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feature request #7417

Make pro parte and partial synonym relationships always visible in data portals

Added by Andreas Müller 7 months ago. Updated 6 months ago.

Status:
Feedback
Priority:
Highest
Category:
cdm-dataportal
Target version:
Start date:
05/15/2018
Due date:
% Done:

50%

Severity:
critical

Description

Pro parte and partial synonyms will only be handled by concept relations starting in v5.0.
Therefor the 2 concept relationships should always be visible in data portals by default.

This is similar to the handling of misapplied names which, by default, are also always visible.
Other relationships usually need to be switched on explicitly by side admin.

Also we need to check the correct formatting (icon, p.p. at end or start, ...)

picture875-1.png View (3.34 KB) Andreas Müller, 06/04/2018 01:52 PM

picture656-1.png View (11.6 KB) Andreas Müller, 06/04/2018 01:53 PM

picture168-1.png View (10.1 KB) Andreas Müller, 06/26/2018 01:42 PM


Related issues

Related to Edit - feature request #7334: Make pro parte and partial synonyms real concept relationships Resolved 03/28/2018
Related to Edit - feature request #7157: interim solution to mark pro parte synonyms in the dataportal Rejected 01/08/2018
Related to Edit - bug #7478: Fix pro parte synonym search Resolved 06/15/2018
Related to Edit - bug #7514: Change direct and inverse symbol for pro parte synonym and misapplied name relationship types. In Progress 06/26/2018
Duplicated by Edit - feature request #5627: Display pro parte (and partial) information in data portal Duplicate 03/09/2016

Associated revisions

Revision baebfef3 (diff)
Added by Andreas Kohlbecker 6 months ago

fix #7417 using DefinedTermBase.symbol and inverseSymbol instead of abbreviated labels as taxon relationship labels

Revision f95ba88b (diff)
Added by Andreas Kohlbecker 6 months ago

fix #7417 defaults for TAXON_RELATIONSHIP_TYPES and bumping module version number to 5.x

Revision eafb60f0 (diff)
Added by Andreas Kohlbecker 6 months ago

fix #7417 defaults for TAXON_RELATIONSHIP_TYPES - bugfix

History

#1 Updated by Andreas Müller 7 months ago

#2 Updated by Andreas Kohlbecker 7 months ago

  • Target version changed from Release 5.0 to Release 5.1

#3 Updated by Andreas Kohlbecker 7 months ago

#4 Updated by Andreas Kohlbecker 7 months ago

#5 Updated by Andreas Müller 7 months ago

IN the attachement you find how currently the default configuration in ...portal/admin/config/cdm_dataportal/settings/layout/taxon looks like. These 4 should be switched on.

As an example for existing pp synonym you may take Nepenthes, e.g. http://caryophyllales.org/nepenthaceae/cdm_dataportal/taxon/63d01d64-7e2d-49b9-8a41-493611692899 . Unfortunately the formatting is not yet correct there. in one direction it shows "-" instead of "p.p.". It looks like the symbol does not yet come from the database because there the symbols looks different (see 2nd attachement).

#6 Updated by Andreas Müller 7 months ago

#7 Updated by Andreas Müller 7 months ago

Other example uuids in Nepenthes: cdm_production_caryo_nepenthaceae

SELECT acc.titleCache, acc.uuid, pp.titleCache, pp.uuid, rel.type_id
FROM TaxonRelationship rel INNER JOIN TaxonBase acc ON acc.id = rel.relatedTo_id 
INNER JOIN TaxonBase pp ON pp.id = rel.relatedFrom_id
WHERE rel.type_id IN ( 942, 2641, 944)
ORDER BY rel.type_id, acc.titleCache

#8 Updated by Andreas Müller 6 months ago

  • Related to bug #7478: Fix pro parte synonym search added

#9 Updated by Andreas Kohlbecker 6 months ago

  • Status changed from New to Resolved
  • % Done changed from 0 to 50

#10 Updated by Andreas Kohlbecker 6 months ago

  • Assignee changed from Andreas Kohlbecker to Andreas Müller

Hi Andreas,

this is fixed now, please review.

Andreas

#11 Updated by Andreas Kohlbecker 6 months ago

  • Status changed from Resolved to In Progress
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

I forgot about updating the default settings regarding the pp synonyms

#12 Updated by Andreas Kohlbecker 6 months ago

As these new TaxonRelationshipTypes already are available in the production systems the accoring settings may already be stored in the drupal db with arbitrary settings. There is now no reliable method to find out if one of these 4 rel types has been set to disabled by purpose or if this has done accidentally. Therefore it is advised to enable these taxon-rel-types (PROPARTE_MISAPPLIEDNAME_FOR, PARTIAL_MISAPPLIEDNAME_FOR, PROPARTE_SYNONYM_FOR, PARTIAL_SYNONYM_FOR) for all existing portals and to let the user decide whether to disable them if needed.

