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feature request #6589

Handle protologue as original source with URI link

Added by Andreas Müller over 4 years ago. Updated 11 months ago.

Status:
Closed
Priority:
Highest
Category:
cdm
Target version:
Start date:
04/24/2017
Due date:
% Done:

100%

Severity:
normal

Description

Once #6588 and #6581 is implemented we could move protologue information from NameDescription to nomenclatural reference.


Related issues

Related to Edit - feature request #7653: [DISCUSS] Delete NameFacts => Result: no Closed 08/14/2018
Related to Edit - feature request #8920: Make reference URL available in details view New 03/31/2020
Related to Edit - bug #9241: replace/adapt descriptionPart in render templated New 10/06/2020
Related to Edit - feature request #9225: Make TaxonName.nomenclaturalSource a new DescriptionElementSource subclass Closed 09/14/2020
Related to Edit - task #9265: Adapt dataportal to new protologue handling Closed 10/29/2020
Related to Edit - task #6591: Use name used in source for original spelling Closed 04/25/2017
Blocked by Edit - feature request #6581: Make all microreferenced references OriginalSources Closed 04/24/2017
Blocked by Edit - feature request #6588: Add URL and URL comment to OriginalSource / ExternalLink Closed 04/24/2017
Precedes Edit - task #9266: Remove protologue section from TaxEditor Closed 04/25/2017
Copied to Edit - feature request #9320: Move additional publication information to nomenclatural source In Progress 11/25/2020

Associated revisions

Revision 32d98e19 (diff)
Added by Patrick Plitzner over 4 years ago

ref #6589 Change protologue section label

Revision 139caafa (diff)
Added by Andreas Müller about 1 year ago

ref #6589 add ProtologMover (not yet ready)

Revision cb45d97c (diff)
Added by Andreas Müller 12 months ago

ref #6589 finalize update script for

Revision bee1d8ab (diff)
Added by Andreas Müller 12 months ago

ref #6589 fix update script (incorrect alias) and update remote-webapp h2 test db

Revision 7fea2e65 (diff)
Added by Andreas Müller 12 months ago

ref #6589 update vaadin h2 test db

Revision 9f095f86 (diff)
Added by Andreas Müller 12 months ago

ref #6589 update taxeditor h2 test db

Revision 4f4efaf6 (diff)
Added by Andreas Müller 12 months ago

ref #6589 adapt import scripts to new protologue handling

Revision 6320b0c9 (diff)
Added by Andreas Müller 12 months ago

ref #6589 adapt cdmlib import scripts to new protologue handling

Revision d772a673 (diff)
Added by Andreas Müller 12 months ago

ref #6589 adapt cdmlight export to new protologue handling

History

#1 Updated by Andreas Müller over 4 years ago

#2 Updated by Andreas Müller over 4 years ago

#3 Updated by Andreas Müller over 4 years ago

WGB: Mir aufgefallen, dass die Angabe „Protolog“ im Editor Detail eigentlich nicht richtig ist, es geht ja eigentlich um den „nomenclatural act“, der den Namen validiert (oder eben auch nicht). Hierzu gehört dann auch die Publikation der Veröffentlichung von Kombinationen (das ist dann ja kein „Protolog“).

AM: Damit wir über das gleiche reden, die Kombinations“protologe“ sollen aber bei den Kombinationsnamen bleiben, oder? Es geht dir also v.a. um das Label?

WGB: Ja. Im Prinzip geht’s ja um das Belegen der im Detail der Veröffentlichungsreferenz des Namens genannten exakten Literaturstellen durch Scans derselben. Damit wird ggf. auch die Zuordnung eines nom. status belegt (also z.B. der „Beweis“, dass an der Veröffentlichungsstelle bestimmte Regeln nicht befolgt wurden). Im Grunde kann das Ganze aber auch als eine Art Diskussion des Status gesehen werden – normalerweise mit Verbindung zu den Literaturdetails, aber manchmal auch mit Bezug auf das Datum der Veröffentlichung (z.B. durch die Darstellung einer Einband- oder Titelseite, die das Jahr der Veröffentlichung klarstellt).

