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Revision 6816

inputs/CVS/cvs.~.utils.sql: plantconcept_plantnames(): Use CVS's taxonLevel values, which are different from the VegBank plantLevel values that the original version of this function used

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inputs/CVS/plantConcept_/header.csv
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PLANTCONCEPT_ID,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma
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PLANTCONCEPT_ID,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Division,Class,Subclass,Order,composite family,family,tribe,composite genus,genus,subgenus,section,composite species,species,subspecies,composite variety,variety
inputs/CVS/cvs.~.utils.sql
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-- DROP FUNCTION plantconcept_plantnames(integer);
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CREATE OR REPLACE FUNCTION plantconcept_plantnames(IN "PLANTCONCEPT_ID" integer, OUT "Kingdom" text, OUT "Subkingdom" text, OUT "Superdivision" text, OUT "Division" text, OUT "Subdivision" text, OUT "Class" text, OUT "Subclass" text, OUT "Order" text, OUT "Family" text, OUT "Genus" text, OUT "Species" text, OUT "Subspecies" text, OUT "Variety" text, OUT "Forma" text)
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CREATE OR REPLACE FUNCTION plantconcept_plantnames(IN "PLANTCONCEPT_ID" integer, OUT "Kingdom" text, OUT "Subkingdom" text, OUT "Division" text, OUT "Class" text, OUT "Subclass" text, OUT "Order" text, OUT "composite family" text, OUT "family" text, OUT "tribe" text, OUT "composite genus" text, OUT "genus" text, OUT "subgenus" text, OUT "section" text, OUT "composite species" text, OUT "species" text, OUT "subspecies" text, OUT "composite variety" text, OUT "variety" text)
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  RETURNS record AS
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$BODY$
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WITH "level_plantName" AS (
......
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SELECT
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  (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Kingdom')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Subkingdom')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Superdivision')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Division')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Subdivision')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Class')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Subclass')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Order')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Family')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Genus')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Species')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Subspecies')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Variety')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'Forma')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'composite family')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'family')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'tribe')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'composite genus')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'genus')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'subgenus')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'section')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'composite species')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'species')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'subspecies')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'composite variety')
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, (SELECT "plantName" FROM "level_plantName" WHERE "taxonLevel" = 'variety')
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$BODY$
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  LANGUAGE sql STABLE STRICT
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  COST 100;
inputs/CVS/taxonObservation_/header.csv
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PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PARTY_ID,salutation,givenName,middleName,surName,suffix,entry_userInitials,organizationName,currentName_ID,contactInstructions,email,accessionCode,partyType,dba_src_ID,dba_unsure,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma
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PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PARTY_ID,salutation,givenName,middleName,surName,suffix,entry_userInitials,organizationName,currentName_ID,contactInstructions,email,accessionCode,partyType,dba_src_ID,dba_unsure,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Division,Class,Subclass,Order,composite family,family,tribe,composite genus,genus,subgenus,section,composite species,species,subspecies,composite variety,variety
inputs/CVS/taxonObservation_/map.csv
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usda_growthForm,*usda_growthForm,,
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Kingdom,kingdom,/_alt/2,
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Subkingdom,*Subkingdom,/_alt/2,
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Superdivision,*Superdivision,/_alt/2,
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Division,*Division,/_alt/2,
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Subdivision,*Subdivision,/_alt/2,
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Class,class,/_alt/2,
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Subclass,*Subclass,/_alt/2,
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Order,order,/_alt/2,
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Family,family,/_alt/2,
105
Genus,genus,/_alt/2,
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Species,specificEpithet,/_alt/2,
107
Subspecies,subspecies,/_alt/2,
108
Variety,variety,/_alt/2,
109
Forma,forma,/_alt/2,
102
composite family,*composite family,/_alt/2,
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family,family,/_alt/2,
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tribe,*tribe,/_alt/2,
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composite genus,*composite genus,/_alt/2,
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genus,genus,/_alt/2,
107
subgenus,subgenus,/_alt/2,
108
section,*section,/_alt/2,
109
composite species,*composite species,/_alt/2,
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species,specificEpithet,/_alt/2,
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subspecies,subspecies,/_alt/2,
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composite variety,*composite variety,/_alt/2,
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variety,variety,,
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:plot,observationType,,
inputs/CVS/taxonObservation_/VegBIEN.csv
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TAXONOBSERVATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
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TAXONOBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,
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denorm_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value/_alt/1",
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Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value/_alt/2",
