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Revision 4003

mappings/DwC2-VegBIEN.specimens.csv: Remapped institutionCode/collectionCode/catalogNumber location mappings to location.authorlocationcode

View differences:

inputs/QMOR/maps/VegBIEN.specimens.csv
1 1
QMOR[DwC],VegBIEN:,Comments
2
institutionCode,/location/authorlocationcode/_merge/1,
3
collectionCode,/location/authorlocationcode/_merge/2,
4
catalogNumber,/location/authorlocationcode/_merge/3,
2 5
verbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 6
maximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
4 7
minimumElevationInMeters,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
42 45
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
43 46
locality,/location/locationnarrative/_merge/1,
44 47
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?"
45
id,/location/sourceaccessioncode/_alt/1,
46
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
47
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
48
catalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
48
id,/location/sourceaccessioncode,
49 49
acceptedNameUsage,,** No non-empty join mapping for acceptedNameUsage ** 
50 50
basisOfRecord,,** No non-empty join mapping for basisOfRecord ** 
51 51
behavior,,** No non-empty join mapping for behavior ** 
mappings/for_review/DwC2-VegBIEN.specimens.csv
1 1
DwC,VegBIEN:,Comments
2
institutionCode,//location/authorlocationcode,
3
collectionCode,//location/authorlocationcode,
4
catalogNumber,//location/authorlocationcode,
2 5
verbatimElevation,//location/elevation,
3 6
maximumElevationInMeters,//location/elevation,
4 7
minimumElevationInMeters,//location/elevation,
......
54 57
habitat,"//location/locationnarrative/_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?"
55 58
locationID,//location/sourceaccessioncode,
56 59
occurrenceID,//location/sourceaccessioncode,
57
institutionCode,//location/sourceaccessioncode,
58
collectionCode,//location/sourceaccessioncode,
59
catalogNumber,//location/sourceaccessioncode,
60 60
acceptedNameUsage,,
61 61
acceptedNameUsageID,,
62 62
associatedMedia,,
mappings/DwC.cs-VegBIEN.specimens.csv
1 1
DwC,VegBIEN:,Comments
2
institutionCode,/location/authorlocationcode/_merge/1,
3
collectionCode,/location/authorlocationcode/_merge/2,
4
catalogNumber,/location/authorlocationcode/_merge/3,
2 5
verbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 6
maximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
4 7
maximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
......
83 86
locality,/location/locationnarrative/_merge/1,
84 87
verbatimLocality,/location/locationnarrative/_merge/2,
85 88
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?"
89
globalUniqueIdentifier,/location/sourceaccessioncode,
90
id,/location/sourceaccessioncode,
86 91
locationID,/location/sourceaccessioncode,
87
globalUniqueIdentifier,/location/sourceaccessioncode/_alt/1,
88
id,/location/sourceaccessioncode/_alt/1,
89
occurrenceID,/location/sourceaccessioncode/_alt/1,
90
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
91
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
92
catalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
92
occurrenceID,/location/sourceaccessioncode,
93 93
acceptedNameUsage,,
94 94
acceptedNameUsageID,,
95 95
accessRights,,** No non-empty join mapping for dcterms:accessRights ** 
inputs/MT/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$institutionCode</1>
7
                <2>$collectionCode</2>
8
            </_merge>
9
        </authorlocationcode>
4 10
        <locationdetermination>
5 11
            <namedplace_id>
6 12
                <_simplifyPath>
......
112 118
            </taxonoccurrence>
113 119
        </locationevent>
114 120
        <locationnarrative><_merge><1>$locality</1></_merge></locationnarrative>
115
        <sourceaccessioncode>
116
            <_alt>
117
                <1>$id</1>
118
                <2>
119
                    <_merge>
120
                        <1>$institutionCode</1>
121
                        <2>$collectionCode</2>
122
                    </_merge>
123
                </2>
124
            </_alt>
125
        </sourceaccessioncode>
121
        <sourceaccessioncode>$id</sourceaccessioncode>
126 122
    </location>
127 123
</VegBIEN>
128 124
Inserted 22 new rows into database
inputs/MT/maps/VegBIEN.specimens.csv
1 1
MT[DwC],VegBIEN:,Comments
2
institutionCode,/location/authorlocationcode/_merge/1,
3
collectionCode,/location/authorlocationcode/_merge/2,
2 4
continent,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,country,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=continent]/placename",
3 5
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
4 6
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/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 12
genus,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
11 13
family,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
12 14
locality,/location/locationnarrative/_merge/1,
13
id,/location/sourceaccessioncode/_alt/1,
14
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
15
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
15
id,/location/sourceaccessioncode,
16 16
basisOfRecord,,** No non-empty join mapping for basisOfRecord ** 
17 17
countryCode,,** No non-empty join mapping for countryCode ** 
18 18
datasetName,,** No non-empty join mapping for datasetName ** 
inputs/XAL/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$InstitutionCode</1>
7
                <2>$CollectionCode</2>
8
                <3>$CatalogNumber</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <2>
......
