EDIT

Not yet complete

see also #5082

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check that the import is adapted such that only referenced authors and teams are imported

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check that import is run with a maven compiled code (aspectJ switched on)

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run [s_em_MoveCommonNames] to move common names to structured common names

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remove duplicate parent relationships (see also http://wiki.bgbm.org/bdinotes/index.php/EuroMed#Data_publication)

SELECT * 
FROM (
   SELECT COUNT(pt2.RIdentifier) AS HowMany, pt.PTNameFk, pt.PTRefFk , n.FullNameCache
   FROM PTaxon pt
     INNER JOIN RelPTaxon rel ON pt.PTNameFk = rel.PTNameFk1 AND pt.PTRefFk = rel.PTRefFk1 
     INNER JOIN PTaxon pt2 ON rel.PTNameFk2 = pt2.PTNameFk AND rel.PTRefFk2 = pt2.PTRefFk 
     INNER JOIN Name n ON pt.PTNameFk = n.NameID 
   WHERE (rel.RelQualifierFk = 1) AND (pt.PTRefFk % 100000 = 0) AND (pt.PTRefFk >= 7000000) 
   GROUP BY pt.RIdentifier, pt.PTNameFk, pt.PTRefFk, n.FullNameCache) AS DuplicateParentRelation 
WHERE HowMany > 1 
ORDER BY HowMany DESC;

SELECT n2.fullNameCache, rel.*
FROM PTaxon pt
    INNER JOIN RelPTaxon rel ON pt.PTNameFk = rel.PTNameFk1 AND pt.PTRefFk = rel.PTRefFk1 
    INNER JOIN Name n2 ON rel.PTNameFk2 = n2.NameId
WHERE rel.PTNameFk1 = xxx AND rel.PTRefFk1 = 7xxx

====

remove selfreferencing relations

DELETE RelName WHERE NameFk1 = NameFk2 AND RelNameQualifierFk <> 62;
DELETE RelPTaxon WHERE PTNameFk1 = PTNameFk2 and PTRefFk1 = PTRefFk2

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Taxa without parents (still needs improvements with publish flag and other issues like valueless taxa)

SELECT n.fullNameCache, pt.*
FROM PTaxon pt 
     INNER JOIN Name n ON pt.PTNameFk = n.NameId
WHERE pt.RIdentifier NOT IN
(SELECT p.RIdentifier 
  FROM PTaxon p 
    INNER JOIN RelPTaxon rel ON p.PTNameFk = rel.PTNameFk1 AND p.PTRefFk = rel.PTRefFk1 
  WHERE (rel.RelQualifierFk = 1)
)
AND (pt.PTRefFk % 100000 = 0) AND (pt.PTRefFk >= 7000000) AND pt.StatusFk NOT IN (2,6, 3,4)

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Run Queries in Y:\BDI\PESI\sh\EuroPlusMed\Credits_Publish\Update_before_publication.sql for data integrity

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Run Commands in Y:\BDI\PESI\sh\EuroPlusMed\Credits_Publish\SetPublishAndCredits.sql to set the publish flag correctly and to set last scrutiny

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The export starting point xxx requires that the Treeindex is set correctly in BM.

For this run

UPDATE PTaxon SET TreeIndex=NULL;
UPDATE PTaxon SET TreeIndex=dbo.f_core_getTreeIndex(RIdentifier) WHERE (StatusFk IN (1,5)) 

This differs a bit from http://wiki.bgbm.org/bdinotes/index.php/EuroMed#Data_publication as there unpublished taxa do not need a treeindex.

We may also run

UPDATE PTaxon SET IndexNameString=dbo.f_core_TreeIndex2NameString(TreeIndex) 

but not really necessary for the export

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check for corrupt hierarchies:

SELECT n.fullNameCache,  n.NameCache, pt.*
FROM PTaxon pt INNER JOIN Name n ON n.NameId = pt.PTNameFk 
WHERE pt.TreeIndex NOT LIKE '533921-%' AND pt.TreeIndex NOT LIKE '556619-%' -- AND pt.StatusFk NOT IN (2,3,4,6)
AND pt.PTRefFk >= 7000000 
 AND (PublishFlag = 1 OR pt.PTRefFk <> 8000000)
 AND (pt.PTRefFk % 100000 = 0)
 AND DoubtfulFlag <> 'i'
-- AND IsExcludedMarker = 0
ORDER BY PTRefFk,Treeindex,  StatusFK

; 
SELECT n.fullNameCache,  n.NameCache, pt.*
FROM PTaxon pt INNER JOIN Name n ON n.NameId = pt.PTNameFk 
WHERE ptRefFk <> 500000 AND (pt.PTNameFk IN (
        SELECT pt.PTNameFk
        FROM PTaxon pt 
        WHERE pt.TreeIndex NOT LIKE '533921-%' AND pt.TreeIndex NOT LIKE '556619-%' -- AND pt.StatusFk NOT IN (2,3,4,6)
        AND pt.PTRefFk >= 7000000 
         AND (PublishFlag = 1 OR pt.PTRefFk <> 8000000)
         AND (pt.PTRefFk % 100000 = 0)
         AND DoubtfulFlag <> 'i'
) OR n.nameCache IN ( SELECT   n.NameCache 
    FROM PTaxon pt INNER JOIN Name n ON n.NameId = pt.PTNameFk 
    WHERE pt.TreeIndex NOT LIKE '533921-%' AND pt.TreeIndex NOT LIKE '556619-%' -- AND pt.StatusFk NOT IN (2,3,4,6)
    AND pt.PTRefFk >= 7000000 
    AND (PublishFlag = 1 OR pt.PTRefFk <> 8000000)
    AND (pt.PTRefFk % 100000 = 0)
    AND DoubtfulFlag <> 'i')
    )
ORDER BY n.nameCache, PTNameFK, PTRefFk

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remove incative taxon relationships not needed anymore

SELECT        RelPTaxonId, PTNameFk1, PTRefFk1, PTNameFk2, PTRefFk2, RelQualifierFk, RelRefFk, Created_When, Updated_When, Created_Who, Updated_Who, Notes, Provisional
FROM            RelPTaxon
WHERE        (RelPTaxonId IN
                             (SELECT        rel.RelPTaxonId
                               FROM            RelPTaxon AS rel LEFT OUTER JOIN
                                                         PTaxon AS pt1 ON rel.PTNameFk1 = pt1.PTNameFk AND rel.PTRefFk1 = pt1.PTRefFk LEFT OUTER JOIN
                                                         PTaxon AS pt2 ON rel.PTNameFk2 = pt2.PTNameFk AND rel.PTRefFk2 = pt2.PTRefFk
                               WHERE        (rel.RelQualifierFk = - 99) AND (pt1.DoubtfulFlag <> 'i' OR
                                                         pt1.DoubtfulFlag IS NULL) AND (pt2.DoubtfulFlag <> 'i' OR
                                                         pt2.DoubtfulFlag IS NULL)))

===