Revision 6384
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 24 | 24 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1", |
| 25 | 25 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric |
| 26 | 26 |
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 |
| 27 |
GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 28 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists/_alt/1", |
|
| 29 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
|
| 30 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 27 |
GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 28 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/1", |
|
| 29 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
|
| 30 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 31 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 31 | 32 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 32 | 33 |
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 33 | 34 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",Contains the binomial in addition to the authority |
| inputs/TRT/Specimen/test.xml.ref | ||
|---|---|---|
| 62 | 62 |
<2>$collectionID</2> |
| 63 | 63 |
</_join> |
| 64 | 64 |
</collectioncode_dwc> |
| 65 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 65 |
<institution_id> |
|
| 66 |
<sourcename> |
|
| 67 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 68 |
<name>$institutionCode</name> |
|
| 69 |
</sourcename> |
|
| 70 |
</institution_id> |
|
| 66 | 71 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 67 | 72 |
</specimenreplicate> |
| 68 | 73 |
</plantobservation> |
| ... | ... | |
| 335 | 340 |
</path> |
| 336 | 341 |
</_simplifyPath> |
| 337 | 342 |
</VegBIEN> |
| 338 |
Inserted 42 new rows into database |
|
| 343 |
Inserted 43 new rows into database |
|
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 57 | 57 |
<specimenreplicate> |
| 58 | 58 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 59 | 59 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| 60 |
<institution_id><sourcename><name>$InstitutionCode</name></sourcename></institution_id> |
|
| 60 |
<institution_id> |
|
| 61 |
<sourcename> |
|
| 62 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 63 |
<name>$InstitutionCode</name> |
|
| 64 |
</sourcename> |
|
| 65 |
</institution_id> |
|
| 61 | 66 |
</specimenreplicate> |
| 62 | 67 |
</plantobservation> |
| 63 | 68 |
</aggregateoccurrence> |
| inputs/TRTE/Specimen/test.xml.ref | ||
|---|---|---|
| 43 | 43 |
<2>$collectionID</2> |
| 44 | 44 |
</_join> |
| 45 | 45 |
</collectioncode_dwc> |
| 46 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 46 |
<institution_id> |
|
| 47 |
<sourcename> |
|
| 48 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 49 |
<name>$institutionCode</name> |
|
| 50 |
</sourcename> |
|
| 51 |
</institution_id> |
|
| 47 | 52 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 48 | 53 |
</specimenreplicate> |
| 49 | 54 |
</plantobservation> |
| ... | ... | |
| 297 | 302 |
</path> |
| 298 | 303 |
</_simplifyPath> |
| 299 | 304 |
</VegBIEN> |
| 300 |
Inserted 34 new rows into database |
|
| 305 |
Inserted 35 new rows into database |
|
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 9 | 9 |
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 |
| 10 | 10 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 11 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 12 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 11 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 12 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 13 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 13 | 14 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 14 | 15 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 15 | 16 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 17 | 17 |
<2>$collectionID</2> |
| 18 | 18 |
</_join> |
| 19 | 19 |
</collectioncode_dwc> |
| 20 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 20 |
<institution_id> |
|
| 21 |
<sourcename> |
|
| 22 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 23 |
<name>$institutionCode</name> |
|
| 24 |
</sourcename> |
|
| 25 |
</institution_id> |
|
| 21 | 26 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 22 | 27 |
</specimenreplicate> |
| 23 | 28 |
</plantobservation> |
| ... | ... | |
| 117 | 122 |
</path> |
| 118 | 123 |
</_simplifyPath> |
| 119 | 124 |
</VegBIEN> |
| 120 |
Inserted 25 new rows into database |
|
| 125 |
Inserted 26 new rows into database |
|
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
darwin:Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
| 17 | 17 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 18 | 18 |
darwin: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 |
| 19 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 19 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 21 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 21 | 22 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 22 | 23 |
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 23 | 24 |
darwin:Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 20 | 20 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
| 21 | 21 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 22 | 22 |
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 |
| 23 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
UniqueNYInternalRecordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 23 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
UniqueNYInternalRecordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 26 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 26 | 27 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 27 | 28 |
FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",Usage inconsistent with DwC definition |
| 28 | 29 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
Observations,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 20 | 20 |
Tree number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 21 | 21 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 22 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 22 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 | 23 |
Trunk,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
| 24 | 24 |
Liana presence,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue", |
| 25 | 25 |
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,Assuming units based on the range and precision of values |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 62 | 62 |
<plantobservation> |
| 63 | 63 |
<collectionnumber>$collectno</collectionnumber> |
| 64 | 64 |
<specimenreplicate> |
| 65 |
<institution_id><sourcename><name>$herbarium</name></sourcename></institution_id> |
|
| 65 |
<institution_id> |
|
| 66 |
<sourcename> |
|
| 67 |
<matched_source_id><source><shortname>$herbarium</shortname></source></matched_source_id> |
|
| 68 |
<name>$herbarium</name> |
|
| 69 |
</sourcename> |
|
| 70 |
</institution_id> |
|
| 66 | 71 |
<sourceaccessioncode>$accession</sourceaccessioncode> |
| 67 | 72 |
</specimenreplicate> |
| 68 | 73 |
</plantobservation> |
| ... | ... | |
| 296 | 301 |
</path> |
| 297 | 302 |
</_simplifyPath> |
| 298 | 303 |
</VegBIEN> |
| 299 |
Inserted 28 new rows into database |
|
| 304 |
Inserted 29 new rows into database |
|
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 69 | 69 |
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 70 | 70 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
| 71 | 71 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 72 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
|
|
| 73 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
|
|
| 72 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string |
|
| 73 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 74 | 74 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m, |
| 75 | 75 |
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| 76 | 76 |
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue", |
| inputs/REMIB/Specimen/test.xml.ref | ||
|---|---|---|
| 41 | 41 |
<plantobservation> |
| 42 | 42 |
<specimenreplicate> |
| 43 | 43 |
<catalognumber_dwc>$accession_number</catalognumber_dwc> |
| 44 |
<institution_id><sourcename><name>$acronym</name></sourcename></institution_id> |
|
| 44 |
<institution_id> |
|
| 45 |
<sourcename> |
|
| 46 |
<matched_source_id><source><shortname>$acronym</shortname></source></matched_source_id> |
|
| 47 |
<name>$acronym</name> |
|
| 48 |
</sourcename> |
|
| 49 |
</institution_id> |
|
| 45 | 50 |
</specimenreplicate> |
| 46 | 51 |
</plantobservation> |
| 47 | 52 |
</aggregateoccurrence> |
| ... | ... | |
| 199 | 204 |
</path> |
| 200 | 205 |
</_simplifyPath> |
| 201 | 206 |
</VegBIEN> |
| 202 |
Inserted 32 new rows into database |
|
| 207 |
Inserted 33 new rows into database |
|
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 22 | 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 23 | 23 |
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 |
| 24 | 24 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 27 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 27 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 28 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 28 | 29 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 29 | 30 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 30 | 31 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 17 | 17 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 18 | 18 |
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 |
| 19 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 19 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 21 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 21 | 22 |
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 22 | 23 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 23 | 24 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/TRTE/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 20 |
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 |
| 21 | 21 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 25 | 26 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 26 | 27 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 27 | 28 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
Observation Date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 17 | 17 |
Observation Date,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 18 | 18 |
Observation Date,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 19 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 19 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 | 20 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 21 | 21 |
Diameter at 1.3m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 7 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>)"
