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bug #9302

open

Phycobank related issues for TypeDesignation formatting

Added by Andreas Müller over 3 years ago. Updated almost 3 years ago.

Status:
In Progress
Priority:
New
Category:
cdmlib
Target version:
Start date:
Due date:
% Done:

30%

Estimated time:
Severity:
normal
Found in Version:
Tags:

Description

In the Phycobank context a couple of issues for type formatting have been found, after TypeDesginationSetManager has been refactored. Some of them came from refactoring, some are new.

  • brackets around year in short citation (both designated by and fide citations) lead to double brackets - e.g. "... country, location (lectotpy: B 12345 designated by Miller (2020))" => simply remove brackets around year
  • microcitations for short citations not yet implemented => implement as "Author year: xyz)
  • designation citations can have the form "designated by" or "designated in" (and "vide" - see next issue). The former linking to an authorteam within a reference (if the autorteam differs from the reference authorteam). The second references the reference and does not mention the exact authors => "Designated by" should be used as it is most exact and also with "designated in" it is per se unclear who the authors of a designation, additional information is needed to distinguis if the authors of the designated in references are also the authors of the type designation.
  • A third kind of designation is using "vide". This means that the designation is kind of doubtful, as the type was mentioned in the given reference but it is not clear if the reference is the place of designation or if the reference mentions only a designation that took place elsewhere. => maybe we need a flag indicating if the designation citation is a "vide-citation" so the correct formatting can be done => a mail was sent to users to ask for opinions
  • NameTypeDesignations on the registration page do not show the designation reference at all anymore, before they did show the long form sepated only by empty space. Both is not expected behavior. => Better we should have the name type followed by "designated by" followed by the above mentioned short form of the citation
  • SpecimenTypeDesignations with designations are currently handled different to NameTypeDesignations as the show the "designated by" part in brackets behind the type status but before the specimen information. This should be unified by using the NameTypeDesignation format here as well which is typestatus followed by type followed by designated by short citation
  • The search result in phycobank currently includes citation information, this was not the case before and should be removed again => can be implemented in dataportal code ==> #9306
  • Microreferences for non-lectotypes should be editable => see #9303

Related issues

Related to EDIT - task #9300: Name Page: harmonize media specimen lectotype representationsIn ProgressAndreas Kohlbecker

Actions
Related to EDIT - feature request #9279: Improve type designation formatting and TypeDesignationSetManagerClosedAndreas Müller

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Related to EDIT - bug #9290: stop setting Registration.citation as citation for TypeDesignations in all type editors by defaultClosedAndreas Kohlbecker

Actions
Related to EDIT - task #8546: type specimen editor: published in vs. designated byNewAndreas Kohlbecker

Actions
Related to EDIT - bug #8984: Registration search result list: Format display of two type specimensNewAndreas Kohlbecker

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Related to EDIT - feature request #9596: Open issues for TypeDesignationWorkingSetIn ProgressAndreas Müller

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Related to EDIT - bug #9701: Order and display of different typifications for one name in one referenceClosedAndreas Kohlbecker

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Copied to EDIT - bug #9303: [DISCUSS+IMPLEMENT] Make type designation micro references for non-lectotypes editable in TaxEditorNewAndreas Müller

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Copied to EDIT - task #9306: Registration result list: supress "designated by" reference in portal ClosedAndreas Kohlbecker

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Copied to EDIT - task #9308: Supress "designated by" reference in portal in registration ListView and RegistrationWorkingSetEditorClosedAndreas Kohlbecker

Actions
Actions #1

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #2

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
  • Status changed from New to In Progress
  • % Done changed from 0 to 10
Actions #3

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)

AM:

Bisher war gewünscht, Quellen als Kurzzitat mit „Autor (Jahr)“ anzugeben, was sowohl für die designated by Quellen als auch für die fide Quellen gelten sollte.
Jetzt hat Henning entdeckt, dass die Klammer um die Jahreszahl zu unschönen Doppelklammern bei Specimen Typedesignations führt, z.B.

Viet Nam, Bắc Kạn Province, Ba Bể Lake, benthos, alt. 160 m, 22°23'36.3"N, 105°36'51.36"E, 29 Apr 2015, E. Gusev & M. Kulikovskiy s.n. (lectotype: 02168 designated by Kulikovskiy & al. (2020))

Die Frage daher, ob wir hier nicht einfach auf die Klammer um die Jahreszahl verzichten können.
Die äußere Klammer ist als Klammer um alle Typus + Specimen Information herum gedacht und es wäre gut wenn wir die behalten könnten.
Zudem ist die Stellung der Microreferenz (Seitenzahl etc.) bislang noch nicht besprochen worden. Hier ist der Vorschlag diese durch „:“ getrennt hinter dem Jahr einzufügen, sofern sie existiert.
Dann käme am Ende z.B. raus

Viet Nam, Bắc Kạn Province, Ba Bể Lake, benthos, alt. 160 m, 22°23'36.3"N, 105°36'51.36"E, 29 Apr 2015, E. Gusev & M. Kulikovskiy s.n. (lectotype: 02168 designated by Kulikovskiy & al. 2020: 615)

Gibt es gegen diese Art der Formatierung (zumindest als Default) Einwände?

