Revision 4684
Added by Aaron Marcuse-Kubitza over 12 years ago
inputs/NY/Specimen/map.csv | ||
---|---|---|
20 | 20 |
MonthIdentified,monthIdentified,, |
21 | 21 |
DayIdentified,dayIdentified,, |
22 | 22 |
TypeStatus,TypeStatus,, |
23 |
CollectorNumber,OMIT,,"Not used [1], so does not need to be mapped. |
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24 |
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23 |
CollectorNumber,OMIT,,"Not used [1], so does not need to be mapped.
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24 |
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25 | 25 |
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL" |
26 | 26 |
FieldNumber,recordNumber,,Usage inconsistent with DwC definition |
27 | 27 |
Collector,recordedBy,, |
... | ... | |
34 | 34 |
Country,country,, |
35 | 35 |
StateProvince,stateProvince,, |
36 | 36 |
County,county,, |
37 |
Locality,locality,/_merge/1,
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37 |
Locality,locality,/_join/1,
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38 | 38 |
Longitude,verbatimLongitude,, |
39 | 39 |
Latitude,verbatimLatitude,, |
40 | 40 |
CoordinatePrecision,coordinatePrecision,, |
... | ... | |
49 | 49 |
PreviousCatalogNumber,otherCatalogNumbers,, |
50 | 50 |
RelationshipType,relationshipOfResource,, |
51 | 51 |
RelatedCatalogItem,relatedResourceID,, |
52 |
Notes,fieldNotes,/_merge/1,
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52 |
Notes,fieldNotes,/_join/1,
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53 | 53 |
Habitat,habitat,, |
54 |
PlantFungusDescription,fieldNotes,"/_merge/2/_label[label=""plant fungus""]/value",
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55 |
Substrate,locality,"/_merge/2/_label[label=""substrate""]/value",
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56 |
Vegetation,locality,"/_merge/3/_label[label=""vegetation""]/value",
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54 |
PlantFungusDescription,fieldNotes,"/_join/2/_label[label=""plant fungus""]/value",
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55 |
Substrate,locality,"/_join/2/_label[label=""substrate""]/value",
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56 |
Vegetation,locality,"/_join/3/_label[label=""vegetation""]/value",
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57 | 57 |
UniqueNYInternalRecordNumber,occurrenceID,, |
inputs/NY/Specimen/VegBIEN.csv | ||
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20 | 20 |
MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
21 | 21 |
YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
22 | 22 |
IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
23 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/1,
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24 |
PlantFungusDescription,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/2/_label[label=""plant fungus""]/value",
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23 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1,
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24 |
PlantFungusDescription,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/2/_label[label=""plant fungus""]/value",
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25 | 25 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,Usage inconsistent with DwC definition |
26 | 26 |
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" |
27 | 27 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
... | ... | |
50 | 50 |
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
51 | 51 |
MaximumDepth,"/location/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value", |
52 | 52 |
MinimumDepth,"/location/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value", |
53 |
Locality,/location/locationnarrative/_merge/1/_merge/1,
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54 |
Substrate,"/location/locationnarrative/_merge/1/_merge/2/_label[label=""substrate""]/value",
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55 |
Vegetation,"/location/locationnarrative/_merge/1/_merge/3/_label[label=""vegetation""]/value",
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53 |
Locality,/location/locationnarrative/_merge/1/_join/1,
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54 |
Substrate,"/location/locationnarrative/_merge/1/_join/2/_label[label=""substrate""]/value",
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55 |
Vegetation,"/location/locationnarrative/_merge/1/_join/3/_label[label=""vegetation""]/value",
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56 | 56 |
Habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
57 | 57 |
BasisOfRecord,,** No join mapping for BasisOfRecord ** |
58 |
CollectorNumber,,"** No join mapping for OMIT ** Not used [1], so does not need to be mapped. |
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59 |
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58 |
CollectorNumber,,"** No join mapping for OMIT ** Not used [1], so does not need to be mapped.
