Revision 6558
Added by Aaron Marcuse-Kubitza almost 12 years ago
inputs/NVS/Organism/new_terms.csv | ||
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1 |
Project Abbreviation,projectName,, |
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2 |
Plot,locationName,, |
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3 |
Taxon Growth Form,growthForm,, |
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4 |
Taxon Obs Note,taxonRemarks,, |
inputs/NVS/Organism/unmapped_terms.csv | ||
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1 |
*Method Name |
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2 |
*Species Code |
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3 |
*Verbatim Code |
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4 |
*Taxon Bio Status |
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5 |
*Taxon Palatibility |
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6 |
*Tier |
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7 |
*Tier Description |
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8 |
*Tier ID |
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9 |
*Category |
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10 |
*Category Description |
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11 |
*Parent Plot Obs ID |
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12 |
*Sample Method ID |
inputs/NVS/Organism/map.csv | ||
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1 |
NVS,VegCore,Filter,Comments |
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2 |
Project Abbreviation,projectName,, |
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3 |
Plot,locationName,, |
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4 |
Sub Plot,subplot,, |
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5 |
Method Name,*Method Name,, |
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6 |
Species Code,*Species Code,, |
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7 |
Species Name,specificEpithet,, |
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8 |
Verbatim Code,*Verbatim Code,, |
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9 |
Taxon Bio Status,*Taxon Bio Status,, |
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10 |
Taxon Palatibility,*Taxon Palatibility,, |
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11 |
Taxon Growth Form,growthForm,, |
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12 |
Tier,*Tier,, |
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13 |
Tier Description,*Tier Description,, |
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14 |
Tier ID,*Tier ID,, |
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15 |
Category,*Category,, |
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16 |
Category Description,*Category Description,, |
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17 |
Taxon Obs Note,taxonRemarks,, |
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18 |
Parent Plot Obs ID,*Parent Plot Obs ID,, |
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19 |
Sample Method ID,*Sample Method ID,, |
inputs/NVS/Organism/test.xml.ref | ||
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1 |
Put template: |
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2 |
<VegBIEN> |
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3 |
<_setDefault id="-1"> |
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4 |
<source_id><source><shortname>NVS</shortname></source></source_id> |
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5 |
<path> |
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6 |
<_simplifyPath> |
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7 |
<next>parent_id</next> |
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8 |
<path> |
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9 |
<location> |
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10 |
<parent_id><location><authorlocationcode>$Plot</authorlocationcode></location></parent_id> |
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11 |
<authorlocationcode>$Sub Plot</authorlocationcode> |
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12 |
<locationevent> |
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13 |
<project_id><project><projectname>$Project Abbreviation</projectname></project></project_id> |
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14 |
<taxonoccurrence> |
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15 |
<growthform>$Taxon Growth Form</growthform> |
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16 |
<taxondetermination> |
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17 |
<taxonverbatim_id> |
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18 |
<taxonverbatim> |
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19 |
<taxonlabel_id> |
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20 |
<taxonlabel> |
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21 |
<matched_label_id> |
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22 |
<taxonlabel> |
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23 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
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24 |
<taxonomicname>$Species Name</taxonomicname> |
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25 |
</taxonlabel> |
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26 |
</matched_label_id> |
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27 |
<parent_id> |
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28 |
<taxonlabel> |
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29 |
<parent_id> |
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30 |
<taxonlabel> |
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31 |
<rank>cultivar</rank> |
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32 |
<parent_id> |
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33 |
<taxonlabel> |
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34 |
<rank>forma</rank> |
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35 |
<parent_id> |
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36 |
<taxonlabel> |
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37 |
<rank>variety</rank> |
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38 |
<parent_id> |
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39 |
<taxonlabel> |
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40 |
<rank>subspecies</rank> |
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41 |
<parent_id> |
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42 |
<taxonlabel> |
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<rank>species</rank> |
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44 |
<taxonepithet>$Species Name</taxonepithet> |
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45 |
</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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50 |
</parent_id> |
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</taxonlabel> |
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52 |
