Activity

From 11/20/2019 to 12/19/2019

12/19/2019

05:14 PM bug #8739 (Resolved): remaining issues for description detail page: AS far as I see, this ticket is either solved or remaining issues are copied to new tickets.
Therefore I suggest c... Andreas Kohlbecker
05:08 PM task #8786 (Feedback): Display of mean value with min max: Andreas Kohlbecker
05:08 PM task #8786 (Resolved): Display of mean value with min max: > abgesehen davon, dass die Mittelwertangabe zwischen Min und Max unüblich ist, ... Eine bessere Darstellung wär... Andreas Kohlbecker
03:00 PM feature request #8769 (New): Biocase import configuration should be shown when clicking on import button: Andreas Kohlbecker wrote:
> I fear that just opening the import config dialog does not really help.
> I suggest to ... Andreas Müller
02:59 PM feature request #8471: Computed descriptions should be disabled in TaxEditor: Andreas Müller wrote:
> Andreas Kohlbecker wrote:
> > I find it very useful for debugging that computed description... Andreas Kohlbecker
02:28 PM feature request #8471: Computed descriptions should be disabled in TaxEditor: Andreas Kohlbecker wrote:
> I find it very useful for debugging that computed descriptions can be viewed and modifie... Andreas Müller
02:40 PM bug #8785: Move functionality of buttons to context menu of the character matrix: Katja Luther wrote:
> this should be possible in character matrix. I have to test this.
yes, it should be handled... Andreas Müller
02:35 PM bug #8785 (In Progress): Move functionality of buttons to context menu of the character matrix: this should be possible in character matrix. I have to test this. Katja Luther
11:58 AM bug #8785: Move functionality of buttons to context menu of the character matrix: Also this one I put to current milestone for same reason as #8784 Andreas Müller
11:58 AM bug #8785 (Resolved): Move functionality of buttons to context menu of the character matrix: The issue is described in #8784 but I created a new ticket as it is as deleting a specimen description (which is hand... Andreas Müller
02:30 PM bug #8783: Massive Heap consumption in server instance opening the Description-Matrix editor: As this is a critical issue I suggest to put it into 5.13. (5.12 is probably not possible as the task is difficult). ... Andreas Müller
02:23 PM bug #8784: Deleting a specimen description not possible: fixing the delete handling in deletehandler of the factual data view. Now the deletion of descriptions and descriptio... Katja Luther
11:57 AM bug #8784 (In Progress): Deleting a specimen description not possible: this is already in process because I already found this problem while working on #8782 Katja Luther
11:54 AM bug #8784: Deleting a specimen description not possible: I put this into the current milestone because it is a blocker for undoing incorrect/unwanted data entries. Andreas Müller
11:53 AM bug #8784 (Closed): Deleting a specimen description not possible: Currently it seems to be impossible to delete a specimen description.
In the specimen LIST editor specimen descrip... Andreas Müller
02:21 PM feature request #8781 (Closed): Descriptions (aggregated): futher improvements: Looks fine now Andreas Müller
01:51 PM feature request #8781 (Resolved): Descriptions (aggregated): futher improvements: Andreas Müller wrote:
> Now the semicolon is missing everywhere, it should be removed ONLY at the end:
>
Proble... Andreas Kohlbecker
01:19 PM feature request #8781: Descriptions (aggregated): futher improvements: An example can be found here: http://test.e-taxonomy.eu/dataportal/preview/greece_bupleurum/cdm_dataportal/taxon/8718... Andreas Müller
01:19 PM feature request #8781 (Feedback): Descriptions (aggregated): futher improvements: Andreas Müller
01:19 PM feature request #8781: Descriptions (aggregated): futher improvements: Now the semicolon is missing everywhere, it should be removed ONLY at the end:
![](picture967-1.png)
The capita... Andreas Müller

12/18/2019

04:38 PM feature request #8471: Computed descriptions should be disabled in TaxEditor: I find it very useful for debugging that computed descriptions can be viewed and modified in the editor. Can't we all... Andreas Kohlbecker
02:43 PM bug #8783 (Closed): Massive Heap consumption in server instance opening the Description-Matrix editor: This was observed with a locally running cdmlib-remote-webapp instance configured with 700 MB of Heap:
![](pic... Andreas Kohlbecker
01:39 PM bug #8782 (Closed): Delete a description included in a CdmSource should not be possible: mail AM:
ich habe gerade DescriptionBase gelöscht (aus dem Facts View heraus), die noch verlinkt waren über eine C... Katja Luther
01:24 PM bug #8780: Repair sortindex does not work on TermTree index: This should be fixed. Please review. Andreas Müller
11:57 AM bug #8780 (Resolved): Repair sortindex does not work on TermTree index: Applied in changeset commit:cdmlib|dad659722b698863a2dee711782748b0de216a71. Andreas Müller
09:16 AM bug #8780 (Closed): Repair sortindex does not work on TermTree index: Andreas Müller
12:21 PM feature request #8781 (Resolved): Descriptions (aggregated): futher improvements: ticket complete Andreas Kohlbecker
12:08 PM feature request #8781 (Closed): Descriptions (aggregated): futher improvements: Hallo Andreas,
1. am Ende der aggregated descriptions gibt es derzeit im noch ein überflüssiges Komma. Könntest du... Andreas Kohlbecker
11:22 AM feature request #7981 (In Progress): Add configuration UI for matrix description aggregation: Katja Luther

