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feature request #6682

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

Added by Andreas Müller over 1 year ago. Updated 4 months ago.

Status:
Closed
Priority:
Highest
Category:
cdmlib
Target version:
Start date:
05/31/2017
Due date:
% Done:

100%

Severity:
normal
Tags:

Description

URGENT: Update inverse symbol for MAN rel type

We need a webservice for taxon relationships returning

  • a list of all taxon relationships for a given taxon including

    • direction of relationship (if this taxon is the "from" taxon, the direction is "direct", otherwise it is "inverse"
    • a Entity Holder(?) for the related taxon
    • RelType DTO
    • TaggedTitle for the relationship
    • formatting type (misapplication, synonym, other tscon relationship - see below)
  • a deduplicated list of TaggedText for misapplied names, deduplicated if name and err. sec. are equal (best handling still needs to be discussed, pure list as TaggedText is probably not enough, see also comment in #7658)

This requires a formatter for taxon relationships, which includes

  • symbol for relationship type (depending on relation direction)
  • related name and relation source information

and which differs for

  • misapplications (only inverse - "has misapplied name"),
  • pro parte/partial synonyms
  • all other concept relationships

  • tests

Formatting rules (as discussed with WGB):

  • as marker for relationship citation we use "err. sec.", "syn. sec." and "rel. sec." (for now)
  • authors must not have initials
  • symbol for doubtful relationship and symbol for doubtful taxon
  • MAN non author is full name authorship cache
  • sensu references should have same format as other references (family name + year with whitespace separator)

Also check carefully against results discussed in #5676

Example: http://test.e-taxonomy.eu/cdmserver/rem_conf_am/taxon/7ef2a81e-0e01-4585-ab24-f41b4fc7eecc/taxonRelationshipsDTO.json?directTypes=1ed87175-59dd-437e-959e-0d71583d8417&directTypes=8a896603-0fa3-44c6-9cd7-df2d8792e577&inversTypes=1ed87175-59dd-437e-959e-0d71583d8417&inversTypes=8a896603-0fa3-44c6-9cd7-df2d8792e577&direction=relatedFrom&groupMisapplications=true

further relationship Type: 60974c98-64ab-4574-bb5c-c110f6db634d

Example for old service: http://api.cybertaxonomy.org/caryo_nepenthaceae/portal/taxon/90d47d8d-0f76-47d9-a0c8-20b4361080a4/taxonRelationships.json

new version: http://api.cybertaxonomy.org/caryo_nepenthaceae/taxon/90d47d8d-0f76-47d9-a0c8-20b4361080a4/taxonRelationshipsDTO.json

Nepenthes portal example: http://caryophyllales.org/nepenthaceae/cdm_dataportal/taxon/90d47d8d-0f76-47d9-a0c8-20b4361080a4


Related issues

Related to Edit - feature request #6681: Correct formatting for misapplied names in name editor Closed 05/31/2017
Related to Edit - feature request #6390: Details view for misapplied names Closed 01/27/2017
Related to Edit - bug #5676: Sensu does not show up if no author exists for secundum reference Feedback 07/06/2016
Related to Edit - bug #7656: Adapt inverse symbol for MisappliedName relationship type Duplicate 08/15/2018
Related to Edit - bug #6652: [Discuss] misapplied names: hide protologue icon New 05/18/2017
Related to Edit - feature request #7753: use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editor Closed 09/12/2018
Precedes Edit - feature request #7658: use new taxon relationship DTO webservice in portal Closed 06/01/2017
Copied to Edit - feature request #7666: Remaining issues for "Formatter and DTO for taxon relationships (e.g. misapplied names)" In Progress 08/20/2018

Associated revisions

Revision 33852ad0 (diff)
Added by Andreas Müller 4 months ago

ref #6682 first implementation of taxon relationship formatter and web service

Revision d50a2175 (diff)
Added by Andreas Müller 4 months ago

ref #6682 adapt taxon rel type symbols in test in for MAN inverse type

Revision c6a7335e (diff)
Added by Andreas Müller 4 months ago

ref #6682 adapt inverse MAN symbol in test

Revision 1fab5922 (diff)
Added by Andreas Müller 4 months ago

ref #6682 some changes to test taxon relationship service

Revision 973082b3 (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxonRelationship service