This information should be included into the release notification.

#13 Updated by Andreas Kohlbecker 6 months ago

  • Status changed from In Progress to Resolved

#14 Updated by Andreas Kohlbecker 6 months ago

  • Assignee changed from Andreas Kohlbecker to Andreas Müller

finally done and ready for reviewing

#15 Updated by Andreas Müller 6 months ago

  • Status changed from Resolved to Feedback
  • Assignee changed from Andreas Müller to Andreas Kohlbecker

The symbols are still used in incorrect direction. On the side of the "real" taxon (which takes the role of the toTaxon in the relationship) the inverse symbol is used but the normal symbol should as it reads like

"the following synonym is a pp synonym of the above accepted taxon".

This is maybe confusing but definitely correct.

#16 Updated by Andreas Müller 6 months ago

Also, as symbol is not a required field, we may also think about fallbacks in case symbol is NULL.

E.g. (symbol != null)? symbol : (abbrevLabel != null)? abbrevLabel : idInVocabulary

We may also make it configurable which string to use preferably (including also symbol2).

#17 Updated by Andreas Müller 6 months ago

At least in cichorieae test (http://test.e-taxonomy.eu/dataportal/preview/cichorieae/admin/config/cdm_dataportal/settings/layout/taxon#) the possibility to choose from existing concept or name relationships is now completely missing.

#18 Updated by Andreas Müller 6 months ago

The same is true for euromed on test!!

#19 Updated by Andreas Kohlbecker 6 months ago

this is due to a LazyInitializationException occurring in the procession of the requests like:

http://160.45.63.175/cdmserver/cichorieae/termVocabulary/15db0cf7-7afc-4a86-a7d4-221c73b0c9ac/terms.json?orderBy=BY_ORDER_INDEX_ASC&pageNumber=0&pageSize=500

this has for sure been introduced by the changes made for #7508

#20 Updated by Andreas Müller 6 months ago

The pp synonyms should precede the misapplied names. Currently they come afterwards or the order is undefined.

#21 Updated by Andreas Müller 6 months ago

Andreas Kohlbecker wrote:

this is due to a LazyInitializationException occurring in the procession of the requests like:

http://160.45.63.175/cdmserver/cichorieae/termVocabulary/15db0cf7-7afc-4a86-a7d4-221c73b0c9ac/terms.json?orderBy=BY_ORDER_INDEX_ASC&pageNumber=0&pageSize=500

this has for sure been introduced by the changes made for #7508

This issue is fixed now.

#22 Updated by Andreas Müller 6 months ago

Partial synonyms are not yet shown by default (at least not for cichorieae on test)

#23 Updated by Andreas Müller 6 months ago

  • Related to bug #7514: Change direct and inverse symbol for pro parte synonym and misapplied name relationship types. added

#24 Updated by Andreas Müller 6 months ago

Andreas Müller wrote:

The symbols are still used in incorrect direction. On the side of the "real" taxon (which takes the role of the toTaxon in the relationship) the inverse symbol is used but the normal symbol should as it reads like

"the following synonym is a pp synonym of the above accepted taxon".

This is maybe confusing but definitely correct.

This has been discussed and will be handled by changing the symbols in DB (#7514)

#25 Updated by Andreas Kohlbecker 6 months ago

Andreas Müller wrote:

Partial synonyms are not yet shown by default (at least not for cichorieae on test)

This has worked in the integration databases where I tested the drupal database update. The test dataportal configurations may have been confused through problems in the update functions. Let's wait for the release being installed. It should be ok on the production servers.

If it is ok there we can close this issue.

#26 Updated by Andreas Kohlbecker 6 months ago

  • Target version changed from Release 5.1 to Release 5.2

#27 Updated by Andreas Müller 6 months ago

Isn't this solved (more or less) in 5.1 already?

#28 Updated by Andreas Kohlbecker 6 months ago

  • Target version changed from Release 5.2 to Release 5.1

I guess something went wrong this morning with Redmine I only moved tickets which are "New" or in "Progress", when changing the Targetversion via the batch edit function Redmine was behaving a bit strange, hung for quite some time.

I moving this issue back now ...

after checking the production portal settings we can close this issue.

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