12/17/2019

03:55 PM bug #8566 (Rejected): Recursive aggregation for common parent taxon does not work if not in data set: This is expected behavior, not a bug IMO. However, with the UI aggregation trigger we may have more possibilities to ... Andreas Müller
03:47 PM feature request #8686: Support CdmLink sources in bibliography: An example could be shown here: http://test.e-taxonomy.eu/dataportal/preview/caryophyllales_spp/cdm_dataportal/taxon/... Andreas Müller
03:46 PM feature request #8686 (Feedback): Support CdmLink sources in bibliography: Andreas Kohlbecker wrote:
> **Note**: The links to the taxa are having a fragment which directly focuses on the "Agg... Andreas Müller
03:40 PM bug #8779 (Resolved): Description page: use render_taxon_or_name() for creating the page and description title and taxon links: after harmonization the top of the page now looks like
![](picture451-1.png)
If more detailed display of the ta... Andreas Kohlbecker
03:20 PM bug #8779 (Closed): Description page: use render_taxon_or_name() for creating the page and description title and taxon links: in `compose_description_table()` the `render_taxon_or_name()` method must be used for portal wide consistend display ... Andreas Kohlbecker
03:35 PM feature request #8777: Make visiblity of CDM Source configurable: Andreas Müller wrote:
> ... hmm, maybe an even better solution is to show the field only if data exists. Is this pos... Andreas Müller
03:08 PM feature request #8777: Make visiblity of CDM Source configurable: ... hmm, maybe an even better solution is to show the field only if data exists. Is this possible? Andreas Müller
03:00 PM feature request #8777 (Resolved): Make visiblity of CDM Source configurable: see #8688, for some projects the CDM Source should not be visible (because not used). This is similar to ID in Source... Andreas Müller
03:15 PM feature request #8688 (Feedback): Make OriginalSourceBase.cdmSource visible in TaxEditor: The current solution shows titleCache+uuid for identifiable entities. This is too much. For now we need only the titl... Andreas Müller
03:12 PM feature request #8778 (New): Have explicit subclass for CdmSourceLink sources: copied from #8688: Possible open questions related: do we want to have a new subclass for OriginalSourceBase which on... Andreas Müller
02:27 PM feature request #8724 (Closed): Allow OriginalSource to link to Taxon: I think we can close this. If problems occurr we may reopen or immediately fix. Andreas Müller
02:14 PM feature request #8044 (Feedback): Add "Move to..." menu to term editor: * For this usecase the title and the description in the term selection wizard needs to be adapted. It should be somet... Andreas Müller
01:56 PM bug #7994 (Duplicate): Implement allowDuplicates for term trees in TaxEditor: This is a duplicate for #8477, #8776 Andreas Müller
01:53 PM feature request #8476: Implement support for TermCollection.isFlat in TaxEditor: Note: saving often does not work due to issues to be solved in #8774 Andreas Müller
01:47 PM feature request #8476 (In Progress): Implement support for TermCollection.isFlat in TaxEditor: Only the flag is editable until now so I put this back to InProgress. Andreas Müller
01:53 PM feature request #8474: Make TermCollection.orderRelevant usable for TermTrees: Note: saving often does not work due to issues to be solved in #8774 Andreas Müller
01:50 PM feature request #8474 (In Progress): Make TermCollection.orderRelevant usable for TermTrees: Only editing the flag is implemented until now so I put it back to InProgress Andreas Müller
01:52 PM bug #8776: Open issues for TermCollection.allowDuplicates handling in TaxEditor: Note: saving often does not work due to issues to be solved in #8774 Andreas Müller
01:25 PM bug #8776 (Closed): Open issues for TermCollection.allowDuplicates handling in TaxEditor: * ~~The error message currently looks like an unhandled error. The message should only inform about the fact that dup... Andreas Müller
01:41 PM feature request #8477 (Closed): Implement support for TermCollection.allowDuplicates in TaxEditor: Generally this works but there are some open issues. I moved them all to a new ticket: #8776 Andreas Müller
12:19 PM feature request #8242 (Closed): Implement filtered combo boxes for state selection in CharacterMatrix: This is generally implemented. There are follow up tickets like #8254 and #8775 Andreas Müller
12:14 PM bug #8313 (Closed): Multiple categorical data get deleted when clicked on in Character Matrix: This seems to work now. There are issues with the general (rapid) data entry of categorical data into the matrix. The... Andreas Müller
12:12 PM feature request #8775 (In Progress): Improve (rapid) data entry into characater matrix for categorical data: Quantitative data can be entered into the matrix very fast by only using the keyboard via return, left, right and num... Andreas Müller
11:50 AM feature request #8665 (Closed): Rename "New" to "New Tree" in Term Tree editors: Andreas Müller
11:44 AM bug #8751: Replace saveOrUpdate() in AbstractTermTreeEditor: This is probably more or less a duplicate for #8774 and will be fixed by #8774 Andreas Müller
11:41 AM bug #8663 (Duplicate): LIE when trying to save a tree node: This is probably a duplicate for #8744 Andreas Müller
11:38 AM bug #8744 (Closed): LazyInitializationException (LIE) saving the Character Editor: The LIE itself seems to be fixed by switching to merge() but there are still very serious issues related to saving of... Andreas Müller
11:28 AM bug #8744: LazyInitializationException (LIE) saving the Character Editor: Andreas Müller wrote:
> hmm, it does not really seem to be the problem, but I found that there seems no session to b... Andreas Müller
11:36 AM bug #8774 (Closed): Reimplement term tree editors to implement the general save strategy: Currently term trees save changes in the hierarchy (including new terms/nodes) immediately in the DB. This is against... Andreas Müller
11:24 AM bug #8748 (Closed): Supported state vocabularies should be ordered: This is fixed and is a very nice and important feature. Andreas Müller
11:22 AM feature request #8755 (Closed): Show all structure/property trees in CharacterEditor: Follow up issues are moved to extra tickets so we can close this one. Andreas Müller
11:20 AM feature request #8773 (New): [DISCUSS] Allow editing structure and properties tree in Character Editor: copied from #8755#note-3:
"with the current state of the structure tree it is sometimes wanted to extend this tree... Andreas Müller
10:23 AM feature request #8772 (New): Recognize Character duplicates: Characters constructed from structure and property (and structural modifier) can be recognized as duplicates by this ... Andreas Müller
09:10 AM feature request #8771 (Feedback): display of average value with precision so that it differs from min and max by one digit: do you agree with my suggestion? Andreas Kohlbecker
09:07 AM feature request #8771 (Resolved): display of average value with precision so that it differs from min and max by one digit: The display of decimal place for average value should be adjusted so that it differs from the values on min and max (... Andreas Kohlbecker

