Revision 6432
Added by Aaron Marcuse-Kubitza almost 12 years ago
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 6 | 6 |
institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| 7 | 7 |
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
| 8 | 8 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 9 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 10 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 10 | 11 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 11 | 12 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 12 | 13 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode>$id</authorlocationcode> |
| 11 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 11 | 12 |
<locationevent> |
| 12 | 13 |
<taxonoccurrence> |
| 13 | 14 |
<aggregateoccurrence> |
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 9 | 9 |
darwin:MaximumElevation,/location/elevation_m/_alt/2/_avg/max, |
| 10 | 10 |
darwin:MinimumElevation,/location/elevation_m/_alt/2/_avg/min, |
| 11 |
darwin:CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 11 |
darwin:CollectorNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 12 |
darwin:Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 12 | 13 |
darwin:DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 13 | 14 |
darwin:MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 14 | 15 |
darwin:YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 6 | 6 |
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", |
| 7 | 7 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 8 | 8 |
Subplot Number,/location/authorlocationcode, |
| 9 |
Id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
Id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 10 | 10 |
Site Name,/location/locationevent/*_id/project/projectname, |
| 11 | 11 |
Subplot Number,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 12 | 12 |
Observation Date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 6 | 6 |
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", |
| 7 | 7 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 8 | 8 |
Subplot Number,/location/authorlocationcode, |
| 9 |
Id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
Id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 10 | 10 |
Site Name,/location/locationevent/*_id/project/projectname, |
| 11 | 11 |
Subplot Number,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 12 | 12 |
Observation Date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
<value>$verbatimElevation</value> |
| 32 | 32 |
</_units> |
| 33 | 33 |
</elevation_m> |
| 34 |
<iscultivated> |
|
| 35 |
<_locationnarrative_is_cultivated> |
|
| 36 |
<locationnarrative> |
|
| 37 |
<_join> |
|
| 38 |
<1>$locality</1> |
|
| 39 |
<3>$habitat</3> |
|
| 40 |
</_join> |
|
| 41 |
</locationnarrative> |
|
| 42 |
</_locationnarrative_is_cultivated> |
|
| 43 |
</iscultivated> |
|
| 34 | 44 |
<locationevent> |
| 35 | 45 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 36 | 46 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 | 14 |
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min, |
| 15 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 17 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 18 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 19 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 36 | 36 |
<2><_avg><min>$minimumElevationInMeters</min></_avg></2> |
| 37 | 37 |
</_alt> |
| 38 | 38 |
</elevation_m> |
| 39 |
<iscultivated> |
|
| 40 |
<_locationnarrative_is_cultivated> |
|
| 41 |
<locationnarrative> |
|
| 42 |
<_join> |
|
| 43 |
<1>$locality</1> |
|
| 44 |
<3>$habitat</3> |
|
| 45 |
</_join> |
|
| 46 |
</locationnarrative> |
|
| 47 |
</_locationnarrative_is_cultivated> |
|
| 48 |
</iscultivated> |
|
| 39 | 49 |
<locationevent> |
| 40 | 50 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 41 | 51 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/CTFS/StemObservation/VegBIEN.csv | ||
|---|---|---|
| 4 | 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
| 5 | 5 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| 6 | 6 |
QuadratID,/location/authorlocationcode,Not globally unique; unique only within Site |
| 7 |
MeasureID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 7 |
MeasureID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 8 | 8 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
| 9 | 9 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
| 10 | 10 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| inputs/CTFS/TaxonOccurrence/VegBIEN.csv | ||