|
| 22 | 22 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
Observation Date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 17 | 17 |
Observation Date,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 18 | 18 |
Observation Date,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 19 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 19 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 | 20 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 21 | 21 |
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 7 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>)"
|
| 22 | 22 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 20 |
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 |
| 21 | 21 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 25 | 26 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 26 | 27 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 27 | 28 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 43 | 43 |
<2>$collectionID</2> |
| 44 | 44 |
</_join> |
| 45 | 45 |
</collectioncode_dwc> |
| 46 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 46 |
<institution_id> |
|
| 47 |
<sourcename> |
|
| 48 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 49 |
<name>$institutionCode</name> |
|
| 50 |
</sourcename> |
|
| 51 |
</institution_id> |
|
| 47 | 52 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 48 | 53 |
</specimenreplicate> |
| 49 | 54 |
</plantobservation> |
| ... | ... | |
| 299 | 304 |
</path> |
| 300 | 305 |
</_simplifyPath> |
| 301 | 306 |
</VegBIEN> |
| 302 |
Inserted 46 new rows into database |
|
| 307 |
Inserted 47 new rows into database |
|
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 20 | 20 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
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 |
| 22 | 22 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 23 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 23 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 26 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 26 | 27 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 27 | 28 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 28 | 29 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 48 | 48 |
<2>$collectionID</2> |
| 49 | 49 |
</_join> |
| 50 | 50 |
</collectioncode_dwc> |
| 51 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 51 |
<institution_id> |
|
| 52 |
<sourcename> |
|
| 53 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 54 |
<name>$institutionCode</name> |
|
| 55 |
</sourcename> |
|
| 56 |
</institution_id> |
|
| 52 | 57 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 53 | 58 |
</specimenreplicate> |
| 54 | 59 |
</plantobservation> |
| ... | ... | |
| 273 | 278 |
</path> |
| 274 | 279 |
</_simplifyPath> |
| 275 | 280 |
</VegBIEN> |
| 276 |
Inserted 36 new rows into database |
|
| 281 |
Inserted 37 new rows into database |
|
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 103 | 103 |
catalogNumber,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 104 | 104 |
collectionCode,//specimenreplicate/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 105 | 105 |
collectionID,//specimenreplicate/collectioncode_dwc, |
| 106 |
catalogNumber,"//sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 107 |
occurrenceID,"//sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 108 |
institutionCode,"//sourcename/name/_if[@name=""if specimen""]/then", |
|
| 106 |
catalogNumber,"//institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 107 |
occurrenceID,"//institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 108 |
institutionCode,"//institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 109 |
institutionCode,"//institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 109 | 110 |
occurrenceID,//specimenreplicate/sourceaccessioncode, |
| 110 | 111 |
stemCount,//plantobservation/stemcount, |
| 111 | 112 |
authorStemCode,//stemobservation/authorstemcode, |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 70 | 70 |
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 71 | 71 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
| 72 | 72 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 73 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
|
|
| 74 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
|
|
| 73 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string |
|
| 74 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 75 | 75 |
canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| 76 | 76 |
canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue", |
| 77 | 77 |
liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue", |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 13 | 13 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 14 | 14 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 15 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 16 |
ID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 15 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 |
ID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 17 | 17 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 18 | 18 |
Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 19 | 19 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/1, |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 20 |
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 |
