Revision 6406
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/CTFS/Plot/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS/projects/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
project_name,/location/locationevent/*_id/project/projectname, |
| 3 | 3 |
project_id,/location/locationevent/*_id/project/sourceaccessioncode, |
| 4 | 4 |
allow_download_all,,** No join mapping for *allow_download_all ** |
| inputs/SALVIAS/stems/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS/plotMetadata_/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
SiteCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project) |
| 3 | 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata." |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata." |
| inputs/CTFS/PlotObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 3 | 3 |
PlotCensusNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/CTFS/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:primary database,/source/sourcetype, |
| inputs/CTFS/TaxonOccurrence/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 3 | 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| inputs/CTFS/SubplotObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
| 3 | 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/CTFS/Plot/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
PlotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 3 | 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/SALVIAS/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS/stems/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
PlotObsID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 3 | 3 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
| 4 | 4 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| inputs/SALVIAS/plotObservations/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
U,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
U,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
MT,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
MT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 4 |
institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>MT</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>MT</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/test_taxonomic_names/Taxon/VegBIEN.csv | ||
|---|---|---|
| 1 |
test_taxonomic_names,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
test_taxonomic_names,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 3 | 3 |
scientificName,"/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/1/_taxon_family_require_std/family/_nullIf/null/_first/1", |
| 4 | 4 |
scientificName,"/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/1", |
| inputs/test_taxonomic_names/Taxon/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>test_taxonomic_names</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>test_taxonomic_names</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
XAL:/content/record/,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
XAL:/content/record/,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 3 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 4 |
darwin:InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| inputs/TEAM/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
TEAM,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:primary database,/source/sourcetype, |
| inputs/TEAM/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TEAM</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TEAM</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 1 |
TEAM,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Subplot Number,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 3 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 4 |
Id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| inputs/TEAM/VL/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TEAM</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TEAM</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 1 |
TEAM,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Subplot Number,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 3 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 4 |
Id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| inputs/TEAM/VT/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TEAM</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TEAM</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/TEAM/TEAM_Sites/VegBIEN.csv | ||
|---|---|---|
| 1 |
TEAM,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Name,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 3 | 3 |
Name,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 4 | 4 |
Site Name,/location/locationevent/*_id/project/projectname, |
| inputs/TEAM/TEAM_Sites/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TEAM</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TEAM</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/.geoscrub/geoscrub_output/VegBIEN.csv | ||
|---|---|---|
| 1 |
geoscrub,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
geoscrub,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
countryvalidity,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/cond/_exists/_map:[""-1""=,./{0,1,2}=false,3=true]/value",
|
| 3 | 3 |
decimallatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
| 4 | 4 |
decimallongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
| inputs/.geoscrub/geoscrub_output/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>geoscrub</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
ACAD,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
ACAD,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>ACAD</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>ACAD</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/.NCBI/nodes/VegBIEN.csv | ||
|---|---|---|
| 1 |
NCBI,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
| 3 | 3 |
rank,"/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/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 4 | 4 |
parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode, |
| inputs/.NCBI/nodes/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>NCBI</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>NCBI</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
WIN,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
WIN,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>WIN</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>WIN</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CTFS/StemObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
| 3 | 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/CTFS/StemObservation/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CTFS/Subplot/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
| 3 | 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/CTFS/Subplot/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CTFS/PlotObservation/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CTFS/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CTFS/TaxonOccurrence/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CTFS/SubplotObservation/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CTFS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:aggregator,/source/sourcetype, |
| inputs/SALVIAS/projects/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Line,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 3 |
PlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| inputs/SALVIAS/plotMetadata_/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/GBIF/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
GBIF,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:aggregator,/source/sourcetype, |
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
JBM,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
JBM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/SpeciesLink/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
SpeciesLink,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SpeciesLink,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:aggregator,/source/sourcetype, |
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
UBC,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
UBC,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
NY,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
NY,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
UniqueNYInternalRecordNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/Madidi/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
Madidi,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:primary database,/source/sourcetype, |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
UNCC,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
UNCC,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
accession,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1","Globally unique, although occasionally duplicated. [1] |
| 3 | 3 |
|
| 4 | 4 |
[1] Using the following query: |
| inputs/CVS/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:primary database,/source/sourcetype, |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS-CSV,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS-CSV,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 3 |
plot_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 4 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| inputs/SALVIAS-CSV/Plot/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS-CSV,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS-CSV,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
plot_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project) |
| 3 | 3 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata." |
| 4 | 4 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata." |
| inputs/U/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>U</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>U</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/GBIF/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>GBIF</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>GBIF</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/JBM/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>JBM</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>JBM</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SpeciesLink/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SpeciesLink</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SpeciesLink</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/UBC/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>UBC</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>UBC</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>NY</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>NY</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/Madidi/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>Madidi</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>Madidi</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>UNCC</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>UNCC</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CVS/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CVS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS-CSV/Organism/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS-CSV</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS-CSV</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS-CSV/Plot/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS-CSV</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS-CSV</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/QFA/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>QFA</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>QFA</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/GBIF/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>GBIF</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>GBIF</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/HIBG/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>HIBG</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>HIBG</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SpeciesLink</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SpeciesLink</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/bien_web/observation/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>bien_web</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>bien_web</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/Madidi/Organism/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>Madidi</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>Madidi</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/Madidi/Plot/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>Madidi</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>Madidi</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/CVS/Organism/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>CVS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/.herbaria/herbaria/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>herbaria</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>herbaria</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/SALVIAS-CSV/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>SALVIAS-CSV</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>SALVIAS-CSV</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/REMIB/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>REMIB</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>REMIB</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
