Revision 3224
Added by Aaron Marcuse-Kubitza over 12 years ago
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref | ||
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7 | 7 |
<voucher> |
8 | 8 |
<specimenreplicate_id> |
9 | 9 |
<specimenreplicate> |
10 |
<taxonoccurrence_id><taxonoccurrence/></taxonoccurrence_id> |
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11 | 10 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
12 | 11 |
<catalognumber_dwc>14598</catalognumber_dwc> |
13 | 12 |
</specimenreplicate> |
... | ... | |
127 | 126 |
<voucher> |
128 | 127 |
<specimenreplicate_id> |
129 | 128 |
<specimenreplicate> |
130 |
<taxonoccurrence_id><taxonoccurrence/></taxonoccurrence_id> |
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131 | 129 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
132 | 130 |
<catalognumber_dwc>14669</catalognumber_dwc> |
133 | 131 |
</specimenreplicate> |
inputs/SALVIAS-CSV/test/import.organisms.out.ref | ||
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1 |
Inserted 48 new rows into database |
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1 |
Inserted 46 new rows into database |
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
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1 | 1 |
SALVIAS-CSV,VegBIEN:/plantobservation,Comments |
2 |
coll_number,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string
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voucher_string,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
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coll_number,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
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voucher_string,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
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4 | 4 |
census_date,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_date/year, |
5 | 5 |
plot_code,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}","Brad: Same as plotCode, above" |
6 | 6 |
PLOT_ID,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}","Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
inputs/CTFS/test/import.organisms.out.ref | ||
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1 |
Inserted 43 new rows into database |
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1 |
Inserted 41 new rows into database |
inputs/CTFS/maps/VegBIEN.organisms.csv | ||
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1 | 1 |
CTFS[VegX]:/*s/individualOrganismObservation,VegBIEN:/plantobservation,Comments |
2 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
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3 |
/simpleUserdefined[name=collectionDate]/value,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate",
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/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
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/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc", |
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/simpleUserdefined[name=collectionDate]/value,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate", |
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/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1", |
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5 | 5 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/area,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/area, |
6 | 6 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/elevation/_alt/1, |
7 | 7 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/CoordinateUncertaintyInMeters,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy, |
inputs/SALVIAS/test/VegBIEN.stems.xml.ref | ||
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9 | 9 |
<voucher> |
10 | 10 |
<specimenreplicate_id> |
11 | 11 |
<specimenreplicate> |
12 |
<taxonoccurrence_id><taxonoccurrence/></taxonoccurrence_id> |
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13 | 12 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
14 | 13 |
<catalognumber_dwc>1</catalognumber_dwc> |
15 | 14 |
</specimenreplicate> |
... | ... | |
32 | 31 |
<voucher> |
33 | 32 |
<specimenreplicate_id> |
34 | 33 |
<specimenreplicate> |
35 |
<taxonoccurrence_id><taxonoccurrence/></taxonoccurrence_id> |
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36 | 34 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
37 | 35 |
<catalognumber_dwc>2</catalognumber_dwc> |
38 | 36 |
</specimenreplicate> |
inputs/SALVIAS/test/import.stems.out.ref | ||
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1 |
Inserted 30 new rows into database |
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1 |
Inserted 28 new rows into database |
inputs/SALVIAS/maps/VegBIEN.stems.csv | ||
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1 | 1 |
SALVIAS,VegBIEN:/stemobservation,Comments |
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PlotObsID,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
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PlotObsID,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc", |
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3 | 3 |
NoInd,/*_id/plantobservation/stemcount, |
4 | 4 |
basal_diam,/basaldiameter, |
5 | 5 |
stem_canopy_form,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
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1 | 1 |
SALVIAS,VegBIEN:/plantobservation,Comments |
2 |
coll_number,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string
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SourceVoucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
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census_date,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date",
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coll_number,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
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SourceVoucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
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census_date,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date", |
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5 | 5 |
PlotCode,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}","Brad: Same as plotCode, above" |
6 | 6 |
PlotID,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}","Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
7 | 7 |
Line,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}", |
mappings/VegX-VegBIEN.organisms.csv | ||
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1 | 1 |
"VegX::[@xmlns:tcs=""http://www.tdwg.org/schemas/tcs/1.01""]/*s/individualOrganismObservation",VegBIEN:/plantobservation,Comments |
2 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
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/simpleUserdefined[name=collectionDate]/value,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate",
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/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
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/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc", |
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/simpleUserdefined[name=collectionDate]/value,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate", |
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/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1", |
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5 | 5 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/area,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/area, |
6 | 6 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/elevation/_alt/1, |
7 | 7 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/CoordinateUncertaintyInMeters,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy, |
mappings/VegX-VegBIEN.stems.csv | ||
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1 | 1 |
"VegX::[@xmlns:tcs=""http://www.tdwg.org/schemas/tcs/1.01""]/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]",VegBIEN:/stemobservation,Comments |
2 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
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/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/simpleUserdefined[name=collectionDate]/value,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate",
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/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
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/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc", |
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/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/simpleUserdefined[name=collectionDate]/value,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate", |
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/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/*_id/plantobservation/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1", |
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5 | 5 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/area,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/area, |
6 | 6 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/elevation/_alt/1, |
7 | 7 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/CoordinateUncertaintyInMeters,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy, |
Also available in: Unified diff
mappings/VegX-VegBIEN.stems.csv: Indirect voucher mappings: Removed no longer needed ":[*_id/taxonoccurrence]" because a specimenreplicate is a taxonoccurrence, so it doesn't need to have an empty taxonoccurrence