|---|---|---|
| 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", |
| 5 |
SpeciesInvID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 5 |
SpeciesInvID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 6 | 6 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
| 7 | 7 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 8 | 8 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| inputs/CTFS/Plot/VegBIEN.csv | ||
|---|---|---|
| 14 | 14 |
GROUP BY ""Elevation""::real , ""LocationName"" |
| 15 | 15 |
ORDER BY ""Elevation""::real DESC |
| 16 | 16 |
-----" |
| 17 |
DescriptionOfSite,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 18 |
LocationName,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 | 19 |
PlotName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
| 18 | 20 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| 19 | 21 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| inputs/CTFS/Plot/test.xml.ref | ||
|---|---|---|
| 11 | 11 |
<sourceaccessioncode>$PlotID</sourceaccessioncode> |
| 12 | 12 |
<area_m2><_ha_to_m2><value>$SizeOfSite</value></_ha_to_m2></area_m2> |
| 13 | 13 |
<elevation_m>$Elevation</elevation_m> |
| 14 |
<iscultivated> |
|
| 15 |
<_locationnarrative_is_cultivated> |
|
| 16 |
<locationnarrative> |
|
| 17 |
<_alt> |
|
| 18 |
<0>$DescriptionOfSite</0> |
|
| 19 |
<1>$LocationName</1> |
|
| 20 |
</_alt> |
|
| 21 |
</locationnarrative> |
|
| 22 |
</_locationnarrative_is_cultivated> |
|
| 23 |
</iscultivated> |
|
| 14 | 24 |
<locationnarrative> |
| 15 | 25 |
<_alt> |
| 16 | 26 |
<0>$DescriptionOfSite</0> |
| inputs/SALVIAS/stems/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
PlotObsID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 2 |
PlotObsID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 3 | 3 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
| 4 | 4 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| 5 | 5 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m, |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
PlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 16 | 16 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| 17 | 17 |
Line,/location/authorlocationcode, |
| 18 |
Ind,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot." |
|
| 19 |
PlotObsID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 18 |
Ind,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
|
|
| 19 |
PlotObsID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 20 | 20 |
Line,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 21 | 21 |
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists","This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows: |
| 22 | 22 |
----- |
| inputs/SALVIAS/plotMetadata_/VegBIEN.csv | ||
|---|---|---|
| 9 | 9 |
Elev,/location/elevation_m/_alt/1,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick. |
| 10 | 10 |
elev_max_m,/location/elevation_m/_alt/2/_avg/max, |
| 11 | 11 |
elev_min_m,/location/elevation_m/_alt/2/_avg/min, |
| 12 |
Locality_Description,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX" |
|
| 13 |
Habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 12 | 14 |
topography_desc,/location/landform, |
| 13 | 15 |
PlotMethod,/location/locationevent/*_id/method/name, |
| 14 | 16 |
lookup_MethodCode_Description,/location/locationevent/*_id/method/observationmeasure, |
| inputs/SALVIAS/plotMetadata_/test.xml.ref | ||
|---|---|---|
| 29 | 29 |
</2> |
| 30 | 30 |
</_alt> |
| 31 | 31 |
</elevation_m> |
| 32 |
<iscultivated> |
|
| 33 |
<_locationnarrative_is_cultivated> |
|
| 34 |
<locationnarrative> |
|
| 35 |
<_join> |
|
| 36 |
<1>$Locality_Description</1> |
|
| 37 |
<3>$Habitat</3> |
|
| 38 |
</_join> |
|
| 39 |
</locationnarrative> |
|
| 40 |
</_locationnarrative_is_cultivated> |
|
| 41 |
</iscultivated> |
|
| 32 | 42 |
<landform>$topography_desc</landform> |
| 33 | 43 |
<locationevent> |
| 34 | 44 |
<method_id> |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 6 | 6 |
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", |
| 7 | 7 |
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", |
| 8 | 8 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 9 |
ID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 10 |
Number,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 10 |
Number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 11 |
Gazetteer,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_join/1/_label[label=""gazetteer""]/value/_join/1", |
