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Revision 11809

fix: inputs/CVS/taxonObservation_/create.sql: mapped identifiedBy, which involves joining to party

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inputs/CVS/taxonObservation_/create.sql
1 1
SELECT *
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FROM "taxonObservation"
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LEFT JOIN "taxonInterpretation" USING ("TAXONOBSERVATION_ID")
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LEFT JOIN party USING ("PARTY_ID")
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LEFT JOIN "plantConcept_" USING ("PLANTCONCEPT_ID")
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;
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; -- runtime: 10 s ("12372.322 ms") @starscream
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,*PLANTNAME_ID,*plantConcept_reference_ID,taxonName,scientificName,*plantCode,*plantDescription,*plantConcept_accessionCode,*plantConcept_dba_src_ID,*plantConcept_entry_sppID,*USDAPlantsCode,*VascularPlant,kingdom,division_main,*category,family,genus_main,specificEpithet,infraspecificRank,infraspecificEpithet,infraspecificRank2,infraspecificEpithet2,*hybridX,taxonRank,OMIT#taxonRank,*lowestParentName,*lowestParentConcept_ID,*lowestChildRank,vernacularName,*growthForm_short,*woody,*exotic,*usda_code,*usda_growthForm,*sensitiveSpeciesFuzzPlot,DUPLICATE#of:denorm_kingdom#Kingdom,*Subkingdom,division_normalized,class,*Subclass,order,*composite family,DUPLICATE#of:denorm_family#family,*tribe,*composite genus,genus_normalized,subgenus,*section,*composite species,speciesBinomial,EQUIV#to:species#subspecies,EQUIV#to:species#composite variety,EQUIV#to:species#variety,division,genus
1
PLANTCONCEPT_ID,PARTY_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,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,salutation,givenName,middleName,surName,suffix,entry_userInitials,organizationName,currentName_ID,contactInstructions,email,accessionCode,partyType,dba_src_ID,dba_unsure,*plantConcept_--PLANTNAME_ID,*plantConcept_--plantConcept_reference_ID,taxonName,scientificName,*plantConcept_--plantCode,*plantConcept_--plantDescription,*plantConcept_--plantConcept_accessionCode,*plantConcept_--plantConcept_dba_src_ID,*plantConcept_--plantConcept_entry_sppID,*plantConcept_--USDAPlantsCode,*plantConcept_--VascularPlant,kingdom,division_main,*plantConcept_--category,family,genus_main,specificEpithet,infraspecificRank,infraspecificEpithet,infraspecificRank2,infraspecificEpithet2,*hybridX,taxonRank,OMIT#taxonRank,*plantConcept_--lowestParentName,*plantConcept_--lowestParentConcept_ID,*plantConcept_--lowestChildRank,vernacularName,*plantConcept_--growthForm_short,*plantConcept_--woody,*plantConcept_--exotic,*plantConcept_--usda_code,*plantConcept_--usda_growthForm,*plantConcept_--sensitiveSpeciesFuzzPlot,DUPLICATE#of:denorm_kingdom#Kingdom,*Subkingdom,division_normalized,class,*Subclass,order,*composite family,DUPLICATE#of:denorm_family#family,*tribe,*composite genus,genus_normalized,subgenus,*section,*composite species,speciesBinomial,EQUIV#to:species#subspecies,EQUIV#to:species#composite variety,EQUIV#to:species#variety,division,genus
inputs/CVS/taxonObservation_/postprocess.sql
12 12
genus_main = trim(genus_main, '{}') -- applies to 6 rows
13 13
WHERE genus_main LIKE '{%}' -- applies to 6 rows
14 14
; -- rerun time: 0.5 s ("492.670 ms") @starscream; runtime: 0.5 s ("543.942 ms") @starscream
15

  
16

  
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SELECT mk_derived_col((:table_str, 'identifiedBy'),
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$$_join_words("identifiedBy__first", "identifiedBy__middle", "identifiedBy__last")$$)
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; -- runtime: 15 s ("14351.532 ms") @starscream
inputs/CVS/taxonObservation_/map.csv
1 1
CVS,VegCore,Filter,Comments
2 2
PLANTCONCEPT_ID,*taxonObservation_--PLANTCONCEPT_ID,,
3
PARTY_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,,
3 4
TAXONOBSERVATION_ID,taxonOccurrenceID__overall_plot,,
4 5
OBSERVATION_ID,eventID,,
5 6
authorPlantName,OMIT#authorPlantName,,omitted because not specific to the taxonInterpretation row (this is in a separate taxonInterpretation for the original determination instead). = originalTaxonName
......
25 26
stemLocation_ID,stemID,,
26 27
interpretationDate,dateIdentified,,
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taxonInterpretation_PLANTNAME_ID,*taxonObservation_--taxonInterpretation_PLANTNAME_ID,,
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PARTY_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,,
29 29
ROLE_ID,*taxonObservation_--ROLE_ID,,
30 30
interpretationType,identificationType,,
31 31
reference_ID,*taxonObservation_--reference_ID,,
......
