Revision 11254
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/VegBank/taxon_observation.**.sample/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
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| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
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| inputs/VegBank/taxon_observation.**.sample/map.csv | ||
|---|---|---|
| 1 |
VegBank,VegCore,Filter,Comments |
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| 2 |
sort_col,sort_col,, |
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| 3 |
country,country,, |
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| 4 |
continent,continent,, |
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| 5 |
stateProvince,stateProvince,, |
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| 6 |
county,county,, |
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| 7 |
landform,landform,, |
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| 8 |
locality,locality,, |
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| 9 |
decimalLatitude,decimalLatitude,, |
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| 10 |
decimalLongitude,decimalLongitude,, |
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| 11 |
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,, |
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| 12 |
coordinateUncertaintyInMeters__from_coords,coordinateUncertaintyInMeters__from_coords,, |
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| 13 |
coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters__from_fuzzing,, |
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| 14 |
accessRights,accessRights,, |
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| 15 |
accessRights_verbatim,accessRights_verbatim,, |
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| 16 |
projectID,projectID,, |
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| 17 |
locationID,locationID,, |
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| 18 |
locationName,locationName,, |
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| 19 |
parentLocationID,parentLocationID,, |
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| 20 |
footprintWKT,footprintWKT,, |
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| 21 |
elevationInMeters,elevationInMeters,, |
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| 22 |
slopeAspect,slopeAspect,, |
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| 23 |
minSlopeAspect,minSlopeAspect,, |
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maxSlopeAspect,maxSlopeAspect,, |
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slopeGradient,slopeGradient,, |
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minSlopeGradient,minSlopeGradient,, |
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maxSlopeGradient,maxSlopeGradient,, |
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| 28 |
plotArea_m2,plotArea_m2,, |
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| 29 |
eventID,eventID,, |
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authorEventCode,authorEventCode,, |
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| 31 |
startDate,startDate,, |
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| 32 |
endDate,endDate,, |
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| 33 |
samplingProtocol,samplingProtocol,, |
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| 34 |
organic_percent,organic_percent,, |
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| 35 |
texture,texture,, |
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| 36 |
sand_percent,sand_percent,, |
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| 37 |
silt_percent,silt_percent,, |
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| 38 |
clay_percent,clay_percent,, |
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| 39 |
ph,ph,, |
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| 40 |
cationExchangeCapacity_cmol_kg,cationExchangeCapacity_cmol_kg,, |
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| 41 |
baseSaturation_percent,baseSaturation_percent,, |
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| 42 |
emb_soilobs,emb_soilobs,, |
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| 43 |
stratum__name,stratum__name,, |
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*stratum_id,*stratum_id,, |
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*stratumtype_id,*stratumtype_id,, |
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| 46 |
collectorNumber,collectorNumber,, |
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| 47 |
dateCollected,dateCollected,, |
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| 48 |
originalScientificName,originalScientificName,, |
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| 49 |
originalTaxonName,originalTaxonName,, |
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originalVernacularName,originalVernacularName,, |
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| 51 |
scientificName_verbatim,scientificName_verbatim,, |
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| 52 |
dateIdentified,dateIdentified,, |
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kingdom,kingdom,, |
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*Subkingdom,*Subkingdom,, |
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*Superdivision,*Superdivision,, |
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*Division,*Division,, |
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*Subdivision,*Subdivision,, |
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class,class,, |
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*Subclass,*Subclass,, |
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order,order,, |
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family,family,, |
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| 62 |
genus,genus,, |
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taxonName,taxonName,, |
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scientificName,scientificName,, |