|
| 12 |
Newgazett,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_join/1/_label[label=""gazetteer""]/value/_join/2",Only used in 1 row |
|
| 13 |
Locnotes,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_join/2, |
|
| 14 |
Ecology,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 11 | 15 |
Colldd,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 12 | 16 |
Collmm,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 13 | 17 |
Collyy,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/U/Specimen/test.xml.ref | ||
|---|---|---|
| 13 | 13 |
<2>$Barcode</2> |
| 14 | 14 |
</_alt> |
| 15 | 15 |
</authorlocationcode> |
| 16 |
<iscultivated> |
|
| 17 |
<_locationnarrative_is_cultivated> |
|
| 18 |
<locationnarrative> |
|
| 19 |
<_join> |
|
| 20 |
<2> |
|
| 21 |
<_join> |
|
| 22 |
<1> |
|
| 23 |
<_label> |
|
| 24 |
<label>gazetteer</label> |
|
| 25 |
<value> |
|
| 26 |
<_join> |
|
| 27 |
<1>$Gazetteer</1> |
|
| 28 |
<2>$Newgazett</2> |
|
| 29 |
</_join> |
|
| 30 |
</value> |
|
| 31 |
</_label> |
|
| 32 |
</1> |
|
| 33 |
<2>$Locnotes</2> |
|
| 34 |
</_join> |
|
| 35 |
</2> |
|
| 36 |
<3>$Ecology</3> |
|
| 37 |
</_join> |
|
| 38 |
</locationnarrative> |
|
| 39 |
</_locationnarrative_is_cultivated> |
|
| 40 |
</iscultivated> |
|
| 16 | 41 |
<locationevent> |
| 17 | 42 |
<taxonoccurrence> |
| 18 | 43 |
<aggregateoccurrence> |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/QFA/Specimen/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
<value>$verbatimElevation</value> |
| 32 | 32 |
</_units> |
| 33 | 33 |
</elevation_m> |
| 34 |
<iscultivated> |
|
| 35 |
<_locationnarrative_is_cultivated> |
|
| 36 |
<locationnarrative> |
|
| 37 |
<_join> |
|
| 38 |
<1>$locality</1> |
|
| 39 |
<3>$habitat</3> |
|
| 40 |
</_join> |
|
| 41 |
</locationnarrative> |
|
| 42 |
</_locationnarrative_is_cultivated> |
|
| 43 |
</iscultivated> |
|
| 34 | 44 |
<locationevent> |
| 35 | 45 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 36 | 46 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
CatalogNO,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 9 | 9 |
MaximumElevationInMeter,/location/elevation_m/_alt/2/_avg/max, |
| 10 | 10 |
MinimumElevationInMeter,/location/elevation_m/_alt/2/_avg/min, |
| 11 |
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 11 | 12 |
LatestDateCollected,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 12 | 13 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 13 | 14 |
CollectionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| inputs/GBIF/Specimen/test.xml.ref | ||
|---|---|---|
| 20 | 20 |
<min>$MinimumElevationInMeter</min> |
| 21 | 21 |
</_avg> |
| 22 | 22 |
</elevation_m> |
| 23 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$Locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 23 | 24 |
<locationevent> |
| 24 | 25 |
<taxonoccurrence> |
| 25 | 26 |
<aggregateoccurrence> |
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min, |
| 14 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/JBM/Specimen/test.xml.ref | ||
|---|---|---|
| 25 | 25 |
</_alt> |
| 26 | 26 |
</authorlocationcode> |
| 27 | 27 |
<elevation_m><_avg><min>$minimumElevationInMeters</min></_avg></elevation_m> |
| 28 |
<iscultivated> |
|
| 29 |
<_locationnarrative_is_cultivated> |
|
| 30 |
<locationnarrative> |
|
| 31 |
<_join> |
|
| 32 |
<1>$locality</1> |
|
| 33 |
<3>$habitat</3> |
|
| 34 |
</_join> |
|
| 35 |
</locationnarrative> |
|
| 36 |
</_locationnarrative_is_cultivated> |
|
| 37 |
</iscultivated> |
|
| 28 | 38 |
<locationevent> |
| 29 | 39 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 30 | 40 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/HIBG/Specimen/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
<value>$verbatimElevation</value> |
| 32 | 32 |
</_units> |
| 33 | 33 |
</elevation_m> |
| 34 |
<iscultivated> |
|
| 35 |
<_locationnarrative_is_cultivated> |
|
| 36 |
<locationnarrative> |
|
| 37 |
<_join> |
|
| 38 |
<1>$locality</1> |
|
| 39 |
<3>$habitat</3> |
|
| 40 |
</_join> |
|
| 41 |
</locationnarrative> |
|
| 42 |
</_locationnarrative_is_cultivated> |
|
| 43 |
</iscultivated> |
|
| 34 | 44 |
<locationevent> |
| 35 | 45 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 36 | 46 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 60 | 60 |
</min> |
| 61 | 61 |
</_avg> |
| 62 | 62 |
</elevation_m> |
| 63 |
<iscultivated> |
|
| 64 |
<_locationnarrative_is_cultivated> |
|
| 65 |
<locationnarrative> |
|
| 66 |
<_alt> |
|
| 67 |