12/11/2019

09:54 PM bug #8511: The structure path in the character details view should have a line break: .. and this is probably a no-brainer? Andreas Müller
09:52 PM bug #8338: Newly created structural modifier terms are not available in details view: This is also a bit annoying, therefore I move it to 5.12 in case time is there to fix it. Andreas Müller
06:19 PM bug #8736 (Resolved): LazyInitializationException (LIE) during adding Specimens to Matrix Editor: Applied in changeset commit:cdmlib|9e89976076d8a735426f40e4cebb49c42bd5ab33. Patrick Plitzner
06:09 PM feature request #8688: Make OriginalSourceBase.cdmSource visible in TaxEditor: Current implementation shows the titleCache if it is an IdentifiableEntity. It shows the UUID if it is a CdmBase. Oth... Patrick Plitzner
06:08 PM feature request #8688 (Resolved): Make OriginalSourceBase.cdmSource visible in TaxEditor: Applied in changeset commit:taxeditor|5d945a6ece2394f970845815a0dc7f08bb70e1b4. Patrick Plitzner
05:43 PM task #8716 (Feedback): Configure taxeditor to run with GTK2 in linux: On my home desktop PC with Linux Mint, Cinnamon desktop I have no problems but I also did not have any problems befor... Patrick Plitzner
05:26 PM feature request #8044: Add "Move to..." menu to term editor: This is not not experimental anymore.
Known issues when reviewing:
* It is still possible to select multiple te... Patrick Plitzner
05:25 PM bug #8763 (Duplicate): Remaining issues for "Move term" in term editor: Known issues:
* ~~It is still possible to select multiple terms in the term search dialog but a warning will appea... Patrick Plitzner
05:07 PM feature request #8755: Show all structure/property trees in CharacterEditor: Andreas Müller wrote:
> We tested intensively today during the integrated taxonomy course. It worked fine.
>
> 2 ... Patrick Plitzner
12:36 PM feature request #8755 (Feedback): Show all structure/property trees in CharacterEditor: I am passing this ticket to you since the questions in comment 3 are addressed to the implementer. Andreas Kohlbecker
03:36 PM feature request #8762 (New): [DISCUSS] Do we need/want to report a count for missing data in aggregated descriptions: ... for reasons why this could be useful see #8759#note-4 Andreas Müller
03:33 PM feature request #8759: Description aggregation : suppress state present when more details are available: This case usually is dirty or incomplete data. Dirty data should be shown on the portal to make it findable (correcta... Andreas Müller
03:00 PM feature request #8759 (Feedback): Description aggregation : suppress state present when more details are available: I adapted the description to avoid misunderstandings
In your comment you seem to suggest to show the following si... Andreas Kohlbecker
02:43 PM feature request #8759: Description aggregation : suppress state present when more details are available: No this is a misunderstanding. The requirement is:
Do not show character and value for characters of property pres... Andreas Müller
01:19 PM feature request #8759: Description aggregation : suppress state present when more details are available: This should be handled already during the aggregation process. Andreas Kohlbecker
01:18 PM feature request #8759 (Resolved): Description aggregation : suppress state present when more details are available: In character trees frequently a parent character is being used to determine the presence or absence of subordinate ch... Andreas Kohlbecker
03:17 PM bug #8718 (Resolved): polytomousKey page: better handling of invalid uuids: Andreas Müller wrote:
> Instead of saying "page not found" can't we do the same as for taxa and say "xxx does not ex... Andreas Kohlbecker
02:49 PM bug #8718 (Feedback): polytomousKey page: better handling of invalid uuids: Instead of saying "page not found" can't we do the same as for taxa and say "xxx does not exist". This sounds a bit m... Andreas Müller
02:41 PM bug #8718: polytomousKey page: better handling of invalid uuids: done
please review I you have time to:
http://test.e-taxonomy.eu/dataportal/preview/cichorieae/cdm_dataportal/n... Andreas Kohlbecker
01:58 PM bug #8718 (Resolved): polytomousKey page: better handling of invalid uuids: Applied in changeset commit:cdm-dataportal|4d9660ef5a78a9d741385db13549716889ceabb1. Andreas Kohlbecker
02:24 PM feature request #8756 (Resolved): Refresh button for structure tree and property tree in Character Editor: Applied in changeset commit:taxeditor|a0f4664b4135fac8549cf6a0b0836acb248abbb8. Patrick Plitzner
01:46 PM feature request #8756 (In Progress): Refresh button for structure tree and property tree in Character Editor: Patrick Plitzner
02:13 PM feature request #8761 (Closed): Remove TaxonName_NomenclaturalStatus MN table: As a status belongs always to exactly 1 name an MN table is not necessary Andreas Müller
01:41 PM bug #8760 (New): Presentation and linking of molecular data in specimen table too unclear: Hallo,
mir ist auf http://test.e-taxonomy.eu/dataportal/preview/campanulaceae/cdm_dataportal/taxon/48249487-e921... Patrick Plitzner
01:10 PM feature request #8758 (Closed): Aggregated Descriptions: order states by frequency: Most frequent states should be displayed first.
Another option to order the stated would be the term order as defi... Andreas Kohlbecker
10:36 AM bug #8757 (Resolved): ArrayIndexOutOfBoundsException in term combo: Katja Luther
10:34 AM bug #8757 (Closed): ArrayIndexOutOfBoundsException in term combo: … im Details View, beim Versuch Leaf length über Facts View einzugeben. Leaf length hat recommendedMeasurementUnit „... Katja Luther

