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Revision 4684

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)

View differences:

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.
24

  
23
CollectorNumber,OMIT,,"Not used [1], so does not need to be mapped.

24

  
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,
37
Locality,locality,/_join/1,
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,
52
Notes,fieldNotes,/_join/1,
53 53
Habitat,habitat,,
54
PlantFungusDescription,fieldNotes,"/_merge/2/_label[label=""plant fungus""]/value",
55
Substrate,locality,"/_merge/2/_label[label=""substrate""]/value",
56
Vegetation,locality,"/_merge/3/_label[label=""vegetation""]/value",
54
PlantFungusDescription,fieldNotes,"/_join/2/_label[label=""plant fungus""]/value",
55
Substrate,locality,"/_join/2/_label[label=""substrate""]/value",
56
Vegetation,locality,"/_join/3/_label[label=""vegetation""]/value",
57 57
UniqueNYInternalRecordNumber,occurrenceID,,
inputs/NY/Specimen/VegBIEN.csv
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,
24
PlantFungusDescription,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/2/_label[label=""plant fungus""]/value",
23
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1,
24
PlantFungusDescription,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/2/_label[label=""plant fungus""]/value",
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,
54
Substrate,"/location/locationnarrative/_merge/1/_merge/2/_label[label=""substrate""]/value",
55
Vegetation,"/location/locationnarrative/_merge/1/_merge/3/_label[label=""vegetation""]/value",
53
Locality,/location/locationnarrative/_merge/1/_join/1,
54
Substrate,"/location/locationnarrative/_merge/1/_join/2/_label[label=""substrate""]/value",
55
Vegetation,"/location/locationnarrative/_merge/1/_join/3/_label[label=""vegetation""]/value",
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.
59