<0>$conceptual_darwin_2003_1_0_Locality</0> |
|
| 68 |
<1>$dwc_dwcore_Locality</1> |
|
| 69 |
<2>$dwc_terms_locality</2> |
|
| 70 |
</_alt> |
|
| 71 |
</locationnarrative> |
|
| 72 |
</_locationnarrative_is_cultivated> |
|
| 73 |
</iscultivated> |
|
| 63 | 74 |
<locationevent> |
| 64 | 75 |
<taxonoccurrence> |
| 65 | 76 |
<aggregateoccurrence> |
| inputs/UBC/Specimen/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
<value>$verbatimElevation</value> |
| 32 | 32 |
</_units> |
| 33 | 33 |
</elevation_m> |
| 34 |
<iscultivated> |
|
| 35 |
<_locationnarrative_is_cultivated> |
|
| 36 |
<locationnarrative> |
|
| 37 |
<_join> |
|
| 38 |
<1>$locality</1> |
|
| 39 |
<3>$habitat</3> |
|
| 40 |
</_join> |
|
| 41 |
</locationnarrative> |
|
| 42 |
</_locationnarrative_is_cultivated> |
|
| 43 |
</iscultivated> |
|
| 34 | 44 |
<locationevent> |
| 35 | 45 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 36 | 46 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 12 | 12 |
MaximumElevation,/location/elevation_m/_alt/2/_avg/max, |
| 13 | 13 |
MinimumElevation,/location/elevation_m/_alt/2/_avg/min/_nullIf:[null=.]/value, |
| 14 |
FieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",Usage inconsistent with DwC definition |
|
| 15 |
UniqueNYInternalRecordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
FieldNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",Usage inconsistent with DwC definition |
|
| 15 |
UniqueNYInternalRecordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/1, |
|
| 17 |
Substrate,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/2/_label[label=""substrate""]/value", |
|
| 18 |
Vegetation,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/3/_label[label=""vegetation""]/value", |
|
| 19 |
Habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 20 |
DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 17 | 21 |
MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 18 | 22 |
YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/Madidi/Plot/VegBIEN.csv | ||
|---|---|---|
| 56 | 56 |
GROUP BY ""Minimum altitude"" , ""Locality"" |
| 57 | 57 |
----- |
| 58 | 58 |
[2] This map shows both flat and mountainous regions: <https://maps.google.com/maps/ms?ie=UTF8&hl=en&t=h&msa=0&msid=103363035880599665829.00047e9cf84b87448387d&ll=-13.96448,-68.380065&spn=3.730927,4.669189&z=7>" |
| 59 |
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 59 | 60 |
Topographical situation,/location/landform, |
| 60 | 61 |
Expedition name,/location/locationevent/*_id/project/projectname,Consistent (globally unique) between PPM and PT data |
| 61 | 62 |
Expedition number,/location/locationevent/*_id/project/sourceaccessioncode,Consistent (globally unique) between PPM and PT data |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode>$accession</authorlocationcode> |
| 11 |
<iscultivated> |
|
| 12 |
<_locationnarrative_is_cultivated> |
|
| 13 |
<locationnarrative> |
|
| 14 |
<_join> |
|
| 15 |
<1>$locality</1> |
|
| 16 |
<3>$habitat</3> |
|
| 17 |
</_join> |
|
| 18 |
</locationnarrative> |
|
| 19 |
</_locationnarrative_is_cultivated> |
|
| 20 |
</iscultivated> |
|
| 11 | 21 |
<locationevent> |
| 12 | 22 |
<taxonoccurrence> |
| 13 | 23 |
<aggregateoccurrence> |
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 10 | 10 |
Inventory name,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 11 | 11 |
Inventory code,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| 12 | 12 |
Number of subplot,/location/authorlocationcode, |
| 13 |
Tree number,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 13 |
Tree number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 14 | 14 |
Expedition,/location/locationevent/*_id/project/projectname, |
| 15 | 15 |
Number of subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 16 | 16 |
Number of subplot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2", |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 28 | 28 |
HAVING count(*) > 1 |
| 29 | 29 |
-----" |
| 30 | 30 |
herbarium,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| 31 |
accession,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Globally unique, although occasionally duplicated. [1] |
|
| 31 |
accession,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Globally unique, although occasionally duplicated. [1]
|
|
| 32 | 32 |
|
| 33 | 33 |
[1] Using the following query: |
| 34 | 34 |
----- |
| ... | ... | |
| 37 | 37 |
GROUP BY herbarium, accession |
| 38 | 38 |
HAVING count(*) > 1 |
| 39 | 39 |
-----" |
| 40 |
