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feature request #7666

Remaining issues for "Formatter and DTO for taxon relationships (e.g. misapplied names)"

Added by Andreas Müller 9 months ago. Updated 3 months ago.

Status:
In Progress
Priority:
Highest
Category:
cdmlib
Start date:
08/20/2018
Due date:
% Done:

0%

Severity:
normal
Tags:

Description

copied from #6682

for requirements see #6682

  • correct symbols for relationships in databases
    • EN_DASH for inverse MAN
    • "p.p. MAN for" for MAN direct symbol
    • pro parte synonyms: WGB: [Symbol overlaps] oder [Symbol includes + p.p.]
  • protologue links (see screen shot below)
  • TODOs in code
  • compare with other formatters, especially reference part
  • how to handle doubtful information (tag type, combined with following tag, ...)
  • grouping for MANs, current solution will not work
  • adapt existing data (e.g. remove work arounds in Nepenthes in appended phrases and others, maybe also show other users how to use the new MAN framework correctly and adapt some example data in these databases, e.g. deduplication of names)
  • should we include protologue link to name, see comment below (maybe configurable in data portal?)
  • Check for Nepenthes abalata and MAN N. alata that the currently existing reference to the type does not exist anymore (see attachement)
  • Teams are currently not yet correctly formatted (wrong index of ambersand)
  • TBC
  • add NARROW NO-BREAK (\u202F) after doubtful marker as requested in #5492
  • "Empty" whitespace separator in response http://int.e-taxonomy.eu/cdmserver/integration_reference/taxon/c6716cee-2039-4ba8-a239-4b1b353f9c84/taxonRelationshipsDTO.json:
--
{
    "entityReference": null,
    "text": "\"",
    "type": "postSeparator",
    "class": "TaggedText"
},
{
    "entityReference": null,
    "text": " ", <===== !!!!!!
    "type": "separator",
    "class": "TaggedText"
},
{
    "entityReference": null,
    "text": "auctrs. afr.",
    "type": "appendedPhrase",
    "class": "TaggedText"
}
...

incorrect reference link to type

Also check carefully against results discussed in #5676

Example for pro parte synonym: Nepenthes boschiana http://caryophyllales.org/nepenthaceae/cdm_dataportal/taxon/a0f4770e-5076-43e4-950f-01166e65669d

picture990-1.png View - incorrect reference link to type (14.7 KB) Andreas Müller, 08/20/2018 06:06 PM


Related issues

Related to Edit - feature request #7658: use new taxon relationship DTO webservice in portal Closed 06/01/2017
Related to Edit - bug #6652: [Discuss] misapplied names: hide protologue icon New 05/18/2017
Related to Edit - bug #7656: Adapt inverse symbol for MisappliedName relationship type Duplicate 08/15/2018
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 #6681: Correct formatting for misapplied names in name editor Closed 05/31/2017
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 #7753: use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editor Closed 09/12/2018
Related to Edit - task #8055: Correct formatting for invalid designations New 02/01/2019
Related to Edit - task #8275: [DISCUSS] Relationship between invalid designations and invalid names / nom. inval. New 05/14/2019
Copied from Edit - feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names) Closed 05/31/2017

Associated revisions

Revision 9c8dc025 (diff)
Added by Andreas Müller 9 months ago

ref #6682 split doubtful in rel doubtful and taxon doubtful + use full authorshipCache for MAN non-authors

Revision 5c5d1f1f (diff)
Added by Andreas Müller 9 months ago

ref #7666 adapt test for new doubtful handling in formatter

Revision b7f100e5 (diff)
Added by Andreas Kohlbecker 9 months ago

ref #7666 adding NARROW NO-BREAK after doubtful marker

Revision 5e7f22d8 (diff)
Added by Andreas Kohlbecker 9 months ago

ref #7666 adding NARROW NO-BREAK after doubtful marker - adapting test

Revision 530b3394 (diff)
Added by Andreas Kohlbecker 9 months ago

ref #7666 NARROW NO-BREAK in UTF8 class

Revision c331fa7e (diff)
Added by Andreas Müller 9 months ago

ref #7666 fix team formatting (incorrect index of ambersand)

Revision b127d201 (diff)
Added by Andreas Müller 8 months ago

ref #7666 allow formatting without name part

Revision 013e3b2f (diff)
Added by Andreas Müller 8 months ago

ref #7666 allow formatting without name part (2. test)

Revision dd3ea7ac (diff)
Added by Andreas Müller 8 months ago

ref #7666 replace StringUtils dependency by correct one

Revision 603aecbe (diff)
Added by Andreas Kohlbecker 8 months ago

ref #7666 doGetTaxonRelationshipsDTO groupMisapplications paramter default = false

History

#1 Updated by Andreas Müller 9 months ago

  • Description updated (diff)

#2 Updated by Andreas Müller 9 months ago

  • Description updated (diff)

#3 Updated by Andreas Müller 9 months ago

#4 Updated by Andreas Müller 9 months ago

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

#5 Updated by Andreas Müller 9 months ago

  • Related to bug #7656: Adapt inverse symbol for MisappliedName relationship type added

#6 Updated by Andreas Müller 9 months ago

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

#7 Updated by Andreas Müller 9 months ago

#8 Updated by Andreas Müller 9 months ago

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

#9 Updated by Andreas Müller 9 months ago

  • Description updated (diff)

#10 Updated by Andreas Müller 9 months ago

  • Description updated (diff)

#11 Updated by Andreas Müller 9 months ago

WGB: Der Buchlink verweist auf den Protolog von N. blancoi Blume – der hat ja aber gerade nichts mit dieser Namensanwendung zu tun (also: Protologbildlinks müssen bei MAN weggelassen werden oder der Link muss nach dem
eingefügt werden)

#12 Updated by Andreas Müller 9 months ago

  • Description updated (diff)

#13 Updated by Andreas Kohlbecker 9 months ago

Problems with current implementation of the new webservice:

  1. relations.representation_L10n and relations.representation_L10n_abbreviatedLabel is always an empty string
  2. The TaggedText lists in the misapplications field of the DTO need the relation ship type as additional information: "Im Portal können ALLE TaxonRelationen ein und ausgeschaltet werden, so auch die MAs und INVALID_DESIGNATION_FORs. Daher muss ich die misapplications im DTO unterscheiden können . Ein einfaches Feld misapplications mit einer Liste von TaggedTitle reicht nicht aus. Der Relationstype fehlt hier." --> use an DTO class which has two fields, taggedText and relationshiptype

#14 Updated by Andreas Kohlbecker 9 months ago

A disadvantage of the current implememtation of the taxon relationships webservice and DTO when being used in the dataportal:

The secRefs are returned in the taggedText of the DTO only as authorship - good! The dataportal needs to show the full citation of the secRef in as footnote. The fullCitation is not included in the DTO, so the dataportal would need to fetch the reference from the webservice. Therefore I suggest to add the reference titlecache as label to the typedEntityReference:

{

    "entityReference": {
        "label": ">>>>>TITLE_CACHE<<<<<",
        "type": "Reference",
        "class": "TypedEntityReference",
        "uuid": "206add8c-3eae-4d9c-872c-e15409d2a3d9"
    },
    "text": "Cheek, Jebb 2001",
    "type": "secReference",
    "class": "TaggedText"

},

#15 Updated by Andreas Müller 9 months ago

  • Status changed from New to In Progress

Andreas Kohlbecker wrote:

A disadvantage of the current implememtation of the taxon relationships webservice and DTO when being used in the dataportal:

The secRefs are returned in the taggedText of the DTO only as authorship - good! The dataportal needs to show the full citation of the secRef in as footnote. The fullCitation is not included in the DTO, so the dataportal would need to fetch the reference from the webservice. Therefore I suggest to add the reference titlecache as label to the typedEntityReference:

I am not sure if the titleCache is enough. The information we need is the finally the full OriginalSource information (soon it will be OriginalSource including external links, currently it is Reference + Detail).
Also Sources need to allow different types of formatting again and need deduplication functionality. This is hard to implement in TypedEntityReference without having to make this class too complex.
Also, as the relationship reference should be able to fully integrate into the general bibliography model the way how references/sources are loaded should be similar to the way all other references/sources are loaded. And I don't think those currently use TypedEntityReference.

General we need to define what TaggedText can be used for. Originally it was only for formatting taxon names and to transfer the results of a formatter/cacheStrategy class to the client. We more and more use it as a data holder/DTO for various CDM types, which needs to be discussed further.

#16 Updated by Andreas Müller 9 months ago

#17 Updated by Andreas Kohlbecker 9 months ago

Ok from this future perspective it makes sense to decouple the loading of the references and the display of the MANs. Extending the ReationshipDTO could be an alternative but bloating the tagged text list to transport the full source information makes not much sense.
As the full reference information will be displayed in the footnotes we could do bulk loading of all references/sources when processing this page part. By this we can limit the overhead imposed by the required additional requests.

#18 Updated by Andreas Kohlbecker 9 months ago

  • Description updated (diff)

#19 Updated by Andreas Kohlbecker 9 months ago

  • Description updated (diff)

#20 Updated by Andreas Müller 9 months ago

When implementing:

add NARROW NO-BREAK (\u202F) after doubtful marker as requested in #5492

can you please add the marker to the class UTF8 in cdmlib commons?

#21 Updated by Andreas Müller 9 months ago

should we change Assignee of this ticket?

#22 Updated by Andreas Kohlbecker 9 months ago

Andreas Müller wrote:

should we change Assignee of this ticket?

No need to, the NARROW_NO_BREAK is now a constant in the UTF8 class.

But what about the

String doubtfulRelationStr = taxonRelationship.isDoubtful() ? "?" : "";

do we also need to append the NARROW_NO_BREAK to the doubtful relation marker?

#23 Updated by Andreas Müller 9 months ago

Andreas Kohlbecker wrote:

the NARROW_NO_BREAK is now a constant in the UTF8 class.

But what about the

String doubtfulRelationStr = taxonRelationship.isDoubtful() ? "?" : "";

do we also need to append the NARROW_NO_BREAK to the doubtful relation marker?

Yes I think we should handle them both similar.

By the way, probably you have realized, that the handling of the doubtful marker is not very implemented yet. One time it is part of Tag type "symbol" one time it is part of "separator" which is not really correct. There might be better ways. E.g. we could have "doubtful" as a separate Tag type instead. And then use NARROW_NO_BREAK as post-separator. Needs to be discussed.

#24 Updated by Andreas Müller 9 months ago

  • Description updated (diff)

#25 Updated by Andreas Müller 8 months ago

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

#26 Updated by Andreas Müller 8 months ago

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

#27 Updated by Katja Luther 8 months ago

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

#28 Updated by Andreas Kohlbecker 8 months ago

  • Description updated (diff)

#29 Updated by Andreas Müller 8 months ago

  • Target version changed from Release 5.3 to Release 5.4

#30 Updated by Andreas Müller 7 months ago

  • Target version changed from Release 5.4 to Release 5.5

#31 Updated by Andreas Kohlbecker 5 months ago

  • Tags set to formatter

#32 Updated by Andreas Kohlbecker 5 months ago

  • Tags changed from formatter to formatting

#33 Updated by Andreas Müller 3 months ago

  • Target version changed from Release 5.5 to Release 5.6

#34 Updated by Andreas Müller 3 months ago

  • Priority changed from New to Highest
  • Target version changed from Release 5.6 to Reviewed Next Major Release

#35 Updated by Andreas Müller 10 days ago

  • Related to task #8055: Correct formatting for invalid designations added

#36 Updated by Andreas Müller 10 days ago

  • Related to task #8275: [DISCUSS] Relationship between invalid designations and invalid names / nom. inval. added

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