Actions #4

Updated by Andreas Müller over 3 years ago

AM: Bei der Diskussion ums Typusmodul vor ca. 2 Jahren hatten wir diskutiert und später auch implementiert, dass es 2 Arten von Quellen für Typen geben soll, die „designated by“ Quelle für Lecto (Epi, Neo, ..)typen und allgemeine Quellen, die wir inzwischen mit „[fide xxx, yyy, zzz] angeben, worunter Sekundärquellen und Quellen für textuelle Typuszitate fallen, wenn ich es richtig verstanden habe.

Henning erwähnte jetzt auch noch Quellenangaben mit „vide“ wobei es sich wohl quasi um „designated by“ Zitate handelt, aus denen im Original aber nicht eindeutig hervorgeht, ob sie einen Typus designieren oder ob sie die Information von woanders abschreiben, da die Information, dass es sich um eine Designation handelt, noch nicht solange verpflichtend ist.

Beispiel:
Amphora C. G. Ehrenberg ex Kützing, Kies. Bacill. Diat. 107. 7-9 Nov 1844.
LT.: A. ovalis (C. G. Ehrenberg) Kützing (Navicula amphora C. G. Zitat Zitat aus Index Nominum Genericorum:Ehrenberg) (vide C. S. Boyer, Proc. Acad. Nat. Sci. Philadelphia 79 (Suppl.): 253. 1928)

Die Frage ist, ob dieser Fall bereits vom Modell abgedeckt wird. Für mich sieht es aus wie eine Art „doubtful designated by“, also ein doubtful oder vide Flag, welches zur designated by Referenz gehören würde und welches bewirkt, dass nicht „designated by“ sondern „vide“ im Output erscheint.

Macht das für euch Sinn? Gibt es andere Vorschläge? Wird was falsch interpretiert?

Actions #5

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #6

Updated by Andreas Müller over 3 years ago

  • Copied to bug #9303: [DISCUSS+IMPLEMENT] Make type designation micro references for non-lectotypes editable in TaxEditor added
Actions #7

Updated by Andreas Müller over 3 years ago

AM:

ich habe, wie besprochen versucht den Punkt

"The search result in phycobank currently includes citation information, this was not the case before and should be removed again " (Punkt 4 in Hennings Mail)

des Tickets https://dev.e-taxonomy.eu/redmine/issues/9302 über Verwendung des withCitaion Parameters beim Aufruf des print bzw. toTaggedText Methoden des TypeDesignationSetManagers zu lösen.

Grundsätzlich ist das möglich, würde aber an sehr vielen Stellen im Stellen die Einführung dieses Parameters im Code verlangen, da die aufgerufenen Methoden auch von vielen anderen Stellen her aufgerufen werden, bei denen i.d.R. das Weglassen der Citation nicht gewünscht sein dürfte. Die Aufrufkette ist:

/registrationDTO/find => RegistrationWorkingSetService.pageDTOs => RegistrationWorkingSetService .convertToDTOPager => RegistrationWorkingSetService.makeDTOs => new RegistrationDTO(Registration)

Bei letzerer wollte ich den Parameter einführen, was problemlos ging, allerdings warden die vorangehenden Methoden teilweise sehr häufig verwendet.

Daher jetzt meine Frage: Die DTO gibt die summary ja auch als TaggedText zurück. Benutzt du diesen oder die String Version? Falls ersteres wäre es vermutlich deutlich leichter und sauberer die Referenz einfach aus dem TaggedText herauszufiltern.
Kannst du mal schauen, ob das ginge?

Actions #8

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #9

Updated by Andreas Müller over 3 years ago

  • Related to task #9300: Name Page: harmonize media specimen lectotype representations added
Actions #10

Updated by Andreas Müller over 3 years ago

  • Related to feature request #9279: Improve type designation formatting and TypeDesignationSetManager added
Actions #11

Updated by Andreas Müller over 3 years ago

  • Related to bug #9290: stop setting Registration.citation as citation for TypeDesignations in all type editors by default added
Actions #12

Updated by Andreas Müller over 3 years ago

  • Related to task #8546: type specimen editor: published in vs. designated by added
Actions #13

Updated by Andreas Müller over 3 years ago

  • Related to bug #8984: Registration search result list: Format display of two type specimens added
Actions #14

Updated by Andreas Kohlbecker over 3 years ago

  • Copied to task #9306: Registration result list: supress "designated by" reference in portal added
Actions #15

Updated by Andreas Kohlbecker over 3 years ago

  • Description updated (diff)
Actions #16

Updated by Andreas Kohlbecker over 3 years ago

  • Copied to task #9308: Supress "designated by" reference in portal in registration ListView and RegistrationWorkingSetEditor added
Actions #17

Updated by Andreas Müller about 3 years ago

Actions #18

Updated by Andreas Müller about 3 years ago

  • % Done changed from 10 to 30

Check how far this is still open.
Closed issues where implemented in 5.18 or prior.

Actions #19

Updated by Andreas Müller about 3 years ago

  • Target version changed from Release 5.18 to Release 5.25
Actions #20

Updated by Andreas Müller about 3 years ago

  • Tags set to formatting
Actions #21

Updated by Andreas Müller almost 3 years ago

  • Target version changed from Release 5.25 to Release 5.45
Actions #22

Updated by Andreas Kohlbecker almost 3 years ago

  • Related to bug #9701: Order and display of different typifications for one name in one reference added
Actions

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