collectno,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 41 |
cultivated,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/else/_alt/2",Ignore other values |
|
| 40 |
collectno,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 41 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2",Ignore other values |
|
| 42 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 43 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 42 | 44 |
collday,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 43 | 45 |
collmonth,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 44 | 46 |
collyear,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 30 | 30 |
conceptual_darwin_2003_1_0_MinimumElevation,/location/elevation_m/_alt/2/_avg/min, |
| 31 | 31 |
dwc_dwcore_MinimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min, |
| 32 | 32 |
dwc_terms_minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min, |
| 33 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 34 |
dwc_terms_recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1", |
|
| 35 |
conceptual_darwin_2003_1_0_FieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec) |
|
| 33 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 34 |
dwc_terms_recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",
|
|
| 35 |
conceptual_darwin_2003_1_0_FieldNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 36 | 36 |
----- |
| 37 | 37 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
| 38 | 38 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
|
| 39 | 39 |
-----" |
| 40 |
dwc_curatorial_FieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec) |
|
| 40 |
dwc_curatorial_FieldNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 41 | 41 |
----- |
| 42 | 42 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
| 43 | 43 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
|
| 44 | 44 |
-----" |
| 45 |
dwc_terms_fieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec) |
|
| 45 |
dwc_terms_fieldNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 46 | 46 |
----- |
| 47 | 47 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
| 48 | 48 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
|
| 49 | 49 |
-----" |
| 50 |
conceptual_darwin_2003_1_0_CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3", |
|
| 51 |
dwc_curatorial_CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3", |
|
| 50 |
conceptual_darwin_2003_1_0_CollectorNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3", |
|
| 51 |
dwc_curatorial_CollectorNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3", |
|
| 52 |
conceptual_darwin_2003_1_0_Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 53 |
dwc_dwcore_Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 54 |
dwc_terms_locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 52 | 55 |
conceptual_darwin_2003_1_0_DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 53 | 56 |
conceptual_darwin_2003_1_0_MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 54 | 57 |
conceptual_darwin_2003_1_0_YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
plotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| 12 | 12 |
plotAreaHa,/location/area_m2/_ha_to_m2/value, |
| 13 | 13 |
elevation_m,/location/elevation_m/_alt/1, |
| 14 |
collectionNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
observationID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
isCultivated,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/else/_alt/2", |
|
| 14 |
collectionNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 15 |
observationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 16 |
isCultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2",
|
|
| 17 | 17 |
plotMethod,/location/locationevent/*_id/method/name, |
| 18 | 18 |
plotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
| 19 | 19 |
plotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 30 | 30 |
</min> |
| 31 | 31 |
</_avg> |
| 32 | 32 |
</elevation_m> |
| 33 |
<iscultivated> |
|
| 34 |
<_locationnarrative_is_cultivated> |
|
| 35 |
<locationnarrative> |
|
| 36 |
<_join> |
|
| 37 |
<1> |
|
| 38 |
<_join> |
|
| 39 |
<1>$Locality</1> |
|
| 40 |
<2> |
|
| 41 |
<_label> |
|
| 42 |
<label>substrate</label> |
|
| 43 |
<value>$Substrate</value> |
|
| 44 |
</_label> |
|
| 45 |
</2> |
|
| 46 |
<3> |
|
| 47 |
<_label> |
|
| 48 |
<label>vegetation</label> |
|
| 49 |
<value>$Vegetation</value> |
|
| 50 |
</_label> |
|
| 51 |
</3> |
|
| 52 |
</_join> |
|
| 53 |
</1> |
