Revision 14786
Added by Aaron Marcuse-Kubitza over 9 years ago
| trunk/inputs/Cyrille_traits/Source/header.csv | ||
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row_num |
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| trunk/inputs/Cyrille_traits/Source/data.csv | ||
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| trunk/inputs/Cyrille_traits/Source/run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| trunk/inputs/Cyrille_traits/Source/map.csv | ||
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Cyrille_traits,VegCore,Filter,Comments |
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row_num,*row_num,, |
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:primary database,sourceType,, |
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:specimen,observationGranularity,, |
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| trunk/inputs/Cyrille_traits/Source/test.xml.ref | ||
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<!--put template--> |
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<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>Cyrille_traits.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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<source> |
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<shortname>Cyrille_traits.new</shortname> |
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<observationtype>specimen</observationtype> |
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<sourcetype>primary database</sourcetype> |
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</source> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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Inserted 1 new rows into database |
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| trunk/inputs/Cyrille_traits/Source/VegBIEN.csv | ||
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link ../../../mappings/VegCore-VegBIEN.csv |
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| trunk/inputs/Cyrille_traits/Source/unmapped_terms.csv | ||
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*row_num |
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| trunk/inputs/Cyrille_traits/import_order.txt | ||
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Source |
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trait_observation |
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| trunk/inputs/Cyrille_traits/run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
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| trunk/inputs/Cyrille_traits/table.run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/table.run
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| trunk/inputs/Cyrille_traits/Makefile | ||
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include ../input.Makefile |
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| trunk/inputs/Cyrille_traits/trait_observation/header.csv | ||
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row_num,Family,Genus,Species,Intraspecific rank,var./subsp.,Taxon,Authority,Trait name,Trait value,Unit,Method,Region,Country,State/province,Lower political,Locality description,latitude,Longitude,Elevation,Source,URL source,Source citation,Source Id,Visiting date,Reference number,Access,Project PI,Project PI contact,Observation,Authorship,Authorship contact |
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| trunk/inputs/Cyrille_traits/trait_observation/run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| trunk/inputs/Cyrille_traits/trait_observation/header.txt | ||
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Family,Genus,Species,Intraspecific rank,var./subsp.,Taxon,Authority,Trait name,Trait value,Unit,Method,Region,Country,State/province,Lower political,Locality description,latitude,Longitude,Elevation,Source,URL source,Source citation,Source Id,Visiting date,Reference number,Access,Project PI,Project PI contact,Observation,Authorship,Authorship contact |
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| trunk/inputs/Cyrille_traits/trait_observation/map.csv | ||
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Cyrille_traits,VegCore,Filter,Comments |
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row_num,dataProviderRecordID,, |
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Family,family,, |
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Genus,genus,, |
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Species,specificEpithet,, |
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Intraspecific rank,infraspecificRank,, |
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var./subsp.,infraspecificEpithet,, |
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Taxon,taxonName,, |
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Authority,scientificNameAuthorship,, |
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Trait name,measurementName,, |
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Trait value,measurementValue,, |
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Unit,measurementUnit,, |
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Method,samplingProtocol,, |
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Region,continent,, |
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Country,country,, |
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State/province,stateProvince,, |
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Lower political,county,, |
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Locality description,locality,, |
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latitude,latitude_DMS,, |
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Longitude,longitude_DMS,, |
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Elevation,verbatimElevation_m,, |
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Source,projectName,,"should also be firstPublisher and dataset, but those aren’t mapped yet" |
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URL source,*URL source,,"should be datasetURL, but that isn’t mapped yet for occurrence records" |
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Source citation,bibliographicCitation,,bibliographicCitation of the dataset |
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Source Id,collectorNumber,, |
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Visiting date,dateCollected,, |
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Reference number,projectID,, |
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Access,accessRights,, |
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Project PI,recordedBy,, |
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Project PI contact,*Project PI contact,, |
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Observation,occurrenceRemarks,,sometimes contains basisOfRecord |
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Authorship,*Authorship,, |
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Authorship contact,*Authorship contact,, |
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| trunk/inputs/Cyrille_traits/trait_observation/test.xml.ref | ||
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<!--put template--> |
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<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>Cyrille_traits.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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<location> |
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<authorlocationcode>$dataProviderRecordID</authorlocationcode> |
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<accesslevel>$accessRights</accesslevel> |
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<elevation_m> |
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<_avg> |
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<1><_rangeStart><value>$verbatimElevation_m</value></_rangeStart></1> |
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<2><_rangeEnd><value>$verbatimElevation_m</value></_rangeEnd></2> |
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</_avg> |
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</elevation_m> |
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<elevationrange_m> |
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<_range> |
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<from><_rangeStart><value>$verbatimElevation_m</value></_rangeStart></from> |
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<to><_rangeEnd><value>$verbatimElevation_m</value></_rangeEnd></to> |
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</_range> |
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</elevationrange_m> |
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<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
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<locationevent> |
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<method_id><method><name>$samplingProtocol</name></method></method_id> |
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<project_id> |
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<project> |
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<projectname>$projectName</projectname> |
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<sourceaccessioncode>$projectID</sourceaccessioncode> |
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</project> |
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</project_id> |
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<locationevent fkey="parent_id"> |
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<taxonoccurrence> |
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<aggregateoccurrence> |
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<collectiondate>$dateCollected</collectiondate> |
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<notes>$occurrenceRemarks</notes> |
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<plantobservation> |
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<authorplantcode>$collectorNumber</authorplantcode> |
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<specimenreplicate> |
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<collectionnumber>$collectorNumber</collectionnumber> |
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<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode> |
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</specimenreplicate> |
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</plantobservation> |
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</aggregateoccurrence> |
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<collector_id><party><fullname>$recordedBy</fullname></party></collector_id> |
