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feature request #7658

use new taxon relationship DTO webservice in portal

Added by Andreas Kohlbecker 4 months ago. Updated 3 months ago.

Status:
Closed
Priority:
Highest
Category:
cdm-dataportal
Target version:
Start date:
06/01/2017
Due date:
% Done:

100%

Severity:
normal

Description

for details see #6682

Example taxa:

  • Chichorieae: Pilosella acutifolia coll.
  • Cihochorieae: Hieracium dermophyllum

New test data copied from
Nepenthes abalata in the integrationtest reference database

http://int.e-taxonomy.eu/dataportal/integration/reference/cdm_dataportal/taxon/9b588d8a-c4fa-430a-b9c7-026bf715ecf6/synonymy?destination=cdm_dataportal/taxon/9b588d8a-c4fa-430a-b9c7-026bf715ecf6/synonymy

Still to discuss: how to handle misapplied name deduplication (1 line per same name/rel.sec. but for different sensu/appended phrases, the later need to be concatenated with "," as separator. This can either be handled on server or client side (discussion).

picture970-1.png View (17.8 KB) Andreas Müller, 09/06/2018 02:44 PM

picture970-2.png View (41 KB) Andreas Müller, 09/06/2018 02:44 PM

picture38-1.png View (7.79 KB) Andreas Müller, 09/06/2018 03:27 PM

picture944-1.png View (3.35 KB) Andreas Müller, 09/06/2018 03:45 PM

picture400-1.png View (8.17 KB) Andreas Müller, 09/12/2018 12:32 PM

picture979-1.png View (24.4 KB) Andreas Müller, 09/16/2018 05:40 PM


Related issues

Related to Edit - bug #6652: [Discuss] misapplied names: hide protologue icon New 05/18/2017
Related to Edit - bug #5676: Sensu does not show up if no author exists for secundum reference Feedback 07/06/2016
Related to Edit - feature request #7666: Remaining issues for "Formatter and DTO for taxon relationships (e.g. misapplied names)" In Progress 08/20/2018
Related to Edit - feature request #5232: use TaxonBase.getTaggedTitle to get the sec reference in theme_cdm_taxonRelationships() New 09/10/2015
Related to Edit - feature request #5647: Aggregate misapplied names with multiple sensu references Closed 03/14/2016 06/02/2016
Related to Edit - feature request #6681: Correct formatting for misapplied names in name editor Closed 05/31/2017
Related to Edit - feature request #7753: use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editor Closed 09/12/2018
Follows Edit - feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names) Closed 05/31/2017
Copied to Edit - feature request #7720: use new taxonRelationshipsDTO webservice for all taxon relations Resolved 06/01/2017
Copied to Edit - bug #7766: Remaining issues for using relationship DTO webservice in portal Resolved 06/01/2017

Associated revisions

Revision 5cfd066c (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658 test case for Nepenthes abalata

Revision 116fb348 (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658 work in progress with errors

Revision 83dc60b9 (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658 adapting cdm_taxonRelationships() to new taxon relationship DTO webservice
- test case
- extending tagged text functions
- adapting misapplied name redering

Revision 2978b0c8 (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658 moving all tagged text functions to separate file

Revision 67c8cca9 (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658 miapplied names and invalid designations modified to use the taxonRelationshipsDTO webservice

Revision 27c31249 (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658 test for invalid designation

Revision 13bd883d (diff)
Added by Andreas Kohlbecker 4 months ago

ref #7658, ref #7720 restoring css rule for .relation_sign

Revision 439f531a (diff)
Added by Andreas Kohlbecker 3 months ago

ref #7658 MAN deduplication by full MAN representation except sensu reference

Revision 23ebb91f (diff)
Added by Andreas Kohlbecker 3 months ago

ref #7658 fixing final problems in MAN display related to appendedPhrase, citationDetail, footnotes

Revision 18c71cd1 (diff)
Added by Andreas Kohlbecker 3 months ago

ref #7658 using the taxonRelationDTO for other relationshipt also - footnotes are missing

Revision a9dc4b35 (diff)
Added by Andreas Kohlbecker 3 months ago

ref #7658 other relationship reprentation based on DTOs fully implemented

Revision bafcf277 (diff)
Added by Andreas Kohlbecker 3 months ago

adapting xpaths in test framework to modified rendering of footnotes, related to ref #7658

Revision e56e5d1c (diff)
Added by Andreas Kohlbecker 3 months ago

adding test case for no sensu but with Combination Authors and fixing according bug

Revision 45aaf1fe (diff)
Added by Andreas Kohlbecker 3 months ago

depuplication of p.p.MAN and partial MAN with test

History

#1 Updated by Andreas Kohlbecker 4 months ago

  • Copied from feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names) added