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59 |
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60 | 60 |
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL" |
61 | 61 |
DateLastModified,,** No join mapping for dcterms:modified ** |
62 | 62 |
JulianDay,,** No join mapping for day ** |
inputs/NY/Specimen/test.xml.ref | ||
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185 | 185 |
</collectiondate> |
186 | 186 |
<count>$IndividualCount</count> |
187 | 187 |
<notes> |
188 |
<_merge>
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188 |
<_join>
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189 | 189 |
<1>$Notes</1> |
190 | 190 |
<2> |
191 | 191 |
<_label> |
... | ... | |
193 | 193 |
<value>$PlantFungusDescription</value> |
194 | 194 |
</_label> |
195 | 195 |
</2> |
196 |
</_merge>
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196 |
</_join>
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197 | 197 |
</notes> |
198 | 198 |
<plantobservation> |
199 | 199 |
<collectionnumber>$FieldNumber</collectionnumber> |
... | ... | |
354 | 354 |
<locationnarrative> |
355 | 355 |
<_merge> |
356 | 356 |
<1> |
357 |
<_merge>
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357 |
<_join>
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358 | 358 |
<1>$Locality</1> |
359 | 359 |
<2> |
360 | 360 |
<_label> |
... | ... | |
368 | 368 |
<value>$Vegetation</value> |
369 | 369 |
</_label> |
370 | 370 |
</3> |
371 |
</_merge>
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371 |
</_join>
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372 | 372 |
</1> |
373 | 373 |
<3> |
374 | 374 |
<_label> |
inputs/UNCC/Specimen/map.csv | ||
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9 | 9 |
infraname,infraspecificEpithet,, |
10 | 10 |
SciName,scientificName,, |
11 | 11 |
authors,scientificNameAuthorship,, |
12 |
collector,recordedBy,/_merge/1,
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13 |
collector1,recordedBy,/_merge/2,
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14 |
collector2,recordedBy,/_merge/3,
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15 |
collector3,recordedBy,/_merge/4,
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12 |
collector,recordedBy,/_join/1,
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13 |
collector1,recordedBy,/_join/2,
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14 |
collector2,recordedBy,/_join/3,
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15 |
collector3,recordedBy,/_join/4,
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16 | 16 |
collectno,recordNumber,, |
17 | 17 |
collmonth,monthCollected,, |
18 | 18 |
collday,dayCollected,, |
... | ... | |
20 | 20 |
country,country,, |
21 | 21 |
state,stateProvince,, |
22 | 22 |
county,county,, |
23 |
campus,fieldNotes,"/_merge/5/_label[label=""campus""]/value",
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23 |
campus,fieldNotes,"/_join/5/_label[label=""campus""]/value",
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24 | 24 |
leaves,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
25 | 25 |
flower,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
26 | 26 |
fruit,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
27 | 27 |
root,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?" |
28 | 28 |
locality,locality,, |
29 | 29 |
habitat,habitat,, |
30 |
comment1,fieldNotes,/_merge/1,
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31 |
comment2,fieldNotes,/_merge/2,
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32 |
comment3,fieldNotes,/_merge/3,
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33 |
comment4,fieldNotes,/_merge/4,
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34 |
loanto,fieldNotes,"/_merge/6/_label[label=""loaned to""]/value",
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35 |
inorout,fieldNotes,"/_merge/7/_label[label=""in or out""]/value",
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30 |
comment1,fieldNotes,/_join/1,
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31 |
comment2,fieldNotes,/_join/2,
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32 |
comment3,fieldNotes,/_join/3,
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33 |
comment4,fieldNotes,/_join/4,
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34 |
loanto,fieldNotes,"/_join/6/_label[label=""loaned to""]/value",
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35 |
inorout,fieldNotes,"/_join/7/_label[label=""in or out""]/value",
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36 | 36 |
sheetno,associatedMedia,,? |
37 | 37 |
cultivated,cultivated,,Ignore other values |
38 | 38 |
filler,filler,,"Where used, same as family" |
inputs/UNCC/Specimen/VegBIEN.csv | ||
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7 | 7 |
collday,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
8 | 8 |
collmonth,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
9 | 9 |
collyear,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
10 |
comment1,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/1,
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11 |
comment2,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/2,
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12 |
comment3,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/3,
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13 |
comment4,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/4,
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14 |
campus,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/5/_label[label=""campus""]/value",
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15 |
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/6/_label[label=""loaned to""]/value",
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16 |
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/7/_label[label=""in or out""]/value",
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10 |
comment1,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1,
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11 |
comment2,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/2,
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12 |
comment3,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/3,
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13 |
comment4,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/4,
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14 |
campus,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/5/_label[label=""campus""]/value",
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15 |
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/6/_label[label=""loaned to""]/value",
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16 |
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/7/_label[label=""in or out""]/value",
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17 | 17 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
18 | 18 |
herbarium,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
19 | 19 |
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
... | ... | |
28 | 28 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname", |
29 | 29 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
30 | 30 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
31 |
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/1,
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32 |
collector1,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/2,
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33 |
collector2,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/3,