45 45
revisions,*taxonObservation_--revisions,,
46 46
taxonInterpretation_dba_src_ID,*taxonObservation_--taxonInterpretation_dba_src_ID,,
47 47
taxonInterpretation_accessionCode,*taxonObservation_--taxonInterpretation_accessionCode,,
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salutation,*taxonObservation_--party--salutation,,
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givenName,identifiedBy__first,,
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middleName,identifiedBy__middle,,
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surName,identifiedBy__last,,
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suffix,*taxonObservation_--party--suffix,,
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entry_userInitials,*taxonObservation_--party--entry_userInitials,,
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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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accessionCode,*taxonObservation_--party--accessionCode,,
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partyType,*taxonObservation_--party--partyType,,
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dba_src_ID,*taxonObservation_--party--dba_src_ID,,
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dba_unsure,*taxonObservation_--party--dba_unsure,,
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*plantConcept_--PLANTNAME_ID,*plantConcept_--PLANTNAME_ID,,
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*plantConcept_--plantConcept_reference_ID,*plantConcept_--plantConcept_reference_ID,,
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taxonName,taxonName,,
inputs/CVS/taxonObservation_/test.xml.ref
26 26
                                    </aggregateoccurrence>
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                                    <authortaxoncode>$collectorNumber</authortaxoncode>
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                                    <taxondetermination>
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                                        <party_id><party><fullname>$identifiedBy</fullname></party></party_id>
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                                        <taxonverbatim_id>
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                                            <taxonverbatim>
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                                                <taxonlabel_id>
......
155 156
        </path>
156 157
    </_setDefault>
157 158
</VegBIEN>
158
Inserted 21 new rows into database
159
Inserted 22 new rows into database
inputs/CVS/taxonObservation_/new_terms.csv
1 1
PLANTCONCEPT_ID,*taxonObservation_--PLANTCONCEPT_ID,,
2
PARTY_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,,
2 3
OBSERVATION_ID,eventID,,
3 4
currentTaxonInterpPlantConcept_ID,*taxonObservation_--currentTaxonInterpPlantConcept_ID,,
4 5
taxonInferenceArea,*taxonObservation_--taxonInferenceArea,,
......
21 22
stemLocation_ID,stemID,,
22 23
interpretationDate,dateIdentified,,
23 24
taxonInterpretation_PLANTNAME_ID,*taxonObservation_--taxonInterpretation_PLANTNAME_ID,,
24
taxonInterpretation_PARTY_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,,
25 25
ROLE_ID,*taxonObservation_--ROLE_ID,,
26 26
reference_ID,*taxonObservation_--reference_ID,,
27 27
collectionDate,dateCollected,,
......
32 32
revisions,*taxonObservation_--revisions,,
33 33
taxonInterpretation_dba_src_ID,*taxonObservation_--taxonInterpretation_dba_src_ID,,
34 34
taxonInterpretation_accessionCode,*taxonObservation_--taxonInterpretation_accessionCode,,
35
salutation,*taxonObservation_--party--salutation,,
36
givenName,identifiedBy__first,,
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middleName,identifiedBy__middle,,
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surName,identifiedBy__last,,
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suffix,*taxonObservation_--party--suffix,,
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entry_userInitials,*taxonObservation_--party--entry_userInitials,,
41
organizationName,*taxonObservation_--party--organizationName,,
42
currentName_ID,*taxonObservation_--party--currentName_ID,,
43
contactInstructions,*taxonObservation_--party--contactInstructions,,
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email,*taxonObservation_--party--email,,
45
accessionCode,*taxonObservation_--party--accessionCode,,
46
partyType,*taxonObservation_--party--partyType,,
47
dba_src_ID,*taxonObservation_--party--dba_src_ID,,
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dba_unsure,*taxonObservation_--party--dba_unsure,,
inputs/CVS/taxonObservation_/unmapped_terms.csv
1 1
*taxonObservation_--PLANTCONCEPT_ID
2
*taxonObservation_--taxonInterpretation_PARTY_ID
2 3
taxonOccurrenceID__overall_plot
3 4
*taxonObservation_--taxonObservation_reference_ID
4 5
*taxonObservation_--currentTaxonInterpPlantConcept_ID
......
20 21
*taxonObservation_--temp_taxonUpToDate
21 22
identificationID
22 23