  
58
CollectorNumber,,"** No join mapping for OMIT ** Not used [1], so does not need to be mapped.

59

  
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
185 185
                            </collectiondate>
186 186
                            <count>$IndividualCount</count>
187 187
                            <notes>
188
                                <_merge>
188
                                <_join>
189 189
                                    <1>$Notes</1>
190 190
                                    <2>
191 191
                                        <_label>
......
193 193
                                            <value>$PlantFungusDescription</value>
194 194
                                        </_label>
195 195
                                    </2>
196
                                </_merge>
196
                                </_join>
197 197
                            </notes>
198 198
                            <plantobservation>
199 199
                                <collectionnumber>$FieldNumber</collectionnumber>
......
354 354
                <locationnarrative>
355 355
                    <_merge>
356 356
                        <1>
357
                            <_merge>
357
                            <_join>
358 358
                                <1>$Locality</1>
359 359
                                <2>
360 360
                                    <_label>
......
368 368
                                        <value>$Vegetation</value>
369 369
                                    </_label>
370 370
                                </3>
371
                            </_merge>
371
                            </_join>
372 372
                        </1>
373 373
                        <3>
374 374
                            <_label>
inputs/UNCC/Specimen/map.csv
9 9
infraname,infraspecificEpithet,,
10 10
SciName,scientificName,,
11 11
authors,scientificNameAuthorship,,
12
collector,recordedBy,/_merge/1,
13
collector1,recordedBy,/_merge/2,
14
collector2,recordedBy,/_merge/3,
15
collector3,recordedBy,/_merge/4,
12
collector,recordedBy,/_join/1,
13
collector1,recordedBy,/_join/2,
14
collector2,recordedBy,/_join/3,
15
collector3,recordedBy,/_join/4,
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",
23
campus,fieldNotes,"/_join/5/_label[label=""campus""]/value",
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,
31
comment2,fieldNotes,/_merge/2,
32
comment3,fieldNotes,/_merge/3,
33
comment4,fieldNotes,/_merge/4,
34
loanto,fieldNotes,"/_merge/6/_label[label=""loaned to""]/value",
35
inorout,fieldNotes,"/_merge/7/_label[label=""in or out""]/value",
30
comment1,fieldNotes,/_join/1,
31
comment2,fieldNotes,/_join/2,
32
comment3,fieldNotes,/_join/3,
33
comment4,fieldNotes,/_join/4,
34
loanto,fieldNotes,"/_join/6/_label[label=""loaned to""]/value",
35
inorout,fieldNotes,"/_join/7/_label[label=""in or out""]/value",
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
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,
11
comment2,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/2,
12
comment3,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/3,
13
comment4,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/4,
14
campus,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/5/_label[label=""campus""]/value",
15
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/6/_label[label=""loaned to""]/value",
16
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/7/_label[label=""in or out""]/value",
10
comment1,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1,
11
comment2,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/2,
12
comment3,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/3,
13
comment4,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/4,
14
campus,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/5/_label[label=""campus""]/value",
15
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/6/_label[label=""loaned to""]/value",
16
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/7/_label[label=""in or out""]/value",
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,
32
collector1,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/2,
33
collector2,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/3,
34
collector3,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/4,
31
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
32
collector1,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/2,
33
collector2,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/3,
34
collector3,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/4,
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
59 59
                                </_date>
60 60
                            </collectiondate>
61 61
                            <notes>
62
                                <_merge>
62
                                <_join>
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>
85
                                </_join>
86 86
                            </notes>
87 87
                            <plantobservation>
88 88
                                <collectionnumber>$collectno</collectionnumber>
......
152 152
                            </plantconcept_id>
153 153
                        </taxondetermination>
154 154
                        <verbatimcollectorname>
155
                            <_merge>
155
                            <_join>
156 156
                                <1>$collector</1>
157 157
                                <2>$collector1</2>
158 158
                                <3>$collector2</3>
159 159
                                <4>$collector3</4>
160
                            </_merge>
160
                            </_join>
161 161
                        </verbatimcollectorname>
162 162
                    </taxonoccurrence>
163 163
                </locationevent>
inputs/U/Specimen/map.csv
1 1
U,VegCore,Filter,Comments
2 2
ID,occurrenceID,,
3 3
Barcode,catalogNumber,,
4
Collector,recordedBy,/_merge/1,
4
Collector,recordedBy,/_join/1,
5 5
Prefix,Prefix,,Not used
6 6
Number,recordNumber,,
7 7
Suffix,Suffix,,Not used
8
Addcoll,recordedBy,/_merge/2,
8
Addcoll,recordedBy,/_join/2,
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",
19
Newgazett,verbatimLocality,"/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row
18
Gazetteer,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/1",
19
Newgazett,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/2",Only used in 1 row
20 20
Majorarea,Majorarea,,
21 21
Country,country,,
22
Locnotes,verbatimLocality,/_merge/2,
22
Locnotes,verbatimLocality,/_join/2,
23 23
Coorsyst,Coorsyst,,
24 24
Lat,decimalLatitude,,
25 25
NS,NS,,
inputs/U/Specimen/VegBIEN.csv
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,
23
Addcoll,/location/locationevent/taxonoccurrence/verbatimcollectorname/_merge/2,
22
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
23
Addcoll,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/2,
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",
26
Newgazett,"/location/locationnarrative/_merge/2/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row
27
Locnotes,/location/locationnarrative/_merge/2/_merge/2,
25
Gazetteer,"/location/locationnarrative/_merge/2/_join/1/_label[label=""gazetteer""]/value/_join/1",
26
Newgazett,"/location/locationnarrative/_merge/2/_join/1/_label[label=""gazetteer""]/value/_join/2",Only used in 1 row
27
Locnotes,/location/locationnarrative/_merge/2/_join/2,
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>
141
                            <_join>
142 142
                                <1>$Collector</1>
143 143
                                <2>$Addcoll</2>
144
                            </_merge>
144
                            </_join>
145 145
                        </verbatimcollectorname>
146 146
                    </taxonoccurrence>
147 147
                </locationevent>
148 148
                <locationnarrative>
149 149
                    <_merge>
150 150
                        <2>
151
                            <_merge>
151
                            <_join>
152 152
                                <1>
153 153
                                    <_label>
154 154
                                        <label>gazetteer</label>
155 155
                                        <value>
156
                                            <_merge>
156
                                            <_join>
157 157
                                                <1>$Gazetteer</1>
158 158
                                                <2>$Newgazett</2>
159
                                            </_merge>
159
                                            </_join>
160 160
                                        </value>
161 161
                                    </_label>
162 162
                                </1>
163 163
                                <2>$Locnotes</2>
164
                            </_merge>
164
                            </_join>
165 165
                        </2>
166 166
                        <3>
167 167
                            <_label>

Also available in: Unified diff