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value/_alt/2",
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denorm_genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/1",
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Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/2",
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/2",
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denorm_species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/1",
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Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/2",
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Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4/_alt/2",
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species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/2",
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subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4/_alt/2",
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taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
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Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""var. ""]/2/_alt/2",
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Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""fm. ""]/2/_alt/2",
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variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""var. ""]/2",
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interpretationDate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
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taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
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taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank",
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Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=forma]/taxonepithet/_alt/2",
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Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet/_alt/2",
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Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet/_alt/2",
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variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet",
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subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet/_alt/2",
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denorm_species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet/_alt/1",
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Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet/_alt/2",
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species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet/_alt/2",
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denorm_genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname/_alt/1",
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Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname/_alt/2",
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname/_alt/2",
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denorm_genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet/_alt/1",
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Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet/_alt/2",
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet/_alt/2",
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denorm_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname/_alt/1",
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Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname/_alt/2",
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname/_alt/2",
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denorm_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet/_alt/1",
48
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet/_alt/2",
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet/_alt/2",
49 47
Order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet/_alt/2",
50 48
Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet/_alt/2",
51 49
denorm_kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet/_alt/1",
......
53 51
taxonLevel,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
54 52
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
55 53
denorm_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value/_alt/1,
56
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value/_alt/2,
54
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value/_alt/2,
57 55
denorm_genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/1,
58
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/2,
56
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/2,
59 57
denorm_species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/1,
60
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/2,
61
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4/_alt/2,
58
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/2,
59
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4/_alt/2,
62 60
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
63
Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2/_alt/2",
64
Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2/_alt/2",
61
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2",
65 62
denorm_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family/_alt/1,
66
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family/_alt/2,
63
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family/_alt/2,
67 64
denorm_genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/1,
68
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,
65
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,
69 66
denorm_species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet/_alt/1,
70
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet/_alt/2,
67
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet/_alt/2,
71 68
taxonLevel,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
72 69
interpretationDate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
73 70
taxonFit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
......
83 80
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID ** 
84 81
ROLE_ID,,** No join mapping for *ROLE_ID ** 
85 82
Subclass,,** No join mapping for *Subclass/_alt/2 ** 
86
Subdivision,,** No join mapping for *Subdivision/_alt/2 ** 
87 83
Subkingdom,,** No join mapping for *Subkingdom/_alt/2 ** 
88
Superdivision,,** No join mapping for *Superdivision/_alt/2 ** 
89 84
TAXONINTERPRETATION_ID,,** No join mapping for *TAXONINTERPRETATION_ID ** 
90 85
USDAPlantsCode,,** No join mapping for *USDAPlantsCode ** 
91 86
VascularPlant,,** No join mapping for *VascularPlant ** 
......
93 88
collectionNumber,,** No join mapping for *collectionNumber ** 
94 89
collector_ID,,** No join mapping for *collector_ID ** 
95 90
commonName,,** No join mapping for *commonName ** 
91
composite family,,** No join mapping for *composite family/_alt/2 ** 
92
composite genus,,** No join mapping for *composite genus/_alt/2 ** 
93
composite species,,** No join mapping for *composite species/_alt/2 ** 
94
composite variety,,** No join mapping for *composite variety/_alt/2 ** 
96 95
contactInstructions,,** No join mapping for *contactInstructions ** 
97 96
currentInterpretation,,** No join mapping for *currentInterpretation ** 
98 97
currentName_ID,,** No join mapping for *currentName_ID ** 
......
143 142
reference_ID,,** No join mapping for *reference_ID ** 
144 143
revisions,,** No join mapping for *revisions ** 
145 144
salutation,,** No join mapping for *salutation ** 
145
section,,** No join mapping for *section/_alt/2 ** 
146
subgenus,,** No join mapping for subgenus/_alt/2 ** 
146 147
suffix,,** No join mapping for *suffix ** 
147 148
taxonConfidence,,** No join mapping for *taxonConfidence ** 
148 149
taxonInferenceArea,,** No join mapping for *taxonInferenceArea ** 
......
157 158
taxonObservation_reference_ID,,** No join mapping for *taxonObservation_reference_ID ** 
158 159
taxonRank,,** No non-empty join mapping for OMIT ** Omitted because taxonLevel contains this information in text form
159 160
temp_taxonUpToDate,,** No join mapping for *temp_taxonUpToDate ** 
161
tribe,,** No join mapping for *tribe/_alt/2 ** 
160 162
usda_code,,** No join mapping for *usda_code ** 
161 163
usda_growthForm,,** No join mapping for *usda_growthForm ** 
162 164
woody,,** No join mapping for *woody ** 
inputs/CVS/taxonObservation_/test.xml.ref
45 45
                                                                            <family>
46 46
                                                                                <_alt>
47 47
                                                                                    <1>$denorm_family</1>
48
                                                                                    <2>$Family</2>
48
                                                                                    <2>$family</2>
49 49
                                                                                </_alt>
50 50
                                                                            </family>
51 51
                                                                        </_taxon_family_require_std>
......
55 55
                                                                            <2>
56 56
                                                                                <_alt>
57 57
                                                                                    <1>$denorm_genus</1>
58
                                                                                    <2>$Genus</2>
58
                                                                                    <2>$genus</2>
59 59
                                                                                </_alt>
60 60
                                                                            </2>
61 61
                                                                            <3>
62 62
                                                                                <_alt>
63 63
                                                                                    <1>$denorm_species</1>
64
                                                                                    <2>$Species</2>
64
                                                                                    <2>$species</2>
65 65
                                                                                </_alt>
66 66
                                                                            </3>
67
                                                                            <4>$Subspecies</4>
67
                                                                            <4>$subspecies</4>
68 68
                                                                            <7>
69 69
                                                                                <_join_words>
70 70
                                                                                    <1>var. </1>
71
                                                                                    <2>$Variety</2>
71
                                                                                    <2>$variety</2>
72 72
                                                                                </_join_words>
73 73
                                                                            </7>
74
                                                                            <8>
75
                                                                                <_join_words>
76
                                                                                    <1>fm. </1>
77
                                                                                    <2>$Forma</2>
78
                                                                                </_join_words>
79
                                                                            </8>
80 74
                                                                        </_join_words>
81 75
                                                                    </2>
82 76
                                                                </_join_words>
......
94 88
                                                                    <parent_id>
95 89
                                                                        <taxonlabel>
96 90
                                                                            <rank>forma</rank>
97
                                                                            <taxonepithet>$Forma</taxonepithet>
98 91
                                                                            <parent_id>
99 92
                                                                                <taxonlabel>
100 93
                                                                                    <rank>variety</rank>
101
                                                                                    <taxonepithet>$Variety</taxonepithet>
94
                                                                                    <taxonepithet>$variety</taxonepithet>
102 95
                                                                                    <parent_id>
103 96
                                                                                        <taxonlabel>
104 97
                                                                                            <rank>subspecies</rank>
105
                                                                                            <taxonepithet>$Subspecies</taxonepithet>
98
                                                                                            <taxonepithet>$subspecies</taxonepithet>
106 99
                                                                                            <parent_id>
107 100
                                                                                                <taxonlabel>
108 101
                                                                                                    <rank>species</rank>
109 102
                                                                                                    <taxonepithet>
110 103
                                                                                                        <_alt>
111 104
                                                                                                            <1>$denorm_species</1>
112
                                                                                                            <2>$Species</2>
105
                                                                                                            <2>$species</2>
113 106
                                                                                                        </_alt>
114 107
                                                                                                    </taxonepithet>
115 108
                                                                                                    <parent_id>
......
