Revision 4879
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/TEAM/VL/map.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegCore,Filter,Comments |
| 2 |
ID,occurrenceID,,
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|
| 3 |
SiteName,projectName,, |
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| 4 |
1haPlotCode,plotName,,
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|
| 5 |
ObservationDate,eventDate,, |
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| 2 |
Id,occurrenceID,,
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|
| 3 |
Site Name,projectName,,
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|
| 4 |
1ha Plot Number,plotName,,
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|
| 5 |
Observation Date,eventDate,,
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|
| 6 | 6 |
Family,family,, |
| 7 | 7 |
Genus,genus,, |
| 8 |
SpecificEpithet,specificEpithet,,
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|
| 9 |
Collectors,recordedBy,, |
|
| 10 |
dbh,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 11 |
max_diam,max_diam,,
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| 12 |
max_diam_pom,max_diam_pom,,
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|
| 13 |
ConditionCodes,ConditionCodes,,
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| 14 |
LocationCodes,LocationCodes,,
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|
| 15 |
SamplingPeriod,SamplingPeriod,,
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|
| 8 |
Species,specificEpithet,,
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| 9 |
Names of Collectors,recordedBy,,
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|
| 10 |
Diameter at 1.3m,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
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| 11 |
Max Diameter,Max Diameter,,
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|
| 12 |
Max Diameter POM,Max Diameter POM,,
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| 13 |
Condition Codes,Condition Codes,,
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| 14 |
Location Codes,Location Codes,,
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|
| 15 |
Sampling Period,Sampling Period,,
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|
| 16 | 16 |
Comments,Comments,, |
| 17 |
SamplingUnitName,SamplingUnitName,,
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|
| 17 |
Sampling Unit Name,Sampling Unit Name,,
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|
| 18 | 18 |
Latitude,verbatimLatitude,, |
| 19 | 19 |
Longitude,verbatimLongitude,, |
| 20 | 20 |
Method,samplingProtocol,, |
| 21 |
Subplot,subplot,, |
|
| 22 |
X_1haPlot,organismX,, |
|
| 23 |
Y_1haPlot,organismY,, |
|
| 24 |
TreeNumber,tag,, |
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| 25 |
ProtocolVersion,ProtocolVersion,, |
|
| 26 |
ResponsibleInstitution,ResponsibleInstitution,, |
|
| 27 |
ProtocolLeadScientist,ProtocolLeadScientist,, |
|
| 28 |
ProtocolLeadScientistInstitution,ProtocolLeadScientistInstitution,, |
|
| 21 |
Subplot Number,subplot,, |
|
| 22 |
1ha Plot X Coordinate,organismX,, |
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| 23 |
1ha Plot Y Coordinate,organismY,, |
|
| 24 |
Tree Number,tag,, |
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| 25 |
Protocol Version,Protocol Version,, |
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| 26 |
Responsible Institution,Responsible Institution,, |
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| 27 |
Protocol Lead Scientist,Protocol Lead Scientist,, |
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| 28 |
Protocol Lead Scientist Institution,Protocol Lead Scientist Institution,, |
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| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2", |
|
| 3 |
1haPlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
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| 4 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