355 362
            </waterdepth>
356 363
        </locationevent>
357 364
        <locationnarrative><_merge><1>$Locality</1></_merge></locationnarrative>
358
        <sourceaccessioncode>
359
            <_alt>
360
                <2>
361
                    <_merge>
362
                        <1>$InstitutionCode</1>
363
                        <2>$CollectionCode</2>
364
                        <3>$CatalogNumber</3>
365
                    </_merge>
366
                </2>
367
            </_alt>
368
        </sourceaccessioncode>
369 365
    </location>
370 366
</VegBIEN>
371 367
Inserted 47 new rows into database
inputs/XAL/maps/VegBIEN.specimens.csv
1 1
"XAL[DwC,darwin:]:/content/record/",VegBIEN:,Comments
2
InstitutionCode,/location/authorlocationcode/_merge/1,
3
CollectionCode,/location/authorlocationcode/_merge/2,
4
CatalogNumber,/location/authorlocationcode/_merge/3,
2 5
MaximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
3 6
MinimumElevation,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
4 7
MinimumElevation,"/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
42 45
MaximumDepth,"/location/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
43 46
MinimumDepth,"/location/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
44 47
Locality,/location/locationnarrative/_merge/1,
45
InstitutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
46
CollectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
47
CatalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
48 48
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord ** 
49 49
DateLastModified,,** No non-empty join mapping for DateLastModified ** 
50 50
JulianDay,,** No non-empty join mapping for JulianDay ** 
inputs/NY/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$InstitutionCode</1>
7
                <2>$CollectionCode</2>
8
                <3>$CatalogNumber</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <2>
......
412 419
                </3>
413 420
            </_merge>
414 421
        </locationnarrative>
415
        <sourceaccessioncode>
416
            <_alt>
417
                <1>$UniqueNYInternalRecordNumber</1>
418
                <2>
419
                    <_merge>
420
                        <1>$InstitutionCode</1>
421
                        <2>$CollectionCode</2>
422
                        <3>$CatalogNumber</3>
423
                    </_merge>
424
                </2>
425
            </_alt>
426
        </sourceaccessioncode>
422
        <sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode>
427 423
    </location>
428 424
</VegBIEN>
429 425
Inserted 39 new rows into database
inputs/NY/maps/VegBIEN.specimens.csv
1 1
NY[DwC],VegBIEN:,Comments
2
InstitutionCode,/location/authorlocationcode/_merge/1,
3
CollectionCode,/location/authorlocationcode/_merge/2,
4
CatalogNumber,/location/authorlocationcode/_merge/3,
2 5
MaximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
3 6
MinimumElevation,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value/_nullIf:[null=.]/value",
4 7
MinimumElevation,"/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value/_nullIf:[null=.]/value",
......
48 51
Substrate,"/location/locationnarrative/_merge/1/_merge/2/_label[label=""substrate""]/value",
49 52
Vegetation,"/location/locationnarrative/_merge/1/_merge/3/_label[label=""vegetation""]/value",
50 53
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?"
51
UniqueNYInternalRecordNumber,/location/sourceaccessioncode/_alt/1,
52
InstitutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
53
CollectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
54
CatalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
54
UniqueNYInternalRecordNumber,/location/sourceaccessioncode,
55 55
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord ** 
56 56
DateLastModified,,** No non-empty join mapping for DateLastModified ** 
57 57
JulianDay,,** No non-empty join mapping for JulianDay ** 
inputs/UNCC/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode><_merge><2>$herbarium</2></_merge></authorlocationcode>
4 5
        <locationdetermination>
5 6
            <namedplace_id>
6 7
                <_simplifyPath>
......
