing deletion was added with the last ... Katja Luther
11:46 AM bug #8224 (Worksforme): Misleading initial language selection in TranslationWizard: This is fixed in the meanwhile, no language and no text is selected in the right part of the translation wizard Katja Luther

08/17/2022

02:25 PM bug #10102 (Closed): Non-names formatted in italics: Walter reviewed the export, sowe can close this ticket. Katja Luther

08/16/2022

03:06 PM bug #10114: Problem with parser for author string with whitespace between initials: This exception also appears when trying to update sortindex in caryo_amaranthaceae. Katja Luther

08/12/2022

01:38 PM Revision 55e5323a (taxeditor): ref #10108: with new implementation createTitle is not necessary and wrong: Katja Luther
12:27 PM feature request #10062: Migrate TaxEditor word documentation to markdown: Created all md files for Editor documentation. Katja Luther
12:27 PM bug #10114: Problem with parser for author string with whitespace between initials: The exception appears while session.flush() before starting search for matching persons in CdmGenericDaoImpl (line 638) Katja Luther
09:39 AM bug #10114 (Closed): Problem with parser for author string with whitespace between initials: mail ERS:
irgendetwas stimmt mit dem Parser nicht.
Ich bekomme diese Fehlermeldung, wenn ich lediglich eine Ini... Katja Luther

08/11/2022

01:13 PM bug #10108 (In Progress): Description for MediaSpecimen not shown even if it exists (i18n): Katja Luther
01:10 PM bug #10108: Description for MediaSpecimen not shown even if it exists (i18n): I would add the description not only a warning if a description exist.
Maybe we can make it collapsable, then it is ... Katja Luther
01:12 PM Revision 5dec995b (taxeditor): ref #10108: add description field and handling i18n text like in media element: Katja Luther
01:11 PM Revision 2fac67f3 (taxeditor): in multiLanguageText use preferredLanguage also for refresh: Katja Luther
12:06 PM bug #9007 (Closed): Enable i18n support for media description UI: The ticket can be closed because now the language text is get by "getPreferedLanguageText" Katja Luther
09:39 AM Revision cafa2d8c (cdm-dataportal): revert test: Katja Luther
09:37 AM Revision 90ddfcaa (cdm-dataportal): fix compile error: Katja Luther
09:23 AM Revision 436e6bdf (cdm-dataportal): ref #10081: remove whitespace in front of separator: Katja Luther

08/10/2022

04:07 PM Revision b403a6b1 (cdm-dataportal): ref #10081: add test for secundum name in source: Katja Luther
02:39 PM bug #10102: Non-names formatted in italics: This should be fixed, send an example to Walter for review. Katja Luther
02:39 PM bug #10102 (Resolved): Non-names formatted in italics: Applied in changeset commit:cdmlib|241046afcdfe91c97acf02d438b5c4e0f57e3c4d. Katja Luther
02:39 PM Revision 241046af (cdmlib): fix #10102: non names should be in italics: Katja Luther
02:13 PM bug #10113: Exception when opening map in details view for linux: Katja Luther wrote in #note-1:
> mail KL:
>
> ich habe mal ein bisschen recherchiert und es scheint an einer fehl... Katja Luther
02:12 PM bug #10113: Exception when opening map in details view for linux: mail KL:
ich habe mal ein bisschen recherchiert und es scheint an einer fehlenden library zu liegen, könntest Du e... Katja Luther
02:08 PM bug #10113 (New): Exception when opening map in details view for linux: mail NK:
nur in der Linux Version des TaxEditor bekomme ich nachfolgende Fehlermeldung, wenn ich in den Faktendate... Katja Luther
02:06 PM bug #10112 (New): Add a delay for the search in search dialogs: mail WB:
kann man im Auswahldialog Referenzen irgendwie eine * Eingabe am Anfang abfangen, sodass nicht gleich all... Katja Luther
01:29 PM bug #10111: Data loss e.g. when entering type information: Sometimes the dirty flag is not set when changing the status and I think that I had a case where the specimen was rem... Katja Luther
09:09 AM bug #8764 (Worksforme): moving subtree results in NPE: This should be fixed because the sortindex problem is fixed. Katja Luther