12/10/2019

11:56 PM feature request #8028: Better representation of web app media in the image gallery: AM:
Grundsätzlich sollten wir zwischen wirklichen Media und ExternalLinks unterscheiden. Das sind 2 Dinge, Media k... Andreas Müller
05:25 PM feature request #8028 (New): Better representation of web app media in the image gallery: Andreas Kohlbecker
05:24 PM feature request #8028: Better representation of web app media in the image gallery: Alternative suggestion from Walter [06.12.19]:
Am wichtigsten wäre es mir, den grauen Kasten loszuwerden (das find... Andreas Kohlbecker
06:57 PM feature request #8755: Show all structure/property trees in CharacterEditor: We tested intensively today during the integrated taxonomy course. It worked fine.
2 questions:
1) with the cu... Andreas Müller
06:57 PM feature request #8756: Refresh button for structure tree and property tree in Character Editor: I assigned this to KL for now. PP if you think it is a no-brainer and you can immediately do it please feel free to t... Andreas Müller
06:55 PM feature request #8756 (Feedback): Refresh button for structure tree and property tree in Character Editor: copied from #8755, explanations see there Andreas Müller
05:36 PM task #8741 (Closed): Create test for MapServices to test if they support https: done, see https://dev.e-taxonomy.eu/gitweb/edit-map-service-test.git/commit/9603e65de34cde146ba1020f0ed5e1290bf558c7 Andreas Kohlbecker
11:00 AM bug #8747: Matrix Editor: Can not unset categorical data: Sorry, but I consider the priority of this ticket here as being much higher than the priority of #8755. #8755 does no... Andreas Kohlbecker
09:59 AM bug #8747 (New): Matrix Editor: Can not unset categorical data: This should be done sooner or later but it has not highest priority so not a task for PP anymore. Change user and ver... Andreas Müller
09:15 AM bug #8747 (In Progress): Matrix Editor: Can not unset categorical data: Please change it so that checkbox state is toggled each time when being clicked. Andreas Kohlbecker

12/09/2019

06:16 PM feature request #8755 (Resolved): Show all structure/property trees in CharacterEditor: Applied in changeset commit:taxeditor|6803fca4a0c8065b5c4227de7ee853b7969e5332. Patrick Plitzner
03:55 PM feature request #8755 (Closed): Show all structure/property trees in CharacterEditor: Currently you can only choose one tree for each term type Patrick Plitzner
04:08 PM bug #8663 (Feedback): LIE when trying to save a tree node: I cannot reproduce this. I also tested saving some changes for this character tree on rem_conf_am.
If you cannot r... Patrick Plitzner
01:38 PM bug #8663 (New): LIE when trying to save a tree node: No this is not a duplicate. It looks like it happened in the term tree editor, not in the Character editor. Andreas Müller
12:57 PM bug #8663 (In Progress): LIE when trying to save a tree node: Is this a duplicate for 8744? Andreas Müller
04:03 PM bug #8747 (Feedback): Matrix Editor: Can not unset categorical data: Andreas Kohlbecker wrote:
> I don't consider this as user friendly. Is this default behavior of the nattable?
>
>... Patrick Plitzner
03:27 PM bug #8748 (Resolved): Supported state vocabularies should be ordered: This should be fixed now, please review. Katja Luther
12:51 PM bug #8748: Supported state vocabularies should be ordered: This is handled by KL as far as I know. Andreas Müller
01:59 PM bug #8746: Multiple representations problem on saving Matrix Editor: Is this reproducable? Otherwise I would close this ticket because MRE occurr everywhere from time to time. Andreas Müller
01:30 PM feature request #8656 (Resolved): [DISCUSS] Should only characters be allowed for DescriptiveDataSets/Character Matrix?: Andreas Müller
01:19 PM bug #7990: Moving a feature via d&d does not make the Feature Tree Editor dirty: In general the feature tree editor should persist data only after pushing save and therefore needs to be refactored. ... Andreas Müller
01:03 PM bug #7994: Implement allowDuplicates for term trees in TaxEditor: There is a flag now for term trees which defines if duplicates are allowed: "allowDuplicates"
But the according fu... Andreas Müller
12:42 PM feature request #7701 (Resolved): Add link to typified name on specimen page of data portal: So I put this to resolved in current milestone so it can be reviewed. Please change back if not yet solved. Andreas Müller
12:40 PM feature request #7701: Add link to typified name on specimen page of data portal: maybe this is already solved Katja Luther

12/07/2019

06:11 PM bug #8312 (In Progress): Test, fix, improve and run Transmission engine for E+M: Andreas Müller
06:07 PM feature request #6352 (Duplicate): Add Transmission Engine trigger to Admin menu: Andreas Müller

