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Revision 7162

mappings/VegCore-VegBIEN.csv: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead

View differences:

inputs/JBM/Specimen/VegBIEN.csv
37 37
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
38 38
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
39 39
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
40
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
41
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
43
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
44 40
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
45 41
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
46 42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
inputs/UBC/Specimen/test.xml.ref
82 82
                                        <taxonverbatim>
83 83
                                            <taxonlabel_id>
84 84
                                                <taxonlabel>
85
                                                    <matched_label_id>
86
                                                        <taxonlabel>
87
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
88
                                                            <taxonomicname>
89
                                                                <_merge_prefix>
90
                                                                    <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
91
                                                                    <value>
92
                                                                        <_alt>
93
                                                                            <1>$scientificName</1>
94
                                                                            <2>
95
                                                                                <_join_words>
96
                                                                                    <1>
97
                                                                                        <_join_words>
98
                                                                                            <2>$genus</2>
99
                                                                                            <3>$specificEpithet</3>
100
                                                                                            <5>
101
                                                                                                <_join_words>
102
                                                                                                    <1>
103
                                                                                                        <_if name="if has infraspecificEpithet">
104
                                                                                                            <cond>$infraspecificEpithet</cond>
105
                                                                                                            <then>$taxonRank</then>
106
                                                                                                        </_if>
107
                                                                                                    </1>
108
                                                                                                    <2>$infraspecificEpithet</2>
109
                                                                                                </_join_words>
110
                                                                                            </5>
111
                                                                                        </_join_words>
112
                                                                                    </1>
113
                                                                                    <2>$scientificNameAuthorship</2>
114
                                                                                </_join_words>
115
                                                                            </2>
116
                                                                        </_alt>
117
                                                                    </value>
118
                                                                </_merge_prefix>
119
                                                            </taxonomicname>
120
                                                        </taxonlabel>
121
                                                    </matched_label_id>
122 85
                                                    <creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate>
123 86
                                                    <parent_id>
124 87
                                                        <taxonlabel>
......
308 271
        </path>
309 272
    </_setDefault>
310 273
</VegBIEN>
311
Inserted 41 new rows into database
274
Inserted 38 new rows into database
inputs/SpeciesLink/Specimen/VegBIEN.csv
145 145
conceptual_darwin_2003_1_0_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
146 146
dwc_curatorial_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
147 147
dwc_terms_identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
148
conceptual_darwin_2003_1_0_Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
149
dwc_dwcore_Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
150
dwc_terms_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
151
conceptual_darwin_2003_1_0_ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
152
dwc_dwcore_ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
153
dwc_terms_scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
154
conceptual_darwin_2003_1_0_Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
155
dwc_dwcore_Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
156
dwc_terms_genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
157
conceptual_darwin_2003_1_0_Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
158
dwc_dwcore_SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
159
dwc_terms_specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
160
conceptual_darwin_2003_1_0_Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4",
161
dwc_dwcore_InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
162
dwc_terms_infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
163
dwc_dwcore_InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
164
dwc_terms_infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
165
dwc_terms_scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_alt/1",
166
conceptual_darwin_2003_1_0_ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_alt/2",
167
dwc_dwcore_AuthorYearOfScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_alt/3",
168 148
dwc_terms_dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
169 149
conceptual_darwin_2003_1_0_DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
170 150
conceptual_darwin_2003_1_0_MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
inputs/MT/Specimen/VegBIEN.csv
20 20
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value",
21 21
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value",
22 22
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
23
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
24
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
25 23
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
26 24
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
27 25
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
inputs/MT/Specimen/test.xml.ref
61 61
                                        <taxonverbatim>
62 62
                                            <taxonlabel_id>
63 63
                                                <taxonlabel>
64
                                                    <matched_label_id>
65
                                                        <taxonlabel>
66
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
67
                                                            <taxonomicname>
68
                                                                <_merge_prefix>
69
                                                                    <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
70
                                                                    <value>$genus</value>
71
                                                                </_merge_prefix>
72
                                                            </taxonomicname>
73
                                                        </taxonlabel>
74
                                                    </matched_label_id>
75 64
                                                    <parent_id>
76 65
                                                        <taxonlabel>
77 66
                                                            <parent_id>
......