| 21 | 21 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 25 | 26 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 26 | 27 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 27 | 28 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/QFA/Specimen/test.xml.ref | ||
|---|---|---|
| 43 | 43 |
<2>$collectionID</2> |
| 44 | 44 |
</_join> |
| 45 | 45 |
</collectioncode_dwc> |
| 46 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 46 |
<institution_id> |
|
| 47 |
<sourcename> |
|
| 48 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 49 |
<name>$institutionCode</name> |
|
| 50 |
</sourcename> |
|
| 51 |
</institution_id> |
|
| 47 | 52 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 48 | 53 |
</specimenreplicate> |
| 49 | 54 |
</plantobservation> |
| ... | ... | |
| 312 | 317 |
</path> |
| 313 | 318 |
</_simplifyPath> |
| 314 | 319 |
</VegBIEN> |
| 315 |
Inserted 46 new rows into database |
|
| 320 |
Inserted 47 new rows into database |
|
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 9 | 9 |
LatestDateCollected,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 10 | 10 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 11 | 11 |
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 |
| 12 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 13 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 12 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 13 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 14 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 14 | 15 |
ScientificNameOriginal,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
| 15 | 16 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 16 | 17 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/GBIF/Specimen/test.xml.ref | ||
|---|---|---|
| 25 | 25 |
<specimenreplicate> |
| 26 | 26 |
<catalognumber_dwc>$CatalogNO</catalognumber_dwc> |
| 27 | 27 |
<collectioncode_dwc>$CollectionCD</collectioncode_dwc> |
| 28 |
<institution_id><sourcename><name>$InstitutionCD</name></sourcename></institution_id> |
|
| 28 |
<institution_id> |
|
| 29 |
<sourcename> |
|
| 30 |
<matched_source_id><source><shortname>$InstitutionCD</shortname></source></matched_source_id> |
|
| 31 |
<name>$InstitutionCD</name> |
|
| 32 |
</sourcename> |
|
| 33 |
</institution_id> |
|
| 29 | 34 |
</specimenreplicate> |
| 30 | 35 |
</plantobservation> |
| 31 | 36 |
</aggregateoccurrence> |
| ... | ... | |
| 317 | 322 |
</path> |
| 318 | 323 |
</_simplifyPath> |
| 319 | 324 |
</VegBIEN> |
| 320 |
Inserted 46 new rows into database |
|
| 325 |
Inserted 47 new rows into database |
|
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 20 | 20 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
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 |
| 22 | 22 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 23 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 23 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 26 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 26 | 27 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 27 | 28 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 28 | 29 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/JBM/Specimen/test.xml.ref | ||
|---|---|---|
| 46 | 46 |
<2>$collectionID</2> |
| 47 | 47 |
</_join> |
| 48 | 48 |
</collectioncode_dwc> |
| 49 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 49 |
<institution_id> |
|
| 50 |
<sourcename> |
|
| 51 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 52 |
<name>$institutionCode</name> |
|
| 53 |
</sourcename> |
|
| 54 |
</institution_id> |
|
| 50 | 55 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 51 | 56 |
</specimenreplicate> |
| 52 | 57 |
</plantobservation> |
| ... | ... | |
| 260 | 265 |
</path> |
| 261 | 266 |
</_simplifyPath> |
| 262 | 267 |
</VegBIEN> |
| 263 |
Inserted 37 new rows into database |
|
| 268 |
Inserted 38 new rows into database |
|
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 20 |
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 |
| 21 | 21 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 25 | 26 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 26 | 27 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 27 | 28 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/HIBG/Specimen/test.xml.ref | ||
|---|---|---|
| 43 | 43 |
<2>$collectionID</2> |
| 44 | 44 |
</_join> |
| 45 | 45 |
</collectioncode_dwc> |
| 46 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 46 |
<institution_id> |
|
| 47 |
<sourcename> |
|
| 48 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 49 |
<name>$institutionCode</name> |
|
| 50 |
</sourcename> |
|
| 51 |
</institution_id> |
|
| 47 | 52 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 48 | 53 |
</specimenreplicate> |
| 49 | 54 |
</plantobservation> |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 77 | 77 |
dwc_dwcore_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 |
| 78 | 78 |
dwc_terms_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 |
| 79 | 79 |
dwc_terms_collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 80 |
conceptual_darwin_2003_1_0_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 81 |
dwc_dwcore_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 82 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 83 |