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| 5 |
1haPlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
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| 6 |
Subplot,/location/authorlocationcode, |
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| 2 |
Subplot Number,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
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| 3 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
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| 4 |
Id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
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| 5 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
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| 6 |
Subplot Number,/location/authorlocationcode,
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| 7 | 7 |
Latitude,"/location/locationcoords/latitude_deg/_alt/2/_nullIf:[null=0,type=float]/value", |
| 8 | 8 |
Longitude,"/location/locationcoords/longitude_deg/_alt/2/_nullIf:[null=0,type=float]/value", |
| 9 | 9 |
Method,/location/locationevent/*_id/method/name, |
| 10 |
SiteName,/location/locationevent/*_id/project/projectname, |
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| 11 |
Subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2", |
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| 12 |
1haPlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode",
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| 13 |
ObservationDate,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value, |
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| 14 |
ObservationDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value, |
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| 15 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
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| 16 |
dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
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| 17 |
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
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| 18 |
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
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| 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
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| 20 |
1haPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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| 21 |
TreeNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
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| 22 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
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| 10 |
Site Name,/location/locationevent/*_id/project/projectname,
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| 11 |
Subplot Number,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
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| 12 |
1ha Plot Number,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode",
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| 13 |
Observation Date,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value,
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| 14 |
Observation Date,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value,
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| 15 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
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| 16 |
Diameter at 1.3m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
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| 17 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
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| 18 |
1ha Plot X Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
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| 19 |
1ha Plot Y Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
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| 20 |