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scientificName__for_nearest_taxon_concept,scientificName__for_nearest_taxon_concept,, |
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| 66 |
vernacularName,vernacularName,, |
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| 67 |
occurrenceRemarks,occurrenceRemarks,, |
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| 68 |
observationGranularity,observationGranularity,, |
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| 69 |
coverPercent,coverPercent,, |
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| 70 |
diameterBreastHeight_cm,diameterBreastHeight_cm,, |
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| 71 |
height_m,height_m,, |
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| 72 |
individualCount,individualCount,, |
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| 73 |
taxonOccurrenceID,taxonOccurrenceID,, |
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| 74 |
taxonOccurrenceID__overall_plot,taxonOccurrenceID__overall_plot,, |
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| 75 |
identificationID,identificationID,, |
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| 76 |
identificationType,identificationType,, |
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| 77 |
identificationQualifier,identificationQualifier,, |
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| 78 |
identificationVerificationStatus,identificationVerificationStatus,, |
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| 79 |
aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__taxon_presence,, |
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| 80 |
aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID__individual_count,, |
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| 81 |
aggregateOrganismObservationID,aggregateOrganismObservationID,, |
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| 82 |
individualID,individualID,, |
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| 83 |
stemID,stemID,, |
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| 84 |
accessionNumber,accessionNumber,, |
|
| inputs/VegBank/taxon_observation.**.sample/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>VegBank.new</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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| 9 |
<location> |
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<authorlocationcode>$locationName</authorlocationcode> |
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| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode> |
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| 12 |
<accesslevel>$accessRights</accesslevel> |
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| 13 |
<area_m2>$plotArea_m2</area_m2> |
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| 14 |
<elevation_m>$elevationInMeters</elevation_m> |
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| 15 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
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| 16 |
<landform>$landform</landform> |
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| 17 |
<locationevent> |
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| 18 |
<method_id><method><name>$samplingProtocol</name></method></method_id> |
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| 19 |
<project_id><project><sourceaccessioncode>$projectID</sourceaccessioncode></project></project_id> |
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| 20 |
<authoreventcode>$authorEventCode</authoreventcode> |
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| 21 |
<sourceaccessioncode>$eventID</sourceaccessioncode> |
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| 22 |
<locationevent fkey="parent_id"> |
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| 23 |
<stratum_id><stratum><stratumname>$stratum__name</stratumname></stratum></stratum_id> |
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| 24 |
<sourceaccessioncode>$eventID</sourceaccessioncode> |
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| 25 |
<taxonoccurrence> |
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| 26 |
<aggregateoccurrence> |
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| 27 |
<collectiondate>$dateCollected</collectiondate> |
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| 28 |
<count>$individualCount</count> |
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| 29 |
<cover_fraction><_percent_to_fraction><value>$coverPercent</value></_percent_to_fraction></cover_fraction> |
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| 30 |
<notes>$occurrenceRemarks</notes> |
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| 31 |
<plantobservation> |
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| 32 |
<authorplantcode>$collectorNumber</authorplantcode> |
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| 33 |
<sourceaccessioncode>$individualID</sourceaccessioncode> |
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| 34 |
<specimenreplicate> |
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| 35 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc> |
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| 36 |
<collectionnumber>$collectorNumber</collectionnumber> |
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| 37 |
</specimenreplicate> |
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| 38 |
<stemobservation> |
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| 39 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m> |
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| 40 |
<height_m>$height_m</height_m> |
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| 41 |
<sourceaccessioncode>$stemID</sourceaccessioncode> |
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| 42 |
</stemobservation> |
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| 43 |
</plantobservation> |
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| 44 |
<sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode> |
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| 45 |