202 203
                </3>
203 204
            </_merge>
204 205
        </locationnarrative>
205
        <sourceaccessioncode>
206
            <_alt>
207
                <1>$accession</1>
208
                <2><_merge><2>$herbarium</2></_merge></2>
209
            </_alt>
210
        </sourceaccessioncode>
206
        <sourceaccessioncode>$accession</sourceaccessioncode>
211 207
    </location>
212 208
</VegBIEN>
213 209
Inserted 21 new rows into database
inputs/UNCC/maps/VegBIEN.specimens.csv
1 1
UNCC[DwC],VegBIEN:,Comments
2
herbarium,/location/authorlocationcode/_merge/2,
2 3
county,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
3 4
state,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",
4 5
country,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",
......
29 30
collector3,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/4,
30 31
locality,/location/locationnarrative/_merge/1,
31 32
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?"
32
accession,/location/sourceaccessioncode/_alt/1,
33
herbarium,/location/sourceaccessioncode/_alt/2/_merge/2,
33
accession,/location/sourceaccessioncode,
34 34
filler,,"Where used, same as family"
35 35
flower,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
36 36
fruit,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
inputs/ACAD/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$institutionCode</1>
7
                <2>$collectionCode</2>
8
                <3>$catalogNumber</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <1>
......
180 187
                </3>
181 188
            </_merge>
182 189
        </locationnarrative>
183
        <sourceaccessioncode>
184
            <_alt>
185
                <1>$id</1>
186
                <2>
187
                    <_merge>
188
                        <1>$institutionCode</1>
189
                        <2>$collectionCode</2>
190
                        <3>$catalogNumber</3>
191
                    </_merge>
192
                </2>
193
            </_alt>
194
        </sourceaccessioncode>
190
        <sourceaccessioncode>$id</sourceaccessioncode>
195 191
    </location>
196 192
</VegBIEN>
197 193
Inserted 38 new rows into database
inputs/ACAD/maps/VegBIEN.specimens.csv
1 1
ACAD[DwC],VegBIEN:,Comments
2
institutionCode,/location/authorlocationcode/_merge/1,
3
collectionCode,/location/authorlocationcode/_merge/2,
4
catalogNumber,/location/authorlocationcode/_merge/3,
2 5
verbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 6
decimalLatitude,"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value",
4 7
decimalLongitude,"/location/locationdetermination/longitude/_alt/1/_nullIf:[null=0,type=float]/value",
......
30 33
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
31 34
locality,/location/locationnarrative/_merge/1,
32 35
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?"
33
id,/location/sourceaccessioncode/_alt/1,
34
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
35
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
36
catalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
36
id,/location/sourceaccessioncode,
37 37
basisOfRecord,,** No non-empty join mapping for basisOfRecord ** 
38 38
bibliographicCitation,,** No non-empty join mapping for bibliographicCitation ** 
39 39
dynamicProperties,,** No non-empty join mapping for dynamicProperties ** 
inputs/REMIB/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode><_merge><2>$acronym</2></_merge></authorlocationcode>
4 5
        <locationdetermination>
5 6
            <latitude>
6 7
                <_alt>
......
157 158
                </3>
158 159
            </_merge>
159 160
        </locationnarrative>
160
        <sourceaccessioncode>
161
            <_alt>
162
                <1>$accession_number</1>
163
                <2><_merge><2>$acronym</2></_merge></2>
164
            </_alt>
165
        </sourceaccessioncode>
161
        <sourceaccessioncode>$accession_number</sourceaccessioncode>
166 162
    </location>
167 163
</VegBIEN>
168 164
Inserted 26 new rows into database
inputs/REMIB/maps/VegBIEN.specimens.csv
1 1
REMIB[DwC],VegBIEN:,Comments
2
acronym,/location/authorlocationcode/_merge/2,
2 3
lat_deg,"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value",
3 4
long_deg,"/location/locationdetermination/longitude/_alt/1/_nullIf:[null=0,type=float]/value",
4 5
county,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
......
15 16
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
16 17
locality,/location/locationnarrative/_merge/1,
17 18
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?"