08/04/2022

08:37 AM bug #10007 (Resolved): fix reindex jobs on jobber: Andreas Müller wrote in #note-11:
> upgrading some plugins lead to a cycle in dependencies which disabled many plugi... Andreas Müller
08:34 AM bug #10007 (Feedback): fix reindex jobs on jobber: upgrading some plugins lead to a cycle in dependencies which disabled many plugins. The main reason seems to be
~... Andreas Müller

08/02/2022

11:57 PM task #10072: Upgrade fully to log4j2: Also we may want to handle jboss logging via jsl4j, this is not yet added. Andreas Müller
11:48 PM task #10072: Upgrade fully to log4j2: Maybe this helps: https://stackoverflow.com/questions/30045873/log4j2-api-cannot-find-log4j2-core-in-osgi-environment Andreas Müller
11:48 PM task #10072: Upgrade fully to log4j2: Andreas Müller wrote in #note-15:
> There is still an issue with log4j-slf4j-impl in TaxEditor. For some reason it i... Andreas Müller
11:19 PM task #10009: Cleanup dependencies in TaxEditor: Andreas Müller wrote in #note-7:
> Seems to work but still needs intensive testing and maybe some cleanup.
Cleanu... Andreas Müller
10:55 PM task #10009: Cleanup dependencies in TaxEditor: Andreas Müller wrote in #note-10:
> For the following dependencies it is unclear if they are needed. They are marked... Andreas Müller
03:43 PM task #10009: Cleanup dependencies in TaxEditor: Testing needs to be done in the "with java" verson. Andreas Müller
03:43 PM task #10009: Cleanup dependencies in TaxEditor: For the following dependencies it is unclear if they are needed. They are marked as "Only added for correct package e... Andreas Müller
10:50 PM Revision 4066bda3 (taxeditor): ref #10009 fully delete jcl-over-slf4j and log4j-slf4j-impl from git repo: Andreas Müller
10:49 PM Revision 09e461a6 (taxeditor): cleanup: Andreas Müller
10:45 PM Revision 670685c3 (taxeditor): ref #10009 re-add imaging to build.properties: Andreas Müller
10:26 PM task #10067: Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5: Please review and check if there is any remaining issue not mentioned in followup ticket #10104.
Close afterwards. Andreas Müller
10:17 PM Revision 091d1413 (taxeditor): ref #10009 try to remove spring-security-config: Andreas Müller
10:13 PM Revision 224f68c5 (taxeditor): ref #10009 try to remove spring-orm: Andreas Müller
10:09 PM Revision 42df8aed (taxeditor): ref #10009 try to remove spring-context-support: Andreas Müller
10:06 PM Revision 6c63036b (taxeditor): ref #10009 try to remove json-lib-2.4-jdk15: Andreas Müller
10:00 PM Revision 2988a396 (taxeditor): ref #10009 try to remove hibernate-commons-annotations (cont.): Andreas Müller
09:59 PM Revision 8de239c1 (taxeditor): ref #10009 try to remove hibernate-search (cont.): Andreas Müller
09:59 PM Revision 8e45e5fb (taxeditor): ref #10009 try to remove hibernate-search: Andreas Müller
09:50 PM Revision aed150fb (taxeditor): Revert "ref #10009 try to remove commons-imaging" (cont.): Andreas Müller
09:39 PM Revision caf6fb19 (taxeditor): Revert "ref #10009 try to remove commons-imaging": This reverts commit 2656c76547245cbe1b8abb2ddf597c5c95e16d95. Andreas Müller
09:32 PM Revision fde5fee1 (taxeditor): ref #10009 try to remove hibernate-commons-annotations: Andreas Müller
09:23 PM Revision 289bddaa (taxeditor): ref #10009 try to remove xercesImpl: Andreas Müller
09:17 PM Revision 2656c765 (taxeditor): ref #10009 try to remove commons-imaging (cont.): Andreas Müller
09:16 PM Revision da85ff94 (taxeditor): ref #10009 try to remove commons-imaging: Andreas Müller