</aggregateoccurrence> |
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| 46 |
<authortaxoncode>$collectorNumber</authortaxoncode> |
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| 47 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode> |
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| 48 |
<taxondetermination> |
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| 49 |
<taxonverbatim_id> |
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| 50 |
<taxonverbatim> |
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| 51 |
<taxonlabel_id> |
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| 52 |
<taxonlabel> |
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| 53 |
<parent_id> |
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| 54 |
<taxonlabel> |
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| 55 |
<parent_id> |
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| 56 |
<taxonlabel> |
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| 57 |
<rank>cultivar</rank> |
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| 58 |
<parent_id> |
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| 59 |
<taxonlabel> |
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| 60 |
<rank>forma</rank> |
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| 61 |
<parent_id> |
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| 62 |
<taxonlabel> |
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| 63 |
<rank>variety</rank> |
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| 64 |
<parent_id> |
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| 65 |
<taxonlabel> |
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| 66 |
<rank>subspecies</rank> |
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| 67 |
<parent_id> |
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| 68 |
<taxonlabel> |
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| 69 |
<rank>species</rank> |
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| 70 |
<parent_id> |
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| 71 |
<taxonlabel> |
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| 72 |
<rank>genus</rank> |
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| 73 |
<taxonepithet>$genus</taxonepithet> |
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| 74 |
<parent_id> |
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| 75 |
<taxonlabel> |
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<rank>family</rank> |
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| 77 |
<taxonepithet>$family</taxonepithet> |
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| 78 |
<parent_id> |
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| 79 |
<taxonlabel> |
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| 80 |
<rank>order</rank> |
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| 81 |
<taxonepithet>$order</taxonepithet> |
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| 82 |
<parent_id> |
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| 83 |
<taxonlabel> |
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| 84 |
<rank>class</rank> |
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| 85 |
<taxonepithet>$class</taxonepithet> |
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| 86 |
<parent_id> |
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| 87 |
<taxonlabel> |
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| 88 |
<rank>phylum</rank> |
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| 89 |
<parent_id> |
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| 90 |
<taxonlabel> |
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| 91 |
<rank>kingdom</rank> |
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| 92 |
<taxonepithet>$kingdom</taxonepithet> |
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</taxonlabel> |
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| 94 |
</parent_id> |
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| 95 |
</taxonlabel> |
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</parent_id> |
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| 97 |
</taxonlabel> |
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| 98 |
</parent_id> |
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| 99 |
</taxonlabel> |
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| 100 |
</parent_id> |
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| 101 |
</taxonlabel> |
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| 102 |
</parent_id> |
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| 103 |
</taxonlabel> |
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| 104 |
</parent_id> |
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| 105 |
</taxonlabel> |
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| 106 |
</parent_id> |
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| 107 |
</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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| 112 |
</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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| 116 |
</parent_id> |
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| 117 |
<taxonomicname> |
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| 118 |
<_merge_prefix> |
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| 119 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
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| 120 |
<value> |
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| 121 |
<_alt> |
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| 122 |
<1>$scientificName</1> |
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| 123 |
<2> |
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| 124 |
<_alt> |
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| 125 |
<1>$taxonName</1> |
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| 126 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
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| 127 |
</_alt> |
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| 128 |