136 125
        </path>
137 126
    </_setDefault>
138 127
</VegBIEN>
139
Inserted 26 new rows into database
128
Inserted 24 new rows into database
inputs/test_taxonomic_names/Taxon/VegBIEN.csv
1 1
test_taxonomic_names,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 2
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
3
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
4 3
scientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,
5 4
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
6 5
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
inputs/test_taxonomic_names/Taxon/test.xml.ref
14 14
                                        <taxonverbatim>
15 15
                                            <taxonlabel_id>
16 16
                                                <taxonlabel>
17
                                                    <matched_label_id>
18
                                                        <taxonlabel>
19
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
20
                                                            <taxonomicname>$scientificName</taxonomicname>
21
                                                        </taxonlabel>
22
                                                    </matched_label_id>
23 17
                                                    <sourceaccessioncode>$scientificNameID</sourceaccessioncode>
24 18
                                                    <taxonomicname>$scientificName</taxonomicname>
25 19
                                                </taxonlabel>
......
36 30
        </path>
37 31
    </_setDefault>
38 32
</VegBIEN>
39
Inserted 8 new rows into database
33
Inserted 5 new rows into database
inputs/XAL/Specimen/VegBIEN.csv
27 27
darwin:Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
28 28
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
29 29
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
30
darwin:Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
31
darwin:ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
32
darwin:Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
33
darwin:Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
34
darwin:Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4",
35
darwin:ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
36 30
darwin:DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
37 31
darwin:MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
38 32
darwin:YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
inputs/NCU/Specimen/VegBIEN.csv
36 36
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Actually the collector's number, not remarks"
37 37
Cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2/_nullIf:[null=""-1""]/value",
38 38
SpecimenPK,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
39
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
40
CurrentScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
41 39
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
42 40
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
43 41
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
44 42
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
45
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1,
46 43
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
47 44
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname,
48 45
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
inputs/NCU/Specimen/test.xml.ref
84 84
                                        <taxonverbatim>
85 85
                                            <taxonlabel_id>
86 86
                                                <taxonlabel>
87
                                                    <matched_label_id>
88
                                                        <taxonlabel>
89
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
90
                                                            <taxonomicname>
91
                                                                <_alt>
92
                                                                    <1>$CurrentScientificNameWithAuthor</1>
93
                                                                    <2>$CurrentScientificName</2>
94
                                                                </_alt>
95
                                                            </taxonomicname>
96
                                                        </taxonlabel>
97
                                                    </matched_label_id>
98 87
                                                    <taxonomicname>
99 88
                                                        <_alt>
100 89
                                                            <1>$CurrentScientificNameWithAuthor</1>
......
112 101
                                    <isoriginal>true</isoriginal>
113 102
                                    <taxonverbatim_id>
114 103
                                        <taxonverbatim>
115
                                            <taxonlabel_id>
116
                                                <taxonlabel>
117
                                                    <matched_label_id>
118
                                                        <taxonlabel>
119
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
120
                                                            <taxonomicname>$OriginalTaxonLabel</taxonomicname>
121
                                                        </taxonlabel>
122
                                                    </matched_label_id>
123
                                                    <taxonomicname>$OriginalTaxonLabel</taxonomicname>
124
                                                </taxonlabel>
125
                                            </taxonlabel_id>
104
                                            <taxonlabel_id><taxonlabel><taxonomicname>$OriginalTaxonLabel</taxonomicname></taxonlabel></taxonlabel_id>
126 105
                                            <taxonomicname>$OriginalTaxonLabel</taxonomicname>
127 106
                                        </taxonverbatim>
128 107
                                    </taxonverbatim_id>
......
197 176
        </path>
198 177
    </_setDefault>
199 178
</VegBIEN>
200
Inserted 40 new rows into database
179
Inserted 36 new rows into database
inputs/bien2_traits/TraitObservation/VegBIEN.csv
11 11
Habit,/location/locationevent/taxonoccurrence/growthform,
12 12
TraitObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
13 13
TraitObservationID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
14
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
15
Taxon,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
16
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
17
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
18
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
19
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
20
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
21
AuthorOfScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
22 14
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
23 15
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
24 16
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
inputs/bien2_traits/TraitObservation/test.xml.ref
26 26
                                        <taxonverbatim>
27 27
                                            <taxonlabel_id>
28 28
                                                <taxonlabel>
29
                                                    <matched_label_id>
30
                                                        <taxonlabel>
31
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
32
                                                            <taxonomicname>
33
                                                                <_merge_prefix>
34
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
35
                                                                    <value>
36
                                                                        <_join_words>
37
                                                                            <1>
38
                                                                                <_alt>
39
                                                                                    <1>$Taxon</1>
40
                                                                                    <2>
41
                                                                                        <_join_words>
42
                                                                                            <2>$Genus</2>
43
                                                                                            <3>$SpecificEpithet</3>
44
                                                                                            <5>
45
                                                                                                <_join_words>
46
                                                                                                    <1>
47
                                                                                                        <_if name="if has infraspecificEpithet">
48
                                                                                                            <cond>$InfraspecificEpithet</cond>
49
                                                                                                            <then>$InfraspecificRank</then>
50
                                                                                                        </_if>
51
                                                                                                    </1>
52
                                                                                                    <2>$InfraspecificEpithet</2>
53
                                                                                                </_join_words>
54
                                                                                            </5>
55
                                                                                        </_join_words>
56
                                                                                    </2>
57
                                                                                </_alt>
58
                                                                            </1>
59
                                                                            <2>$AuthorOfScientificName</2>
60
                                                                        </_join_words>
61
                                                                    </value>
62
                                                                </_merge_prefix>
63
                                                            </taxonomicname>
64
                                                        </taxonlabel>
65
                                                    </matched_label_id>
66 29
                                                    <parent_id>
67 30
                                                        <taxonlabel>
68 31
                                                            <rank>$InfraspecificRank</rank>
......