Revision 977a388a (diff)
Added by Andreas Müller 4 months ago

ref #6682 fix directions for taxonRelationship service

Revision d7909683 (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxon relationship service

Revision 82eb3374 (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxon relationship service

Revision 81502ddd (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxon relationship service - better separators

Revision 90ec321a (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxon relationship formatting - relsec and authors

Revision d6c56cdc (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxon relationship formatting - fix referenced entity issues

Revision 8a17aa3e (diff)
Added by Andreas Müller 4 months ago

ref #6682 further fixes for taxon relationship formatting - remove sensu tags, include Invalid Designation, use ordinary term for type

Revision 8b98d482 (diff)
Added by Andreas Müller 4 months ago

ref #6682 use TaggedTextBuilder

Revision 576743e2 (diff)
Added by Andreas Müller 4 months ago

ref #6682 include doubtful

Revision 4e6e568a (diff)
Added by Andreas Müller 4 months ago

ref #6682 fix misapplication deduplication issues

Revision 78614c1a (diff)
Added by Andreas Müller 4 months ago

ref #6682 add typeUuid and try to fix missing type issue

Revision a089c5d4 (diff)
Added by Andreas Müller 4 months ago

ref #6682 add types and deduplicateMisapplications parameter to web service

Revision 1fc33b39 (diff)
Added by Andreas Müller 4 months ago

ref #6682 add types and deduplicateMisapplications parameter to web service

Revision 1e1d5695 (diff)
Added by Andreas Müller 4 months ago

ref #6682 revert relType DTO

Revision 5576f79c (diff)
Added by Andreas Müller 4 months ago

ref #6682 try to fix failing query in TaxonDao

Revision ef5174f6 (diff)
Added by Andreas Müller 4 months ago

ref #6682 try to fix failing query in TaxonDao

Revision a9c1e5d6 (diff)
Added by Andreas Müller 4 months ago

ref #6682 types for both directions

Revision 9c8dc025 (diff)
Added by Andreas Müller 4 months ago

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

History

#1 Updated by Andreas Müller over 1 year ago

#2 Updated by Andreas Müller over 1 year ago

#3 Updated by Andreas Müller over 1 year ago

  • Description updated (diff)

#4 Updated by Andreas Müller over 1 year ago

  • Status changed from New to In Progress
  • Target version changed from Release 4.8 to Release 4.9

#5 Updated by Andreas Müller over 1 year ago

  • Target version changed from Release 4.9 to Release 4.10

#6 Updated by Andreas Müller about 1 year ago

  • Target version changed from Release 4.10 to Release 4.11

#7 Updated by Andreas Müller about 1 year ago

  • Target version changed from Release 4.11 to Release 4.12

#8 Updated by Andreas Müller about 1 year ago

  • Target version changed from Release 4.12 to Release 4.13

#9 Updated by Andreas Müller 10 months ago

  • Target version changed from Release 4.13 to Release 4.14

#10 Updated by Andreas Müller 10 months ago

  • Target version changed from Release 4.14 to Release 5.0

#11 Updated by Andreas Müller 7 months ago

  • Target version changed from Release 5.0 to Release 5.1

#12 Updated by Andreas Müller 6 months ago

  • Target version changed from Release 5.1 to Release 5.2

#13 Updated by Andreas Müller 4 months ago

  • Tags set to euro+med

This should rather be a formatter for concept relations and a new DTO service in remote.