</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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78 |
</VegBIEN> |
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79 |
Inserted 17 new rows into database |
inputs/NVS/Organism/VegBIEN.csv | ||
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1 |
NVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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2 |
Sub Plot,"/location/_if[@name=""if subplot""]/cond/_exists", |
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3 |
Plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
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4 |
Plot,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
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5 |
Sub Plot,/location/authorlocationcode, |
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6 |
Project Abbreviation,/location/locationevent/*_id/project/projectname, |
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7 |
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
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8 |
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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10 |
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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11 |
Plot,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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12 |
Taxon Growth Form,/location/locationevent/taxonoccurrence/growthform, |
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13 |
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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14 |
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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15 |
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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16 |
Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
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17 |
Taxon Obs Note,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes, |
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18 |
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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20 |
Sub Plot,/location/sourceaccessioncode/_join/2, |
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21 |
Category,,** No join mapping for *Category ** |
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22 |
Category Description,,** No join mapping for *Category Description ** |
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23 |
Method Name,,** No join mapping for *Method Name ** |
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24 |
Parent Plot Obs ID,,** No join mapping for *Parent Plot Obs ID ** |
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25 |
Sample Method ID,,** No join mapping for *Sample Method ID ** |
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26 |
Species Code,,** No join mapping for *Species Code ** |
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27 |
Taxon Bio Status,,** No join mapping for *Taxon Bio Status ** |
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28 |
Taxon Palatibility,,** No join mapping for *Taxon Palatibility ** |
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29 |
Tier,,** No join mapping for *Tier ** |
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30 |
Tier Description,,** No join mapping for *Tier Description ** |
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31 |
Tier ID,,** No join mapping for *Tier ID ** |
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32 |
Verbatim Code,,** No join mapping for *Verbatim Code ** |
inputs/NVS/AggregateOccurrence/map.csv | ||
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1 |
NVS,VegCore,Filter,Comments |
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2 |
Project Abbreviation,projectName,, |
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3 |
Plot,locationName,, |
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4 |
Sub Plot,subplot,, |
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5 |
Method Name,*Method Name,, |
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6 |
Species Code,*Species Code,, |
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7 |
Species Name,specificEpithet,, |
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8 |
Verbatim Code,*Verbatim Code,, |
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9 |
Taxon Bio Status,*Taxon Bio Status,, |
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10 |
Taxon Palatibility,*Taxon Palatibility,, |
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11 |
Taxon Growth Form,growthForm,, |
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12 |
Tier,*Tier,, |
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13 |
Tier Description,*Tier Description,, |
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14 |
Tier ID,*Tier ID,, |
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15 |
Category,*Category,, |
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16 |
Category Description,*Category Description,, |
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17 |
Taxon Obs Note,taxonRemarks,, |
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18 |
Parent Plot Obs ID,*Parent Plot Obs ID,, |
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19 |
Sample Method ID,*Sample Method ID,, |
inputs/NVS/AggregateOccurrence/VegBIEN.csv | ||
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1 |
NVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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2 |
Sub Plot,"/location/_if[@name=""if subplot""]/cond/_exists", |
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3 |
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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5 |
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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10 |
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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12 |
Taxon Growth Form,/location/locationevent/taxonoccurrence/growthform, |
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13 |
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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14 |
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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15 |
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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16 |
Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
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17 |
Taxon Obs Note,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes, |
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18 |
Sub Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/cond/_exists", |
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19 |
Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
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20 |
Sub Plot,/location/sourceaccessioncode/_join/2, |