AM: Wenn ja, hast du einen Vorschlag. Grundsätzlich wäre es sicherlich auch sinnvoll, das intern anders zu modellieren. Derzeit wird es quasi als NameFact vom Typ „Protolog“ abgespeichert. Auf das Konstrukt „NameFact“ (bzw. NameDescription) würde ich eigentlich gerne völlig verzichten, das ist ein Konstrukt aus den Anfangszeiten welches wir eigentlich nicht brauchen und welches wir für die Protologe als workaround missbraucht haben. Daher wäre hier eine Modelländerung auf jeden Fall sinnvoll. Da bräuchten wir dann auch noch ein Label für das Attribut im Model (nicht nur im UI).

WGB: Ich denke, die Modellierung sollten wir noch mal eingehend diskutieren. Einerseits ist es in vielen Fällen nur ein einfacher Link zum seitengenauen Bild des Textes der Erstveröffentlichung. Das kann aber teilweise schon durch die Nennung mehrere Textstellen komplizierter werden, und dann in eine ganze Diskussion mit Verweis auf Code-Artikel etc. ausarten. Eigentlich denke ich, dass das alles eigentlich zu den Reference Details gehört und beim Zitat des Namens hinterlegt werden sollte (das bedeutet aber, dass das Detail doch geparst modelliert werden müsste); weitere Details könnten dann in einem Text „nomenclatural evaluation“ hinterlegt werden, der dann ggf. mit in-line Referenzen versehen werden könnte. Siehe übernächste Notiz, wie man das mit der jetzigen Lösung einfacher lösen könnte.

AM: Im UI sollte es aber ein eingängliches Label sein. Mit Protolog konnten die User bislang alle was anfangen, deswegen fände ich es nicht gut, wenn wir da etwas zu abstraktes nehmen.
Was wäre mit „Original Publication“, das wird ja auch öfters verwendet?

WGB: Im UI würde ich (bei der jetzigen Lösung) einfach „Protologue / original publication“ benutzen. Das deckt das dann ab.

#4 Updated by Andreas Müller over 4 years ago

  • Priority changed from New to Priority14

#5 Updated by Andreas Müller over 4 years ago

  • Target version changed from CDM UML 4.7 to CDM UML 5.0

#7 Updated by Andreas Müller over 3 years ago

  • Target version changed from CDM UML 5.0 to CDM UML 5.5

#9 Updated by Andreas Müller about 3 years ago

#10 Updated by Andreas Müller almost 3 years ago

  • Priority changed from Priority14 to Priority13

#11 Updated by Andreas Müller over 2 years ago

  • Target version changed from CDM UML 5.5 to CDM UML 5.15

#12 Updated by Andreas Müller over 1 year ago

#13 Updated by Andreas Müller over 1 year ago

  • Target version changed from CDM UML 5.15 to CDM UML 5.28

#14 Updated by Andreas Müller about 1 year ago

  • Status changed from New to In Progress
  • Priority changed from Priority13 to Highest

#15 Updated by Andreas Kohlbecker about 1 year ago

  • Related to bug #9241: replace/adapt descriptionPart in render templated added

#16 Updated by Andreas Müller 12 months ago

  • Related to feature request #9225: Make TaxonName.nomenclaturalSource a new DescriptionElementSource subclass added

#17 Updated by Andreas Müller 12 months ago

The following records (sources for textdata) should also be deleted from AUD tables in Cichorieae . All other DBs do not have sources in for these TextData. => DONE for all relevant DBs on production, test and integration (except for cichoreae on test which somehow is corrupt but will be updated anyway)