#2 Updated by Andreas Kohlbecker 4 months ago

  • Tags changed from euro+med to euro+med, caryophyllales

#3 Updated by Andreas Kohlbecker 4 months ago

  • Description updated (diff)

#4 Updated by Andreas Müller 4 months ago

  • Related to bug #6652: [Discuss] misapplied names: hide protologue icon added

#5 Updated by Andreas Müller 4 months ago

  • Related to bug #5676: Sensu does not show up if no author exists for secundum reference added

#6 Updated by Andreas Kohlbecker 4 months ago

  • Target version changed from Release 5.2 to Release 5.3

#7 Updated by Andreas Müller 4 months ago

  • Related to feature request #7666: Remaining issues for "Formatter and DTO for taxon relationships (e.g. misapplied names)" added

#8 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#9 Updated by Andreas Müller 4 months ago

  • Copied from deleted (feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names))

#10 Updated by Andreas Müller 4 months ago

  • Due date set to 06/01/2017
  • Start date changed from 05/31/2017 to 06/01/2017
  • Follows feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names) added

#11 Updated by Andreas Müller 4 months ago

  • Due date deleted (06/01/2017)

#12 Updated by Andreas Kohlbecker 4 months ago

  • Description updated (diff)

#13 Updated by Andreas Kohlbecker 4 months ago

  • Copied to feature request #7720: use new taxonRelationshipsDTO webservice for all taxon relations added

#14 Updated by Andreas Kohlbecker 4 months ago

  • Status changed from In Progress to Resolved
  • Assignee changed from Andreas Kohlbecker to Andreas Müller
  • % Done changed from 0 to 60

implementation complete, please review

#15 Updated by Andreas Müller 3 months ago

  • Related to feature request #5232: use TaxonBase.getTaggedTitle to get the sec reference in theme_cdm_taxonRelationships() added

#16 Updated by Andreas Müller 3 months ago

  • Status changed from Resolved to Feedback
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

Does not yet work for pro parte and partial MANs.

#17 Updated by Andreas Müller 3 months ago

Exception for second MAN of Achillea santolinoides Lag.

for this data on test.cyprus

#18 Updated by Andreas Müller 3 months ago

But it works when adding an explicit sensu reference. But explicit sensu is not a requirement.

#19 Updated by Andreas Müller 3 months ago

Strange, with this entry:

the webservice even does not return a second entry though it exists. Need to check why.

#20 Updated by Andreas Müller 3 months ago

Andreas Müller wrote:

Strange, with this entry:

the webservice even does not return a second entry though it exists. Need to check why.

ohh, sorry, it was on unpublish (so unpublish works !! ;-)

#21 Updated by Andreas Müller 3 months ago

Deduplication must NOT take place if the rel. sec. differs (e.g. only one of the MANs has a rel. sec.). This is not yet correctly implemented.
Also everything else needs to be equal except for MAN.sec and MAN.secDetail. E.g. if the doubtful flag differs either for the MAN taxon or for relation also no deduplication should take place (as it is no duplicate).
Also the relationship type needs to be equal (once pro parte and partial works).

#22 Updated by Andreas Müller 3 months ago

& handling does not yet work correctly in teams. Probably a formatter issue #7666.

#24 Updated by Andreas Müller 3 months ago

Andreas Müller wrote:

& handling does not yet work correctly in teams. Probably a formatter issue #7666.

This was a formatter problem (#7666) which was fixed by cdmlib|c331fa7e

#25 Updated by Andreas Müller 3 months ago

#26 Updated by Andreas Kohlbecker 3 months ago

  • Status changed from Feedback to Resolved
  • Assignee changed from Andreas Kohlbecker to Andreas Müller
  • % Done changed from 60 to 70

finally fully solved, please review

#27 Updated by Andreas Müller 3 months ago

#28 Updated by Andreas Müller 3 months ago

  • Related to feature request #7753: use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editor added

#29 Updated by Andreas Müller 3 months ago

  • File picture400-1.png View added
  • Status changed from Resolved to Feedback
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

Deduplication still does not work if everything is similar except for sensu and sensu detail. In the following screeshot the 2nd and 3rd entry should be deduplicated:

#30 Updated by Andreas Müller 3 months ago

I tested the above behavior. The reason is that secDetail differs (or misses in one case). secDetail is part of the secSource and may be different.

#31 Updated by Andreas Müller 3 months ago

The MANs are still unsorted. In the above example you can see that Achillea santolina sensu Chrtek ... is before Achillea santolina sensu Baumel but shouldn't.

As far as I know Katja implemented a Comparator for same issue in TaxEditor. If possible we should try to reuse it. But may be this is not possible because of the deduplications that do not exist in TaxEditor.