1ha Plot Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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| 21 |
Tree Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
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| 22 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
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| 23 | 23 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 24 | 24 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 25 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
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| 26 |
Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
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| 25 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
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| 26 |
Names of Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname,
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| 27 | 27 |
Comments,,** No join mapping for Comments ** |
| 28 |
ConditionCodes,,** No join mapping for ConditionCodes ** |
|
| 29 |
LocationCodes,,** No join mapping for LocationCodes ** |
|
| 30 |
ProtocolLeadScientist,,** No join mapping for ProtocolLeadScientist ** |
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| 31 |
ProtocolLeadScientistInstitution,,** No join mapping for ProtocolLeadScientistInstitution ** |
|
| 32 |
ProtocolVersion,,** No join mapping for ProtocolVersion ** |
|
| 33 |
ResponsibleInstitution,,** No join mapping for ResponsibleInstitution ** |
|
| 34 |
SamplingPeriod,,** No join mapping for SamplingPeriod ** |
|
| 35 |
SamplingUnitName,,** No join mapping for SamplingUnitName ** |
|
| 36 |
max_diam,,** No join mapping for max_diam ** |
|
| 37 |
max_diam_pom,,** No join mapping for max_diam_pom ** |
|
| 28 |
Condition Codes,,** No join mapping for Condition Codes ** |
|
| 29 |
Location Codes,,** No join mapping for Location Codes ** |
|
| 30 |
Max Diameter,,** No join mapping for Max Diameter ** |
|
| 31 |
Max Diameter POM,,** No join mapping for Max Diameter POM ** |
|
| 32 |
Protocol Lead Scientist,,** No join mapping for Protocol Lead Scientist ** |
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| 33 |
Protocol Lead Scientist Institution,,** No join mapping for Protocol Lead Scientist Institution ** |
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| 34 |
Protocol Version,,** No join mapping for Protocol Version ** |
|
| 35 |
Responsible Institution,,** No join mapping for Responsible Institution ** |
|
| 36 |
Sampling Period,,** No join mapping for Sampling Period ** |
|
| 37 |
Sampling Unit Name,,** No join mapping for Sampling Unit Name ** |
|
| inputs/TEAM/VL/test.xml.ref | ||
|---|---|---|
| 4 | 4 |
<next>parent_id</next> |
| 5 | 5 |
<path> |
| 6 | 6 |
<location> |
| 7 |
<parent_id><location><authorlocationcode>$1haPlotCode</authorlocationcode></location></parent_id>
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| 8 |
<authorlocationcode>$Subplot</authorlocationcode> |
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| 7 |
<parent_id><location><authorlocationcode>$1ha Plot Number</authorlocationcode></location></parent_id>
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| 8 |
<authorlocationcode>$Subplot Number</authorlocationcode>
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| 9 | 9 |
<locationcoords> |
| 10 | 10 |
<latitude_deg> |
| 11 | 11 |
<_nullIf> |
| ... | ... | |
| 24 | 24 |
</locationcoords> |
| 25 | 25 |
<locationevent> |
| 26 | 26 |
<method_id><method><name>$Method</name></method></method_id> |
| 27 |
<project_id><project><projectname>$SiteName</projectname></project></project_id> |
|
| 28 |
<obsenddate><_date><date><_dateRangeEnd><value>$ObservationDate</value></_dateRangeEnd></date></_date></obsenddate> |
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| 29 |
<obsstartdate><_date><date><_dateRangeStart><value>$ObservationDate</value></_dateRangeStart></date></_date></obsstartdate> |
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| 27 |