dwc_terms_catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 84 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 85 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 86 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 80 |
conceptual_darwin_2003_1_0_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 81 |
dwc_dwcore_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 82 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 83 |
dwc_terms_catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 84 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 85 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 86 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 87 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 88 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 89 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 87 | 90 |
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 88 | 91 |
dwc_terms_recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/1", |
| 89 | 92 |
conceptual_darwin_2003_1_0_FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec) |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 149 | 149 |
</collectioncode_dwc> |
| 150 | 150 |
<institution_id> |
| 151 | 151 |
<sourcename> |
| 152 |
<matched_source_id> |
|
| 153 |
<source> |
|
| 154 |
<shortname> |
|
| 155 |
<_alt> |
|
| 156 |
<0>$conceptual_darwin_2003_1_0_InstitutionCode</0> |
|
| 157 |
<1>$dwc_dwcore_InstitutionCode</1> |
|
| 158 |
<2>$dwc_terms_institutionCode</2> |
|
| 159 |
</_alt> |
|
| 160 |
</shortname> |
|
| 161 |
</source> |
|
| 162 |
</matched_source_id> |
|
| 152 | 163 |
<name> |
| 153 | 164 |
<_alt> |
| 154 | 165 |
<0>$conceptual_darwin_2003_1_0_InstitutionCode</0> |
| ... | ... | |
| 723 | 734 |
</path> |
| 724 | 735 |
</_simplifyPath> |
| 725 | 736 |
</VegBIEN> |
| 726 |
Inserted 46 new rows into database |
|
| 737 |
Inserted 47 new rows into database |
|
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 20 |
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 |
| 21 | 21 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 22 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 24 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 25 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 25 | 26 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 26 | 27 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 27 | 28 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/UBC/Specimen/test.xml.ref | ||
|---|---|---|
| 43 | 43 |
<2>$collectionID</2> |
| 44 | 44 |
</_join> |
| 45 | 45 |
</collectioncode_dwc> |
| 46 |
<institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id> |
|
| 46 |
<institution_id> |
|
| 47 |
<sourcename> |
|
| 48 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 49 |
<name>$institutionCode</name> |
|
| 50 |
</sourcename> |
|
| 51 |
</institution_id> |
|
| 47 | 52 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 48 | 53 |
</specimenreplicate> |
| 49 | 54 |
</plantobservation> |
| ... | ... | |
| 298 | 303 |
</path> |
| 299 | 304 |
</_simplifyPath> |
| 300 | 305 |
</VegBIEN> |
| 301 |
Inserted 42 new rows into database |
|
| 306 |
Inserted 43 new rows into database |
|
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 18 | 18 |
observationDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 19 | 19 |
pctCover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
| 20 | 20 |
collectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 21 |
observationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 22 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 21 |
observationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 22 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 23 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 23 | 24 |
observationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 24 | 25 |
plotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| 25 | 26 |
plotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| inputs/bien_web/observation/test.xml.ref | ||
|---|---|---|
| 17 | 17 |
<plantobservation> |
| 18 | 18 |
<collectionnumber>$collectionNumber</collectionnumber> |
| 19 | 19 |
<specimenreplicate> |
| 20 |
<institution_id><sourcename><name>$dataSourceName</name></sourcename></institution_id> |
|
| 20 |
<institution_id> |
|
| 21 |
<sourcename> |
|
| 22 |
<matched_source_id><source><shortname>$dataSourceName</shortname></source></matched_source_id> |
|
| 23 |
<name>$dataSourceName</name> |
|
| 24 |
</sourcename> |
|
| 25 |
</institution_id> |
|
| 21 | 26 |
<sourceaccessioncode>$observationID</sourceaccessioncode> |
| 22 | 27 |
</specimenreplicate> |
| 23 | 28 |
</plantobservation> |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 81 | 81 |
<specimenreplicate> |
| 82 | 82 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 83 | 83 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| 84 |
<institution_id><sourcename><name>$InstitutionCode</name></sourcename></institution_id> |
|
| 84 |
<institution_id> |
|
| 85 |
<sourcename> |
|
| 86 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 87 |
<name>$InstitutionCode</name> |
|
| 88 |
</sourcename> |
|
| 89 |
</institution_id> |
|
| 85 | 90 |
<sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode> |
| 86 | 91 |
</specimenreplicate> |
| 87 | 92 |
</plantobservation> |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 40 | 40 |
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/6/_label[label=""loaned to""]/value", |
