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Revision 11523

Added by Aaron Marcuse-Kubitza over 10 years ago

inputs/VegBank/taxonobservation_/create.sql: also join party_id to get the identifiedBy (not mapped yet). note that the inserted row count changes, because taxonobservation_ does not yet have a pkey to do a stable ordering with.

View differences:

inputs/VegBank/taxonobservation_/create.sql
1 1 
SELECT *
2 2 
FROM taxonobservation
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LEFT JOIN taxoninterpretation USING (taxonobservation_id)
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LEFT JOIN party               USING (party_id)
4 5 
LEFT JOIN plantconcept_       USING (plantconcept_id)
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LEFT JOIN plantname           USING (plantname_id)
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; -- runtime: 20 s ("18564.276") @starscream
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; -- runtime: 25 s ("23094.379 ms") @starscream
inputs/VegBank/taxonobservation_/header.csv
1 
plantname_id,plantconcept_id,taxonobservation_id,observation_id,authorplantname,taxonobservation_reference_id,taxoninferencearea,emb_taxonobservation,int_origplantconcept_id,int_origplantscifull,int_origplantscinamenoauth,int_origplantcommon,int_origplantcode,int_currplantconcept_id,int_currplantscifull,int_currplantscinamenoauth,int_currplantcommon,int_currplantcode,taxonobservation_accessioncode,taxoninterpretation_id,stemlocation_id,taxoninterpretation_plantname_id,party_id,role_id,interpretationtype,reference_id,originalinterpretation,currentinterpretation,taxonfit,taxonconfidence,collector_id,collectionnumber,museum_id,museumaccessionnumber,grouptype,notes,notespublic,notesmgt,revisions,interpretationdate,collectiondate,emb_taxoninterpretation,taxoninterpretation_accessioncode,*plantconcept_--plantconcept_reference_id,scientificName__for_nearest_taxon_concept,*plantconcept_--plantcode,*plantconcept_--plantdescription,*plantconcept_--d_obscount,*plantconcept_--d_currentaccepted,*plantconcept_--plantconcept_accessioncode,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,speciesBinomial,EQUIV#to:Species#Subspecies,EQUIV#to:Species#Variety,EQUIV#to:Species#Forma,plantname,plantname_reference_id,dateentered
1 
plantname_id,plantconcept_id,party_id,taxonobservation_id,observation_id,authorplantname,taxonobservation_reference_id,taxoninferencearea,emb_taxonobservation,int_origplantconcept_id,int_origplantscifull,int_origplantscinamenoauth,int_origplantcommon,int_origplantcode,int_currplantconcept_id,int_currplantscifull,int_currplantscinamenoauth,int_currplantcommon,int_currplantcode,taxonobservation_accessioncode,taxoninterpretation_id,stemlocation_id,taxoninterpretation_plantname_id,role_id,interpretationtype,reference_id,originalinterpretation,currentinterpretation,taxonfit,taxonconfidence,collector_id,collectionnumber,museum_id,museumaccessionnumber,grouptype,notes,notespublic,notesmgt,revisions,interpretationdate,collectiondate,emb_taxoninterpretation,taxoninterpretation_accessioncode,salutation,givenname,middlename,surname,organizationname,currentname_id,contactinstructions,email,partytype,partypublic,party_d_obscount,accessioncode,*plantconcept_--plantconcept_reference_id,scientificName__for_nearest_taxon_concept,*plantconcept_--plantcode,*plantconcept_--plantdescription,*plantconcept_--d_obscount,*plantconcept_--d_currentaccepted,*plantconcept_--plantconcept_accessioncode,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,speciesBinomial,EQUIV#to:Species#Subspecies,EQUIV#to:Species#Variety,EQUIV#to:Species#Forma,plantname,plantname_reference_id,dateentered
inputs/VegBank/taxonobservation_/map.csv
1 1 
VegBank,VegCore,Filter,Comments
2 2 
plantname_id,*taxonobservation_--plantname_id,,
3 3 
plantconcept_id,*taxonobservation_--plantconcept_id,,
4 
party_id,*taxonobservation_--party_id,,
4 5 
taxonobservation_id,taxonOccurrenceID__overall_plot,,
5 6 
observation_id,eventID,,
6 7 
authorplantname,OMIT#authorplantname,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = originalScientificName
......
21 22 
taxoninterpretation_id,identificationID,,
22 23 
stemlocation_id,*taxonobservation_--stemlocation_id,,
23 24 
taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_plantname_id,,
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party_id,*taxonobservation_--party_id,,
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role_id,*taxonobservation_--role_id,,
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interpretationtype,identificationType,,
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reference_id,*taxonobservation_--reference_id,,
......
42 42 
collectiondate,dateCollected,,
43 43 
emb_taxoninterpretation,*taxonobservation_--emb_taxoninterpretation,,
44 44 
taxoninterpretation_accessioncode,*taxonobservation_--taxoninterpretation_accessioncode,,
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salutation,*taxonobservation--party--salutation,,
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givenname,*taxonobservation--party--givenname,,
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middlename,*taxonobservation--party--middlename,,
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surname,*taxonobservation--party--surname,,
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organizationname,*taxonobservation--party--organizationname,,
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currentname_id,*taxonobservation--party--currentname_id,,
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contactinstructions,*taxonobservation--party--contactinstructions,,
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email,*taxonobservation--party--email,,
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partytype,*taxonobservation--party--partytype,,
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partypublic,*taxonobservation--party--partypublic,,
