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Revision 6549

Added inputs/NVS/Organism/

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inputs/NVS/Organism/map.csv
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NVS,VegCore,Filter,Comments
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Project Abbreviation,projectName,,
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Plot,locationName,,
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Sub Plot,subplot,,
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Method Name,*Method Name,,
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Species Code,*Species Code,,
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Species Name,specificEpithet,,
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Verbatim Code,*Verbatim Code,,
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Taxon Bio Status,*Taxon Bio Status,,
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Taxon Palatibility,*Taxon Palatibility,,
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Taxon Growth Form,growthForm,,
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Tier,*Tier,,
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Tier Description,*Tier Description,,
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Tier ID,*Tier ID,,
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Category,*Category,,
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Category Description,*Category Description,,
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Taxon Obs Note,taxonRemarks,,
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Parent Plot Obs ID,*Parent Plot Obs ID,,
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Sample Method ID,*Sample Method ID,,
inputs/NVS/Organism/VegBIEN.csv
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NVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
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Sub Plot,"/location/_if[@name=""if subplot""]/cond/_exists",
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Plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
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Plot,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
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Sub Plot,/location/authorlocationcode,
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Project Abbreviation,/location/locationevent/*_id/project/projectname,
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Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
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Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",
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Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
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Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",
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Plot,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
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Taxon Growth Form,/location/locationevent/taxonoccurrence/growthform,
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Species Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
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Species Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
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Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
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Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
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Taxon Obs Note,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes,
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Sub Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/cond/_exists",
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Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2",
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Sub Plot,/location/sourceaccessioncode/_join/2,
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Category,,** No join mapping for *Category ** 
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Category Description,,** No join mapping for *Category Description ** 
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Method Name,,** No join mapping for *Method Name ** 
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Parent Plot Obs ID,,** No join mapping for *Parent Plot Obs ID ** 
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Sample Method ID,,** No join mapping for *Sample Method ID ** 
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Species Code,,** No join mapping for *Species Code ** 
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Taxon Bio Status,,** No join mapping for *Taxon Bio Status ** 
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Taxon Palatibility,,** No join mapping for *Taxon Palatibility ** 
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Tier,,** No join mapping for *Tier ** 
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Tier Description,,** No join mapping for *Tier Description ** 
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Tier ID,,** No join mapping for *Tier ID ** 
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Verbatim Code,,** No join mapping for *Verbatim Code ** 
inputs/NVS/Organism/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>NVS</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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                        <parent_id><location><authorlocationcode>$Plot</authorlocationcode></location></parent_id>
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                        <authorlocationcode>$Sub Plot</authorlocationcode>
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                        <locationevent>
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                            <project_id><project><projectname>$Project Abbreviation</projectname></project></project_id>
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                            <taxonoccurrence>
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                                <growthform>$Taxon Growth Form</growthform>
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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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                                                    <matched_label_id>
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                                                        <taxonlabel>
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                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
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                                                            <taxonomicname>$Species Name</taxonomicname>
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                                                        </taxonlabel>
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                                                    </matched_label_id>
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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>$Species Name</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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                                                    <taxonomicname>$Species Name</taxonomicname>
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                                                </taxonlabel>
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                                            </taxonlabel_id>
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                                            <specific_epithet>$Species Name</specific_epithet>
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                                        </taxonverbatim>
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                                    </taxonverbatim_id>
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                                    <notes>$Taxon Obs Note</notes>
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                                </taxondetermination>
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                            </taxonoccurrence>
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                        </locationevent>
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                        <sourceaccessioncode>
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                            <_join>
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                                <1>$Plot</1>
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                                <2>$Sub Plot</2>
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                            </_join>
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                        </sourceaccessioncode>
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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 17 new rows into database
inputs/NVS/Organism/new_terms.csv
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Project Abbreviation,projectName,,
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Plot,locationName,,
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Taxon Growth Form,growthForm,,
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Taxon Obs Note,taxonRemarks,,
inputs/NVS/Organism/unmapped_terms.csv
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*Method Name
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*Species Code
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*Verbatim Code
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*Taxon Bio Status
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*Taxon Palatibility
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*Tier
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*Tier Description
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*Tier ID
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*Category
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*Category Description
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*Parent Plot Obs ID
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*Sample Method ID

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