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<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode> |
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<taxondetermination> |
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<taxonverbatim_id> |
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<taxonverbatim> |
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<taxonlabel_id> |
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<taxonlabel> |
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<parent_id> |
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<taxonlabel> |
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<parent_id> |
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<taxonlabel> |
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<rank>cultivar</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>forma</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>variety</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>subspecies</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>species</rank> |
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<taxonepithet>$specificEpithet</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>genus</rank> |
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<taxonepithet>$genus</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>family</rank> |
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<taxonepithet>$family</taxonepithet> |
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</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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</parent_id> |
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</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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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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<taxonepithet>$infraspecificEpithet</taxonepithet> |
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</taxonlabel> |
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</parent_id> |
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<taxonomicname> |
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<_merge_prefix> |
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<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
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<value> |
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<_join_words> |
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<1> |
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<_alt> |
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<1>$taxonName</1> |
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<2> |
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<_join_words> |
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<2><_filter_genus><value>$genus</value></_filter_genus></2> |
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<3>$specificEpithet</3> |
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<5>$infraspecificEpithet</5> |
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</_join_words> |
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</2> |
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</_alt> |
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</1> |
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<2>$scientificNameAuthorship</2> |
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</_join_words> |
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</value> |
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</_merge_prefix> |
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</taxonomicname> |
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</taxonlabel> |
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</taxonlabel_id> |
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<author>$scientificNameAuthorship</author> |
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<family>$family</family> |
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<genus>$genus</genus> |
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<specific_epithet>$specificEpithet</specific_epithet> |
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<taxonname>$taxonName</taxonname> |
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</taxonverbatim> |
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</taxonverbatim_id> |
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</taxondetermination> |
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<trait> |
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<name>$measurementName</name> |
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<units>$measurementUnit</units> |
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<value>$measurementValue</value> |
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</trait> |
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</taxonoccurrence> |
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</locationevent> |
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</locationevent> |
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<locationnarrative>$locality</locationnarrative> |
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<locationplace> |
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<place_id> |
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<place> |
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<coordinates_id> |
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<coordinates> |
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<latitude_deg><_dms_to_dd><value>$latitude_DMS</value></_dms_to_dd></latitude_deg> |
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<longitude_deg><_dms_to_dd><value>$longitude_DMS</value></_dms_to_dd></longitude_deg> |
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<verbatimlatitude>$latitude_DMS</verbatimlatitude> |
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<verbatimlongitude>$longitude_DMS</verbatimlongitude> |
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</coordinates> |
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</coordinates_id> |
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<continent>$continent</continent> |
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<country>$country</country> |
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<county>$county</county> |
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<matched_place_id> |
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<place> |
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<source_id><source><shortname>geoscrub</shortname></source></source_id> |
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<coordinates_id> |
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<coordinates> |
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<source_id><source><shortname>geoscrub</shortname></source></source_id> |
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<latitude_deg><_dms_to_dd><value>$latitude_DMS</value></_dms_to_dd></latitude_deg> |
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<longitude_deg><_dms_to_dd><value>$longitude_DMS</value></_dms_to_dd></longitude_deg> |
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</coordinates> |
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</coordinates_id> |
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<country>$country</country> |
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<county>$county</county> |
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<stateprovince>$stateProvince</stateprovince> |
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</place> |
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</matched_place_id> |
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<stateprovince>$stateProvince</stateprovince> |
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</place> |
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</place_id> |
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</locationplace> |
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<verbatimelevation>$verbatimElevation_m</verbatimelevation> |
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</location> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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Inserted 33 new rows into database |
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| trunk/inputs/Cyrille_traits/trait_observation/VegBIEN.csv | ||
|---|---|---|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
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| 0 | 2 | |
| trunk/inputs/Cyrille_traits/trait_observation/new_terms.csv | ||
|---|---|---|
| 1 |
row_num,dataProviderRecordID,, |
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| 2 |
Intraspecific rank,infraspecificRank,, |
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| 3 |
var./subsp.,infraspecificEpithet,, |
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| 4 |
Taxon,taxonName,, |
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| 5 |
Authority,scientificNameAuthorship,, |
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| 6 |
Region,continent,, |
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| 7 |
Lower political,county,, |
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| 8 |
Locality description,locality,, |
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| 9 |
Source citation,bibliographicCitation,,bibliographicCitation of the dataset |
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| 10 |
Source Id,collectorNumber,, |
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| 11 |
Visiting date,dateCollected,, |
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| 12 |
Reference number,projectID,, |
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| 13 |
Access,accessRights,, |
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| 14 |
Project PI,recordedBy,, |
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| 15 |
Observation,occurrenceRemarks,,sometimes contains basisOfRecord |
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| trunk/inputs/Cyrille_traits/trait_observation/unmapped_terms.csv | ||
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| 1 |
infraspecificRank |
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| 2 |
*URL source |
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| 3 |
bibliographicCitation |
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*Project PI contact |
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*Authorship |
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| 6 |
*Authorship contact |
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Also available in: Unified diff
added inputs/Cyrille_traits/