118 111
                                                                                                            <taxonepithet>
119 112
                                                                                                                <_alt>
120 113
                                                                                                                    <1>$denorm_genus</1>
121
                                                                                                                    <2>$Genus</2>
114
                                                                                                                    <2>$genus</2>
122 115
                                                                                                                </_alt>
123 116
                                                                                                            </taxonepithet>
124 117
                                                                                                            <parent_id>
......
127 120
                                                                                                                    <taxonepithet>
128 121
                                                                                                                        <_alt>
129 122
                                                                                                                            <1>$denorm_family</1>
130
                                                                                                                            <2>$Family</2>
123
                                                                                                                            <2>$family</2>
131 124
                                                                                                                        </_alt>
132 125
                                                                                                                    </taxonepithet>
133 126
                                                                                                                    <parent_id>
......
182 175
                                                                    <family>
183 176
                                                                        <_alt>
184 177
                                                                            <1>$denorm_family</1>
185
                                                                            <2>$Family</2>
178
                                                                            <2>$family</2>
186 179
                                                                        </_alt>
187 180
                                                                    </family>
188 181
                                                                </_taxon_family_require_std>
......
192 185
                                                                    <2>
193 186
                                                                        <_alt>
194 187
                                                                            <1>$denorm_genus</1>
195
                                                                            <2>$Genus</2>
188
                                                                            <2>$genus</2>
196 189
                                                                        </_alt>
197 190
                                                                    </2>
198 191
                                                                    <3>
199 192
                                                                        <_alt>
200 193
                                                                            <1>$denorm_species</1>
201
                                                                            <2>$Species</2>
194
                                                                            <2>$species</2>
202 195
                                                                        </_alt>
203 196
                                                                    </3>
204
                                                                    <4>$Subspecies</4>
197
                                                                    <4>$subspecies</4>
205 198
                                                                    <6>
206 199
                                                                        <_join_words>
207 200
                                                                            <1>var. </1>
208
                                                                            <2>$Variety</2>
201
                                                                            <2>$variety</2>
209 202
                                                                        </_join_words>
210 203
                                                                    </6>
211
                                                                    <7>
212
                                                                        <_join_words>
213
                                                                            <1>fm. </1>
214
                                                                            <2>$Forma</2>
215
                                                                        </_join_words>
216
                                                                    </7>
217 204
                                                                </_join_words>
218 205
                                                            </2>
219 206
                                                        </_join_words>
......
223 210
                                            <family>
224 211
                                                <_alt>
225 212
                                                    <1>$denorm_family</1>
226
                                                    <2>$Family</2>
213
                                                    <2>$family</2>
227 214
                                                </_alt>
228 215
                                            </family>
229 216
                                            <genus>
230 217
                                                <_alt>
231 218
                                                    <1>$denorm_genus</1>
232
                                                    <2>$Genus</2>
219
                                                    <2>$genus</2>
233 220
                                                </_alt>
234 221
                                            </genus>
235 222
                                            <specific_epithet>
236 223
                                                <_alt>
237 224
                                                    <1>$denorm_species</1>
238
                                                    <2>$Species</2>
225
                                                    <2>$species</2>
239 226
                                                </_alt>
240 227
                                            </specific_epithet>
241 228
                                            <verbatimrank>$taxonLevel</verbatimrank>
......
271 258
        </path>
272 259
    </_setDefault>
273 260
</VegBIEN>
274
Inserted 29 new rows into database
261
Inserted 31 new rows into database
inputs/CVS/taxonObservation_/unmapped_terms.csv
76 76
*usda_code
77 77
*usda_growthForm
78 78
*Subkingdom
79
*Superdivision
80 79
*Division
81
*Subdivision
82 80
*Subclass
81
*composite family
82
*tribe
83
*composite genus
84
subgenus
85
*section
86
*composite species
87
*composite variety

Also available in: Unified diff