<project_id><project><projectname>$Site Name</projectname></project></project_id>
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| 28 |
<obsenddate><_date><date><_dateRangeEnd><value>$Observation Date</value></_dateRangeEnd></date></_date></obsenddate>
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| 29 |
<obsstartdate><_date><date><_dateRangeStart><value>$Observation Date</value></_dateRangeStart></date></_date></obsstartdate>
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| 30 | 30 |
<taxonoccurrence> |
| 31 | 31 |
<aggregateoccurrence> |
| 32 | 32 |
<plantobservation> |
| 33 |
<specimenreplicate><sourceaccessioncode>$ID</sourceaccessioncode></specimenreplicate>
|
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| 33 |
<specimenreplicate><sourceaccessioncode>$Id</sourceaccessioncode></specimenreplicate>
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| 34 | 34 |
<stemobservation> |
| 35 |
<diameterbreastheight_m><_cm_to_m><value>$dbh</value></_cm_to_m></diameterbreastheight_m>
|
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| 36 |
<tag>$TreeNumber</tag> |
|
| 37 |
<xposition_m>$X_1haPlot</xposition_m>
|
|
| 38 |
<yposition_m>$Y_1haPlot</yposition_m>
|
|
| 35 |
<diameterbreastheight_m><_cm_to_m><value>$Diameter at 1.3m</value></_cm_to_m></diameterbreastheight_m>
|
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| 36 |
<tag>$Tree Number</tag>
|
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| 37 |
<xposition_m>$1ha Plot X Coordinate</xposition_m>
|
|
| 38 |
<yposition_m>$1ha Plot Y Coordinate</yposition_m>
|
|
| 39 | 39 |
</stemobservation> |
| 40 | 40 |
</plantobservation> |
| 41 | 41 |
</aggregateoccurrence> |
| 42 |
<authortaxoncode>$TreeNumber</authortaxoncode> |
|
| 43 |
<sourceaccessioncode>$ID</sourceaccessioncode>
|
|
| 42 |
<authortaxoncode>$Tree Number</authortaxoncode>
|
|
| 43 |
<sourceaccessioncode>$Id</sourceaccessioncode>
|
|
| 44 | 44 |
<taxondetermination> |
| 45 | 45 |
<taxonpath_id> |
| 46 | 46 |
<taxonpath> |
| 47 | 47 |
<family>$Family</family> |
| 48 | 48 |
<genus>$Genus</genus> |
| 49 |
<species>$SpecificEpithet</species>
|
|
| 49 |
<species>$Species</species>
|
|
| 50 | 50 |
</taxonpath> |
| 51 | 51 |
</taxonpath_id> |
| 52 | 52 |
</taxondetermination> |
| 53 |
<verbatimcollectorname>$Collectors</verbatimcollectorname> |
|
| 53 |
<verbatimcollectorname>$Names of Collectors</verbatimcollectorname>
|
|
| 54 | 54 |
</taxonoccurrence> |
| 55 | 55 |
</locationevent> |
| 56 | 56 |
</location> |
| inputs/TEAM/VL/new_terms.csv | ||
|---|---|---|
| 1 |
SiteName,projectName,, |
|
| 2 |
1haPlotCode,plotName,, |
|
| 3 |
ObservationDate,eventDate,, |
|
| 4 |
Collectors,recordedBy,, |
|
| 1 |
Site Name,projectName,, |
|
| 2 |
1ha Plot Number,plotName,, |
|
| 3 |
Observation Date,eventDate,, |
|
| 4 |
Names of Collectors,recordedBy,, |
|
| 5 |
Diameter at 1.3m,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 5 | 6 |
Method,samplingProtocol,, |
| 6 |
X_1haPlot,organismX,, |
|
| 7 |
Y_1haPlot,organismY,, |
|
| 8 |
TreeNumber,tag,, |
|
| 7 |
Subplot Number,subplot,, |
|
| 8 |
1ha Plot X Coordinate,organismX,, |
|
| 9 |
1ha Plot Y Coordinate,organismY,, |
|
| 10 |
Tree Number,tag,, |
|
| inputs/TEAM/VL/unmapped_terms.csv | ||
|---|---|---|
| 1 |
max_diam
|
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| 2 |
max_diam_pom
|
|
| 3 |
ConditionCodes |
|
| 4 |
LocationCodes |
|
| 5 |
SamplingPeriod |
|
| 1 |
Max Diameter
|
|
| 2 |
Max Diameter POM
|
|
| 3 |
Condition Codes
|
|
| 4 |
Location Codes
|
|
| 5 |
Sampling Period
|
|
| 6 | 6 |
Comments |
| 7 |
SamplingUnitName |
|
| 8 |
ProtocolVersion |
|
| 9 |
ResponsibleInstitution |
|
| 10 |
ProtocolLeadScientist |
|
| 11 |
ProtocolLeadScientistInstitution |
|
| 7 |
Sampling Unit Name |
|
| 8 |
Protocol Version |
|
| 9 |
Responsible Institution |
|
| 10 |
Protocol Lead Scientist |
|
| 11 |
Protocol Lead Scientist Institution |
|
| inputs/TEAM/VT/map.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegCore,Filter,Comments |
| 2 |
ID,occurrenceID,,
|
|
| 3 |
ObservationDate,eventDate,, |
|
| 2 |
Id,occurrenceID,,
|
|
| 3 |
Observation Date,eventDate,,
|
|
| 4 | 4 |
Family,family,, |
| 5 | 5 |
Genus,genus,, |
| 6 |
SpecificEpithet,specificEpithet,,
|
|
| 7 |
Collectors,recordedBy,, |
|
| 8 |
dbh,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 9 |
dbh_pom,dbh_pom,,
|
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| 10 |
dbh_new,dbh_new,,
|
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| 11 |
dbh_new_pom,dbh_new_pom,,
|
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| 12 |
ConditionCodes,ConditionCodes,,
|
|
| 13 |
SamplingPeriod,SamplingPeriod,,
|
|
| 6 |
Species,specificEpithet,,
|
|
| 7 |
Names of Collectors,recordedBy,,
|
|
| 8 |
Diameter,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 9 |
POM Height,POM Height,,
|
|
| 10 |
New Diameter,New Diameter,,
|
|
| 11 |
New POM Height,New POM Height,,
|
|
| 12 |
Condition Codes,Condition Codes,,
|
|
| 13 |
Sampling Period,Sampling Period,,
|
|
| 14 | 14 |
Comments,Comments,, |
| 15 |
SamplingUnitName,SamplingUnitName,,
|
|
| 15 |
Sampling Unit Name,Sampling Unit Name,,
|
|
| 16 | 16 |
Latitude,verbatimLatitude,, |
| 17 | 17 |
Longitude,verbatimLongitude,, |
| 18 | 18 |
Method,samplingProtocol,, |
| 19 |
Subplot,subplot,, |
|
| 20 |
X_1haPlot,organismX,, |
|
| 21 |
Y_1haPlot,organismY,, |
|
| 22 |
TreeNumber,tag,, |
|
| 23 |
SiteName,projectName,, |
|
| 24 |
1haPlotCode,plotName,, |
|
| 25 |
ProtocolVersion,ProtocolVersion,, |
|
| 26 |
ResponsibleInstitution,ResponsibleInstitution,, |
|
| 27 |
ProtocolLeadScientist,ProtocolLeadScientist,, |
|
| 28 |
ProtocolLeadScientistInstitution,ProtocolLeadScientistInstitution,, |
|
| 19 |
Subplot Number,subplot,, |
|
| 20 |
1ha Plot X Coordinate,organismX,, |
|
| 21 |
1ha Plot Y Coordinate,organismY,, |
|
| 22 |
Tree Number,tag,, |
|
| 23 |
Site Name,projectName,, |
|
| 24 |
1ha Plot Number,plotName,, |
|
| 25 |
Protocol Version,Protocol Version,, |
|
| 26 |
Responsible Institution,Responsible Institution,, |
|
| 27 |
Protocol Lead Scientist,Protocol Lead Scientist,, |
|
| 28 |
Protocol Lead Scientist Institution,Protocol Lead Scientist Institution,, |
|
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2", |
|
| 3 |
1haPlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
|
|
| 4 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
|
|
| 5 |
1haPlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
|
|
| 6 |
Subplot,/location/authorlocationcode, |
|
| 2 |
Subplot Number,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 3 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
|
|
| 4 |
Id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
|
|
| 5 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
|
|
| 6 |
Subplot Number,/location/authorlocationcode,
|
|
| 7 | 7 |
Latitude,"/location/locationcoords/latitude_deg/_alt/2/_nullIf:[null=0,type=float]/value", |
| 8 | 8 |
Longitude,"/location/locationcoords/longitude_deg/_alt/2/_nullIf:[null=0,type=float]/value", |
| 9 | 9 |
Method,/location/locationevent/*_id/method/name, |
| 10 |
SiteName,/location/locationevent/*_id/project/projectname, |
|
| 11 |
Subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2", |
|
| 12 |
1haPlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode",
|
|
| 13 |
ObservationDate,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value, |
|
| 14 |
ObservationDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value, |
|
| 15 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
|
|
| 16 |
dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 17 |
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
|
| 18 |
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
|
|
| 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
|
|
| 20 |
1haPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
| 21 |
TreeNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
|
| 22 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