#32 Updated by Andreas Müller 3 months ago

Andreas Müller wrote:

Exception for second MAN of Achillea santolinoides Lag.

for this data on test.cyprus

This is not yet fixed. The exception still exists. #7658#note-17

#33 Updated by Andreas Müller 3 months ago

Deduplication should include appendedPhrase part I think (this is also not yet implemented in the server side misapplication deduplication and also has not yet been discussed in our last discussion on deduplication).

E.g. - "Achillea santolina" auctrs. afr.; Meikle 1988 should be deduplicated and not 2 entries.

This is because the appendedPhrase for MANs is usually used as kind of freetext for the sensu reference like in the above example.

#34 Updated by Andreas Müller 3 months ago

Andreas Müller wrote:

Does not yet work for pro parte and partial MANs.

This is also still an open issue.

#35 Updated by Andreas Kohlbecker 3 months ago

  • % Done changed from 70 to 80

please review again

#36 Updated by Andreas Müller 3 months ago

  • Status changed from Feedback to Resolved
  • Assignee changed from Andreas Kohlbecker to Andreas Müller

#37 Updated by Andreas Kohlbecker 3 months ago

Fehler wie bei Achillea santolinoides beseitigt, aber die Fußnoten bei den nicht MANs fehlen noch - kommt in 3.4!

#38 Updated by Andreas Kohlbecker 3 months ago

Andreas Kohlbecker wrote:

Fehler wie bei Achillea santolinoides beseitigt, aber die Fußnoten bei den nicht MANs fehlen noch - kommt in 3.4!

jetzt müsste es perfekt sein!

der Review lohnt sich nun.

#39 Updated by Andreas Müller 3 months ago

"auct." (appended phrase) does not show up, e.g.

  • "Achillea santolina" , non Test , but should be "Achillea santolina" auct., non Test

The auct. is in the webservice but seems to get lost in the portal code

#40 Updated by Andreas Müller 3 months ago

  • Status changed from Resolved to Feedback
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

#41 Updated by Andreas Müller 3 months ago

Andreas Müller wrote:

"auct." (appended phrase) does not show up, e.g.

  • "Achillea santolina" , non Test , but should be "Achillea santolina" auct., non Test

The auct. is in the webservice but seems to get lost in the portal code

This is only the case, if no sensu reference is defined

#42 Updated by Andreas Müller 3 months ago

Deduplication takes not yet place when the relationship is of type "pro parte Misaplied Name" or "partial Misapplied Name", but should. But of course only if both types are equal, so don't mix MAN with ppMAN or partialMAN with ppMAN ...

#43 Updated by Andreas Kohlbecker 3 months ago

Andreas Müller wrote:

Deduplication takes not yet place when the relationship is of type "pro parte Misaplied Name" or "partial Misapplied Name", but should. But of course only if both types are equal, so don't mix MAN with ppMAN or partialMAN with ppMAN ...

Oops, this is a new requirement.

#44 Updated by Andreas Kohlbecker 3 months ago

Andreas Müller wrote:

Andreas Müller wrote:

"auct." (appended phrase) does not show up, e.g.

  • "Achillea santolina" , non Test , but should be "Achillea santolina" auct., non Test

The auct. is in the webservice but seems to get lost in the portal code

This is only the case, if no sensu reference is defined

It is actually the "Combination Authors" data which causes the problem.

#45 Updated by Andreas Kohlbecker 3 months ago

  • Status changed from Feedback to Resolved
  • Assignee changed from Andreas Kohlbecker to Andreas Müller

all mentioned bugs fixed!

#46 Updated by Andreas Müller 3 months ago

The sort order is still not correct. We should first have pro parte/partial synonyms, then invalid designations, then MANs followed (or including?) pro parte/partial MAN and finally concept relationships.

Currently they come mixed up:

#47 Updated by Andreas Müller 3 months ago

#48 Updated by Andreas Müller 3 months ago

This problem is not release critical. We can fix it in 5.4. Maybe only moving up ppSyn to top would be nice but if not it is acceptable.

#49 Updated by Andreas Müller 3 months ago

Andreas Kohlbecker wrote:

all mentioned bugs fixed!

Tested the 2 issues. Both work.

So the only open issue is the sorting #7658#note-46

We may move this to 5.4 if not easy to fix.

#50 Updated by Andreas Müller 3 months ago

  • Status changed from Resolved to Feedback
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

#51 Updated by Andreas Müller 3 months ago

And ofcourse the footnotes for non-MAN data are still missing. #7658#note-37 or should this be fixed already? If yes, it doesn't seem to work.

#52 Updated by Andreas Kohlbecker 3 months ago

  • Copied to bug #7766: Remaining issues for using relationship DTO webservice in portal added

#53 Updated by Andreas Müller 3 months ago

  • Status changed from Feedback to Closed

Close this ticket. Remaining (and new) issues moved to #7766

#54 Updated by Andreas Müller 3 months ago

  • % Done changed from 80 to 100

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