08:52 PM Revision 92ecc4db (taxeditor): remove duplicated commons-collections4 entry: Andreas Müller
08:51 PM Revision 1b54fed6 (taxeditor): ref #10009 fully remove commons-collections dependeny: Andreas Müller
08:28 PM Revision e941d346 (cdmlib): ref #10009 replace CircularFifoBuffer by ArrayBlockingQueue to avoid commons-collections: Andreas Müller
08:14 PM Revision 6779d238 (taxeditor): ref #10009 re-add log4j-slf4j-impl and jcl-over-slf4j to gitignore: Andreas Müller
08:11 PM Revision 544ca435 (taxeditor): ref #10009 add spring-jdbc for running tests (cont.): Andreas Müller
08:05 PM Revision 16fa9188 (taxeditor): ref #10009 add spring-jdbc for running tests: Andreas Müller
07:31 PM Revision dbc272fa (taxeditor): ref #10009 fix classpath entry for jcl-over-slf4j (cont.): Andreas Müller
07:18 PM Revision f875753d (taxeditor): ref #10009 fix classpath entry for jcl-over-slf4j: Andreas Müller
06:05 PM Revision 3075786e (taxeditor): ref #10009 add jcl-over-slf4j and log4j-slf4j-impl as non-ignored libraries: Andreas Müller
05:42 PM Revision fae1500b (taxeditor): cleanup: Andreas Müller
05:40 PM Revision fe77d8d4 (taxeditor): ref #10009 add commons-maths again as it is required by editor: Andreas Müller
04:54 PM task #9975: Create new UML diagramms for the CDM: UPDATE:
three tools were reconsidered:
| |UML_Designer(alignt center) |Papyrus(align cente... Belen Escobari
04:38 PM feature request #10083: Add name relationship type "avoids homonym of"/"causes replacement name": Mail sent to datamanager to adapt their data (list of effected DBs see #note-5).
Katja, could you please check if ... Andreas Müller
03:52 PM Revision bf76e3f5 (taxeditor): ref #10009 remove invalid line in build.properties: Andreas Müller
03:40 PM Revision 81bc5519 (taxeditor): ref #10009 remove maybe unused dependecies in build.properties: Andreas Müller
03:39 PM Revision 1d6dedc4 (taxeditor): ref #10009 put maybe unused dependecies to the end in build.properties: Andreas Müller
03:30 PM feature request #10087: Add taxon node source to status notes in cdmlight: Sent mail to WGB for final testing.
Katja, could you please review? Andreas Müller
03:27 PM bug #10089: Order TypeDesignationSetContainer by status type: Only implemented for cdmlight. Data portal does not use the TypeDesignationSetContainer yet. Andreas Müller
03:22 PM bug #10089: Order TypeDesignationSetContainer by status type: Asked WGB for testing (2022-08-02).
Katja, can you please review? Andreas Müller
02:59 PM Revision 8923a5b4 (taxeditor): ref #10009 check if the "Only added for correct package export" dependencies are realy needed (including commons-math3): Andreas Müller
02:42 PM Revision f2f77749 (taxeditor): javadoc: Andreas Müller
02:19 PM bug #10078 (Feedback): Symbol and details view title of misapplied name type is not the same as shown in the type combo element: Bug is fixed. Notification sent to data managers.
Katja, can you still clean up the code a bit and then close the ... Andreas Müller
01:46 PM bug #10078: Symbol and details view title of misapplied name type is not the same as shown in the type combo element: Instances with Non-default-MAN:
Nepenthaceae: 1 partial, ~10 pp => Mail sent to WGB
Caryo_spp: 1 partial => Mail se... Andreas Müller
01:45 PM bug #10078: Symbol and details view title of misapplied name type is not the same as shown in the type combo element: Non-default MAN:
~~~
SELECT tr.id relId, dtb.titleCache relType, tb1.titleCache MAN, tb2.titleCache accTaxon
FROM De... Andreas Müller

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