#14 Updated by Andreas Müller 4 months ago

  • Subject changed from Cache strategy for misapplied names to Formatter and DTO for taxon relationships (e.g. misapplied names)
  • Description updated (diff)

#15 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#16 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#17 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#18 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#19 Updated by Andreas Müller 4 months ago

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

#20 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#21 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#22 Updated by Andreas Müller 4 months ago

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

#23 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#24 Updated by Andreas Kohlbecker 4 months ago

#25 Updated by Andreas Müller 4 months ago

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

#26 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#27 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#28 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#29 Updated by Andreas Müller 4 months ago

  • Status changed from In Progress to Resolved

#30 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#31 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#32 Updated by Andreas Müller 4 months ago

  • Description updated (diff)
  • Status changed from Resolved to Closed
  • % Done changed from 0 to 100

close this ticket as released in 5.2, open issues moved to #7666

#33 Updated by Andreas Müller 4 months ago

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

#34 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

Sensu references and relation references should be formatted similarly:

WGB: Wenn die exakte Referenz über die Bibliographie auf der gleichen Seite ausgegeben wird, kann man das weglassen, sonst sollte die Jahreszahl stehen.

AM: Das soll heißen, keine gesonderte Behandlung von sensu im Vergleich zu anderen Referenzen (also z.B. beim ersten ohne Jahr, z.B. weil gängige Konvention, oder weil aufgrund von Deduplizierung möglichst eng, oder, oder, …, beim anderen mit Jahr)? Ich frage nach, weil bei dir Macfarlane keine Jahreszahl hat, Cheek & Jebb aber eine haben. War das nur versehentlich?

WGB: stimmt. Cheek & Jebb hatten hier ja auch einen Verweis – da macht meine Antwort keinen Sinn. Ich denke, am besten immer mit Jahr, dann braucht man keine verschiedenen Outputs für Portal (mit Fußnotenreferenz) und anderem Output (ohne, Zitat dann als Bibliographieverweis).

#35 Updated by Andreas Müller 4 months ago

  • Description updated (diff)

#36 Updated by Andreas Müller 4 months ago

#37 Updated by Andreas Müller 4 months ago

#38 Updated by Andreas Müller 4 months ago

AM: … und noch etwas: bei der „sensu“ Referenz ist ja vermutlich die Jahreszahl bewusst weggelassen um es an die gängigen Gepflogenheiten anzupassen, oder soll dieses genauso aussehen wie alle sonstigen Zitate auch, also z.B. Cheek & Jebb 2013.

WGB: Wenn die exakte Referenz über die Bibliographie auf der gleichen Seite ausgegeben wird, kann man das weglassen, sonst sollte die Jahreszahl stehen.

==

AM: Gilt gleiches für die Initialien? Diese werden grundsätzlich weggelassen, auch bei den anderen Referenzen? Ist ja im Portal auch nicht wirklich wichtig, da man noch verlinkte Fußnote mit der vollen Angabe hat.

WGB: Initialen würde ich gerne los sein – die Angabe Autor (Jahr) oder so ist ja ein in der Botanik gängiger Bibliographieverweis.

==

AM: Die Frage ist auch, in wiefern die Details/MicroRefs hier bereits im Zitat erscheinen sollen. Ich werde sie mal auf jeden Fall mit aufnehmen, sie können dann über den sog. TaggedText Typ per default im Portal wieder ausgeschaltet werden.

WGB: Gut – wenn man sie angibt, hat man sich ja vermutlich etwas dabei gedacht. Noch besser, wenn man das ggf. unterdrücken kann.

==

AM “Bad name“ sensu Griesbach1, Mill.2, L.3 (Evtl. Ist das auch jedesmal mit sensu vor dem Namen, muss ich nochmal schauen)
Hier ist auch die Frage, wie die „err. sec.“ hier zu handeln ist. Ich würde davon ausgehen, dass bei unterschiedlicher „err. sec.“ keine Deduplizierung stattfinden soll und dass bei gleicher err. sec. diese am Ende stehen soll, also hinter L.3. Korrekt?

WGB: Deduplizierung korrekt.
Eine Wiederholung des „sensu“ ist nicht notwendig; wird ja auch durch das folgende „non “ zusätzlich zusammengehalten.

#39 Updated by Andreas Müller 3 months ago

  • Copied from deleted (feature request #7666: Remaining issues for "Formatter and DTO for taxon relationships (e.g. misapplied names)")

#40 Updated by Andreas Müller 3 months ago

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

#41 Updated by Katja Luther 3 months ago

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

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