12/06/2019

10:04 PM bug #8754 (Resolved): DescriptionElements are not deleted with the Descriptive Data Set: Based on the dump and situation in #8752:
* deleted both descriptive datasets
* delete the Character trees (for p... Andreas Kohlbecker
09:53 PM bug #8753 (Closed): EagerLoadingException on opening Character Tree Editor after deleting all Desciptive Data Sets: Based on the dump and situation in #8752:
* deleted both descriptive datasets
* Immediately open the Character T... Andreas Kohlbecker
09:44 PM bug #8752 (Worksforme): Matrix Editor: Can fail showing all SpecimenDescriptions in the dataset: It seems as if the DescriptiveDataset has been corrupted somehow.
1. I removed all "specimens" from the matrix at ... Andreas Kohlbecker
06:19 PM bug #8747 (New): Matrix Editor: Can not unset categorical data: I don't consider this as user friendly. Is this default behavior of the nattable?
Since there are check boxes in t... Andreas Kohlbecker
12:21 PM bug #8747 (Resolved): Matrix Editor: Can not unset categorical data: You have to hold CTRL and select the chosen state again to de-select. Patrick Plitzner
06:16 PM bug #8746: Multiple representations problem on saving Matrix Editor: Patrick Plitzner wrote:
> Did you just enter categorical and quantitative data?
> Did you only enter data for this... Andreas Kohlbecker
12:23 PM bug #8746 (Feedback): Multiple representations problem on saving Matrix Editor: Did you just enter categorical and quantitative data?
Did you only enter data for this one specimen?
Did you edit a... Patrick Plitzner
03:44 PM bug #8744 (Resolved): LazyInitializationException (LIE) saving the Character Editor: This seems to be fixed now by using merge(). We still have to have a look at TermTreeEditor which currently still use... Patrick Plitzner
02:05 PM bug #8744: LazyInitializationException (LIE) saving the Character Editor: hmm, it does not really seem to be the problem, but I found that there seems no session to be defined
![](picture1... Andreas Müller
01:25 PM bug #8744: LazyInitializationException (LIE) saving the Character Editor: After changing the users such that only 1 user was attached to all data like TermRelation, DefinedTermBase, TermVocab... Andreas Müller
01:13 PM bug #8744: LazyInitializationException (LIE) saving the Character Editor: We need to test the behavior if data is edited with different users, it seems like at least one user (former user - u... Andreas Müller
01:11 PM bug #8744: LazyInitializationException (LIE) saving the Character Editor: I do not understand how we can have a LIE within a save. With save all objects should be within the session by Merge.... Andreas Müller
03:42 PM bug #8751 (Duplicate): Replace saveOrUpdate() in AbstractTermTreeEditor: Unexpectedly saveOrUpdate() is used instead of merge().
Currently, if you change to merge() an exception is thrown... Patrick Plitzner
01:41 PM feature request #8750 (New): Write tests for service layer methods getting the specimens for an assiociated taxon: The service method for getting all specimen for an associated taxon needs tests:
The method should return all spec... Katja Luther
01:18 PM bug #8748 (In Progress): Supported state vocabularies should be ordered: Now there is a filter for the combo boxes. Katja Luther
11:17 AM bug #8748 (Closed): Supported state vocabularies should be ordered: For characters there is a long list of state vocabularies now. Therefore they are difficult to find in the dropdown. ... Andreas Müller
01:17 PM feature request #8749 (Duplicate): Add proposalProvider to AbstractComboElement: Katja Luther
01:15 PM feature request #8749 (Closed): Add proposalProvider to AbstractComboElement: To provide the filter to all combo elements add the proposalProvider to the AbstractComboElement.
This is used for... Katja Luther
11:59 AM feature request #7071: Reenable restore functionality: Idea:
* After CdmStore has connected invoke "open Part" command on saved editors.
* EditorInput/UUID can be sav... Patrick Plitzner

12/05/2019

05:20 PM bug #8747 (New): Matrix Editor: Can not unset categorical data: Once categorical data state has been set in a cell this cell can not be made blank Andreas Kohlbecker
05:01 PM bug #8744 (In Progress): LazyInitializationException (LIE) saving the Character Editor: Patrick Plitzner
04:59 PM bug #8744 (Resolved): LazyInitializationException (LIE) saving the Character Editor: Applied in changeset commit:taxeditor|5fa6172961481d22d6282abc10b4c350fe1c8bce. Patrick Plitzner
04:38 PM bug #8746 (Rejected): Multiple representations problem on saving Matrix Editor: we did several edits in the matrix for multiple specimens.
Last edit was setting the the state for leave architect... Andreas Kohlbecker
04:33 PM bug #8745 (Resolved): Type designations of synonyms missing on specimen page: please review Katja Luther
04:31 PM bug #8745 (Closed): Type designations of synonyms missing on specimen page: Type designations of synonyms are missing in the compressed specimen page.
mail NK:
Es geht darum, dass von den... Katja Luther
02:20 PM feature request #8677 (In Progress): Add distribution aggregation to set subtree menu: Open issues:
* ~~highest rank should include the rank of the selected taxon~~
* ~~lowest rank should inlcude th... Andreas Müller

12/04/2019

10:40 PM bug #6629 (Closed): TransmissionEngineDistribution misses aggregating Uzebkistan (UZB-OO) to higher rank levels: NK: Ist jetzt OK. Andreas Müller
02:34 PM bug #6629 (Resolved): TransmissionEngineDistribution misses aggregating Uzebkistan (UZB-OO) to higher rank levels: For Acanthoscephalus, Heteroderis, Crepis and Lagoseriopsis the aggregation seems to work now. For Cichorium intybus ... Andreas Müller
06:57 PM bug #8744 (Closed): LazyInitializationException (LIE) saving the Character Editor: saving the Character Editor after changing the Character Node details causes an LazyInitializationException every tim... Andreas Kohlbecker
05:29 PM bug #8743 (New): BioCASE specimen import: ignore invalid biocase accesspoint urls: This is especially important for the DNA import. If an URL is specified which is not pointing to a BioCase provider t... Andreas Kohlbecker
02:50 PM feature request #8742 (New): Allow deleting vocabularies: Currently it is not possible to delete a vocabulary if it contains terms.
With OWL import (additivity) it is now pos... Andreas Müller
10:12 AM task #8741 (Closed): Create test for MapServices to test if they support https: This especially tests if the existing certificate is still valid. Andreas Müller

12/03/2019

06:37 PM feature request #8721: Use webservice to get all biocase provider listed by gbif: I agree with the above. Maybe the title is enough. Users usually recognize a collection by its title not it's service... Andreas Müller
06:24 PM feature request #8721: Use webservice to get all biocase provider listed by gbif: The access points should be searchable also by the accesspoint title, For the BGBM Herbarium the webservice lists th... Andreas Kohlbecker
06:32 PM feature request #8740 (New): BioCASE specimen import: implement data set filter in specimen import dialog page 2: once an access point has been selected in the fist step it should be possible to limit the search to a specific data ... Andreas Kohlbecker
04:35 PM feature request #8657: Order description element in portal according to CharacterTree: Can you provide an example url? Andreas Müller
12:14 PM feature request #8657: Order description element in portal according to CharacterTree: Assignin to you Andreas M.
But maybe also Andreas K. needs to look at the code Patrick Plitzner
03:15 PM feature request #8713 (Resolved): Improve structured descriptive data aggregation: At least tests exist now and also base class algorithm is used. Can you please review and put open issues into a foll... Andreas Müller
02:15 PM bug #8670: Unwanted distribution aggregation/display on 2 levels: Auch hier bitte einen letzten Check ob noch was offen ist.
Anschließend können wir das Ticket schließen. Andreas Müller
02:14 PM bug #4134: Transmissionengine Distribution seems to miss distributions for higher Taxa: I think this is fully fixed with the new implementation of the transmission engine (which allows the user to decide t... Andreas Müller
02:08 PM feature request #5176 (Closed): TransmissionEngineDistribution can run on selected taxa: This should be fully fixed. As it has been used already and also a TaxEditor UI for using it has been developped I cl... Andreas Müller
01:49 PM feature request #8472 (Closed): Transmission engine for distribution aggregation needs to be adapted to new DescriptionBase.types: Andreas Müller
01:41 PM task #8468 (Closed): Remove old InapplicableIf tables: Andreas Müller
01:40 PM bug #8738 (Closed): CdmLink.startPos and .endPos should allow Null: Andreas Müller
01:40 PM bug #8702 (Closed): Remove Not null constraint for uuid in AUD tables: Andreas Müller
12:21 PM feature request #8714: description page: Show multiple datasets per description as list of links: To review you would have to manually add a description to multiple datasets in the database. There is no test data li... Patrick Plitzner
12:19 PM feature request #8595: Create description detail page: created new ticket for remaining issues and discussion -> #8739
Patrick Plitzner
12:17 PM bug #8739 (Closed): remaining issues for description detail page: Copied from #8595
* Evtl. will man auf aggr. Description von höheren Taxa nicht die Specimen als Quellen anzeigen,... Patrick Plitzner