18
accession_number,/location/sourceaccessioncode/_alt/1,
19
acronym,/location/sourceaccessioncode/_alt/2/_merge/2,
19
accession_number,/location/sourceaccessioncode,
20 20
lat_min,,** No input mapping for lat_min ** 
21 21
lat_sec,,** No input mapping for lat_sec ** 
22 22
long_min,,** No input mapping for long_min ** 
inputs/U/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode><_merge><3>$Barcode</3></_merge></authorlocationcode>
4 5
        <locationdetermination>
5 6
            <latitude>
6 7
                <_alt>
......
207 208
                </3>
208 209
            </_merge>
209 210
        </locationnarrative>
210
        <sourceaccessioncode>
211
            <_alt>
212
                <1>$ID</1>
213
                <2><_merge><3>$Barcode</3></_merge></2>
214
            </_alt>
215
        </sourceaccessioncode>
211
        <sourceaccessioncode>$ID</sourceaccessioncode>
216 212
    </location>
217 213
</VegBIEN>
218 214
Inserted 26 new rows into database
inputs/U/maps/VegBIEN.specimens.csv
1 1
U[DwC],VegBIEN:,Comments
2
Barcode,/location/authorlocationcode/_merge/3,
2 3
Lat,"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value",
3 4
Long,"/location/locationdetermination/longitude/_alt/1/_nullIf:[null=0,type=float]/value",
4 5
Country,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",
......
22 23
Newgazett,"/location/locationnarrative/_merge/2/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row
23 24
Locnotes,/location/locationnarrative/_merge/2/_merge/2,
24 25
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?"
25
ID,/location/sourceaccessioncode/_alt/1,
26
Barcode,/location/sourceaccessioncode/_alt/2/_merge/3,
26
ID,/location/sourceaccessioncode,
27 27
Alt,,What is this?
28 28
Alt2,,What is this?
29 29
Coorsyst,,** No input mapping for Coorsyst ** 
inputs/ARIZ/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$InstitutionCode</1>
7
                <2>$CollectionCode</2>
8
                <3>$CatalogNumberNumeric</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <1>
......
384 391
            </waterdepth>
385 392
        </locationevent>
386 393
        <locationnarrative><_merge><1>$Locality</1></_merge></locationnarrative>
387
        <sourceaccessioncode>
388
            <_alt>
389
                <1>$GlobalUniqueIdentifier</1>
390
                <2>
391
                    <_merge>
392
                        <1>$InstitutionCode</1>
393
                        <2>$CollectionCode</2>
394
                        <3>$CatalogNumberNumeric</3>
395
                    </_merge>
396
                </2>
397
            </_alt>
398
        </sourceaccessioncode>
394
        <sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode>
399 395
    </location>
400 396
</VegBIEN>
401 397
Inserted 38 new rows into database
inputs/ARIZ/maps/VegBIEN.specimens.csv
1 1
ARIZ[DwC],VegBIEN:,Comments
2
InstitutionCode,/location/authorlocationcode/_merge/1,
3
CollectionCode,/location/authorlocationcode/_merge/2,
4
CatalogNumberNumeric,/location/authorlocationcode/_merge/3,
2 5
VerbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 6
MaximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
4 7
MinimumElevationInMeters,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
50 53
MaximumDepthInMeters,"/location/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
51 54
MinimumDepthInMeters,"/location/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
52 55
Locality,/location/locationnarrative/_merge/1,
53
GlobalUniqueIdentifier,/location/sourceaccessioncode/_alt/1,
54
InstitutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
55
CollectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
56
CatalogNumberNumeric,/location/sourceaccessioncode/_alt/2/_merge/3,
56
GlobalUniqueIdentifier,/location/sourceaccessioncode,
57 57
AgeClass,,** No non-empty join mapping for lifeStage ** 
58 58
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord ** 
59 59
CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric
inputs/GBIF/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$InstitutionCD</1>
7
                <2>$CollectionCD</2>
8
                <3>$CatalogNO</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <2>
......