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21 |
Category,,** No join mapping for *Category ** |
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22 |
Category Description,,** No join mapping for *Category Description ** |
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23 |
Method Name,,** No join mapping for *Method Name ** |
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24 |
Parent Plot Obs ID,,** No join mapping for *Parent Plot Obs ID ** |
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25 |
Sample Method ID,,** No join mapping for *Sample Method ID ** |
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26 |
Species Code,,** No join mapping for *Species Code ** |
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27 |
Taxon Bio Status,,** No join mapping for *Taxon Bio Status ** |
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28 |
Taxon Palatibility,,** No join mapping for *Taxon Palatibility ** |
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29 |
Tier,,** No join mapping for *Tier ** |
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30 |
Tier Description,,** No join mapping for *Tier Description ** |
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31 |
Tier ID,,** No join mapping for *Tier ID ** |
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32 |
Verbatim Code,,** No join mapping for *Verbatim Code ** |
inputs/NVS/AggregateOccurrence/test.xml.ref | ||
---|---|---|
1 |
Put template: |
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2 |
<VegBIEN> |
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3 |
<_setDefault id="-1"> |
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4 |
<source_id><source><shortname>NVS</shortname></source></source_id> |
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5 |
<path> |
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6 |
<_simplifyPath> |
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7 |
<next>parent_id</next> |
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8 |
<path> |
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9 |
<location> |
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10 |
<parent_id><location><authorlocationcode>$Plot</authorlocationcode></location></parent_id> |
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11 |
<authorlocationcode>$Sub Plot</authorlocationcode> |
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12 |
<locationevent> |
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13 |
<project_id><project><projectname>$Project Abbreviation</projectname></project></project_id> |
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14 |
<taxonoccurrence> |
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15 |
<growthform>$Taxon Growth Form</growthform> |
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16 |
<taxondetermination> |
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17 |
<taxonverbatim_id> |
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18 |
<taxonverbatim> |
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19 |
<taxonlabel_id> |
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20 |
<taxonlabel> |
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21 |
<matched_label_id> |
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22 |
<taxonlabel> |
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23 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
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24 |
<taxonomicname>$Species Name</taxonomicname> |
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25 |
</taxonlabel> |
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26 |
</matched_label_id> |
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27 |
<parent_id> |
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28 |
<taxonlabel> |
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29 |
<parent_id> |
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30 |
<taxonlabel> |
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31 |
<rank>cultivar</rank> |
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32 |
<parent_id> |
|
33 |
<taxonlabel> |
|
34 |
<rank>forma</rank> |
|
35 |
<parent_id> |
|
36 |
<taxonlabel> |
|
37 |
<rank>variety</rank> |
|
38 |
<parent_id> |
|
39 |
<taxonlabel> |
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40 |
<rank>subspecies</rank> |
|
41 |
<parent_id> |
|
42 |
<taxonlabel> |
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43 |
<rank>species</rank> |
|
44 |
<taxonepithet>$Species Name</taxonepithet> |
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45 |
</taxonlabel> |
|
46 |
</parent_id> |
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47 |
</taxonlabel> |
|
48 |
</parent_id> |
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49 |
</taxonlabel> |
|
50 |
</parent_id> |
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51 |
</taxonlabel> |
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52 |
</parent_id> |
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53 |
</taxonlabel> |
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54 |
</parent_id> |
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55 |
</taxonlabel> |
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56 |
</parent_id> |
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57 |
<taxonomicname>$Species Name</taxonomicname> |
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58 |
</taxonlabel> |
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59 |
</taxonlabel_id> |
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60 |
<specific_epithet>$Species Name</specific_epithet> |
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61 |
</taxonverbatim> |
|
62 |
</taxonverbatim_id> |
|
63 |
<notes>$Taxon Obs Note</notes> |
|
64 |
</taxondetermination> |
|
65 |
</taxonoccurrence> |
|
66 |
</locationevent> |
|
67 |
<sourceaccessioncode> |
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68 |
<_join> |
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69 |
<1>$Plot</1> |
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70 |
<2>$Sub Plot</2> |
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71 |
</_join> |
|
72 |
</sourceaccessioncode> |
|
73 |
</location> |
|
74 |
</path> |
|
75 |
</_simplifyPath> |
|
76 |
</path> |
|
77 |
</_setDefault> |
|
78 |
</VegBIEN> |
|
79 |
Inserted 17 new rows into database |
inputs/NVS/AggregateOccurrence/new_terms.csv | ||
---|---|---|
1 |
Project Abbreviation,projectName,, |
|
2 |
Plot,locationName,, |
|
3 |
Taxon Growth Form,growthForm,, |
|
4 |
Taxon Obs Note,taxonRemarks,, |
inputs/NVS/AggregateOccurrence/unmapped_terms.csv | ||
---|---|---|
1 |
*Method Name |
|
2 |
*Species Code |
|
3 |
*Verbatim Code |
|
4 |
*Taxon Bio Status |
|
5 |
*Taxon Palatibility |
|
6 |
*Tier |
|
7 |
*Tier Description |
|
8 |
*Tier ID |
|
9 |
*Category |
|
10 |
*Category Description |
|
11 |
*Parent Plot Obs ID |
|
12 |
*Sample Method ID |
Also available in: Unified diff
inputs/NVS/: Renamed Organism to AggregateOccurrence because this actually contains aggregated samplings