|
| 54 |
<3>$Habitat</3> |
|
| 55 |
</_join> |
|
| 56 |
</locationnarrative> |
|
| 57 |
</_locationnarrative_is_cultivated> |
|
| 58 |
</iscultivated> |
|
| 33 | 59 |
<locationevent> |
| 34 | 60 |
<taxonoccurrence> |
| 35 | 61 |
<aggregateoccurrence> |
| inputs/Madidi/Plot/test.xml.ref | ||
|---|---|---|
| 27 | 27 |
<to><_rangeEnd><value>$Minimum altitude</value></_rangeEnd></to> |
| 28 | 28 |
</_range> |
| 29 | 29 |
</elevationrange_m> |
| 30 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$Locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 30 | 31 |
<landform>$Topographical situation</landform> |
| 31 | 32 |
<locationevent> |
| 32 | 33 |
<project_id> |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
plot_code,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
| 16 | 16 |
PLOT_ID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| 17 | 17 |
subplot,/location/authorlocationcode, |
| 18 |
OBSERVATION_ID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 19 |
individual_code,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot." |
|
| 18 |
OBSERVATION_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 19 |
individual_code,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
|
|
| 20 | 20 |
subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 21 | 21 |
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists","This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows: |
| 22 | 22 |
----- |
| inputs/SALVIAS-CSV/Plot/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
elev_m,/location/elevation_m/_alt/1,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick. |
| 9 | 9 |
elev_max_m,/location/elevation_m/_alt/2/_avg/max, |
| 10 | 10 |
elev_min_m,/location/elevation_m/_alt/2/_avg/min, |
| 11 |
locality_description,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX" |
|
| 11 | 12 |
plot_methodology,/location/locationevent/*_id/method/name, |
| 12 | 13 |
project,/location/locationevent/*_id/project/projectname, |
| 13 | 14 |
date_finish,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric |
| 16 | 16 |
MaximumElevationInMeters,/location/elevation_m/_alt/2/_avg/max,"Contains some verbatim values, including ranges and units" |
| 17 | 17 |
MinimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min,"Contains some verbatim values, including ranges and units" |
| 18 |
CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 19 |
GlobalUniqueIdentifier,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 18 |
CollectorNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 19 |
GlobalUniqueIdentifier,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 20 |
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 20 | 21 |
VerbatimCollectingDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1/_alt/0, |
| 21 | 22 |
DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 22 | 23 |
MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
SeriesName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
| 9 | 9 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 10 | 10 |
Elevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 11 |
Accession Number,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 12 |
Cultivated?,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/else/_alt/2", |
|
| 11 |
Accession Number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 12 |
Cultivated?,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2",
|
|
| 13 | 13 |
Collect Date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 14 | 14 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 15 | 15 |
SeriesName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| inputs/VegBank/stemlocation/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
stemcount_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 2 |
stemcount_id,"/location/iscultivated/_or/1/_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, |
| 5 | 5 |
stemlocation_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode, |
| inputs/VegBank/plot_/test.xml.ref | ||
|---|---|---|
| 23 | 23 |
</accesslevel> |
| 24 | 24 |
<area_m2>$area</area_m2> |
| 25 | 25 |
<elevation_m>$elevation</elevation_m> |
| 26 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locationnarrative</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 26 | 27 |
<landform>$landform</landform> |
| 27 | 28 |
<locationnarrative>$locationnarrative</locationnarrative> |
| 28 | 29 |
<locationplace> |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 40 | 40 |