218 225
            </taxonoccurrence>
219 226
        </locationevent>
220 227
        <locationnarrative><_merge><1>$Locality</1></_merge></locationnarrative>
221
        <sourceaccessioncode>
222
            <_alt>
223
                <2>
224
                    <_merge>
225
                        <1>$InstitutionCD</1>
226
                        <2>$CollectionCD</2>
227
                        <3>$CatalogNO</3>
228
                    </_merge>
229
                </2>
230
            </_alt>
231
        </sourceaccessioncode>
232 228
    </location>
233 229
</VegBIEN>
234 230
Inserted 31 new rows into database
inputs/GBIF/maps/VegBIEN.specimens.csv
1 1
GBIF[DwC],VegBIEN:,Comments
2
InstitutionCD,/location/authorlocationcode/_merge/1,
3
CollectionCD,/location/authorlocationcode/_merge/2,
4
CatalogNO,/location/authorlocationcode/_merge/3,
2 5
MaximumElevationInMeter,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
3 6
MinimumElevationInMeter,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
4 7
MinimumElevationInMeter,"/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
26 29
Family,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
27 30
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
28 31
Locality,/location/locationnarrative/_merge/1,
29
InstitutionCD,/location/sourceaccessioncode/_alt/2/_merge/1,
30
CollectionCD,/location/sourceaccessioncode/_alt/2/_merge/2,
31
CatalogNO,/location/sourceaccessioncode/_alt/2/_merge/3,
32 32
GBIFFamilyOriginal,,** No non-empty join mapping for originalNameUsage/_alt/2/_name/first ** DwC doesn't fully support taxonomic redeterminations
33 33
GBIFGenusOriginal,,** No non-empty join mapping for originalNameUsage/_alt/2/_name/middle ** DwC doesn't fully support taxonomic redeterminations
34 34
LastDateModified,,** No non-empty join mapping for DateLastModified ** 
inputs/NCU-NCSC/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <2>$SeriesName</2>
7
                <3>$Barcode</3>
8
            </_merge>
9
        </authorlocationcode>
4 10
        <elevation>
5 11
            <_alt>
6 12
                <1>
......
132 138
                </taxondetermination>
133 139
            </taxonoccurrence>
134 140
        </locationevent>
135
        <sourceaccessioncode>
136
            <_alt>
137
                <1>$Accession Number</1>
138
                <2>
139
                    <_merge>
140
                        <2>$SeriesName</2>
141
                        <3>$Barcode</3>
142
                    </_merge>
143
                </2>
144
            </_alt>
145
        </sourceaccessioncode>
141
        <sourceaccessioncode>$Accession Number</sourceaccessioncode>
146 142
    </location>
147 143
</VegBIEN>
148 144
Inserted 26 new rows into database
inputs/NCU-NCSC/maps/VegBIEN.specimens.csv
1 1
NCU-NCSC[DwC],VegBIEN:,Comments
2
SeriesName,/location/authorlocationcode/_merge/2,
3
Barcode,/location/authorlocationcode/_merge/3,
2 4
Elevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 5
Accuracy,/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,
4 6
Lat (-=S),"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",
......
13 15
Cultivated?,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Yes=cultivated,No=wild]/value",
14 16
Cultivated?,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Yes=cultivated,No=wild]/value",
15 17
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
16
Accession Number,/location/sourceaccessioncode/_alt/1,
17
SeriesName,/location/sourceaccessioncode/_alt/2/_merge/2,
18
Barcode,/location/sourceaccessioncode/_alt/2/_merge/3,
18
Accession Number,/location/sourceaccessioncode,
19 19
Alt E/W,,** No input mapping for Alt E/W ** 
20 20
Alt N/S,,** No input mapping for Alt N/S ** 
21 21
FIPS,,FIPS county code
inputs/SpeciesLink/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>
7
                    <_alt>
8
                        <0>$dwc_dwcore_InstitutionCode</0>
9
                        <1>$conceptual_darwin_2003_1_0_InstitutionCode</1>
10
                        <2>$dwc_terms_institutionCode</2>
11
                    </_alt>
12
                </1>
13
                <2>
14
                    <_alt>
15
                        <0>$dwc_dwcore_CollectionCode</0>
16
                        <1>$conceptual_darwin_2003_1_0_CollectionCode</1>
17
                        <2>$dwc_terms_collectionCode</2>
18
                    </_alt>
19
                </2>
20
                <3>
21
                    <_alt>
22
                        <0>$dwc_dwcore_CatalogNumber</0>
23
                        <1>$conceptual_darwin_2003_1_0_CatalogNumber</1>
24
                        <2>$dwc_terms_catalogNumber</2>
25
                    </_alt>
26
                </3>
27
            </_merge>
28
        </authorlocationcode>
4 29
        <elevation>
5 30
            <_alt>
6 31
                <2>
......