12/02/2019

12:31 PM feature request #8433 (Duplicate): Disallow user names with whitespace: This is a duplicate for #8454 and has been fixed in CDM UML 5.8 Andreas Müller
12:26 PM task #8468 (Resolved): Remove old InapplicableIf tables: Applied in changeset commit:cdmlib|73391892ccf6af23d1f83357e460ea9b55df4e2d. Andreas Müller
12:12 PM bug #8702 (Resolved): Remove Not null constraint for uuid in AUD tables: Andreas Müller
12:12 PM bug #8738 (Resolved): CdmLink.startPos and .endPos should allow Null: Andreas Müller
10:55 AM bug #8738 (Closed): CdmLink.startPos and .endPos should allow Null: The table was IntextReference before. After using it for class CdmLinkSource also the originally NOT NULL columns mus... Andreas Müller
11:32 AM bug #8737 (Resolved): delete taxon included in two classifications deletes taxonname: Now there is also the possibility to set the taxonnode configurator to deletetaxon = false. This was missing in the d... Katja Luther
09:42 AM bug #8737: delete taxon included in two classifications deletes taxonname: please review. Katja Luther
09:35 AM bug #8737 (Closed): delete taxon included in two classifications deletes taxonname: when deleting a taxon used in two classifications, the taxon still exist, but the name is deleted. This is because of... Katja Luther
10:35 AM bug #8733: Descriptive data set: Specimens of a newly added taxon are not listed in Select Specimen dialog of the matrix editor: This ticket is complex. In the ticket description is not written HOW the taxon is added. In general the underlying se... Andreas Müller
08:24 AM bug #8733 (Feedback): Descriptive data set: Specimens of a newly added taxon are not listed in Select Specimen dialog of the matrix editor: Currently the specimens listed in the specimen selection dialog are cached after the first time opening the dialog be... Patrick Plitzner
08:40 AM feature request #8665 (Resolved): Rename "New" to "New Tree" in Term Tree editors: Applied in changeset commit:taxeditor|210af90ccae0c45e1234bdb8fe216285293546c6. Patrick Plitzner
08:37 AM bug #8732 (Duplicate): Descriptive Data Set Navigator: label not refreshed after change in Descriptive Dataset Editor: This is already solved for release 5.12 with #8661
Please validate with the current nightly build. Patrick Plitzner