*taxonObservation_--taxonInterpretation_PLANTNAME_ID
23
*taxonObservation_--taxonInterpretation_PARTY_ID
24 24
*taxonObservation_--ROLE_ID
25 25
*taxonObservation_--reference_ID
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identificationVerificationStatus
......
31 31
*taxonObservation_--revisions
32 32
*taxonObservation_--taxonInterpretation_dba_src_ID
33 33
*taxonObservation_--taxonInterpretation_accessionCode
34
*taxonObservation_--party--salutation
35
identifiedBy__first
36
identifiedBy__middle
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identifiedBy__last
38
*taxonObservation_--party--suffix
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*taxonObservation_--party--entry_userInitials
40
*taxonObservation_--party--organizationName
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*taxonObservation_--party--currentName_ID
42
*taxonObservation_--party--contactInstructions
43
*taxonObservation_--party--email
44
*taxonObservation_--party--accessionCode
45
*taxonObservation_--party--partyType
46
*taxonObservation_--party--dba_src_ID
47
*taxonObservation_--party--dba_unsure
34 48
*plantConcept_--PLANTNAME_ID
35 49
*plantConcept_--plantConcept_reference_ID
36 50
*plantConcept_--plantCode
inputs/CVS/taxon_observation.**/header.csv
1
sort_col,locationID,eventID,*STRATUMTYPE_ID,*STRATUM_ID,taxonOccurrenceID__overall_plot,*taxonObservation_--PLANTCONCEPT_ID,OMIT#authorPlantName,*taxonObservation_--taxonObservation_reference_ID,*taxonObservation_--currentTaxonInterpPlantConcept_ID,*taxonObservation_--taxonInferenceArea,*taxonObservation_--taxonObservation_accessionCode,*taxonObservation_--taxonObservation_dba_src_ID,*taxonObservation_--cust_cvs_corner1Presence,*taxonObservation_--cust_cvs_corner2Presence,*taxonObservation_--cust_cvs_corner3Presence,*taxonObservation_--cust_cvs_corner4Presence,*taxonObservation_--cust_cvs_corner5Presence,*taxonObservation_--entry_herbLineID,*taxonObservation_--entry_treeLineID,*taxonObservation_--taxonObservation_entry_sppID,*taxonObservation_--entry_unknownSp,*taxonObservation_--entry_sortOrder,*taxonObservation_--cust_cvs_collectionFlag,*taxonObservation_--taxonObservationNotes,*taxonObservation_--temp_taxonUpToDate,identificationID,stemID,dateIdentified,*taxonObservation_--taxonInterpretation_PLANTNAME_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,*taxonObservation_--ROLE_ID,identificationType,*taxonObservation_--reference_ID,taxon_determination__is_original,taxon_determination__is_current,identificationQualifier,identificationVerificationStatus,UNUSED#collector_ID,collectorNumber,dateCollected,*taxonObservation_--museum_ID,accessionNumber,*taxonObservation_--groupType,occurrenceRemarks,*taxonObservation_--notesPublic,*taxonObservation_--notesMgt,*taxonObservation_--revisions,*taxonObservation_--taxonInterpretation_dba_src_ID,*taxonObservation_--taxonInterpretation_accessionCode,*plantConcept_--PLANTNAME_ID,*plantConcept_--plantConcept_reference_ID,taxonName,scientificName,*plantConcept_--plantCode,*plantConcept_--plantDescription,*plantConcept_--plantConcept_accessionCode,*plantConcept_--plantConcept_dba_src_ID,*plantConcept_--plantConcept_entry_sppID,*plantConcept_--USDAPlantsCode,*plantConcept_--VascularPlant,kingdom,division_main,*plantConcept_--category,family,genus_main,specificEpithet,infraspecificRank,infraspecificEpithet,infraspecificRank2,infraspecificEpithet2,*hybridX,taxonRank,OMIT#taxonRank,*plantConcept_--lowestParentName,*plantConcept_--lowestParentConcept_ID,*plantConcept_--lowestChildRank,vernacularName,*plantConcept_--growthForm_short,*plantConcept_--woody,*plantConcept_--exotic,*plantConcept_--usda_code,*plantConcept_--usda_growthForm,*plantConcept_--sensitiveSpeciesFuzzPlot,DUPLICATE#of:denorm_kingdom#Kingdom,*Subkingdom,division_normalized,class,*Subclass,order,*composite family,DUPLICATE#of:denorm_family#family,*tribe,*composite genus,genus_normalized,subgenus,*section,*composite species,speciesBinomial,EQUIV#to:species#subspecies,EQUIV#to:species#composite variety,EQUIV#to:species#variety,*division,genus,observationGranularity,aggregateOrganismObservationID__taxon_presence,coverPercent,*stemCount_--basalarea,*stemCount_--biomass,*stemCount_--inferencearea,*stemCount_--cust_cvs_StemFrequency,*stemCount_--taxonImportance_dba_src_ID,*stemCount_--taxonImportance_entry_herbLineID,*stemCount_--taxonImportance_entry_treeLineID,*stemCount_--cust_cvs_corner1Presence,*stemCount_--cust_cvs_corner2Presence,*stemCount_--cust_cvs_corner3Presence,*stemCount_--cust_cvs_corner4Presence,*stemCount_--cust_cvs_corner5Presence,*stemCount_--cust_cvs_originalCoverCode,aggregateOrganismObservationID__individual_count,diameterBreastHeight_cm,*stemCount_--stemdiameteraccuracy,height_m,*stemCount_--stemheightaccuracy,individualCount,*stemCount_--stemtaxonarea,*stemCount_--stemCount_dba_src_ID,*stemCount_--cust_cvs_ddh,*stemCount_--cust_cvs_ddhAccuracy,*stemCount_--cust_cvs_isPlanted,*stemCount_--cust_cvs_subsamplingFactor,*stemCount_--stemCount_entry_herbLineID,*stemCount_--stemCount_entry_treeLineID,*stemCount_--entry_recordCount,*stemCount_--entry_sortOrder,aggregateOrganismObservationID,*stratum--OBSERVATION_ID,*stratum--STRATUMMETHOD_ID,*stratum--stratumName,*stratum--stratumHeight,*stratum--stratumBase,*stratum--stratumCover,*stratum--stratumDescription,*stratum--dba_src_ID,*stratum--stratumArea,*stratum--stratumLabel,*stratumType--STRATUMMETHOD_ID,*stratumType--stratumIndex,stratum__name,*stratumType--stratumDescription,*stratumType--dba_src_ID,*stratumType--stratumOrder,*observation_--PREVIOUSOBS_ID,projectID,authorEventCode,startDate,endDate,*observation_--dateAccuracy,*observation_--dateEntered,*observation_--COVERMETHOD_ID,*observation_--coverDispersion,*observation_--autoTaxonCover,*observation_--STRATUMMETHOD_ID,samplingProtocol,*observation_--taxonObservationArea,*observation_--stemSizeLimit,*observation_--stemObservationArea,*observation_--stemSampleMethod,*observation_--originalData,*observation_--effortLevel,*observation_--plotValidationLevel,*observation_--floristicQuality,*observation_--bryophyteQuality,*observation_--lichenQuality,*observation_--observationNarrative,*observation_--landscapeNarrative,*observation_--homogeneity,*observation_--phenologicAspect,*observation_--representativeness,*observation_--standMaturity,*observation_--successionalStatus,*observation_--basalArea,*observation_--hydrologicRegime,*observation_--soilMoistureRegime,*observation_--soilDrainage,*observation_--waterSalinity,*observation_--waterDepth,*observation_--shoreDistance,*observation_--soilDepth,*observation_--organicDepth,*observation_--SOILTAXON_ID,*observation_--soilTaxonSrc,*observation_--soilTaxonComplex,*observation_--soilMapUnit,*observation_--percentBedRock,*observation_--percentRockGravel,*observation_--percentWood,*observation_--percentLitter,*observation_--percentBareSoil,*observation_--percentWater,*observation_--percentOther,*observation_--nameOther,*observation_--treeHt,*observation_--shrubHt,*observation_--fieldHt,*observation_--nonvascularHt,*observation_--submergedHt,*observation_--treeCover,*observation_--shrubCover,*observation_--fieldCover,*observation_--nonvascularCover,*observation_--floatingCover,*observation_--submergedCover,*observation_--dominantStratum,*observation_--growthform1Type,*observation_--growthform2Type,*observation_--growthform3Type,*observation_--growthform1Cover,*observation_--growthform2Cover,*observation_--growthform3Cover,*observation_--totalCover,*observation_--accessionCode,*observation_--notesPublic,*observation_--notesMgt,*observation_--revisions,*observation_--cust_cvs_CowardinSystem,*observation_--cust_cvs_mcnab_LFI_asp,*observation_--cust_cvs_mcnab_LFI_45,*observation_--cust_cvs_mcnab_LFI_90,*observation_--cust_cvs_mcnab_LFI_135,*observation_--cust_cvs_mcnab_LFI_180,*observation_--cust_cvs_mcnab_LFI_225,*observation_--cust_cvs_mcnab_LFI_270,*observation_--cust_cvs_mcnab_LFI_315,*observation_--cust_cvs_mcnab_TSI_asp,*observation_--cust_cvs_mcnab_TSI_45,*observation_--cust_cvs_mcnab_TSI_90,*observation_--cust_cvs_mcnab_TSI_135,*observation_--cust_cvs_mcnab_TSI_180,*observation_--cust_cvs_mcnab_TSI_225,*observation_--cust_cvs_mcnab_TSI_270,*observation_--cust_cvs_mcnab_TSI_315,*observation_--cust_cvs_mcnab_LFI,*observation_--cust_cvs_mcnab_TSI,*observation_--cust_cvs_LeafType,*observation_--cust_cvs_LeafPhenology,*observation_--cust_cvs_CanopyHeight,*observation_--cust_cvs_compassType,*observation_--cust_cvs_LocationSource,*observation_--cust_cvs_GPSLocationX,*observation_--cust_cvs_GPSLocationY,*observation_--cust_cvs_Ownership,*observation_--cust_cvs_taxaRichness,*observation_--cust_cvs_lengthSoilProbe,*observation_--cust_cvs_percentHistosol,*observation_--cust_cvs_percentBedrock,*observation_--cust_cvs_percentBoulder,*observation_--cust_cvs_percentGravelCobble,*observation_--cust_cvs_percentMineralSoil,*observation_--cust_cvs_percentCWD,*observation_--cust_cvs_percentFWD,*observation_--cust_cvs_percentDuff,*observation_--cust_cvs_percentLitter,*observation_--cust_cvs_percentNonVasc,*observation_--cust_cvs_percentWater,*observation_--cust_cvs_percentOther,*observation_--cust_cvs_percentOtherName,*observation_--cust_cvs_samplingLevel,*observation_--cust_cvs_postDsgPoly,*observation_--cust_cvs_stemsSampled,*observation_--cust_cvs_stemSamplingNarrative,*observation_--cust_eep_plotLastPlantedDate,*observation_--cust_eep_plotNotSampled,*observation_--cust_eep_plotNotSampledReason,*observation_--entry_ares_herbs,*observation_--entry_ares_trees,*observation_--entry_currentLandUse,*observation_--entry_depth,*observation_--entry_elevationUnits,*observation_--entry_formerLandUse,*observation_--entry_identificationNarrative,*observation_--entry_IntensiveModuleList,*observation_--entry_moduleSize_Overall,*observation_--entry_moduleSizeX,*observation_--entry_moduleSizeY,*observation_--entry_photosTaken,*observation_--entry_physClass,*observation_--entry_plot_X,*observation_--entry_plot_Y,*observation_--entry_soilModulesSampled,*observation_--entry_subsequentObsNum,*observation_--entry_taxonomicAuthority_ID,*observation_--entry_taxonomicAuthorityDate,*observation_--entry_team,*observation