|
|
| 10 |
Site Name,/location/locationevent/*_id/project/projectname,
|
|
| 11 |
Subplot Number,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
|
|
| 12 |
1ha Plot Number,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode",
|
|
| 13 |
Observation Date,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value,
|
|
| 14 |
Observation Date,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value,
|
|
| 15 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
|
|
| 16 |
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 17 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
|
|
| 18 |
1ha Plot X Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
|
|
| 19 |
1ha Plot Y Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
|
|
| 20 |
1ha Plot Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
| 21 |
Tree Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
|
|
| 22 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
|
|
| 23 | 23 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 24 | 24 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 25 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
|
|
| 26 |
Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
|
| 25 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
|
|
| 26 |
Names of Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname,
|
|
| 27 | 27 |
Comments,,** No join mapping for Comments ** |
| 28 |
ConditionCodes,,** No join mapping for ConditionCodes ** |
|
| 29 |
ProtocolLeadScientist,,** No join mapping for ProtocolLeadScientist ** |
|
| 30 |
ProtocolLeadScientistInstitution,,** No join mapping for ProtocolLeadScientistInstitution ** |
|
| 31 |
ProtocolVersion,,** No join mapping for ProtocolVersion ** |
|
| 32 |
ResponsibleInstitution,,** No join mapping for ResponsibleInstitution ** |
|
| 33 |
SamplingPeriod,,** No join mapping for SamplingPeriod ** |
|
| 34 |
SamplingUnitName,,** No join mapping for SamplingUnitName ** |
|
| 35 |
dbh_new,,** No join mapping for dbh_new ** |
|
| 36 |
dbh_new_pom,,** No join mapping for dbh_new_pom ** |
|
| 37 |
dbh_pom,,** No join mapping for dbh_pom ** |
|
| 28 |
Condition Codes,,** No join mapping for Condition Codes ** |
|
| 29 |
New Diameter,,** No join mapping for New Diameter ** |
|
| 30 |
New POM Height,,** No join mapping for New POM Height ** |
|
| 31 |
POM Height,,** No join mapping for POM Height ** |
|
| 32 |
Protocol Lead Scientist,,** No join mapping for Protocol Lead Scientist ** |
|
| 33 |
Protocol Lead Scientist Institution,,** No join mapping for Protocol Lead Scientist Institution ** |
|
| 34 |
Protocol Version,,** No join mapping for Protocol Version ** |
|
| 35 |
Responsible Institution,,** No join mapping for Responsible Institution ** |
|
| 36 |
Sampling Period,,** No join mapping for Sampling Period ** |
|
| 37 |
Sampling Unit Name,,** No join mapping for Sampling Unit Name ** |
|
| inputs/TEAM/VT/test.xml.ref | ||
|---|---|---|
| 4 | 4 |
<next>parent_id</next> |
| 5 | 5 |
<path> |
| 6 | 6 |
<location> |
| 7 |
<parent_id><location><authorlocationcode>$1haPlotCode</authorlocationcode></location></parent_id>
|
|
| 8 |
<authorlocationcode>$Subplot</authorlocationcode> |
|
| 7 |
<parent_id><location><authorlocationcode>$1ha Plot Number</authorlocationcode></location></parent_id>
|
|
| 8 |
<authorlocationcode>$Subplot Number</authorlocationcode>
|
|
| 9 | 9 |
<locationcoords> |
| 10 | 10 |
<latitude_deg> |
| 11 | 11 |
<_nullIf> |
| ... | ... | |
| 24 | 24 |
</locationcoords> |
| 25 | 25 |
<locationevent> |
| 26 | 26 |
<method_id><method><name>$Method</name></method></method_id> |
| 27 |
<project_id><project><projectname>$SiteName</projectname></project></project_id> |
|
| 28 |
<obsenddate><_date><date><_dateRangeEnd><value>$ObservationDate</value></_dateRangeEnd></date></_date></obsenddate> |
|
| 29 |
<obsstartdate><_date><date><_dateRangeStart><value>$ObservationDate</value></_dateRangeStart></date></_date></obsstartdate> |
|
| 27 |
<project_id><project><projectname>$Site Name</projectname></project></project_id>
|
|
| 28 |
<obsenddate><_date><date><_dateRangeEnd><value>$Observation Date</value></_dateRangeEnd></date></_date></obsenddate>
|
|
| 29 |
<obsstartdate><_date><date><_dateRangeStart><value>$Observation Date</value></_dateRangeStart></date></_date></obsstartdate>
|
|
| 30 | 30 |
<taxonoccurrence> |
| 31 | 31 |
<aggregateoccurrence> |
| 32 | 32 |
<plantobservation> |
| 33 |
<specimenreplicate><sourceaccessioncode>$ID</sourceaccessioncode></specimenreplicate>
|
|
| 33 |
<specimenreplicate><sourceaccessioncode>$Id</sourceaccessioncode></specimenreplicate>
|
|
| 34 | 34 |
<stemobservation> |
| 35 |
<diameterbreastheight_m><_cm_to_m><value>$dbh</value></_cm_to_m></diameterbreastheight_m>
|
|
| 36 |
<tag>$TreeNumber</tag> |
|
| 37 |
<xposition_m>$X_1haPlot</xposition_m>
|
|
| 38 |
<yposition_m>$Y_1haPlot</yposition_m>
|
|
| 35 |
<diameterbreastheight_m><_cm_to_m><value>$Diameter</value></_cm_to_m></diameterbreastheight_m>
|
|
| 36 |
<tag>$Tree Number</tag>
|
|
| 37 |
<xposition_m>$1ha Plot X Coordinate</xposition_m>
|
|
| 38 |
<yposition_m>$1ha Plot Y Coordinate</yposition_m>
|
|
| 39 | 39 |
</stemobservation> |
| 40 | 40 |
</plantobservation> |
| 41 | 41 |
</aggregateoccurrence> |
| 42 |
<authortaxoncode>$TreeNumber</authortaxoncode> |
|
| 43 |
<sourceaccessioncode>$ID</sourceaccessioncode>
|
|
| 42 |
<authortaxoncode>$Tree Number</authortaxoncode>
|
|
| 43 |
<sourceaccessioncode>$Id</sourceaccessioncode>
|
|
| 44 | 44 |
<taxondetermination> |
| 45 | 45 |
<taxonpath_id> |
| 46 | 46 |
<taxonpath> |
| 47 | 47 |
<family>$Family</family> |
| 48 | 48 |
<genus>$Genus</genus> |
| 49 |
<species>$SpecificEpithet</species>
|
|
| 49 |
<species>$Species</species>
|
|
| 50 | 50 |
</taxonpath> |
| 51 | 51 |
</taxonpath_id> |
| 52 | 52 |
</taxondetermination> |
| 53 |
<verbatimcollectorname>$Collectors</verbatimcollectorname> |
|
| 53 |
<verbatimcollectorname>$Names of Collectors</verbatimcollectorname>
|
|
| 54 | 54 |
</taxonoccurrence> |
| 55 | 55 |
</locationevent> |
| 56 | 56 |
</location> |
| inputs/TEAM/VT/new_terms.csv | ||
|---|---|---|
| 1 |
ObservationDate,eventDate,, |
|
| 2 |
Collectors,recordedBy,, |
|
| 1 |
Observation Date,eventDate,, |
|
| 2 |
Names of Collectors,recordedBy,, |
|
| 3 |
Diameter,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 6 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/ci-team_extract/Vegetation-Metadata-1.4.pdf>)"
|
|
| 3 | 4 |
Method,samplingProtocol,, |
| 4 |
X_1haPlot,organismX,, |
|
| 5 |
Y_1haPlot,organismY,, |
|
| 6 |
TreeNumber,tag,, |
|
| 7 |
SiteName,projectName,, |
|
| 8 |
1haPlotCode,plotName,, |
|
| 5 |
Subplot Number,subplot,, |
|
| 6 |
1ha Plot X Coordinate,organismX,, |
|
| 7 |
1ha Plot Y Coordinate,organismY,, |
|
| 8 |
Tree Number,tag,, |
|
| 9 |
Site Name,projectName,, |
|
| 10 |
1ha Plot Number,plotName,, |
|
| inputs/TEAM/VT/unmapped_terms.csv | ||
|---|---|---|
| 1 |
dbh_pom
|
|
| 2 |
dbh_new
|
|
| 3 |
dbh_new_pom
|
|
| 4 |
ConditionCodes |
|
| 5 |
SamplingPeriod |
|
| 1 |
POM Height
|
|
| 2 |
New Diameter
|
|
| 3 |
New POM Height
|
|
| 4 |
Condition Codes
|
|
| 5 |
Sampling Period
|
|
| 6 | 6 |
Comments |
| 7 |
SamplingUnitName |
|
| 8 |
ProtocolVersion |
|
| 9 |
ResponsibleInstitution |
|
| 10 |
ProtocolLeadScientist |
|
| 11 |
ProtocolLeadScientistInstitution |
|
| 7 |
Sampling Unit Name |
|
| 8 |
Protocol Version |
|
| 9 |
Responsible Institution |
|
| 10 |
Protocol Lead Scientist |
|
| 11 |
Protocol Lead Scientist Institution |
|
Also available in: Unified diff
inputs/TEAM/VL, VT: Split concatenated flat files apart into separate parts each time a header is duplicated, so that the header would be autoremoved by cat_csv. Changed modified BIEN2 flat file headers back to original headers (the duplicated headers) so the headers of all part files would match up. (This is required for cat_csv header autoremoval to work properly.) This results in changes to the input column names in */map.csv.