QFA,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
QFA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
GBIF,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
CatalogNO,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 3 |
CatalogNO,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 4 |
InstitutionCD,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
HIBG,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
HIBG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
SpeciesLink,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SpeciesLink,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
conceptual_darwin_2003_1_0_CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
dwc_dwcore_CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 1 |
bien_web,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
bien_web,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
plotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 3 | 3 |
plotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 4 |
observationID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 |
Madidi,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Number of subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 3 |
Inventory name,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 4 |
Inventory code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| inputs/Madidi/Plot/VegBIEN.csv | ||
|---|---|---|
| 1 |
Madidi,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Inventory name,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 3 | 3 |
Inventory code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 4 |
Inventory code,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/CVS/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
authorObsCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
| 3 | 3 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
| 4 | 4 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| inputs/.herbaria/herbaria/VegBIEN.csv | ||
|---|---|---|
| 1 |
herbaria,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
herbaria,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
herbariumAcronym,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| 3 | 3 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
| 4 | 4 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
| inputs/SALVIAS-CSV/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
SALVIAS-CSV,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
SALVIAS-CSV,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:aggregator,/source/sourcetype, |
| inputs/REMIB/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
REMIB,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
REMIB,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:aggregator,/source/sourcetype, |
| inputs/REMIB/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>REMIB</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>REMIB</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/FIA/Organism/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>FIA</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>FIA</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/.TNRS/tnrs_other/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TNRS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>ARIZ</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>ARIZ</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/NCU-NCSC/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>NCU-NCSC</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>NCU-NCSC</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/REMIB/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
REMIB,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
REMIB,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
accession_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
|
| 3 | 3 |
|
| 4 | 4 |
[1] Using the following query: |
| inputs/FIA/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
PlotCD,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 3 | 3 |
PlotCD,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| 4 | 4 |
PlotCD,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| inputs/.TNRS/tnrs_other/VegBIEN.csv | ||
|---|---|---|
| 1 |
TNRS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TNRS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 3 | 3 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
| 4 | 4 |
Name_matched,"/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/1/_taxon_family_require_std/family/_nullIf/null/_first/1", |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
ARIZ,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
ARIZ,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
GlobalUniqueIdentifier,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
CatalogNumberNumeric,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/1", |
| 4 | 4 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
NCU-NCSC,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
NCU-NCSC,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Accession Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
Accession Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/IUCN/European_Red_List_Plants/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>IUCN</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>IUCN</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/FIA/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>FIA</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>FIA</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/.TNRS/tnrs_accepted/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TNRS</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/TRT/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TRT</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TRT</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>MO</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>MO</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/IUCN/European_Red_List_Plants/VegBIEN.csv | ||
|---|---|---|
| 1 |
IUCN,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
IUCN,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Family,"/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/1/_taxon_family_require_std/family/_nullIf/value", |
| 3 | 3 |
Species,"/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", |
| 4 | 4 |
Species,"/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", |
| inputs/FIA/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:primary database,/source/sourcetype, |
| inputs/.TNRS/tnrs_accepted/VegBIEN.csv | ||
|---|---|---|
| 1 |
TNRS,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TNRS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 3 | 3 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
| 4 | 4 |
Name_matched,"/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/1/_taxon_family_require_std/family/_nullIf/null/_first/1", |
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
TRT,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TRT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
MO,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
MO,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 3 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 4 |
InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| inputs/VASCAN/Taxon/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VASCAN</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VASCAN</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VegBank/observation_/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VegBank/stemlocation/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VegBank/taxonimportance/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/TRTE/Specimen/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>TRTE</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>TRTE</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VASCAN/Taxon/VegBIEN.csv | ||
|---|---|---|
| 1 |
VASCAN,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VASCAN,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| 3 | 3 |
scientificName,"/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/1/_taxon_family_require_std/family/_nullIf/null/_first/2", |
| 4 | 4 |
family,"/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/1/_taxon_family_require_std/family/_nullIf/value", |
| inputs/VegBank/observation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
plot_id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 3 | 3 |
authorobscode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
| 4 | 4 |
plot_id,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| inputs/VegBank/stemlocation/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
stemcount_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 3 | 3 |
stemcount_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
| 4 | 4 |
stemcode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
| inputs/VegBank/taxonimportance/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
taxonobservation_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
| 3 | 3 |
|
| 4 | 4 |
[1] The following query returns rows: |
| inputs/TRTE/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
TRTE,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
TRTE,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 3 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| inputs/VegBank/stemcount/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VegBank/Source/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VegBank/taxonobservation_/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| inputs/VegBank/plot_/test.xml.ref | ||
|---|---|---|
| 1 | 1 |
Put template: |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<_setDefault id="-1"> |
| 4 |
<col>source_id</col> |
|
| 5 |
<value><source><shortname>VegBank</shortname></source></value> |
|
| 4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
| 6 | 5 |
<path> |
| 7 | 6 |
<_simplifyPath> |
| 8 | 7 |
<next>parent_id</next> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 1 |
VegCore,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegCore,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 3 |
subplotID,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 4 | 4 |
plotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| inputs/VegBank/stemcount/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
stemcount_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 3 | 3 |
stemcount_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
| 4 | 4 |
stemcount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| inputs/VegBank/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
:aggregator,/source/sourcetype, |
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,"VegBIEN:/_setDefault:[col=source_id,value/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path",Comments
|
|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
|
|
| 2 | 2 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 3 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 4 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
Also available in: Unified diff
db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names