_--entry_plot,*observation_--entry_numberOfModules,*observation_--errors,*observation_--dba_src_ID,*observation_--dba_notes,*observation_--numberOfTaxa,*observation_--SOILOBS_ID,*observation_--soilHorizon,*observation_--soilDepthTop,*observation_--soilDepthBottom,*observation_--soilColor,organic_percent,texture,sand_percent,silt_percent,clay_percent,*observation_--soilCoarse,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,*observation_--soilDescription,*observation_--cust_cvs_collectionName,*observation_--cust_cvs_Lab,*observation_--cust_cvs_N,*observation_--cust_cvs_S,*observation_--cust_cvs_P,*observation_--cust_cvs_Ca_ppm,*observation_--cust_cvs_Mg_ppm,*observation_--cust_cvs_K_ppm,*observation_--cust_cvs_Na_ppm,*observation_--cust_cvs_percent_Ca,*observation_--cust_cvs_percent_Mg,*observation_--cust_cvs_percent_K,*observation_--cust_cvs_percent_Na,*observation_--cust_cvs_percent_Othr,*observation_--cust_cvs_percent_H,*observation_--cust_cvs_B_ppm,*observation_--cust_cvs_Fe_ppm,*observation_--cust_cvs_Mn_ppm,*observation_--cust_cvs_Cu_ppm,*observation_--cust_cvs_Zn_ppm,*observation_--cust_cvs_Al_ppm,*observation_--cust_cvs_Density,*observation_--cust_cvs_Ca_over_Mg_ppm,*observation_--soilObs_dba_src_ID,locationName,*plot_--reference_ID,UNUSED#PARENT_ID,*plot_--plotObsolete,*plot_--REPLACEMENTPLOT_ID,UNUSED#realLatitude,UNUSED#realLongitude,coordinateUncertaintyInMeters__from_coords,accessRights_verbatim,*plot_--confidentialityFieldsBlocked,*plot_--confidentialityReason,decimalLatitude,decimalLongitude,*plot_--authorCoordinateType,*plot_--authorCoordinateUnits,*plot_--authorE,*plot_--authorN,*plot_--authorZone,*plot_--authorDatum,site_name,directions_to_place,*plot_--plotRationaleNarrative,*plot_--azimuth,*plot_--dsgpoly,footprintWKT,plotArea_m2,*plot_--standSize,*plot_--placementMethod,*plot_--permanence,*plot_--layoutNarrative,elevationInMeters,*plot_--elevationAccuracy,UNUSED#elevationRange,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,*plot_--topoPosition,landform,*plot_--surficialDeposits,*plot_--rockType,county,*plot_--cust_cvs_province,stateProvince,country,*plot_--dateentered,*plot_--submitter_surname,*plot_--submitter_givenname,*plot_--submitter_email,*plot_--accessionCode,*plot_--notesPublic,*plot_--notesMgt,*plot_--revisions,*plot_--cust_eep_reach,*plot_--dba_src_ID,continent,DUPLICATE#of:COUNTRY#area|country|territory,DUPLICATE#of:stateProvince#region|state|province,DUPLICATE#of:county#county_,*plot_--quadrangle,*plot_--Geographic Name,*plot_--River Basin,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters,locality,taxonOccurrenceID
1
sort_col,locationID,eventID,*STRATUMTYPE_ID,*STRATUM_ID,taxonOccurrenceID__overall_plot,*taxonObservation_--PLANTCONCEPT_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,OMIT#authorPlantName,*taxonObservation_--taxonObservation_reference_ID,*taxonObservation_--currentTaxonInterpPlantConcept_ID,*taxonObservation_--taxonInferenceArea,*taxonObservation_--taxonObservation_accessionCode,*taxonObservation_--taxonObservation_dba_src_ID,*taxonObservation_--cust_cvs_corner1Presence,*taxonObservation_--cust_cvs_corner2Presence,*taxonObservation_--cust_cvs_corner3Presence,*taxonObservation_--cust_cvs_corner4Presence,*taxonObservation_--cust_cvs_corner5Presence,*taxonObservation_--entry_herbLineID,*taxonObservation_--entry_treeLineID,*taxonObservation_--taxonObservation_entry_sppID,*taxonObservation_--entry_unknownSp,*taxonObservation_--entry_sortOrder,*taxonObservation_--cust_cvs_collectionFlag,*taxonObservation_--taxonObservationNotes,*taxonObservation_--temp_taxonUpToDate,identificationID,stemID,dateIdentified,*taxonObservation_--taxonInterpretation_PLANTNAME_ID,*taxonObservation_--ROLE_ID,identificationType,*taxonObservation_--reference_ID,taxon_determination__is_original,taxon_determination__is_current,identificationQualifier,identificationVerificationStatus,UNUSED#collector_ID,collectorNumber,dateCollected,*taxonObservation_--museum_ID,accessionNumber,*taxonObservation_--groupType,occurrenceRemarks,*taxonObservation_--notesPublic,*taxonObservation_--notesMgt,*taxonObservation_--revisions,*taxonObservation_--taxonInterpretation_dba_src_ID,*taxonObservation_--taxonInterpretation_accessionCode,*taxonObservation_--party--salutation,identifiedBy__first,identifiedBy__middle,identifiedBy__last,*taxonObservation_--party--suffix,*taxonObservation_--party--entry_userInitials,*taxonObservation_--party--organizationName,*taxonObservation_--party--currentName_ID,*taxonObservation_--party--contactInstructions,*taxonObservation_--party--email,*taxonObservation_--party--accessionCode,*taxonObservation_--party--partyType,*taxonObservation_--party--dba_src_ID,*taxonObservation_--party--dba_unsure,*plantConcept_--PLANTNAME_ID,*plantConcept_--plantConcept_reference_ID,taxonName,scientificName,*plantConcept_--plantCode,*plantConcept_--plantDescription,*plantConcept_--plantConcept_accessionCode,*plantConcept_--plantConcept_dba_src_ID,*plantConcept_--plantConcept_entry_sppID,*plantConcept_--USDAPlantsCode,*plantConcept_--VascularPlant,kingdom,division_main,*plantConcept_--category,family,genus_main,specificEpithet,infraspecificRank,infraspecificEpithet,infraspecificRank2,infraspecificEpithet2,*hybridX,taxonRank,OMIT#taxonRank,*plantConcept_--lowestParentName,*plantConcept_--lowestParentConcept_ID,*plantConcept_--lowestChildRank,vernacularName,*plantConcept_--growthForm_short,*plantConcept_--woody,*plantConcept_--exotic,*plantConcept_--usda_code,*plantConcept_--usda_growthForm,*plantConcept_--sensitiveSpeciesFuzzPlot,DUPLICATE#of:denorm_kingdom#Kingdom,*Subkingdom,division_normalized,class,*Subclass,order,*composite