</2> |
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| 129 |
</_alt> |
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| 130 |
</value> |
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| 131 |
</_merge_prefix> |
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| 132 |
</taxonomicname> |
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| 133 |
</taxonlabel> |
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| 134 |
</taxonlabel_id> |
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| 135 |
<family>$family</family> |
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| 136 |
<genus>$genus</genus> |
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| 137 |
<taxonname>$taxonName</taxonname> |
|
| 138 |
<taxonomicname>$scientificName</taxonomicname> |
|
| 139 |
</taxonverbatim> |
|
| 140 |
</taxonverbatim_id> |
|
| 141 |
<determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate> |
|
| 142 |
<determinationtype>$identificationType</determinationtype> |
|
| 143 |
<taxonfit>$identificationQualifier</taxonfit> |
|
| 144 |
</taxondetermination> |
|
| 145 |
<taxondetermination> |
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| 146 |
<isoriginal>true</isoriginal> |
|
| 147 |
<taxonverbatim_id> |
|
| 148 |
<taxonverbatim> |
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| 149 |
<taxonname>$originalTaxonName</taxonname> |
|
| 150 |
<taxonomicname>$originalScientificName</taxonomicname> |
|
| 151 |
</taxonverbatim> |
|
| 152 |
</taxonverbatim_id> |
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| 153 |
</taxondetermination> |
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| 154 |
</taxonoccurrence> |
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| 155 |
</locationevent> |
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| 156 |
<obsenddate>$endDate</obsenddate> |
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| 157 |
<obsstartdate>$startDate</obsstartdate> |
|
| 158 |
<soilsample> |
|
| 159 |
<basesaturation_fraction><_percent_to_fraction><value>$baseSaturation_percent</value></_percent_to_fraction></basesaturation_fraction> |
|
| 160 |
<cationexchangecapacity_cmol_kg>$cationExchangeCapacity_cmol_kg</cationexchangecapacity_cmol_kg> |
|
| 161 |
<clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction> |
|
| 162 |
<organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction> |
|
| 163 |
<ph>$ph</ph> |
|
| 164 |
<sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction> |
|
| 165 |
<silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction> |
|
| 166 |
<texture>$texture</texture> |
|
| 167 |
</soilsample> |
|
| 168 |
</locationevent> |
|
| 169 |
<locationnarrative>$locality</locationnarrative> |
|
| 170 |
<locationplace> |
|
| 171 |
<place_id> |
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| 172 |
<place> |
|
| 173 |
<coordinates_id> |
|
| 174 |
<coordinates> |
|
| 175 |
<coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m> |
|
| 176 |
<footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc> |
|
| 177 |
<latitude_deg> |
|
| 178 |
<_nullIf> |
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| 179 |
<null>0</null> |
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| 180 |
<type>float</type> |
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| 181 |
<value>$decimalLatitude</value> |
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| 182 |
</_nullIf> |
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| 183 |
</latitude_deg> |
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| 184 |
<longitude_deg> |
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| 185 |
<_nullIf> |
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| 186 |
<null>0</null> |
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| 187 |
<type>float</type> |
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| 188 |
<value>$decimalLongitude</value> |
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| 189 |
</_nullIf> |
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| 190 |
</longitude_deg> |
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| 191 |
</coordinates> |
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| 192 |
</coordinates_id> |
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| 193 |
<continent>$continent</continent> |
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| 194 |
<country>$country</country> |
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| 195 |
<county>$county</county> |
|
| 196 |
<matched_place_id> |
|
| 197 |
<place> |
|
| 198 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 199 |
<coordinates_id> |
|
| 200 |
<coordinates> |
|
| 201 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 202 |
<latitude_deg> |
|
| 203 |
<_nullIf> |
|
| 204 |
<null>0</null> |
|
| 205 |
<type>float</type> |
|
| 206 |
<value>$decimalLatitude</value> |
|
| 207 |
</_nullIf> |
|
| 208 |
</latitude_deg> |
|
| 209 |
<longitude_deg> |
|
| 210 |
<_nullIf> |
|
| 211 |
<null>0</null> |
|
| 212 |
<type>float</type> |
|
| 213 |
<value>$decimalLongitude</value> |
|
| 214 |
</_nullIf> |
|
| 215 |
</longitude_deg> |
|
| 216 |
</coordinates> |
|
| 217 |
</coordinates_id> |
|
| 218 |
<country>$country</country> |
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| 219 |
<county>$county</county> |
|
| 220 |
<stateprovince>$stateProvince</stateprovince> |
|
| 221 |
</place> |
|
| 222 |
</matched_place_id> |
|
| 223 |
<stateprovince>$stateProvince</stateprovince> |
|
| 224 |
</place> |
|
| 225 |
</place_id> |
|
| 226 |
</locationplace> |
|
| 227 |
<parent_id><location><sourceaccessioncode>$parentLocationID</sourceaccessioncode></location></parent_id> |
|
| 228 |
<slopeaspect_deg> |
|
| 229 |
<_alt> |
|
| 230 |
<1><_compass><value>$slopeAspect</value></_compass></1> |
|
| 231 |
<2> |
|
| 232 |
<_avg> |
|
| 233 |
<1>$minSlopeAspect</1> |
|
| 234 |
<2>$maxSlopeAspect</2> |
|
| 235 |
</_avg> |
|
| 236 |
</2> |
|
| 237 |
</_alt> |
|
| 238 |
</slopeaspect_deg> |
|
| 239 |
<slopegradient_fraction> |
|
| 240 |
<_alt> |
|
| 241 |
<1>$slopeGradient</1> |
|
| 242 |
<2> |
|
| 243 |
<_avg> |
|
| 244 |