187 150
        </path>
188 151
    </_setDefault>
189 152
</VegBIEN>
190
Inserted 33 new rows into database
153
Inserted 30 new rows into database
inputs/TEAM/VL/VegBIEN.csv
28 28
Names of Collectors,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
29 29
Id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
30 30
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
31
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
32
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
33
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
34 31
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
35 32
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
36 33
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
inputs/TEAM/VL/test.xml.ref
49 49
                                        <taxonverbatim>
50 50
                                            <taxonlabel_id>
51 51
                                                <taxonlabel>
52
                                                    <matched_label_id>
53
                                                        <taxonlabel>
54
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
55
                                                            <taxonomicname>
56
                                                                <_merge_prefix>
57
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
58
                                                                    <value>
59
                                                                        <_join_words>
60
                                                                            <2>$Genus</2>
61
                                                                            <3>$Species</3>
62
                                                                        </_join_words>
63
                                                                    </value>
64
                                                                </_merge_prefix>
65
                                                            </taxonomicname>
66
                                                        </taxonlabel>
67
                                                    </matched_label_id>
68 52
                                                    <parent_id>
69 53
                                                        <taxonlabel>
70 54
                                                            <parent_id>
......
182 166
        </path>
183 167
    </_setDefault>
184 168
</VegBIEN>
185
Inserted 35 new rows into database
169
Inserted 32 new rows into database
inputs/TEAM/VT/VegBIEN.csv
28 28
Names of Collectors,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
29 29
Id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
30 30
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
31
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
32
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
33
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
34 31
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
35 32
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
36 33
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
inputs/TEAM/VT/test.xml.ref
49 49
                                        <taxonverbatim>
50 50
                                            <taxonlabel_id>
51 51
                                                <taxonlabel>
52
                                                    <matched_label_id>
53
                                                        <taxonlabel>
54
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
55
                                                            <taxonomicname>
56
                                                                <_merge_prefix>
57
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
58
                                                                    <value>
59
                                                                        <_join_words>
60
                                                                            <2>$Genus</2>
61
                                                                            <3>$Species</3>
62
                                                                        </_join_words>
63
                                                                    </value>
64
                                                                </_merge_prefix>
65
                                                            </taxonomicname>
66
                                                        </taxonlabel>
67
                                                    </matched_label_id>
68 52
                                                    <parent_id>
69 53
                                                        <taxonlabel>
70 54
                                                            <parent_id>
......
182 166
        </path>
183 167
    </_setDefault>
184 168
</VegBIEN>
185
Inserted 33 new rows into database
169
Inserted 30 new rows into database
inputs/ACAD/Specimen/VegBIEN.csv
37 37
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
38 38
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
39 39
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
40
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
41
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
43
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
44
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
45
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
46
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
47
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
48 40
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
49 41
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
50 42
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
inputs/ACAD/Specimen/test.xml.ref
82 82
                                        <taxonverbatim>
83 83
                                            <taxonlabel_id>
84 84
                                                <taxonlabel>
85
                                                    <matched_label_id>
86
                                                        <taxonlabel>
87
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
88
                                                            <taxonomicname>
89
                                                                <_merge_prefix>
90
                                                                    <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
91
                                                                    <value>
92
                                                                        <_alt>
93
                                                                            <1>$scientificName</1>
94
                                                                            <2>
95
                                                                                <_join_words>
96
                                                                                    <1>
97
                                                                                        <_join_words>
98
                                                                                            <2>$genus</2>
99
                                                                                            <3>$specificEpithet</3>
100
                                                                                            <5>
101
                                                                                                <_join_words>
102
                                                                                                    <1>
103
                                                                                                        <_if name="if has infraspecificEpithet">
104
                                                                                                            <cond>$infraspecificEpithet</cond>
105
                                                                                                            <then>$taxonRank</then>
106
                                                                                                        </_if>
107
                                                                                                    </1>
108
                                                                                                    <2>$infraspecificEpithet</2>
109
                                                                                                </_join_words>
110
                                                                                            </5>
111
                                                                                        </_join_words>
112
                                                                                    </1>
113
                                                                                    <2>$scientificNameAuthorship</2>
114
                                                                                </_join_words>
115
                                                                            </2>
116
                                                                        </_alt>
117
                                                                    </value>
118
                                                                </_merge_prefix>
119
                                                            </taxonomicname>
120
                                                        </taxonlabel>
121
                                                    </matched_label_id>
122 85
                                                    <creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate>
123 86
                                                    <parent_id>
124 87
                                                        <taxonlabel>
......