11/29/2019

05:17 PM bug #8736 (Closed): LazyInitializationException (LIE) during adding Specimens to Matrix Editor: To reproduce:
* use database: caryophyllales_spp (cactaceae)
* create new Descriptive Dataset (non specimens so f... Andreas Kohlbecker
04:09 PM task #7976 (In Progress): [PESI][ERMS] Erms taxon import: Andreas Müller
04:09 PM task #8509 (In Progress): [PESI][ERMS] Export ERMS data to PESI: Andreas Müller
04:06 PM task #8577 (In Progress): [PESI][E+M] Validation for E+M export: Andreas Müller
03:35 PM bug #8735 (Duplicate): Character Node Editor: allow line breaks at slashes in structure representation: The line wrapping does not work for long structure representation. Breaks only happen where the term labels contain... Andreas Kohlbecker
11:28 AM task #8734 (Closed): Update distributions from TDWG-L4 to TDWG-L3 where L4=L3: Andreas Müller
10:34 AM task #8734 (In Progress): Update distributions from TDWG-L4 to TDWG-L3 where L4=L3: SQL to use
~~~
UPDATE DescriptionElementBase deb
INNER JOIN DefinedTermBase a ON deb.area_id = a.id
INNER JOIN ... Andreas Müller
10:33 AM task #8734 (Closed): Update distributions from TDWG-L4 to TDWG-L3 where L4=L3: This will shorten the textuell representations of distribution data in the data portal Andreas Müller
01:49 AM bug #8731 (Resolved): BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results: now it works again with the nightly build. Katja Luther
12:47 AM bug #8731 (In Progress): BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results: This is strange, I can not reproduce this with an editor started from the workspace, also when using the actual git d... Katja Luther

11/28/2019

06:57 PM bug #8733 (Closed): Descriptive data set: Specimens of a newly added taxon are not listed in Select Specimen dialog of the matrix editor: to reproduce
1. create Descriptive data set in caryophyllales_spp
* adding *Rhipsalis pilocarpa* by drag and dro... Andreas Kohlbecker
06:33 PM bug #8732 (Duplicate): Descriptive Data Set Navigator: label not refreshed after change in Descriptive Dataset Editor: just exactly what is written in the subject.
Andreas Kohlbecker
03:45 PM bug #8731: BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results: An import of specimens is not possible wit the current code base in the development branch. Andreas Kohlbecker
03:40 PM bug #8731 (Closed): BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results: I am not sure about the timing of the situation in which this exception occurred.
I was searching the `http://ww3.... Andreas Kohlbecker
03:23 PM bug #8730 (New): OWL Term export progress monitor reports wrong process percentage: The initial percentage is really funny:
![](picture396-1.png) Andreas Kohlbecker
12:29 PM bug #8720: blank perspective after using "Switch User": the perspective looked like this:
![](picture283-1.png)
today is the first day this is not happening for quite ... Andreas Kohlbecker
12:05 PM bug #8720: blank perspective after using "Switch User": I am not sure if I fully understand the problem. When I try to change the user I get the "Taxonomic" perspective but ... Andreas Müller
11:51 AM bug #8729: Refresh Taxon Navigator after Specimen import: Seems to be very similar to #8659. So we may think about putting it also to 5.12. Katja, what do you think? Andreas Müller
10:54 AM bug #8729 (New): Refresh Taxon Navigator after Specimen import: After a successful specimen import vi BioCASE Provider the Taxon Navigator is not being refreshed.
New created Clas... Andreas Kohlbecker
09:34 AM bug #8728: Specimen import via BioCASE silently fails: Andreas Kohlbecker wrote:
> The problem in one specific case was that the user was not permitted to update a person:... Andreas Müller
09:26 AM bug #8728: Specimen import via BioCASE silently fails: Next Problem:
~~~
[CREATE] not permitted for 'kurs1' on TaxonNode[uuid:79c3deac-ee1d-4622-91fa-746be0894161', toS... Andreas Kohlbecker
08:51 AM bug #8728: Specimen import via BioCASE silently fails: The problem in one specific case was that the user was not permitted to update a person:
~~~
[UPDATE] not permitt... Andreas Kohlbecker

11/27/2019

04:42 PM bug #8728: Specimen import via BioCASE silently fails: As the import works without problems with the `admin` user, it seems as if this is a permission problem.
@Katja: 1... Andreas Kohlbecker
04:24 PM bug #8728: Specimen import via BioCASE silently fails: this is reproducible
once this error has occurred the taxeditor has to be restarted, otherwise further import atte... Andreas Kohlbecker
04:15 PM bug #8728 (New): Specimen import via BioCASE silently fails: ABCD Specimen import via BioCASE provider silently fails
Logged in as user with GAs: `Editor` + `TAXONNODE.[CREATE... Andreas Kohlbecker
03:39 PM EDIT Platform Etablierung task #8727 (In Progress): Test Workshop workflow: Andreas Kohlbecker
03:21 PM EDIT Platform Etablierung task #8727 (Closed): Test Workshop workflow: **Use the simple editor user accounts: kurs1..5**
The section of taxa to test the workflow with is based in the ... Andreas Kohlbecker
02:39 PM feature request #8686: Support CdmLink sources in bibliography: Further more there is a discussion if links to taxa should be direct links from the description(element) to the taxon... Andreas Müller
02:38 PM feature request #8686: Support CdmLink sources in bibliography: Support for link to taxa has been added in #8724. So we need to check or implement that also links to taxa are handle... Andreas Müller
02:36 PM feature request #8724 (Resolved): Allow OriginalSource to link to Taxon: Andreas Müller
02:25 PM feature request #8724 (Closed): Allow OriginalSource to link to Taxon: When aggregating (or moving) data one may want to link to the taxon the data originally comes from so we need a possi... Andreas Müller
02:35 PM feature request #8726 (New): the search preference search field should be a list: The preference defining the search field should be not a single value, but a list of fields on which the seach should... Katja Luther
02:34 PM feature request #8725 (Feedback): Add abbreviation to namedArea text field in distribution details view: Some named areas have the same label therefore it would be nice to show an abbreviation like idInVoc. This should be ... Katja Luther
09:41 AM feature request #8721 (In Progress): Use webservice to get all biocase provider listed by gbif: The prefilled combo and the filtering for entered text is implemented in the specimen dialog now. Katja Luther
09:11 AM bug #8723 (Worksforme): Distribution detailsview: changing the area removes the state: When changing the area of a distribution the status is not displayed anymore. But the distribution still has the stat... Katja Luther

11/26/2019

04:09 PM EDIT Platform Etablierung task #8722 (Closed): Provide Manuals and Dokumentation for the Kurs „Integrated Taxonomy“ WiSe 2019/20: Documentation needed for the Kurs:
* Matrix-Editor manual - is being prepared ...
* List of user accounts for dem... Andreas Kohlbecker
03:59 PM EDIT Platform Etablierung task #8712 (Closed): Kurs "Integrated Taxonomy" : prepare setup for workshop computers: Andreas Kohlbecker
02:53 PM feature request #8721 (Closed): Use webservice to get all biocase provider listed by gbif: For the specimen search it would be nice to have a list of all biocase provider. (Jörg provided us a webservice)
W... Katja Luther
10:43 AM bug #8720 (New): blank perspective after using "Switch User": When switching the user *General > Switch User* all views and editors are closed, making the perspective blank. After... Andreas Kohlbecker
09:19 AM bug #8719 (Resolved): installation profile 'CDM_Portal' causes Integrity constraint violation: 1048 Column 'pages' cannot be null: Applied in changeset commit:cdm-dataportal|56d39875a598bad7e9c7591d5436b0ac63160cae. Andreas Kohlbecker
08:23 AM bug #8719 (Closed): installation profile 'CDM_Portal' causes Integrity constraint violation: 1048 Column 'pages' cannot be null: this bug has been discovered in the process of automatic creation of workshop servers (`server-scripts/workshop-setup... Andreas Kohlbecker

11/25/2019

02:51 PM feature request #8460: Show examples in text field: Try to implement a base functionality.
This is already implemented in taxon search. Andreas Müller

11/22/2019

01:27 PM bug #8718: polytomousKey page: better handling of invalid uuids: Patrick, this is relevant for additivity (currently PKs get a new uuid with every generation) so we may think about m... Andreas Müller
12:53 PM bug #8718 (Closed): polytomousKey page: better handling of invalid uuids: ich habe gerade gesehen, dass ein PolyKey, wenn dessen uuid nicht stimmt unschöne Fehler schmeißt:
http://test.e-t... Andreas Kohlbecker

11/21/2019

04:16 PM task #8716 (Resolved): Configure taxeditor to run with GTK2 in linux: please report if you are having any problems due to the switch to GTK2 Andreas Kohlbecker
04:09 PM task #8716: Configure taxeditor to run with GTK2 in linux: Andreas Kohlbecker wrote:
> as documented in https://wiki.eclipse.org/SWT/Devel/Gtk/GtkVersion the gtk version can b... Andreas Kohlbecker
04:03 PM task #8716 (In Progress): Configure taxeditor to run with GTK2 in linux: as documented in https://wiki.eclipse.org/SWT/Devel/Gtk/GtkVersion the gtk version can be set via
~~~
--launcher... Andreas Kohlbecker
01:12 PM task #8716 (Closed): Configure taxeditor to run with GTK2 in linux: Der Taxeditor verwendet SWT in der Version 3.105.3.v20170228-0512 (Id: org.eclipse.swt, Version: 3.105.3.v20170228-05... Andreas Kohlbecker
03:58 PM bug #8717 (New): Improve display of PolytomousKey nodes which have a feature: If a PKN has a feature and not a statement it is repeated multiple times for the child alternatives. A better layout ... Andreas Müller
03:29 PM bug #8313 (Feedback): Multiple categorical data get deleted when clicked on in Character Matrix: Reopen as it happens again.
How to reproduce: in any categorical cell select 2 states. Leafe the cell (it shows bo... Andreas Müller
03:21 PM feature request #8714 (Resolved): description page: Show multiple datasets per description as list of links: Applied in changeset commit:cdm-dataportal|cf89f7e20f7cbd623d7d373bbf9061003f175179. Patrick Plitzner
11:42 AM feature request #8714 (Resolved): description page: Show multiple datasets per description as list of links: A description can have multiple descriptive data sets. These define which features are displayed and in which order.
... Patrick Plitzner
02:38 PM feature request #8595 (Resolved): Create description detail page: Patrick Plitzner
12:35 PM task #8468 (In Progress): Remove old InapplicableIf tables: Andreas Müller
12:21 PM feature request #8715: Make 'delete Taxonnode' a lonrunning task: Deleting nodes can take some time and results in connection warnings or timeouts. This can be solved by running the d... Katja Luther
12:16 PM feature request #8715 (New): Make 'delete Taxonnode' a lonrunning task: Katja Luther
08:19 AM feature request #8713 (Closed): Improve structured descriptive data aggregation: * Tests
* Remove empty categorical data creation
* use base class algorithm from #8679
* TBC Andreas Müller