<1>$minSlopeGradient</1> |
|
| 245 |
<2>$maxSlopeGradient</2> |
|
| 246 |
</_avg> |
|
| 247 |
</2> |
|
| 248 |
</_alt> |
|
| 249 |
</slopegradient_fraction> |
|
| 250 |
</location> |
|
| 251 |
</path> |
|
| 252 |
</_simplifyPath> |
|
| 253 |
</path> |
|
| 254 |
</_setDefault> |
|
| 255 |
</VegBIEN> |
|
| 256 |
Inserted 30 new rows into database |
|
| inputs/VegBank/taxon_observation.**.sample/VegBIEN.csv | ||
|---|---|---|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 2 | 0 | |
| inputs/VegBank/taxon_observation.**.sample/unmapped_terms.csv | ||
|---|---|---|
| 1 |
sort_col |
|
| 2 |
coordinateUncertaintyInMeters__from_coords |
|
| 3 |
coordinateUncertaintyInMeters__from_fuzzing |
|
| 4 |
accessRights_verbatim |
|
| 5 |
emb_soilobs |
|
| 6 |
*stratum_id |
|
| 7 |
*stratumtype_id |
|
| 8 |
originalVernacularName |
|
| 9 |
scientificName_verbatim |
|
| 10 |
*Subkingdom |
|
| 11 |
*Superdivision |
|
| 12 |
*Division |
|
| 13 |
*Subdivision |
|
| 14 |
*Subclass |
|
| 15 |
scientificName__for_nearest_taxon_concept |
|
| 16 |
vernacularName |
|
| 17 |
taxonOccurrenceID__overall_plot |
|
| 18 |
identificationID |
|
| 19 |
identificationVerificationStatus |
|
| 20 |
aggregateOrganismObservationID__taxon_presence |
|
| 21 |
aggregateOrganismObservationID__individual_count |
|
| inputs/VegBank/taxon_observation.**.sample/create.sql | ||
|---|---|---|
| 1 |
SELECT |
|
| 2 |
"sort_col" |
|
| 3 |
, "country" |
|
| 4 |
, "continent" |
|
| 5 |
, "stateProvince" |
|
| 6 |
, "county" |
|
| 7 |
, "landform" |
|
| 8 |
, "locality" |
|
| 9 |
, "decimalLatitude" |
|
| 10 |
, "decimalLongitude" |
|
| 11 |
, "coordinateUncertaintyInMeters" |
|
| 12 |
, "coordinateUncertaintyInMeters__from_coords" |
|
| 13 |
, "coordinateUncertaintyInMeters__from_fuzzing" |
|
| 14 |
, "accessRights" |
|
| 15 |
, "accessRights_verbatim" |
|
| 16 |
, "projectID" |
|
| 17 |
, "locationID" |
|
| 18 |
, "locationName" |
|
| 19 |
, "parentLocationID" |
|
| 20 |
, "footprintWKT" |
|
| 21 |
, "elevationInMeters" |
|
| 22 |
, "slopeAspect" |
|
| 23 |
, "minSlopeAspect" |
|
| 24 |
, "maxSlopeAspect" |
|
| 25 |
, "slopeGradient" |
|
| 26 |
, "minSlopeGradient" |
|
| 27 |
, "maxSlopeGradient" |
|
| 28 |
, "plotArea_m2" |
|
| 29 |
, "eventID" |
|
| 30 |
, "authorEventCode" |
|
| 31 |
, "startDate" |
|
| 32 |
, "endDate" |
|
| 33 |
, "samplingProtocol" |
|
| 34 |
, "organic_percent" |
|
| 35 |
, "texture" |
|
| 36 |
, "sand_percent" |
|
| 37 |
, "silt_percent" |
|
| 38 |
, "clay_percent" |
|
| 39 |
, "ph" |
|
| 40 |
, "cationExchangeCapacity_cmol_kg" |
|
| 41 |
, "baseSaturation_percent" |
|
| 42 |
, "emb_soilobs" |
|
| 43 |
, "stratum__name" |
|
| 44 |
, "*stratum_id" |
|
| 45 |
, "*stratumtype_id" |
|
| 46 |
, "collectorNumber" |
|
| 47 |
, "dateCollected" |
|
| 48 |
, "originalScientificName" |
|
| 49 |
, "originalTaxonName" |
|
| 50 |
, "originalVernacularName" |
|
| 51 |
, "scientificName_verbatim" |
|
| 52 |
, "dateIdentified" |
|
| 53 |
, "kingdom" |
|
| 54 |
, "*Subkingdom" |
|
| 55 |
, "*Superdivision" |
|
| 56 |
, "*Division" |
|
| 57 |
, "*Subdivision" |
|
| 58 |
, "class" |
|
| 59 |
, "*Subclass" |
|
| 60 |
, "order" |
|
| 61 |
, "family" |
|
| 62 |
, "genus" |
|
| 63 |
, "taxonName" |
|
| 64 |
, "scientificName" |
|
| 65 |
, "scientificName__for_nearest_taxon_concept" |
|
| 66 |
, "vernacularName" |
|
| 67 |
, "occurrenceRemarks" |
|
| 68 |
, "observationGranularity" |
|
| 69 |
, "coverPercent" |
|
| 70 |
, "diameterBreastHeight_cm" |
|
| 71 |
, "height_m" |
|
| 72 |
, "individualCount" |
|
| 73 |
, "taxonOccurrenceID" |
|
| 74 |
, "taxonOccurrenceID__overall_plot" |
|
| 75 |
, "identificationID" |
|
| 76 |
, "identificationType" |
|
| 77 |
, "identificationQualifier" |
|
| 78 |
, "identificationVerificationStatus" |
|
| 79 |
, "aggregateOrganismObservationID__taxon_presence" |
|
| 80 |
, "aggregateOrganismObservationID__individual_count" |
|
| 81 |
, "aggregateOrganismObservationID" |
|
| 82 |
, "individualID" |
|
| 83 |
, "stemID" |
|
| 84 |
, "accessionNumber" |
|
| 85 |
FROM "taxon_observation.**" |
|
| 86 |
WHERE "locationID" IN (/*Heritage*/27581, /*CVS*/80476, /*NPS*/25572, /*GAP*/46073, /*Jennings*/11862, /*soil*/27234) |
|
| 87 |
-- see wiki.vegpath.org/Spot-checking#VegBank |
|
| 88 |
; -- runtime: 1 s ("1289.136 ms") @starscream
|
|
| inputs/VegBank/taxon_observation.**.sample/header.csv | ||
|---|---|---|
| 1 |
sort_col,country,continent,stateProvince,county,landform,locality,decimalLatitude,decimalLongitude,coordinateUncertaintyInMeters,coordinateUncertaintyInMeters__from_coords,coordinateUncertaintyInMeters__from_fuzzing,accessRights,accessRights_verbatim,projectID,locationID,locationName,parentLocationID,footprintWKT,elevationInMeters,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,plotArea_m2,eventID,authorEventCode,startDate,endDate,samplingProtocol,organic_percent,texture,sand_percent,silt_percent,clay_percent,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,emb_soilobs,stratum__name,*stratum_id,*stratumtype_id,collectorNumber,dateCollected,originalScientificName,originalTaxonName,originalVernacularName,scientificName_verbatim,dateIdentified,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,taxonName,scientificName,scientificName__for_nearest_taxon_concept,vernacularName,occurrenceRemarks,observationGranularity,coverPercent,diameterBreastHeight_cm,height_m,individualCount,taxonOccurrenceID,taxonOccurrenceID__overall_plot,identificationID,identificationType,identificationQualifier,identificationVerificationStatus,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,individualID,stemID,accessionNumber |
|
| inputs/VegBank/import_order.txt | ||
|---|---|---|
| 8 | 8 |
stemcount_ |
| 9 | 9 |
stemlocation_ |
| 10 | 10 |
taxon_observation.** |
| 11 |
taxon_observation.**.sample |
|
| 11 |
+taxon_observation.**.sample
|
|
| 12 | 12 |
observationcontributor_ |
| 13 | 13 |
observation__community |
| inputs/VegBank/+taxon_observation.**.sample/create.sql | ||
|---|---|---|
| 1 |
SELECT |
|
| 2 |
"sort_col" |
|
| 3 |
, "country" |
|
| 4 |
, "continent" |
|
| 5 |
, "stateProvince" |
|
| 6 |
, "county" |
|
| 7 |
, "landform" |
|
| 8 |
, "locality" |