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34 |
collector3,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/4,
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31 |
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
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32 |
collector1,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/2,
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33 |
collector2,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/3,
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34 |
collector3,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/4,
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35 | 35 |
locality,/location/locationnarrative/_merge/1, |
36 | 36 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
37 | 37 |
filler,,"** No join mapping for filler ** Where used, same as family" |
inputs/UNCC/Specimen/test.xml.ref | ||
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59 | 59 |
</_date> |
60 | 60 |
</collectiondate> |
61 | 61 |
<notes> |
62 |
<_merge>
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62 |
<_join>
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63 | 63 |
<1>$comment1</1> |
64 | 64 |
<2>$comment2</2> |
65 | 65 |
<3>$comment3</3> |
... | ... | |
82 | 82 |
<value>$inorout</value> |
83 | 83 |
</_label> |
84 | 84 |
</7> |
85 |
</_merge>
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85 |
</_join>
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86 | 86 |
</notes> |
87 | 87 |
<plantobservation> |
88 | 88 |
<collectionnumber>$collectno</collectionnumber> |
... | ... | |
152 | 152 |
</plantconcept_id> |
153 | 153 |
</taxondetermination> |
154 | 154 |
<verbatimcollectorname> |
155 |
<_merge>
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155 |
<_join>
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156 | 156 |
<1>$collector</1> |
157 | 157 |
<2>$collector1</2> |
158 | 158 |
<3>$collector2</3> |
159 | 159 |
<4>$collector3</4> |
160 |
</_merge>
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160 |
</_join>
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161 | 161 |
</verbatimcollectorname> |
162 | 162 |
</taxonoccurrence> |
163 | 163 |
</locationevent> |
inputs/U/Specimen/map.csv | ||
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1 | 1 |
U,VegCore,Filter,Comments |
2 | 2 |
ID,occurrenceID,, |
3 | 3 |
Barcode,catalogNumber,, |
4 |
Collector,recordedBy,/_merge/1,
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4 |
Collector,recordedBy,/_join/1,
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5 | 5 |
Prefix,Prefix,,Not used |
6 | 6 |
Number,recordNumber,, |
7 | 7 |
Suffix,Suffix,,Not used |
8 |
Addcoll,recordedBy,/_merge/2,
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8 |
Addcoll,recordedBy,/_join/2,
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9 | 9 |
Colldd,dayCollected,, |
10 | 10 |
Collmm,monthCollected,, |
11 | 11 |
Collyy,yearCollected,, |
... | ... | |
15 | 15 |
cf,identificationQualifier,, |
16 | 16 |
Detby,identifiedBy,, |
17 | 17 |
Detyy,yearIdentified,, |
18 |
Gazetteer,verbatimLocality,"/_merge/1/_label[label=""gazetteer""]/value/_merge/1",
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19 |
Newgazett,verbatimLocality,"/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row
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18 |
Gazetteer,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/1",
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19 |
Newgazett,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/2",Only used in 1 row
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20 | 20 |
Majorarea,Majorarea,, |
21 | 21 |
Country,country,, |
22 |
Locnotes,verbatimLocality,/_merge/2,
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22 |
Locnotes,verbatimLocality,/_join/2,
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23 | 23 |
Coorsyst,Coorsyst,, |
24 | 24 |
Lat,decimalLatitude,, |
25 | 25 |
NS,NS,, |
inputs/U/Specimen/VegBIEN.csv | ||
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19 | 19 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
20 | 20 |
Detyy,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
21 | 21 |
cf,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
22 |
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/1,
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23 |
Addcoll,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/2,
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22 |
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
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23 |
Addcoll,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/2,
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24 | 24 |
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
25 |
Gazetteer,"/location/locationnarrative/_merge/2/_merge/1/_label[label=""gazetteer""]/value/_merge/1",
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26 |
Newgazett,"/location/locationnarrative/_merge/2/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row
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27 |
Locnotes,/location/locationnarrative/_merge/2/_merge/2,
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25 |
Gazetteer,"/location/locationnarrative/_merge/2/_join/1/_label[label=""gazetteer""]/value/_join/1",
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26 |
Newgazett,"/location/locationnarrative/_merge/2/_join/1/_label[label=""gazetteer""]/value/_join/2",Only used in 1 row
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27 |
Locnotes,/location/locationnarrative/_merge/2/_join/2,
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28 | 28 |
Ecology,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
29 | 29 |
Alt,,** No join mapping for Alt ** What is this? |
30 | 30 |
Alt2,,** No join mapping for Alt2 ** What is this? |
inputs/U/Specimen/test.xml.ref | ||
---|---|---|
138 | 138 |
<taxonfit>$cf</taxonfit> |
139 | 139 |
</taxondetermination> |
140 | 140 |
<verbatimcollectorname> |
141 |
<_merge>
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141 |
<_join>
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142 | 142 |
<1>$Collector</1> |
143 | 143 |
<2>$Addcoll</2> |
144 |
</_merge>
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144 |
</_join>
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145 | 145 |
</verbatimcollectorname> |
146 | 146 |
</taxonoccurrence> |
147 | 147 |
</locationevent> |
148 | 148 |
<locationnarrative> |
149 | 149 |
<_merge> |
150 | 150 |
<2> |
151 |
<_merge>
|
|
151 |
<_join>
|
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152 | 152 |
<1> |
153 | 153 |
<_label> |
154 | 154 |
<label>gazetteer</label> |
155 | 155 |
<value> |
156 |
<_merge>
|
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156 |
<_join>
|
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157 | 157 |
<1>$Gazetteer</1> |
158 | 158 |
<2>$Newgazett</2> |
159 |
</_merge>
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|
159 |
</_join>
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160 | 160 |
</value> |
161 | 161 |
</_label> |
162 | 162 |
</1> |
163 | 163 |
<2>$Locnotes</2> |
164 |
</_merge>
|
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164 |
</_join>
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165 | 165 |
</2> |
166 | 166 |
<3> |
167 | 167 |
<_label> |
Also available in: Unified diff
inputs/*/*/map.csv: Changed _merge to _join everywhere because _merge's (slower) duplicate elimination functionality is not needed (the combined columns do not both contain the same value, so they can simply be concatenated)