DELETE  
FROM DescriptionElementBase_OriginalSourceBase
WHERE sources_id IN 
(
SELECT * FROM (
SELECT DO.sources_id -- osb.id -- deb.id, osb.id, osb.sourceType
FROM TaxonName n
INNER JOIN DescriptionBase db ON db.taxonName_id = n.id 
INNER JOIN DescriptionElementBase deb ON deb.inDescription_id = db.id 
INNER JOIN DescriptionElementBase_Media MN ON deb.id = MN.DescriptionElementBase_id 
INNER JOIN Media m ON m.id = MN.media_id 
INNER JOIN MediaRepresentation mr ON mr.media_id = m.id 
INNER JOIN MediaRepresentationPart mrp ON mrp.representation_id = mr.id 
INNER JOIN DefinedTermBase feature ON feature.id = deb.feature_id 
              AND feature.uuid = '71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f' 
INNER JOIN DescriptionElementBase_OriginalSourceBase DO ON DO.DescriptionElementBase_id = deb.id
-- INNER JOIN OriginalSourceBase osb ON osb.id = DO.sources_id
 ) AS tmp
)
DELETE
FROM OriginalSourceBase
WHERE id IN 
(
SELECT DO.sources_id -- osb.id -- deb.id, osb.id, osb.sourceType
FROM TaxonName n
INNER JOIN DescriptionBase db ON db.taxonName_id = n.id 
INNER JOIN DescriptionElementBase deb ON deb.inDescription_id = db.id 
INNER JOIN DescriptionElementBase_Media MN ON deb.id = MN.DescriptionElementBase_id 
INNER JOIN Media m ON m.id = MN.media_id 
INNER JOIN MediaRepresentation mr ON mr.media_id = m.id 
INNER JOIN MediaRepresentationPart mrp ON mrp.representation_id = mr.id 
INNER JOIN DefinedTermBase feature ON feature.id = deb.feature_id 
              AND feature.uuid = '71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f' 
INNER JOIN DescriptionElementBase_OriginalSourceBase DO ON DO.DescriptionElementBase_id = deb.id
-- INNER JOIN OriginalSourceBase osb ON osb.id = DO.sources_id

)

#18 Updated by Andreas Müller 12 months ago

SQL to find linking data to TextData holding the protologue image

SELECT DO.sources_id -- DO.DescriptionElementBase_id,  -- , osb.sourceType
FROM TaxonName n
INNER JOIN DescriptionBase db ON db.taxonName_id = n.id 
INNER JOIN DescriptionElementBase deb ON deb.inDescription_id = db.id 
INNER JOIN DescriptionElementBase_Media MN ON deb.id = MN.DescriptionElementBase_id 
INNER JOIN Media m ON m.id = MN.media_id 
INNER JOIN MediaRepresentation mr ON mr.media_id = m.id 
INNER JOIN MediaRepresentationPart mrp ON mrp.representation_id = mr.id 
INNER JOIN DefinedTermBase feature ON feature.id = deb.feature_id 
              AND feature.uuid = '71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f' 
LEFT JOIN DescriptionElementBase_OriginalSourceBase DO ON DO.DescriptionElementBase_id = deb.id
LEFT JOIN OriginalSourceBase osb ON osb.id = DO.sources_id

WHERE deb.id IN (
   SELECT DA.DescriptionElementBase_id 
    FROM DescriptionElementBase_Annotation DA 

    UNION ALL

   SELECT DS.TextData_id  
    FROM DescriptionElementBase_LanguageString DS 

    UNION ALL

   SELECT DM.DescriptionElementBase_id  
    FROM DescriptionElementBase_Marker DM 

    UNION ALL

   SELECT DMo.DescriptionElementBase_id  
    FROM DescriptionElementBase_Modifier DMo 

    UNION ALL   
   SELECT DO.DescriptionElementBase_id  
    FROM DescriptionElementBase_OriginalSourceBase DO 
)

#19 Updated by Andreas Müller 12 months ago

SQL to find linking data to DescriptionBase holding the protologue image

SELECT n.titleCache 
FROM TaxonName n
INNER JOIN DescriptionBase db ON db.taxonName_id = n.id 
INNER JOIN DescriptionElementBase deb ON deb.inDescription_id = db.id 
INNER JOIN DescriptionElementBase_Media MN ON deb.id = MN.DescriptionElementBase_id 
INNER JOIN Media m ON m.id = MN.media_id 
INNER JOIN MediaRepresentation mr ON mr.media_id = m.id 
INNER JOIN MediaRepresentationPart mrp ON mrp.representation_id = mr.id 
INNER JOIN DefinedTermBase feature ON feature.id = deb.feature_id 
              AND feature.uuid = '71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f' 

WHERE db.id IN (
   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_Annotation NN 