|
| 9 |
, "decimalLatitude" |
|
| 10 |
, "decimalLongitude" |
|
| 11 |
, "coordinateUncertaintyInMeters" |
|
| 12 |
, "coordinateUncertaintyInMeters__from_coords" |
|
| 13 |
, "coordinateUncertaintyInMeters__from_fuzzing" |
|
| 14 |
, "accessRights" |
|
| 15 |
, "accessRights_verbatim" |
|
| 16 |
, "projectID" |
|
| 17 |
, "locationID" |
|
| 18 |
, "locationName" |
|
| 19 |
, "parentLocationID" |
|
| 20 |
, "footprintWKT" |
|
| 21 |
, "elevationInMeters" |
|
| 22 |
, "slopeAspect" |
|
| 23 |
, "minSlopeAspect" |
|
| 24 |
, "maxSlopeAspect" |
|
| 25 |
, "slopeGradient" |
|
| 26 |
, "minSlopeGradient" |
|
| 27 |
, "maxSlopeGradient" |
|
| 28 |
, "plotArea_m2" |
|
| 29 |
, "eventID" |
|
| 30 |
, "authorEventCode" |
|
| 31 |
, "startDate" |
|
| 32 |
, "endDate" |
|
| 33 |
, "samplingProtocol" |
|
| 34 |
, "organic_percent" |
|
| 35 |
, "texture" |
|
| 36 |
, "sand_percent" |
|
| 37 |
, "silt_percent" |
|
| 38 |
, "clay_percent" |
|
| 39 |
, "ph" |
|
| 40 |
, "cationExchangeCapacity_cmol_kg" |
|
| 41 |
, "baseSaturation_percent" |
|
| 42 |
, "emb_soilobs" |
|
| 43 |
, "stratum__name" |
|
| 44 |
, "*stratum_id" |
|
| 45 |
, "*stratumtype_id" |
|
| 46 |
, "collectorNumber" |
|
| 47 |
, "dateCollected" |
|
| 48 |
, "originalScientificName" |
|
| 49 |
, "originalTaxonName" |
|
| 50 |
, "originalVernacularName" |
|
| 51 |
, "scientificName_verbatim" |
|
| 52 |
, "dateIdentified" |
|
| 53 |
, "kingdom" |
|
| 54 |
, "*Subkingdom" |
|
| 55 |
, "*Superdivision" |
|
| 56 |
, "*Division" |
|
| 57 |
, "*Subdivision" |
|
| 58 |
, "class" |
|
| 59 |
, "*Subclass" |
|
| 60 |
, "order" |
|
| 61 |
, "family" |
|
| 62 |
, "genus" |
|
| 63 |
, "taxonName" |
|
| 64 |
, "scientificName" |
|
| 65 |
, "scientificName__for_nearest_taxon_concept" |
|
| 66 |
, "vernacularName" |
|
| 67 |
, "occurrenceRemarks" |
|
| 68 |
, "observationGranularity" |
|
| 69 |
, "coverPercent" |
|
| 70 |
, "diameterBreastHeight_cm" |
|
| 71 |
, "height_m" |
|
| 72 |
, "individualCount" |
|
| 73 |
, "taxonOccurrenceID" |
|
| 74 |
, "taxonOccurrenceID__overall_plot" |
|
| 75 |
, "identificationID" |
|
| 76 |
, "identificationType" |
|
| 77 |
, "identificationQualifier" |
|
| 78 |
, "identificationVerificationStatus" |
|
| 79 |
, "aggregateOrganismObservationID__taxon_presence" |
|
| 80 |
, "aggregateOrganismObservationID__individual_count" |
|
| 81 |
, "aggregateOrganismObservationID" |
|
| 82 |
, "individualID" |
|
| 83 |
, "stemID" |
|
| 84 |
, "accessionNumber" |
|
| 85 |
FROM "taxon_observation.**" |
|
| 86 |
WHERE "locationID" IN (/*Heritage*/27581, /*CVS*/80476, /*NPS*/25572, /*GAP*/46073, /*Jennings*/11862, /*soil*/27234) |
|
| 87 |
-- see wiki.vegpath.org/Spot-checking#VegBank |
|
| 88 |
; -- runtime: 1 s ("1289.136 ms") @starscream
|
|
| inputs/VegBank/+taxon_observation.**.sample/header.csv | ||
|---|---|---|
| 1 |
sort_col,country,continent,stateProvince,county,landform,locality,decimalLatitude,decimalLongitude,coordinateUncertaintyInMeters,coordinateUncertaintyInMeters__from_coords,coordinateUncertaintyInMeters__from_fuzzing,accessRights,accessRights_verbatim,projectID,locationID,locationName,parentLocationID,footprintWKT,elevationInMeters,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,plotArea_m2,eventID,authorEventCode,startDate,endDate,samplingProtocol,organic_percent,texture,sand_percent,silt_percent,clay_percent,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,emb_soilobs,stratum__name,*stratum_id,*stratumtype_id,collectorNumber,dateCollected,originalScientificName,originalTaxonName,originalVernacularName,scientificName_verbatim,dateIdentified,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,taxonName,scientificName,scientificName__for_nearest_taxon_concept,vernacularName,occurrenceRemarks,observationGranularity,coverPercent,diameterBreastHeight_cm,height_m,individualCount,taxonOccurrenceID,taxonOccurrenceID__overall_plot,identificationID,identificationType,identificationQualifier,identificationVerificationStatus,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,individualID,stemID,accessionNumber |
|
| inputs/VegBank/+taxon_observation.**.sample/map.csv | ||
|---|---|---|
| 1 |
VegBank,VegCore,Filter,Comments |
|
| 2 |
sort_col,sort_col,, |
|
| 3 |
country,country,, |
|
| 4 |
continent,continent,, |
|
| 5 |
stateProvince,stateProvince,, |
|
| 6 |
county,county,, |
|
| 7 |
landform,landform,, |
|
| 8 |
locality,locality,, |
|
| 9 |
decimalLatitude,decimalLatitude,, |
|
| 10 |
decimalLongitude,decimalLongitude,, |
|
| 11 |
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,, |
|
| 12 |
coordinateUncertaintyInMeters__from_coords,coordinateUncertaintyInMeters__from_coords,, |
|
| 13 |
coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters__from_fuzzing,, |
|
| 14 |
accessRights,accessRights,, |
|
| 15 |
accessRights_verbatim,accessRights_verbatim,, |
|
| 16 |
projectID,projectID,, |
|
| 17 |
locationID,locationID,, |
|
| 18 |
locationName,locationName,, |
|
| 19 |
parentLocationID,parentLocationID,, |
|
| 20 |
footprintWKT,footprintWKT,, |
|
| 21 |
elevationInMeters,elevationInMeters,, |
|
| 22 |
slopeAspect,slopeAspect,, |
|
| 23 |
minSlopeAspect,minSlopeAspect,, |
|
| 24 |
maxSlopeAspect,maxSlopeAspect,, |
|
| 25 |
slopeGradient,slopeGradient,, |
|
| 26 |
minSlopeGradient,minSlopeGradient,, |
|
| 27 |
maxSlopeGradient,maxSlopeGradient,, |
|
| 28 |
plotArea_m2,plotArea_m2,, |
|
| 29 |
eventID,eventID,, |
|
| 30 |
authorEventCode,authorEventCode,, |
|
| 31 |
startDate,startDate,, |
|
| 32 |
endDate,endDate,, |
|
| 33 |
samplingProtocol,samplingProtocol,, |
|
| 34 |
organic_percent,organic_percent,, |
|
| 35 |
texture,texture,, |
|
| 36 |
sand_percent,sand_percent,, |
|
| 37 |
silt_percent,silt_percent,, |
|
| 38 |
clay_percent,clay_percent,, |
|
| 39 |
ph,ph,, |
|
| 40 |
cationExchangeCapacity_cmol_kg,cationExchangeCapacity_cmol_kg,, |
|
| 41 |
baseSaturation_percent,baseSaturation_percent,, |
|
| 42 |
emb_soilobs,emb_soilobs,, |
|
| 43 |
stratum__name,stratum__name,, |
|
| 44 |
*stratum_id,*stratum_id,, |
|
| 45 |
*stratumtype_id,*stratumtype_id,, |
|
| 46 |
collectorNumber,collectorNumber,, |
|
| 47 |
dateCollected,dateCollected,, |
|
| 48 |