family,DUPLICATE#of:denorm_family#family,*tribe,*composite genus,genus_normalized,subgenus,*section,*composite species,speciesBinomial,EQUIV#to:species#subspecies,EQUIV#to:species#composite variety,EQUIV#to:species#variety,*division,genus,observationGranularity,identifiedBy,aggregateOrganismObservationID__taxon_presence,coverPercent,*stemCount_--basalarea,*stemCount_--biomass,*stemCount_--inferencearea,*stemCount_--cust_cvs_StemFrequency,*stemCount_--taxonImportance_dba_src_ID,*stemCount_--taxonImportance_entry_herbLineID,*stemCount_--taxonImportance_entry_treeLineID,*stemCount_--cust_cvs_corner1Presence,*stemCount_--cust_cvs_corner2Presence,*stemCount_--cust_cvs_corner3Presence,*stemCount_--cust_cvs_corner4Presence,*stemCount_--cust_cvs_corner5Presence,*stemCount_--cust_cvs_originalCoverCode,aggregateOrganismObservationID__individual_count,diameterBreastHeight_cm,*stemCount_--stemdiameteraccuracy,height_m,*stemCount_--stemheightaccuracy,individualCount,*stemCount_--stemtaxonarea,*stemCount_--stemCount_dba_src_ID,*stemCount_--cust_cvs_ddh,*stemCount_--cust_cvs_ddhAccuracy,*stemCount_--cust_cvs_isPlanted,*stemCount_--cust_cvs_subsamplingFactor,*stemCount_--stemCount_entry_herbLineID,*stemCount_--stemCount_entry_treeLineID,*stemCount_--entry_recordCount,*stemCount_--entry_sortOrder,aggregateOrganismObservationID,*stratum--OBSERVATION_ID,*stratum--STRATUMMETHOD_ID,*stratum--stratumName,*stratum--stratumHeight,*stratum--stratumBase,*stratum--stratumCover,*stratum--stratumDescription,*stratum--dba_src_ID,*stratum--stratumArea,*stratum--stratumLabel,*stratumType--STRATUMMETHOD_ID,*stratumType--stratumIndex,stratum__name,*stratumType--stratumDescription,*stratumType--dba_src_ID,*stratumType--stratumOrder,*observation_--PREVIOUSOBS_ID,projectID,authorEventCode,startDate,endDate,*observation_--dateAccuracy,*observation_--dateEntered,*observation_--COVERMETHOD_ID,*observation_--coverDispersion,*observation_--autoTaxonCover,*observation_--STRATUMMETHOD_ID,samplingProtocol,*observation_--taxonObservationArea,*observation_--stemSizeLimit,*observation_--stemObservationArea,*observation_--stemSampleMethod,*observation_--originalData,*observation_--effortLevel,*observation_--plotValidationLevel,*observation_--floristicQuality,*observation_--bryophyteQuality,*observation_--lichenQuality,*observation_--observationNarrative,*observation_--landscapeNarrative,*observation_--homogeneity,*observation_--phenologicAspect,*observation_--representativeness,*observation_--standMaturity,*observation_--successionalStatus,*observation_--basalArea,*observation_--hydrologicRegime,*observation_--soilMoistureRegime,*observation_--soilDrainage,*observation_--waterSalinity,*observation_--waterDepth,*observation_--shoreDistance,*observation_--soilDepth,*observation_--organicDepth,*observation_--SOILTAXON_ID,*observation_--soilTaxonSrc,*observation_--soilTaxonComplex,*observation_--soilMapUnit,*observation_--percentBedRock,*observation_--percentRockGravel,*observation_--percentWood,*observation_--percentLitter,*observation_--percentBareSoil,*observation_--percentWater,*observation_--percentOther,*observation_--nameOther,*observation_--treeHt,*observation_--shrubHt,*observation_--fieldHt,*observation_--nonvascularHt,*observation_--submergedHt,*observation_--treeCover,*observation_--shrubCover,*observation_--fieldCover,*observation_--nonvascularCover,*observation_--floatingCover,*observation_--submergedCover,*observation_--dominantStratum,*observation_--growthform1Type,*observation_--growthform2Type,*observation_--growthform3Type,*observation_--growthform1Cover,*observation_--growthform2Cover,*observation_--growthform3Cover,*observation_--totalCover,*observation_--accessionCode,*observation_--notesPublic,*observation_--notesMgt,*observation_--revisions,*observation_--cust_cvs_CowardinSystem,*observation_--cust_cvs_mcnab_LFI_asp,*observation_--cust_cvs_mcnab_LFI_45,*observation_--cust_cvs_mcnab_LFI_90,*observation_--cust_cvs_mcnab_LFI_135,*observation_--cust_cvs_mcnab_LFI_180,*observation_--cust_cvs_mcnab_LFI_225,*observation_--cust_cvs_mcnab_LFI_270,*observation_--cust_cvs_mcnab_LFI_315,*observation_--cust_cvs_mcnab_TSI_asp,*observation_--cust_cvs_mcnab_TSI_45,*observation_--cust_cvs_mcnab_TSI_90,*observation_--cust_cvs_mcnab_TSI_135,*observation_--cust_cvs_mcnab_TSI_180,*observation_--cust_cvs_mcnab_TSI_225,*observation_--cust_cvs_mcnab_TSI_270,*observation_--cust_cvs_mcnab_TSI_315,*observation_--cust_cvs_mcnab_LFI,*observation_--cust_cvs_mcnab_TSI,*observation_--cust_cvs_LeafType,*observation_--cust_cvs_LeafPhenology,*observation_--cust_cvs_CanopyHeight,*observation_--cust_cvs_compassType,*observation_--cust_cvs_LocationSource,*observation_--cust_cvs_GPSLocationX,*observation_--cust_cvs_GPSLocationY,*observation_--cust_cvs_Ownership,*observation_--cust_cvs_taxaRichness,*observation_--cust_cvs_lengthSoilProbe,*observation_--cust_cvs_percentHistosol,*observation_--cust_cvs_percentBedrock,*observation_--cust_cvs_percentBoulder,*observation_--cust_cvs_percentGravelCobble,*observation_--cust_cvs_percentMineralSoil,*observation_--cust_cvs_percentCWD,*observation_--cust_cvs_percentFWD,*observation_--cust_cvs_percentDuff,*observation_--cust_cvs_percentLitter,*observation_--cust_cvs_percentNonVasc,*observation_--cust_cvs_percentWater,*observation_--cust_cvs_percentOther,*observation_--cust_cvs_percentOtherName,*observation_--cust_cvs_samplingLevel,*observation_--cust_cvs_postDsgPoly,*observation_--cust_cvs_stemsSampled,*observation_--cust_cvs_stemSamplingNarrative,*observation_--cust_eep_plotLastPlantedDate,*observation_--cust_eep_plotNotSampled,*observation_--cust_eep_plotNotSampledReason,*observation_--entry_ares_herbs,*observation_--entry_ares_trees,*observation_--entry_currentLandUse,*observation_--entry_depth,*observation_--entry_elevationUnits,*observation_--entry_formerLandUse,*observation_--entry_identificationNarrative,*observation_--entry_IntensiveModuleList,*observation_--entry_moduleSize_Overall,*observation_--entry_moduleSizeX,*observation_--entry_moduleSizeY,*observation_--entry_photosTaken,*observation_--entry_physClass,*observation_--entry_plot_X,*observation_--entry_plot_Y,*observation_--entry_soilModulesSampled,*observation_--entry_subsequentObsNum,*observation_--entry_taxonomicAuthority_ID,*observation_--entry_taxonomicAuthorityDate,*observation_--entry_team,*observation_--entry_plot,*observation_--entry_numberOfModules,*observation_--errors,*observation_--dba_src_ID,*observation_--dba_notes,*observation_--numberOfTaxa,*observation_--SOILOBS_ID,*observation_--soilHorizon,*observation_--soilDepthTop,*observation_--soilDepthBottom,*observation_--soilColor,organic_percent,texture,sand_percent,silt_percent,clay_percent,*observation_--soilCoarse,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,*observation_--soilDescription,*observation_--cust_cvs_collectionName,*observation_--cust_cvs_Lab,*observation_--cust_cvs_N,*observation_--cust_cvs_S,*observation_--cust_cvs_P,*observation_--cust_cvs_Ca_ppm,*observation_--cust_cvs_Mg_ppm,*observation_--cust_cvs_K_ppm,*observation_--cust_cvs_Na_ppm,*observation_--cust_cvs_percent_Ca,*observation_--cust_cvs_percent_Mg,*observation_--cust_cvs_percent_K,*observation_--cust_cvs_percent_Na,*observation_--cust_cvs_percent_Othr,*observation_--cust_cvs_percent_H,*observation_--cust_cvs_B_ppm,*observation_--cust_cvs_Fe_ppm,*observation_--cust_cvs_Mn_ppm,*observation_--cust_cvs_Cu_ppm,*observation_--cust_cvs_Zn_ppm,*observation_--cust_cvs_Al_ppm,*observation_--cust_cvs_Density,*observation_--cust_cvs_Ca_over_Mg_ppm,*observation_--soilObs_dba_src_ID,locationName,*plot_--reference_ID,UNUSED#PARENT_ID,*plot_--plotObsolete,*plot_--REPLACEMENTPLOT_ID,UNUSED#realLatitude,UNUSED#realLongitude,coordinateUncertaintyInMeters__from_coords,accessRights_verbatim,*plot_--confidentialityFieldsBlocked,*plot_--confidentialityReason,decimalLatitude,decimalLongitude,*plot_--authorCoordinateType,*plot_--authorCoordinateUnits,*plot_--authorE,*plot_--authorN,*plot_--authorZone,*plot_--authorDatum,site_name,directions_to_place,*plot_--plotRationaleNarrative,*plot_--azimuth,*plot_--dsgpoly,footprintWKT,plotArea_m2,*plot_--standSize,*plot_--placementMethod,*plot_--permanence,*plot_--layoutNarrative,elevationInMeters,*plot_--elevationAccuracy,UNUSED#elevationRange,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,*plot_--topoPosition,landform,*plot_--surficialDeposits,*plot_--rockType,county,*plot_--cust_cvs_province,stateProvince,country,*plot_--dateentered,*plot_--submitter_surname,*plot_--submitter_givenname,*plot_--submitter_email,*plot_--accessionCode,*plot_--notesPublic,*plot_--notesMgt,*plot_--revisions,*plot_--cust_eep_reach,*plot_--dba_src_ID,continent,DUPLICATE#of:COUNTRY#area|country|territory,DUPLICATE#of:stateProvince#region|state|province,DUPLICATE#of:county#county_,*plot_--quadrangle,*plot_--Geographic Name,*plot_--River Basin,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters,locality,taxonOccurrenceID
inputs/CVS/taxon_observation.**/map.csv
6 6
*STRATUM_ID,*STRATUM_ID,,
7 7
taxonOccurrenceID__overall_plot,taxonOccurrenceID__overall_plot,,
8 8
*taxonObservation_--PLANTCONCEPT_ID,*taxonObservation_--PLANTCONCEPT_ID,,
9
*taxonObservation_--taxonInterpretation_PARTY_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,,
9 10
OMIT#authorPlantName,OMIT#authorPlantName,,
10 11
*taxonObservation_--taxonObservation_reference_ID,*taxonObservation_--taxonObservation_reference_ID,,
11 12
*taxonObservation_--currentTaxonInterpPlantConcept_ID,*taxonObservation_--currentTaxonInterpPlantConcept_ID,,
......
