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task #7319

[CHECK] Import synonyms correctly in E+M

Added by Andreas Müller over 1 year ago. Updated 7 months ago.

Status:
Resolved
Priority:
Highest
Category:
cdmadapter
Target version:
Start date:
03/19/2018
Due date:
% Done:

90%

Estimated time:
2.00 h
Severity:
normal
Tags:

Description

Since CDM 4.1 synonyms may belong only to exactly 1 taxon (#5803, #5974). Therefore pro parte/partial synonyms should be handled as different concept with pro parte synonym concept relationships instead.

In E+M there are multiple synonyms having more than 1 accepted taxon. Those being pro parte/partial synonyms should be handled as described above and be converted to accepted taxa, while ordinary synonyms with >1 accepted taxa should be corrected in data.

Possible candidates can be found via

SELECT        ta.PTNameFk AS synNameID, ta.PTRefFk, syn.StatusFk, st.Status synStatus, synName.FullNameCache,   
    rel1.RelQualifierFk relTyp1, relStatus1.RelPTQualifier relTyp1_, acc1.StatusFk st1, acc1.RIdentifier taxon1, accName1.NameId name1, acc1.PTRefFk ref1, accName1.FullNameCache,  
    rel2.RelQualifierFk relTyp2, relStatus2.RelPTQualifier relTyp2_, acc2.StatusFk st2, acc2.RIdentifier taxon2, accName2.NameId name2, acc2.PTRefFk ref2, accName2.FullNameCache   
FROM          dbo.v_cdm_exp_taxaAll ta LEFT OUTER JOIN PTaxon syn ON syn.RIdentifier = ta.RIdentifier   
LEFT OUTER JOIN Status st ON st.StatusId = syn.StatusFk 
LEFT OUTER JOIN Name synName ON syn.PTNameFk = synName.NameId   
LEFT OUTER JOIN RelPTaxon rel1 ON rel1.PTNameFk1 = syn.PTNameFk AND rel1.PTRefFk1 = syn.PTRefFk 
       LEFT OUTER JOIN PTaxon acc1 ON rel1.PTNameFk2 = acc1.PTNameFk AND rel1.PTRefFk2 = acc1.PTRefFk   
       LEFT OUTER JOIN RelPTQualifier relStatus1 ON rel1.RelQualifierFk = relStatus1.RelPTQualifierId
       LEFT OUTER JOIN Name accName1 ON accName1.NameId = acc1.PTNameFk 
LEFT OUTER JOIN RelPTaxon rel2 ON rel2.PTNameFk1 = syn.PTNameFk AND rel2.PTRefFk1 = syn.PTRefFk 
       LEFT OUTER JOIN PTaxon acc2 ON rel2.PTNameFk2 = acc2.PTNameFk AND rel2.PTRefFk2 = acc2.PTRefFk   
       LEFT OUTER JOIN RelPTQualifier relStatus2 ON rel2.RelQualifierFk = relStatus2.RelPTQualifierId
       LEFT OUTER JOIN Name accName2 ON accName2.NameId = acc2.PTNameFk 
WHERE    syn.StatusFk NOT IN ( 1) AND acc1.RIdentifier < acc2.RIdentifier AND rel1.RelQualifierFk <> -99  AND rel2.RelQualifierFk <> -99 
ORDER BY syn.StatusFk, relTyp1, st1, relTyp2, st2, syn.PTRefFk, synNameID   

with

 AND NOT (acc1.StatusFk <> 1 OR acc2.StatusFk <> 1)  -- rel to accepted only

 AND NOT (syn.StatusFk = 4 AND rel1.RelQualifierFk = 4  AND rel2.RelQualifierFk = 4) -- no pure pro parte synonyms

inconsistent pro parte:

AND 
       (
         (syn.StatusFk NOT IN (3,4) AND ( rel1.RelQualifierFk NOT IN (2,6,7) OR rel2.RelQualifierFk NOT IN (2,6,7)))
         OR
         (syn.StatusFk IN (3,4) AND ( rel1.RelQualifierFk IN (2,6,7) OR rel2.RelQualifierFk IN (2,6,7)))

       )

Related issues

Related to Edit - feature request #7334: Make pro parte and partial synonyms real concept relationships Resolved 03/28/2018
Follows Edit - feature request #5974: Remove synonym relationships Closed 11/14/2016
Copied from Edit - task #6521: Check existing imports for handling new synonym structure correctly New 03/17/2017

History

#1 Updated by Andreas Müller over 1 year ago

  • Status changed from New to In Progress

#2 Updated by Andreas Müller over 1 year ago

  • Copied from task #6521: Check existing imports for handling new synonym structure correctly added

#4 Updated by Andreas Müller over 1 year ago

  • Due date set to 11/15/2016
  • Start date changed from 03/19/2018 to 11/15/2016
  • Follows feature request #5974: Remove synonym relationships added

#5 Updated by Andreas Müller over 1 year ago

  • Description updated (diff)
  • Due date deleted (11/15/2016)
  • Start date changed from 11/15/2016 to 03/19/2018

#6 Updated by Andreas Müller over 1 year ago

  • Description updated (diff)

#7 Updated by Andreas Müller over 1 year ago

#8 Updated by Andreas Müller over 1 year ago

  • Estimated time set to 2.00 h

#9 Updated by Andreas Müller over 1 year ago

  • % Done changed from 0 to 70

#10 Updated by Andreas Müller over 1 year ago

  • Priority changed from Highest to Priority13

#11 Updated by Andreas Müller about 1 year ago

  • Target version changed from Euro+Med Portal Release to Euro+Med Migration

#12 Updated by Andreas Müller about 1 year ago

  • Subject changed from Import synonyms correctly in E+M to [CHECK] Import synonyms correctly in E+M
  • Priority changed from Priority13 to Highest

#13 Updated by Andreas Müller 7 months ago

  • Status changed from In Progress to Resolved
  • % Done changed from 70 to 90

This seems to be fixed. There are only pro parte/partial synonyms left in the candidates list. And they seem to be handled correctly.

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