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party_d_obscount,*taxonobservation--party--party_d_obscount,,
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accessioncode,*taxonobservation--party--accessioncode,,
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*plantconcept_--plantconcept_reference_id,*plantconcept_--plantconcept_reference_id,,
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scientificName__for_nearest_taxon_concept,scientificName,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
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*plantconcept_--plantcode,*plantconcept_--plantcode,,
inputs/VegBank/taxonobservation_/test.xml.ref
126 126 
        </path>
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    </_setDefault>
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</VegBIEN>
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Inserted 20 new rows into database
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Inserted 12 new rows into database
inputs/VegBank/taxonobservation_/new_terms.csv
1 1 
plantname_id,*taxonobservation_--plantname_id,,
2 2 
plantconcept_id,*taxonobservation_--plantconcept_id,,
3 
party_id,*taxonobservation_--party_id,,
3 4 
observation_id,eventID,,
4 5 
taxoninferencearea,*taxonobservation_--taxoninferencearea,,
5 6 
emb_taxonobservation,*taxonobservation_--emb_taxonobservation,,
......
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taxoninterpretation_id,identificationID,,
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stemlocation_id,*taxonobservation_--stemlocation_id,,
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taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_plantname_id,,
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party_id,*taxonobservation_--party_id,,
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role_id,*taxonobservation_--role_id,,
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reference_id,*taxonobservation_--reference_id,,
23 23 
museum_id,*taxonobservation_--museum_id,,
......
29 29 
collectiondate,dateCollected,,
30 30 
emb_taxoninterpretation,*taxonobservation_--emb_taxoninterpretation,,
31 31 
taxoninterpretation_accessioncode,*taxonobservation_--taxoninterpretation_accessioncode,,
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salutation,*taxonobservation--party--salutation,,
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givenname,*taxonobservation--party--givenname,,
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middlename,*taxonobservation--party--middlename,,
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surname,*taxonobservation--party--surname,,
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organizationname,*taxonobservation--party--organizationname,,
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currentname_id,*taxonobservation--party--currentname_id,,
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contactinstructions,*taxonobservation--party--contactinstructions,,
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email,*taxonobservation--party--email,,
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partytype,*taxonobservation--party--partytype,,
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partypublic,*taxonobservation--party--partypublic,,
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party_d_obscount,*taxonobservation--party--party_d_obscount,,
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accessioncode,*taxonobservation--party--accessioncode,,
32 44 
scientificName__for_nearest_taxon_concept,scientificName,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
33 45 
plantname,DUPLICATE#of:plantconcept_plantname#plantname,,exact duplicate
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plantname_reference_id,*taxonobservation_--plantname_reference_id,,
inputs/VegBank/taxonobservation_/unmapped_terms.csv
1 1 
*taxonobservation_--plantname_id
2 2 
*taxonobservation_--plantconcept_id
3 
*taxonobservation_--party_id
3 4 
taxonOccurrenceID__overall_plot
4 5 
*taxonobservation_--taxonobservation_reference_id
5 6 
*taxonobservation_--taxoninferencearea
......
8 9 
identificationID
9 10 
*taxonobservation_--stemlocation_id
10 11 
*taxonobservation_--taxoninterpretation_plantname_id
11 
*taxonobservation_--party_id
12 12 
*taxonobservation_--role_id
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*taxonobservation_--reference_id
14 14 
identificationVerificationStatus
......
19 19 
*taxonobservation_--revisions
20 20 
*taxonobservation_--emb_taxoninterpretation
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*taxonobservation_--taxoninterpretation_accessioncode
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*taxonobservation--party--salutation
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*taxonobservation--party--givenname
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*taxonobservation--party--middlename
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*taxonobservation--party--surname
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*taxonobservation--party--organizationname
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*taxonobservation--party--currentname_id
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*taxonobservation--party--contactinstructions
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*taxonobservation--party--email
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*taxonobservation--party--partytype
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*taxonobservation--party--partypublic
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*taxonobservation--party--party_d_obscount
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*taxonobservation--party--accessioncode
22 34 
*plantconcept_--plantconcept_reference_id
23 35 
*plantconcept_--plantcode
24 36 
*plantconcept_--plantdescription

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