    UNION ALL

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_Credit NN 

    UNION ALL 

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_Extension NN 

        UNION ALL 

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_ExternalLink NN 

        UNION ALL 

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_Identifier NN 

    UNION ALL

   SELECT MM.TaxonDescription_id
    FROM DescriptionBase_GeoScope MM 

    UNION ALL

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_Marker NN 

    UNION ALL

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_OriginalSourceBase  NN 

    UNION ALL

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_RightsInfo  NN 

    UNION ALL

   SELECT NN.DescriptionBase_id
    FROM DescriptionBase_Reference  NN 

    UNION ALL

   SELECT NN.TaxonDescription_id
    FROM DescriptionBase_Scope  NN 

    UNION ALL

   SELECT NN.descriptions_id
    FROM DescriptiveDataSet_DescriptionBase  NN 
)

#20 Updated by Andreas Müller 12 months ago

  • Related to task #9265: Adapt dataportal to new protologue handling added

#21 Updated by Andreas Müller 12 months ago

  • Precedes task #9266: Remove protologue section from TaxEditor added

#22 Updated by Andreas Müller 12 months ago

  • Status changed from In Progress to Resolved
  • % Done changed from 0 to 50

This is fixed now with model version 5.18.4.
However, #9266 and #9265 also need to be fixed before release

#23 Updated by Andreas Müller 12 months ago

  • Related to task #6591: Use name used in source for original spelling added

#24 Updated by Andreas Kohlbecker 11 months ago

I found a special case in the data portal code for the feature:

UUID_ADDITIONAL_PUBLICATION = 'cb2eab09-6d9d-4e43-8ad2-873f23400930'

Which is also treated like a secondary nomenclatural reference:

The code expects $description_element->multilanguageText_L10n->text being filled and appends this test to the nomRef like

NOM_REF [& ADDITIONAL_PUBLICATION_TEXT].

I found no current project in the edit-database server which is making use of this, so I think that we can neglect it. So I don't think that this is still relevant but felt it would be better to share this observation with you, just in case you remember something in this context which needs to be handled.

#25 Updated by Andreas Müller 11 months ago

Additional Publications do definetely exist, e.g. in E+M or caryo_spp

SELECT db.DTYPE, db.id, feature.titleCache
FROM DescriptionBase db INNER JOIN DescriptionElementBase deb ON deb.indescription_id = db.id
 INNER JOIN DefinedTermBase feature ON feature.id = deb.feature_id
WHERE feature.titleCache LIKE '%Additio%' -- db.DTYPE like 'TaxonNameDesc%'

in caryo_spp some data is attached to TaxonDescriptions which is not correct. This needs to be corrected.

Andreas K., does the fact that additional publications exist need any action?

#26 Updated by Andreas Kohlbecker 11 months ago

Interesting, that the UUID is different from that in the data portal code ('cb2eab09-6d9d-4e43-8ad2-873f23400930').

I am not sure what do to with these references. ADDITIONAL_PUBLICATION in NameDescriptions could be handled in the NomenclaturalSource, but how can we distinguish them from protologues?

#27 Updated by Andreas Kohlbecker 11 months ago

also in

  • cdm_production_cichorieae
  • cdm_production_euromed
  • cdm_production_euromed_caucasus
  • cdm_production_diptera
  • cdm_production_flora_central_africa
  • cdm_production_flora_cuba
  • cdm_production_flora_malesiana_prospective

#28 Updated by Andreas Müller 11 months ago

Andreas Kohlbecker wrote:

Interesting, that the UUID is different from that in the data portal code ('cb2eab09-6d9d-4e43-8ad2-873f23400930').

I am not sure what do to with these references. ADDITIONAL_PUBLICATION in NameDescriptions could be handled in the NomenclaturalSource, but how can we distinguish them from protologues?

Yes, strange, maybe it was changed when ADDITIONAL_PUBLICATION was moved from Feature to NameFeature vocabulary. But I can't find an according update script.
However, there are some old test data which still use the old uuid (e.g. TermVocabularyDaoImplTest.xml) so it was there at some time in the past.

We should move this discussion to a new ticket (#9320) as it does not really belong to this ticket.

#29 Updated by Andreas Müller 11 months ago

#30 Updated by Andreas Müller 11 months ago

  • Target version changed from CDM UML 5.28 to Release 5.18

#31 Updated by Andreas Müller 11 months ago

  • Status changed from Resolved to Closed
  • % Done changed from 50 to 100

I think we can close this ticket.

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