originalScientificName,originalScientificName,, |
|
| 49 |
originalTaxonName,originalTaxonName,, |
|
| 50 |
originalVernacularName,originalVernacularName,, |
|
| 51 |
scientificName_verbatim,scientificName_verbatim,, |
|
| 52 |
dateIdentified,dateIdentified,, |
|
| 53 |
kingdom,kingdom,, |
|
| 54 |
*Subkingdom,*Subkingdom,, |
|
| 55 |
*Superdivision,*Superdivision,, |
|
| 56 |
*Division,*Division,, |
|
| 57 |
*Subdivision,*Subdivision,, |
|
| 58 |
class,class,, |
|
| 59 |
*Subclass,*Subclass,, |
|
| 60 |
order,order,, |
|
| 61 |
family,family,, |
|
| 62 |
genus,genus,, |
|
| 63 |
taxonName,taxonName,, |
|
| 64 |
scientificName,scientificName,, |
|
| 65 |
scientificName__for_nearest_taxon_concept,scientificName__for_nearest_taxon_concept,, |
|
| 66 |
vernacularName,vernacularName,, |
|
| 67 |
occurrenceRemarks,occurrenceRemarks,, |
|
| 68 |
observationGranularity,observationGranularity,, |
|
| 69 |
coverPercent,coverPercent,, |
|
| 70 |
diameterBreastHeight_cm,diameterBreastHeight_cm,, |
|
| 71 |
height_m,height_m,, |
|
| 72 |
individualCount,individualCount,, |
|
| 73 |
taxonOccurrenceID,taxonOccurrenceID,, |
|
| 74 |
taxonOccurrenceID__overall_plot,taxonOccurrenceID__overall_plot,, |
|
| 75 |
identificationID,identificationID,, |
|
| 76 |
identificationType,identificationType,, |
|
| 77 |
identificationQualifier,identificationQualifier,, |
|
| 78 |
identificationVerificationStatus,identificationVerificationStatus,, |
|
| 79 |
aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__taxon_presence,, |
|
| 80 |
aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID__individual_count,, |
|
| 81 |
aggregateOrganismObservationID,aggregateOrganismObservationID,, |
|
| 82 |
individualID,individualID,, |
|
| 83 |
stemID,stemID,, |
|
| 84 |
accessionNumber,accessionNumber,, |
|
| inputs/VegBank/+taxon_observation.**.sample/unmapped_terms.csv | ||
|---|---|---|
| 1 |
sort_col |
|
| 2 |
coordinateUncertaintyInMeters__from_coords |
|
| 3 |
coordinateUncertaintyInMeters__from_fuzzing |
|
| 4 |
accessRights_verbatim |
|
| 5 |
emb_soilobs |
|
| 6 |
*stratum_id |
|
| 7 |
*stratumtype_id |
|
| 8 |
originalVernacularName |
|
| 9 |
scientificName_verbatim |
|
| 10 |
*Subkingdom |
|
| 11 |
*Superdivision |
|
| 12 |
*Division |
|
| 13 |
*Subdivision |
|
| 14 |
*Subclass |
|
| 15 |
scientificName__for_nearest_taxon_concept |
|
| 16 |
vernacularName |
|
| 17 |
taxonOccurrenceID__overall_plot |
|
| 18 |
identificationID |
|
| 19 |
identificationVerificationStatus |
|
| 20 |
aggregateOrganismObservationID__taxon_presence |
|
| 21 |
aggregateOrganismObservationID__individual_count |
|
| inputs/VegBank/+taxon_observation.**.sample/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>VegBank.new</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode> |
|
| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode> |
|
| 12 |
<accesslevel>$accessRights</accesslevel> |
|
| 13 |
<area_m2>$plotArea_m2</area_m2> |
|
| 14 |
<elevation_m>$elevationInMeters</elevation_m> |
|
| 15 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 16 |
<landform>$landform</landform> |
|
| 17 |
<locationevent> |
|
| 18 |
<method_id><method><name>$samplingProtocol</name></method></method_id> |
|
| 19 |
<project_id><project><sourceaccessioncode>$projectID</sourceaccessioncode></project></project_id> |
|
| 20 |
<authoreventcode>$authorEventCode</authoreventcode> |
|
| 21 |
<sourceaccessioncode>$eventID</sourceaccessioncode> |
|
| 22 |
<locationevent fkey="parent_id"> |
|
| 23 |
<stratum_id><stratum><stratumname>$stratum__name</stratumname></stratum></stratum_id> |
|
| 24 |
<sourceaccessioncode>$eventID</sourceaccessioncode> |
|
| 25 |
<taxonoccurrence> |
|
| 26 |
<aggregateoccurrence> |
|
| 27 |
<collectiondate>$dateCollected</collectiondate> |
|
| 28 |
<count>$individualCount</count> |
|
| 29 |
<cover_fraction><_percent_to_fraction><value>$coverPercent</value></_percent_to_fraction></cover_fraction> |
|
| 30 |
<notes>$occurrenceRemarks</notes> |
|
| 31 |
<plantobservation> |
|
| 32 |
<authorplantcode>$collectorNumber</authorplantcode> |
|
| 33 |
<sourceaccessioncode>$individualID</sourceaccessioncode> |
|
| 34 |
<specimenreplicate> |
|
| 35 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc> |
|
| 36 |
<collectionnumber>$collectorNumber</collectionnumber> |
|
| 37 |
</specimenreplicate> |
|
| 38 |
<stemobservation> |
|
| 39 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m> |
|
| 40 |
<height_m>$height_m</height_m> |
|
| 41 |
<sourceaccessioncode>$stemID</sourceaccessioncode> |
|
| 42 |
</stemobservation> |
|
| 43 |
</plantobservation> |
|
| 44 |
<sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode> |
|
| 45 |
</aggregateoccurrence> |
|
| 46 |
<authortaxoncode>$collectorNumber</authortaxoncode> |
|
| 47 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode> |
|
| 48 |
<taxondetermination> |
|
| 49 |
<taxonverbatim_id> |
|
| 50 |
<taxonverbatim> |
|
| 51 |
<taxonlabel_id> |
|
| 52 |
<taxonlabel> |
|
| 53 |
<parent_id> |
|
| 54 |
<taxonlabel> |
|
| 55 |
<parent_id> |
|
| 56 |
<taxonlabel> |
|
| 57 |
<rank>cultivar</rank> |
|
| 58 |
<parent_id> |
|
| 59 |
<taxonlabel> |
|
| 60 |
<rank>forma</rank> |
|
| 61 |
<parent_id> |
|
| 62 |
<taxonlabel> |
|
| 63 |
<rank>variety</rank> |
|
| 64 |
<parent_id> |
|
| 65 |
<taxonlabel> |
|
| 66 |
<rank>subspecies</rank> |
|
| 67 |
<parent_id> |
|
| 68 |
<taxonlabel> |
|
| 69 |
<rank>species</rank> |
|
| 70 |
<parent_id> |
|
| 71 |
<taxonlabel> |
|
| 72 |
<rank>genus</rank> |
|
| 73 |
<taxonepithet>$genus</taxonepithet> |
|
| 74 |
<parent_id> |
|
| 75 |
<taxonlabel> |
|
| 76 |
<rank>family</rank> |
|
| 77 |
<taxonepithet>$family</taxonepithet> |
|
| 78 |
<parent_id> |
|
| 79 |
<taxonlabel> |
|
| 80 |
<rank>order</rank> |
|
| 81 |
<taxonepithet>$order</taxonepithet> |
|
| 82 |
<parent_id> |
|
| 83 |
<taxonlabel> |
|
| 84 |
<rank>class</rank> |
|
| 85 |
<taxonepithet>$class</taxonepithet> |
|
| 86 |
<parent_id> |
|
| 87 |
<taxonlabel> |
|
| 88 |
<rank>phylum</rank> |
|
| 89 |
<parent_id> |
|
| 90 |
<taxonlabel> |
|
| 91 |
<rank>kingdom</rank> |
|
| 92 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 93 |
</taxonlabel> |
|
| 94 |