615 640
                </1>
616 641
            </_merge>
617 642
        </locationnarrative>
618
        <sourceaccessioncode>
619
            <_alt>
620
                <1>$dwc_dwcore_GlobalUniqueIdentifier</1>
621
                <2>
622
                    <_merge>
623
                        <1>
624
                            <_alt>
625
                                <0>$dwc_dwcore_InstitutionCode</0>
626
                                <1>$conceptual_darwin_2003_1_0_InstitutionCode</1>
627
                                <2>$dwc_terms_institutionCode</2>
628
                            </_alt>
629
                        </1>
630
                        <2>
631
                            <_alt>
632
                                <0>$dwc_dwcore_CollectionCode</0>
633
                                <1>$conceptual_darwin_2003_1_0_CollectionCode</1>
634
                                <2>$dwc_terms_collectionCode</2>
635
                            </_alt>
636
                        </2>
637
                        <3>
638
                            <_alt>
639
                                <0>$dwc_dwcore_CatalogNumber</0>
640
                                <1>$conceptual_darwin_2003_1_0_CatalogNumber</1>
641
                                <2>$dwc_terms_catalogNumber</2>
642
                            </_alt>
643
                        </3>
644
                    </_merge>
645
                </2>
646
            </_alt>
647
        </sourceaccessioncode>
643
        <sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode>
648 644
    </location>
649 645
</VegBIEN>
650 646
Inserted 40 new rows into database
inputs/SpeciesLink/maps/VegBIEN.specimens.csv
1 1
"SpeciesLink[DwC,dwc_dwcore_,dwc_curatorial_,dwc_geospatial_,http__purl_org_,dwc_terms_,conceptual_darwin_2003_1_0_]",VegBIEN:,Comments
2
InstitutionCode,/location/authorlocationcode/_merge/1,
3
institutionCode,/location/authorlocationcode/_merge/1,
4
CollectionCode,/location/authorlocationcode/_merge/2,
5
collectionCode,/location/authorlocationcode/_merge/2,
6
CatalogNumber,/location/authorlocationcode/_merge/3,
7
catalogNumber,/location/authorlocationcode/_merge/3,
2 8
MaximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
3 9
MaximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
4 10
maximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
......
100 106
minimumDepthInMeters,"/location/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
101 107
Locality,/location/locationnarrative/_merge/1,
102 108
locality,/location/locationnarrative/_merge/1,
103
GlobalUniqueIdentifier,/location/sourceaccessioncode/_alt/1,
104
InstitutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
105
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
106
CollectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
107
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
108
CatalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
109
catalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
109
GlobalUniqueIdentifier,/location/sourceaccessioncode,
110 110
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord ** 
111 111
DateLastModified,,** No non-empty join mapping for DateLastModified ** 
112 112
DayOfYear,,** No non-empty join mapping for JulianDay ** 
inputs/MO/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$InstitutionCode</1>
7
                <2>$CollectionCode</2>
8
                <3>$CatalogNumber</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <2>
......
274 281
            </taxonoccurrence>
275 282
        </locationevent>
276 283
        <locationnarrative><_merge><1>$Locality</1></_merge></locationnarrative>
277
        <sourceaccessioncode>
278
            <_alt>
279
                <2>
280
                    <_merge>
281
                        <1>$InstitutionCode</1>
282
                        <2>$CollectionCode</2>
283
                        <3>$CatalogNumber</3>
284
                    </_merge>
285
                </2>
286
            </_alt>
287
        </sourceaccessioncode>
288 284
    </location>
289 285
</VegBIEN>
290 286
Inserted 38 new rows into database
inputs/MO/maps/VegBIEN.specimens.csv
1 1
MO[DwC],VegBIEN:,Comments
2
InstitutionCode,/location/authorlocationcode/_merge/1,
3
CollectionCode,/location/authorlocationcode/_merge/2,
4
CatalogNumber,/location/authorlocationcode/_merge/3,
2 5
MaximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
3 6
MinimumElevation,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
4 7
MinimumElevation,"/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
31 34
Kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",
32 35
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
33 36
Locality,/location/locationnarrative/_merge/1,
34
InstitutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
35
CollectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
36
CatalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
37 37
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord ** 
38 38
DateLastModified,,** No non-empty join mapping for DateLastModified ** 
39 39
TypeStatus,,** No non-empty join mapping for TypeStatus ** 
inputs/QMOR/test/import.specimens.xml.ref
1 1
Put template:
2 2
<VegBIEN>
3 3
    <location id="-1">
4
        <authorlocationcode>
5
            <_merge>
6
                <1>$institutionCode</1>
7
                <2>$collectionCode</2>
8
                <3>$catalogNumber</3>
9
            </_merge>
10
        </authorlocationcode>
4 11
        <elevation>
5 12
            <_alt>
6 13
                <1>
......