11/20/2019

05:11 PM EDIT Platform Etablierung task #8689: Export Flora of Greece Bupleurum using Cdm2Cdm export: I change Project and milestone as it is mostly data related. Andreas Müller
03:37 PM EDIT Platform Etablierung task #8689 (Closed): Export Flora of Greece Bupleurum using Cdm2Cdm export: The data looks complete and did not cause any errors when opening the taxa in the editor.
I consider this issue as... Andreas Kohlbecker
05:01 PM feature request #8281 (Closed): Doubtful flag for TaxonNode: E+M data updated
~~~
UPDATE TaxonNode
Set unplaced = 0, doubtful = 1
WHERE unplaced = 1
~~~
also for _AUD Andreas Müller
05:00 PM feature request #8686 (In Progress): Support CdmLink sources in bibliography: Andreas Kohlbecker
04:51 PM EDIT Platform Etablierung task #8711 (Closed): add additivity ontologies to the bupleurum database: completed a dump is stored at edit-test:/root/cdm_test_bupleurum-2019-11-20-001.sql.bz2 Andreas Kohlbecker
01:25 PM EDIT Platform Etablierung task #8711 (Closed): add additivity ontologies to the bupleurum database: the ontology can be downloaded from https://cybertaxonomy.eu/download/data/ontology/additivity/
the characters mus... Andreas Kohlbecker
04:24 PM feature request #8657 (Resolved): Order description element in portal according to CharacterTree: Patrick Plitzner
01:32 PM EDIT Platform Etablierung task #8712 (Closed): Kurs "Integrated Taxonomy" : prepare setup for workshop computers: * We will be using the edit-demo-2 server for the Kurs "Integrated Taxonomy"
* prepare database: - **DONE**
... Andreas Kohlbecker
12:58 PM task #8710: Decide if sub-area Preference and/or status order preference rule: relevant code:
~~~
define('CDM_DISTRIBUTION_FILTER_DEFAULT', serialize(
array(
'filter_rules' => array(
'statu... Andreas Müller
12:57 PM task #8710: Decide if sub-area Preference and/or status order preference rule: Probably needs discussion with users. Andreas Müller
12:56 PM task #8710 (New): Decide if sub-area Preference and/or status order preference rule: Currently they are switched of in default dataportals.
The setting can be found in the portal settings on the genera... Andreas Müller
12:10 PM feature request #8709 (New): Show last selected name in selection dialog of name in source: mail Eckhard v. Raab-Straube:
was auch nett wäre: wenn sich der Editor bei der Auswahl des „name in source“ an die... Katja Luther
12:05 PM feature request #8708 (Duplicate): Sort taxa in distribution editor same as in navigator: mail Eckhard v. Raab-Straube:
Hallo,
zum Verbreitungseditor:
wenn man den Verbreitungseditor von einem höher... Katja Luther
12:03 PM feature request #8707 (New): Use NAT Table for specimen search result: The search result for the specimen search contains not all informations needed. Therefore it should be shown in a NAT... Katja Luther
11:45 AM feature request #8706 (Closed): taxeditor error report with timestamps: Wie wäre es wenn wir dem Fehlerprotokoll mal einen Timestamp spendierten? Damit wäre es leichter den Fehler einem bes... Andreas Kohlbecker
01:35 AM bug #8670 (Resolved): Unwanted distribution aggregation/display on 2 levels: Dieses Ticket hat primär mit der Kartenanzeige und nicht mit der Aggregation zu tun. Bei der Kartenanzeige gibt es di... Andreas Müller

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