</parent_id> |
|
| 95 |
</taxonlabel> |
|
| 96 |
</parent_id> |
|
| 97 |
</taxonlabel> |
|
| 98 |
</parent_id> |
|
| 99 |
</taxonlabel> |
|
| 100 |
</parent_id> |
|
| 101 |
</taxonlabel> |
|
| 102 |
</parent_id> |
|
| 103 |
</taxonlabel> |
|
| 104 |
</parent_id> |
|
| 105 |
</taxonlabel> |
|
| 106 |
</parent_id> |
|
| 107 |
</taxonlabel> |
|
| 108 |
</parent_id> |
|
| 109 |
</taxonlabel> |
|
| 110 |
</parent_id> |
|
| 111 |
</taxonlabel> |
|
| 112 |
</parent_id> |
|
| 113 |
</taxonlabel> |
|
| 114 |
</parent_id> |
|
| 115 |
</taxonlabel> |
|
| 116 |
</parent_id> |
|
| 117 |
<taxonomicname> |
|
| 118 |
<_merge_prefix> |
|
| 119 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 120 |
<value> |
|
| 121 |
<_alt> |
|
| 122 |
<1>$scientificName</1> |
|
| 123 |
<2> |
|
| 124 |
<_alt> |
|
| 125 |
<1>$taxonName</1> |
|
| 126 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 127 |
</_alt> |
|
| 128 |
</2> |
|
| 129 |
</_alt> |
|
| 130 |
</value> |
|
| 131 |
</_merge_prefix> |
|
| 132 |
</taxonomicname> |
|
| 133 |
</taxonlabel> |
|
| 134 |
</taxonlabel_id> |
|
| 135 |
<family>$family</family> |
|
| 136 |
<genus>$genus</genus> |
|
| 137 |
<taxonname>$taxonName</taxonname> |
|
| 138 |
<taxonomicname>$scientificName</taxonomicname> |
|
| 139 |
</taxonverbatim> |
|
| 140 |
</taxonverbatim_id> |
|
| 141 |
<determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate> |
|
| 142 |
<determinationtype>$identificationType</determinationtype> |
|
| 143 |
<taxonfit>$identificationQualifier</taxonfit> |
|
| 144 |
</taxondetermination> |
|
| 145 |
<taxondetermination> |
|
| 146 |
<isoriginal>true</isoriginal> |
|
| 147 |
<taxonverbatim_id> |
|
| 148 |
<taxonverbatim> |
|
| 149 |
<taxonname>$originalTaxonName</taxonname> |
|
| 150 |
<taxonomicname>$originalScientificName</taxonomicname> |
|
| 151 |
</taxonverbatim> |
|
| 152 |
</taxonverbatim_id> |
|
| 153 |
</taxondetermination> |
|
| 154 |
</taxonoccurrence> |
|
| 155 |
</locationevent> |
|
| 156 |
<obsenddate>$endDate</obsenddate> |
|
| 157 |
<obsstartdate>$startDate</obsstartdate> |
|
| 158 |
<soilsample> |
|
| 159 |
<basesaturation_fraction><_percent_to_fraction><value>$baseSaturation_percent</value></_percent_to_fraction></basesaturation_fraction> |
|
| 160 |
<cationexchangecapacity_cmol_kg>$cationExchangeCapacity_cmol_kg</cationexchangecapacity_cmol_kg> |
|
| 161 |
<clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction> |
|
| 162 |
<organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction> |
|
| 163 |
<ph>$ph</ph> |
|
| 164 |
<sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction> |
|
| 165 |
<silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction> |
|
| 166 |
<texture>$texture</texture> |
|
| 167 |
</soilsample> |
|
| 168 |
</locationevent> |
|
| 169 |
<locationnarrative>$locality</locationnarrative> |
|
| 170 |
<locationplace> |
|
| 171 |
<place_id> |
|
| 172 |
<place> |
|
| 173 |
<coordinates_id> |
|
| 174 |
<coordinates> |
|
| 175 |
<coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m> |
|
| 176 |
<footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc> |
|
| 177 |
<latitude_deg> |
|
| 178 |
<_nullIf> |
|
| 179 |
<null>0</null> |
|
| 180 |
<type>float</type> |
|
| 181 |
<value>$decimalLatitude</value> |
|
| 182 |
</_nullIf> |
|
| 183 |
</latitude_deg> |
|
| 184 |
<longitude_deg> |
|
| 185 |
<_nullIf> |
|
| 186 |
<null>0</null> |
|
| 187 |
<type>float</type> |
|
| 188 |
<value>$decimalLongitude</value> |
|
| 189 |
</_nullIf> |
|
| 190 |
</longitude_deg> |
|
| 191 |
</coordinates> |
|
| 192 |
</coordinates_id> |
|
| 193 |
<continent>$continent</continent> |
|
| 194 |
<country>$country</country> |
|
| 195 |
<county>$county</county> |
|
| 196 |
<matched_place_id> |
|
| 197 |
<place> |
|
| 198 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 199 |
<coordinates_id> |
|
| 200 |
<coordinates> |
|
| 201 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 202 |
<latitude_deg> |
|
| 203 |
<_nullIf> |
|
| 204 |
<null>0</null> |
|
| 205 |
<type>float</type> |
|
| 206 |
<value>$decimalLatitude</value> |
|
| 207 |
</_nullIf> |
|
| 208 |
</latitude_deg> |
|
| 209 |
<longitude_deg> |
|
| 210 |
<_nullIf> |
|
| 211 |
<null>0</null> |
|
| 212 |
<type>float</type> |
|
| 213 |
<value>$decimalLongitude</value> |
|
| 214 |
</_nullIf> |
|
| 215 |
</longitude_deg> |
|
| 216 |
</coordinates> |
|
| 217 |
</coordinates_id> |
|
| 218 |
<country>$country</country> |
|
| 219 |
<county>$county</county> |
|
| 220 |
<stateprovince>$stateProvince</stateprovince> |
|
| 221 |
</place> |
|
| 222 |
</matched_place_id> |
|
| 223 |
<stateprovince>$stateProvince</stateprovince> |
|
| 224 |
</place> |
|
| 225 |
</place_id> |
|
| 226 |
</locationplace> |
|
| 227 |
<parent_id><location><sourceaccessioncode>$parentLocationID</sourceaccessioncode></location></parent_id> |
|
| 228 |
<slopeaspect_deg> |
|
| 229 |
<_alt> |
|
| 230 |
<1><_compass><value>$slopeAspect</value></_compass></1> |
|
| 231 |
<2> |
|
| 232 |
<_avg> |
|
| 233 |
<1>$minSlopeAspect</1> |
|
| 234 |
<2>$maxSlopeAspect</2> |
|
| 235 |
</_avg> |
|
| 236 |
</2> |
|
| 237 |
</_alt> |
|
| 238 |
</slopeaspect_deg> |
|
| 239 |
<slopegradient_fraction> |
|
| 240 |
<_alt> |
|
| 241 |
<1>$slopeGradient</1> |
|
| 242 |
<2> |
|
| 243 |
<_avg> |
|
| 244 |
<1>$minSlopeGradient</1> |
|
| 245 |
<2>$maxSlopeGradient</2> |
|
| 246 |
</_avg> |
|
| 247 |
</2> |
|
| 248 |
</_alt> |
|
| 249 |
</slopegradient_fraction> |
|
| 250 |
</location> |
|
| 251 |
</path> |
|
| 252 |
</_simplifyPath> |
|
| 253 |
</path> |
|
| 254 |
</_setDefault> |
|
| 255 |
</VegBIEN> |
|
| 256 |
Inserted 30 new rows into database |
|
| inputs/VegBank/+taxon_observation.**.sample/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/VegBank/+taxon_observation.**.sample/VegBIEN.csv | ||
|---|---|---|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 0 | 2 | |
Also available in: Unified diff
bugfix: inputs/VegBank/taxon_observation.**.sample/: renamed to +taxon_observation.**.sample so that the -expansion of taxon_observation.* doesn't add taxon_observation.**.sample (which causes it to attempt to install taxon_observation.**.sample before taxon_observation.** is installed)