| 41 | 41 |
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/7/_label[label=""in or out""]/value", |
| 42 | 42 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 43 |
accession,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1]
|
|
| 43 |
accession,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1] |
|
| 44 | 44 |
|
| 45 | 45 |
[1] Using the following query: |
| 46 | 46 |
----- |
| ... | ... | |
| 49 | 49 |
GROUP BY herbarium, accession |
| 50 | 50 |
HAVING count(*) > 1 |
| 51 | 51 |
-----" |
| 52 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 52 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 53 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 53 | 54 |
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,"Globally unique, although occasionally duplicated. [1] |
| 54 | 55 |
|
| 55 | 56 |
[1] Using the following query: |
| inputs/.herbaria/herbaria/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
herbaria,VegBIEN:/_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 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 3 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 4 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 4 | 5 |
herbariumAcronym,"/source/shortname/_if[@name=""if specimen""]/else", |
| 5 | 6 |
:herbarium,/source/sourcetype, |
| 6 | 7 |
City,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| inputs/REMIB/Specimen/VegBIEN.csv | ||
|---|---|---|
| 39 | 39 |
GROUP BY acronym, accession_number |
| 40 | 40 |
HAVING count(*) > 1 |
| 41 | 41 |
-----" |
| 42 |
accession_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/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]
|
|
| 42 |
accession_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/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]
|
|
| 43 | 43 |
|
| 44 | 44 |
[1] Using the following query: |
| 45 | 45 |
----- |
| ... | ... | |
| 48 | 48 |
GROUP BY acronym, accession_number |
| 49 | 49 |
HAVING count(*) > 1 |
| 50 | 50 |
-----" |
| 51 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 51 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 52 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 52 | 53 |
collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 53 | 54 |
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", |
| 54 | 55 |
genus,"/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/2", |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 81 | 81 |
</_alt> |
| 82 | 82 |
</catalognumber_dwc> |
| 83 | 83 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| 84 |
<institution_id><sourcename><name>$InstitutionCode</name></sourcename></institution_id> |
|
| 84 |
<institution_id> |
|
| 85 |
<sourcename> |
|
| 86 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 87 |
<name>$InstitutionCode</name> |
|
| 88 |
</sourcename> |
|
| 89 |
</institution_id> |
|
| 85 | 90 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
| 86 | 91 |
</specimenreplicate> |
| 87 | 92 |
</plantobservation> |
| ... | ... | |
| 360 | 365 |
</path> |
| 361 | 366 |
</_simplifyPath> |
| 362 | 367 |
</VegBIEN> |
| 363 |
Inserted 44 new rows into database |
|
| 368 |
Inserted 45 new rows into database |
|
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
Collect Date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 12 | 12 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 13 | 13 |
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 |
| 14 |
Accession Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 15 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 14 |
Accession Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 15 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 | 16 |
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 17 | 17 |
Full Taxon Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 18 | 18 |
Accession Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 9 | 9 |
collectiondate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 10 | 10 |
notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 11 | 11 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 12 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists",
|
|
| 12 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 13 | 13 |
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| 14 | 14 |
authorplantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
| 15 | 15 |
givenname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/1, |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 103 | 103 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 104 | 104 |
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 |
| 105 | 105 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 106 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 107 |
occurrenceID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/cond/_exists", |
|
| 108 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name/_if[@name=""if specimen""]/then", |
|
| 106 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 107 |
occurrenceID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 108 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 109 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 109 | 110 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 110 | 111 |
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| 111 | 112 |
authorStemCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium