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feature request #7666

open

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

Added by Andreas Müller over 5 years ago. Updated about 5 years ago.

Status:
In Progress
Priority:
Highest
Category:
cdmlib
Start date:
Due date:
% Done:

0%

Estimated time:
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


Files

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

Related issues

Related to EDIT - feature request #7658: use new taxon relationship DTO webservice in portal ClosedAndreas Kohlbecker

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Related to EDIT - bug #6652: [Discuss] misapplied names: hide protologue icon NewAndreas Müller

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Related to EDIT - bug #7656: Adapt inverse symbol for MisappliedName relationship typeDuplicateAndreas Müller

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Related to EDIT - bug #5676: Sensu does not show up if no author exists for secundum referenceClosedAndreas Kohlbecker

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Related to EDIT - feature request #6681: Correct formatting for misapplied names in name editorClosedKatja Luther

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Related to EDIT - feature request #5647: Aggregate misapplied names with multiple sensu referencesClosedAndreas Kohlbecker

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Related to EDIT - feature request #7753: use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editorClosedKatja Luther

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Related to EDIT - task #8055: Correct formatting for invalid designationsRejectedAndreas Müller

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Related to EDIT - task #8275: [DISCUSS] Relationship between invalid designations and invalid names / nom. inval. WorksformeAndreas Müller

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Copied from EDIT - feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names)ClosedAndreas Müller

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Actions #1

Updated by Andreas Müller over 5 years ago

  • Description updated (diff)
Actions #2

Updated by Andreas Müller over 5 years ago

  • Description updated (diff)
Actions #3

Updated by Andreas Müller over 5 years ago

Actions #4

Updated by Andreas Müller over 5 years ago

  • Related to bug #6652: [Discuss] misapplied names: hide protologue icon added
Actions #5

Updated by Andreas Müller over 5 years ago

  • Related to bug #7656: Adapt inverse symbol for MisappliedName relationship type added
Actions #6

Updated by Andreas Müller over 5 years ago

  • Related to bug #5676: Sensu does not show up if no author exists for secundum reference added
Actions #7

Updated by Andreas Müller over 5 years ago

Actions #8

Updated by Andreas Müller over 5 years ago

  • Copied to feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names) added
Actions #9

Updated by Andreas Müller over 5 years ago

  • Description updated (diff)
Actions #10

Updated by Andreas Müller over 5 years ago

  • Description updated (diff)
Actions #11

Updated by Andreas Müller over 5 years 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)

Actions #12

Updated by Andreas Müller over 5 years ago

  • Description updated (diff)
Actions #13

Updated by Andreas Kohlbecker over 5 years 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
Actions #14

Updated by Andreas Kohlbecker over 5 years 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"

},
Actions #15

Updated by Andreas Müller over 5 years 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.

Actions #16

Updated by Andreas Müller over 5 years ago

Actions #17

Updated by Andreas Kohlbecker over 5 years 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.

Actions #18

Updated by Andreas Kohlbecker over 5 years ago

  • Description updated (diff)
Actions #19

Updated by Andreas Kohlbecker over 5 years ago

  • Description updated (diff)
Actions #20

Updated by Andreas Müller over 5 years 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?

Actions #21

Updated by Andreas Müller over 5 years ago

should we change Assignee of this ticket?

Actions #22

Updated by Andreas Kohlbecker over 5 years 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?

Actions #23

Updated by Andreas Müller over 5 years 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.

Actions #24

Updated by Andreas Müller over 5 years ago

  • Description updated (diff)
Actions #25

Updated by Andreas Müller over 5 years ago

  • Copied to deleted (feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names))
Actions #26

Updated by Andreas Müller over 5 years ago

  • Copied from feature request #6682: Formatter and DTO for taxon relationships (e.g. misapplied names) added
Actions #27

Updated by Katja Luther over 5 years ago

  • Related to feature request #7753: use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editor added
Actions #28

Updated by Andreas Kohlbecker over 5 years ago

  • Description updated (diff)
Actions #29

Updated by Andreas Müller over 5 years ago

  • Target version changed from Release 5.3 to Release 5.4
Actions #30

Updated by Andreas Müller over 5 years ago

  • Target version changed from Release 5.4 to Release 5.5
Actions #31

Updated by Andreas Kohlbecker over 5 years ago

  • Tags set to formatter
Actions #32

Updated by Andreas Kohlbecker over 5 years ago

  • Tags changed from formatter to formatting
Actions #33

Updated by Andreas Müller about 5 years ago

  • Target version changed from Release 5.5 to Release 5.6
Actions #34

Updated by Andreas Müller about 5 years ago

  • Priority changed from New to Highest
  • Target version changed from Release 5.6 to Reviewed Next Major Release
Actions #35

Updated by Andreas Müller almost 5 years ago

  • Related to task #8055: Correct formatting for invalid designations added
Actions #36

Updated by Andreas Müller almost 5 years ago

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

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