29 30
stemID,stemID,,
30 31
dateIdentified,dateIdentified,,
31 32
*taxonObservation_--taxonInterpretation_PLANTNAME_ID,*taxonObservation_--taxonInterpretation_PLANTNAME_ID,,
32
*taxonObservation_--taxonInterpretation_PARTY_ID,*taxonObservation_--taxonInterpretation_PARTY_ID,,
33 33
*taxonObservation_--ROLE_ID,*taxonObservation_--ROLE_ID,,
34 34
identificationType,identificationType,,
35 35
*taxonObservation_--reference_ID,*taxonObservation_--reference_ID,,
......
49 49
*taxonObservation_--revisions,*taxonObservation_--revisions,,
50 50
*taxonObservation_--taxonInterpretation_dba_src_ID,*taxonObservation_--taxonInterpretation_dba_src_ID,,
51 51
*taxonObservation_--taxonInterpretation_accessionCode,*taxonObservation_--taxonInterpretation_accessionCode,,
52
*taxonObservation_--party--salutation,*taxonObservation_--party--salutation,,
53
identifiedBy__first,identifiedBy__first,,
54
identifiedBy__middle,identifiedBy__middle,,
55
identifiedBy__last,identifiedBy__last,,
56
*taxonObservation_--party--suffix,*taxonObservation_--party--suffix,,
57
*taxonObservation_--party--entry_userInitials,*taxonObservation_--party--entry_userInitials,,
58
*taxonObservation_--party--organizationName,*taxonObservation_--party--organizationName,,
59
*taxonObservation_--party--currentName_ID,*taxonObservation_--party--currentName_ID,,
60
*taxonObservation_--party--contactInstructions,*taxonObservation_--party--contactInstructions,,
61
*taxonObservation_--party--email,*taxonObservation_--party--email,,
62
*taxonObservation_--party--accessionCode,*taxonObservation_--party--accessionCode,,
63
*taxonObservation_--party--partyType,*taxonObservation_--party--partyType,,
64
*taxonObservation_--party--dba_src_ID,*taxonObservation_--party--dba_src_ID,,
65
*taxonObservation_--party--dba_unsure,*taxonObservation_--party--dba_unsure,,
52 66
*plantConcept_--PLANTNAME_ID,*plantConcept_--PLANTNAME_ID,,
53 67
*plantConcept_--plantConcept_reference_ID,*plantConcept_--plantConcept_reference_ID,,
54 68
taxonName,taxonName,,
......
104 118
*division,*division,,
105 119
genus,genus,,
106 120
observationGranularity,observationGranularity,,
121
identifiedBy,identifiedBy,,
107 122
aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__taxon_presence,,
108 123
coverPercent,coverPercent,,
109 124
*stemCount_--basalarea,*stemCount_--basalarea,,
inputs/CVS/taxon_observation.**/test.xml.ref
45 45
                                    <authortaxoncode>$collectorNumber</authortaxoncode>
46 46
                                    <sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
47 47
                                    <taxondetermination>
48
                                        <party_id><party><fullname>$identifiedBy</fullname></party></party_id>
48 49
                                        <taxonverbatim_id>
49 50
                                            <taxonverbatim>
50 51
                                                <taxonlabel_id>
......
266 267
        </path>
267 268
    </_setDefault>
268 269
</VegBIEN>
269
Inserted 34 new rows into database
270
Inserted 35 new rows into database
inputs/CVS/taxon_observation.**/unmapped_terms.csv
3 3
*STRATUM_ID
4 4
taxonOccurrenceID__overall_plot
5 5
*taxonObservation_--PLANTCONCEPT_ID
6
*taxonObservation_--taxonInterpretation_PARTY_ID
6 7
*taxonObservation_--taxonObservation_reference_ID
7 8
*taxonObservation_--currentTaxonInterpPlantConcept_ID
8 9
*taxonObservation_--taxonInferenceArea
......
23 24
*taxonObservation_--temp_taxonUpToDate
24 25
identificationID
25 26
*taxonObservation_--taxonInterpretation_PLANTNAME_ID
26
*taxonObservation_--taxonInterpretation_PARTY_ID
27 27
*taxonObservation_--ROLE_ID
28 28
*taxonObservation_--reference_ID
29 29
identificationVerificationStatus
......
34 34
*taxonObservation_--revisions
35 35
*taxonObservation_--taxonInterpretation_dba_src_ID
36 36
*taxonObservation_--taxonInterpretation_accessionCode
37
*taxonObservation_--party--salutation
38
identifiedBy__first
39
identifiedBy__middle
40
identifiedBy__last
41
*taxonObservation_--party--suffix
42
*taxonObservation_--party--entry_userInitials
43
*taxonObservation_--party--organizationName
44
*taxonObservation_--party--currentName_ID
45
*taxonObservation_--party--contactInstructions
46
*taxonObservation_--party--email
47
*taxonObservation_--party--accessionCode
48
*taxonObservation_--party--partyType
49
*taxonObservation_--party--dba_src_ID
50
*taxonObservation_--party--dba_unsure
37 51
*plantConcept_--PLANTNAME_ID
38 52
*plantConcept_--plantConcept_reference_ID
39 53
*plantConcept_--plantCode

Also available in: Unified diff