taxonOccurrenceID,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 41 | 41 |
oldGrowth,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/else", |
| 42 | 42 |
cultivated,"//location/iscultivated/_if[@name=""if TaxonOccurrence""]/else", |
| 43 |
locality,//location/iscultivated, |
|
| 44 |
verbatimLocality,//location/iscultivated, |
|
| 45 |
habitat,//location/iscultivated, |
|
| 43 | 46 |
landform,//location/landform, |
| 44 | 47 |
samplingProtocol,//method/name, |
| 45 | 48 |
observationMeasure,//method/observationmeasure, |
| inputs/REMIB/Specimen/test.xml.ref | ||
|---|---|---|
| 13 | 13 |
<3>$accession_number</3> |
| 14 | 14 |
</_join> |
| 15 | 15 |
</authorlocationcode> |
| 16 |
<iscultivated> |
|
| 17 |
<_locationnarrative_is_cultivated> |
|
| 18 |
<locationnarrative> |
|
| 19 |
<_join> |
|
| 20 |
<1>$locality</1> |
|
| 21 |
<3>$habitat</3> |
|
| 22 |
</_join> |
|
| 23 |
</locationnarrative> |
|
| 24 |
</_locationnarrative_is_cultivated> |
|
| 25 |
</iscultivated> |
|
| 16 | 26 |
<locationevent> |
| 17 | 27 |
<taxonoccurrence> |
| 18 | 28 |
<aggregateoccurrence> |
| inputs/TRT/Specimen/test.xml.ref | ||
|---|---|---|
| 41 | 41 |
</2> |
| 42 | 42 |
</_alt> |
| 43 | 43 |
</elevation_m> |
| 44 |
<iscultivated> |
|
| 45 |
<_locationnarrative_is_cultivated> |
|
| 46 |
<locationnarrative> |
|
| 47 |
<_join> |
|
| 48 |
<1>$locality</1> |
|
| 49 |
<3>$habitat</3> |
|
| 50 |
</_join> |
|
| 51 |
</locationnarrative> |
|
| 52 |
</_locationnarrative_is_cultivated> |
|
| 53 |
</iscultivated> |
|
| 44 | 54 |
<locationevent> |
| 45 | 55 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 46 | 56 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
| inputs/VegBank/stemcount/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
stemcount_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 2 |
stemcount_id,"/location/iscultivated/_or/1/_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, |
| 5 | 5 |
stemdiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
| inputs/VegBank/plot_/VegBIEN.csv | ||
|---|---|---|
| 7 | 7 |
confidentialitystatus,"/location/accesslevel/_map:[./{0,1,2,3,4}=public,5=""data by request"",6=private]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
| 8 | 8 |
area,/location/area_m2,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
| 9 | 9 |
elevation,/location/elevation_m/_alt/1,"""The elevation of the plot origin in meters above sea level"" (elevation definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
| 10 |
locationnarrative,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 10 | 11 |
landform,/location/landform, |
| 11 | 12 |
authorplotcode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
| 12 | 13 |
plot_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 34 | 34 |
verbatimElevation_m,/location/elevation_m/_alt/2/_avg/min/_rangeStart/value, |
| 35 | 35 |
verbatimElevation_m,/location/elevationrange_m/_range/from/_rangeStart/value, |
| 36 | 36 |
verbatimElevation_m,/location/elevationrange_m/_range/to/_rangeEnd/value, |
| 37 |
individualID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 38 |
occurrenceID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 39 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 40 |
taxonOccurrenceID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 41 |
oldGrowth,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/else/_alt/1/_not/value", |
|
| 42 |
cultivated,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/else/_alt/2", |
|
| 37 |
individualID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 38 |
occurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 39 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 40 |
taxonOccurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 41 |
oldGrowth,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1/_not/value", |
|
| 42 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2", |
|
| 43 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 44 |
verbatimLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2, |
|
| 45 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 43 | 46 |
landform,/location/landform, |
| 44 | 47 |
samplingProtocol,/location/locationevent/*_id/method/name, |
| 45 | 48 |
observationMeasure,/location/locationevent/*_id/method/observationmeasure, |
| inputs/SALVIAS-CSV/Plot/test.xml.ref | ||
|---|---|---|
| 21 | 21 |
</2> |
| 22 | 22 |
</_alt> |
| 23 | 23 |
</elevation_m> |
| 24 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality_description</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 24 | 25 |