285 292
                </3>
286 293
            </_merge>
287 294
        </locationnarrative>
288
        <sourceaccessioncode>
289
            <_alt>
290
                <1>$id</1>
291
                <2>
292
                    <_merge>
293
                        <1>$institutionCode</1>
294
                        <2>$collectionCode</2>
295
                        <3>$catalogNumber</3>
296
                    </_merge>
297
                </2>
298
            </_alt>
299
        </sourceaccessioncode>
295
        <sourceaccessioncode>$id</sourceaccessioncode>
300 296
    </location>
301 297
</VegBIEN>
302 298
Inserted 34 new rows into database
mappings/DwC2-VegBIEN.specimens.csv
1 1
DwC,VegBIEN:,Comments
2
institutionCode,/location/authorlocationcode/_merge/1,
3
collectionCode,/location/authorlocationcode/_merge/2,
4
catalogNumber,/location/authorlocationcode/_merge/3,
2 5
verbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 6
maximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
4 7
minimumElevationInMeters,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
53 56
verbatimLocality,/location/locationnarrative/_merge/2,
54 57
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?"
55 58
locationID,/location/sourceaccessioncode,
56
occurrenceID,/location/sourceaccessioncode/_alt/1,
57
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
58
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
59
catalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
59
occurrenceID,/location/sourceaccessioncode,
60 60
acceptedNameUsage,,
61 61
acceptedNameUsageID,,
62 62
associatedMedia,,
mappings/DwC-VegBIEN.specimens.csv
1 1
DwC,VegBIEN:,Comments
2
InstitutionCode,/location/authorlocationcode/_merge/1,
3
institutionCode,/location/authorlocationcode/_merge/1,
4
CollectionCode,/location/authorlocationcode/_merge/2,
5
collectionCode,/location/authorlocationcode/_merge/2,
6
CatalogNumber,/location/authorlocationcode/_merge/3,
7
catalogNumber,/location/authorlocationcode/_merge/3,
2 8
VerbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
3 9
verbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
4 10
MaximumElevation,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
......
167 173
verbatimLocality,/location/locationnarrative/_merge/2,
168 174
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?"
169 175
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?"
176
GlobalUniqueIdentifier,/location/sourceaccessioncode,
177
Id,/location/sourceaccessioncode,
170 178
LocationID,/location/sourceaccessioncode,
179
OccurrenceID,/location/sourceaccessioncode,
180
globalUniqueIdentifier,/location/sourceaccessioncode,
181
id,/location/sourceaccessioncode,
171 182
locationID,/location/sourceaccessioncode,
172
GlobalUniqueIdentifier,/location/sourceaccessioncode/_alt/1,
173
Id,/location/sourceaccessioncode/_alt/1,
174
OccurrenceID,/location/sourceaccessioncode/_alt/1,
175
globalUniqueIdentifier,/location/sourceaccessioncode/_alt/1,
176
id,/location/sourceaccessioncode/_alt/1,
177
occurrenceID,/location/sourceaccessioncode/_alt/1,
178
InstitutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
179
institutionCode,/location/sourceaccessioncode/_alt/2/_merge/1,
180
CollectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
181
collectionCode,/location/sourceaccessioncode/_alt/2/_merge/2,
182
CatalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
183
catalogNumber,/location/sourceaccessioncode/_alt/2/_merge/3,
183
occurrenceID,/location/sourceaccessioncode,
184 184
AcceptedNameUsage,,** No non-empty join mapping for acceptedNameUsage ** 
185 185
AcceptedNameUsageID,,** No non-empty join mapping for acceptedNameUsageID ** 
186 186
AccessRights,,** No non-empty join mapping for accessRights ** 

Also available in: Unified diff