<locationevent> |
| 25 | 26 |
<method_id><method><name>$plot_methodology</name></method></method_id> |
| 26 | 27 |
<project_id><project><projectname>$project</projectname></project></project_id> |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 30 | 30 |
<min>$MinimumElevationInMeters</min> |
| 31 | 31 |
</_avg> |
| 32 | 32 |
</elevation_m> |
| 33 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$Locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 33 | 34 |
<locationevent> |
| 34 | 35 |
<taxonoccurrence> |
| 35 | 36 |
<aggregateoccurrence> |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 9 | 9 |
MaximumElevation,/location/elevation_m/_alt/2/_avg/max, |
| 10 | 10 |
MinimumElevation,/location/elevation_m/_alt/2/_avg/min, |
| 11 |
CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 11 |
CollectorNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 12 |
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 12 | 13 |
DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 13 | 14 |
MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 14 | 15 |
YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 3 | 3 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 4 |
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", |
| 5 | 5 |
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", |
| 6 |
taxonobservation_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 6 |
taxonobservation_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
|
|
| 7 | 7 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
| 8 | 8 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 9 | 9 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
| inputs/TRTE/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| 12 | 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 14 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 16 | 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 17 | 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/REMIB/Specimen/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
GROUP BY acronym, accession_number |
| 38 | 38 |
HAVING count(*) > 1 |
| 39 | 39 |
-----" |
| 40 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 41 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 40 | 42 |
coll_day,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 41 | 43 |
coll_month,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 42 | 44 |
coll_year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 13 | 13 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
| 14 | 14 |
maximumElevationInMeters,/location/elevation_m/_alt/2/_avg/max, |
| 15 | 15 |
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min, |
| 16 |
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 17 |
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 17 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 18 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 19 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 18 | 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
| 19 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
| 20 | 22 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 20 | 20 |
<min>$MinimumElevation</min> |
| 21 | 21 |
</_avg> |
| 22 | 22 |
</elevation_m> |
| 23 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$Locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 23 | 24 |
<locationevent> |
| 24 | 25 |
<taxonoccurrence> |
| 25 | 26 |
<aggregateoccurrence> |
| inputs/VegBank/taxonimportance/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
taxonobservation_id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
| 2 |
taxonobservation_id,"/location/iscultivated/_or/1/_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: |
| 5 | 5 |
----- |
| inputs/TRTE/Specimen/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
<value>$verbatimElevation</value> |
| 32 | 32 |
</_units> |
| 33 | 33 |
</elevation_m> |
| 34 |
<iscultivated> |
|
| 35 |
<_locationnarrative_is_cultivated> |
|
| 36 |
<locationnarrative> |
|
| 37 |
<_join> |
|
| 38 |
<1>$locality</1> |
|
| 39 |
<3>$habitat</3> |
|
| 40 |
</_join> |
|
| 41 |
</locationnarrative> |
|
| 42 |
</_locationnarrative_is_cultivated> |
|
| 43 |
</iscultivated> |
|
| 34 | 44 |
<locationevent> |
| 35 | 45 |
<obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate> |
| 36 | 46 |
<obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate> |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()