308 271
        </path>
309 272
    </_setDefault>
310 273
</VegBIEN>
311
Inserted 45 new rows into database
274
Inserted 42 new rows into database
inputs/.NCBI/nodes/VegBIEN.csv
1 1
NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 2
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists",
3
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
4 3
parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode,
5 4
parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists",
6 5
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
inputs/.NCBI/nodes/test.xml.ref
43 43
        </path>
44 44
    </_setDefault>
45 45
</VegBIEN>
46
Inserted 6 new rows into database
46
Inserted 5 new rows into database
inputs/WIN/Specimen/VegBIEN.csv
38 38
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
39 39
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
40 40
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
41
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
43
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
44
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
45
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
46
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
47
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
48 41
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
49 42
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
50 43
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
inputs/WIN/Specimen/test.xml.ref
87 87
                                        <taxonverbatim>
88 88
                                            <taxonlabel_id>
89 89
                                                <taxonlabel>
90
                                                    <matched_label_id>
91
                                                        <taxonlabel>
92
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
93
                                                            <taxonomicname>
94
                                                                <_alt>
95
                                                                    <1>$scientificName</1>
96
                                                                    <2>
97
                                                                        <_join_words>
98
                                                                            <1>
99
                                                                                <_join_words>
100
                                                                                    <2>$genus</2>
101
                                                                                    <3>$specificEpithet</3>
102
                                                                                    <5>
103
                                                                                        <_join_words>
104
                                                                                            <1>
105
                                                                                                <_if name="if has infraspecificEpithet">
106
                                                                                                    <cond>$infraspecificEpithet</cond>
107
                                                                                                    <then>$taxonRank</then>
108
                                                                                                </_if>
109
                                                                                            </1>
110
                                                                                            <2>$infraspecificEpithet</2>
111
                                                                                        </_join_words>
112
                                                                                    </5>
113
                                                                                </_join_words>
114
                                                                            </1>
115
                                                                            <2>$scientificNameAuthorship</2>
116
                                                                        </_join_words>
117
                                                                    </2>
118
                                                                </_alt>
119
                                                            </taxonomicname>
120
                                                        </taxonlabel>
121
                                                    </matched_label_id>
122 90
                                                    <creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate>
123 91
                                                    <parent_id>
124 92
                                                        <taxonlabel>
......
301 269
        </path>
302 270
    </_setDefault>
303 271
</VegBIEN>
304
Inserted 36 new rows into database
272
Inserted 34 new rows into database
inputs/CTFS/StemObservation/VegBIEN.csv
26 26
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",
27 27
MeasureID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
28 28
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2",
29
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
30
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
31
SpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
32
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4",
33
SpeciesAuthority,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
34 29
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet",
35 30
SpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
36 31
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
inputs/CTFS/StemObservation/test.xml.ref
55 55
                                        <taxonverbatim>
56 56
                                            <taxonlabel_id>
57 57
                                                <taxonlabel>
58
                                                    <matched_label_id>
59
                                                        <taxonlabel>
60
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
61
                                                            <taxonomicname>
62
                                                                <_merge_prefix>
63
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
64
                                                                    <value>
65
                                                                        <_join_words>
66
                                                                            <1>
67
                                                                                <_join_words>
68
                                                                                    <2>$Genus</2>
69
                                                                                    <3>$SpeciesName</3>
70
                                                                                    <4>$SubSpeciesName</4>
71
                                                                                </_join_words>
72
                                                                            </1>
73
                                                                            <2>$SpeciesAuthority</2>
74
                                                                        </_join_words>
75
                                                                    </value>
76
                                                                </_merge_prefix>
77
                                                            </taxonomicname>
78
                                                        </taxonlabel>
79
                                                    </matched_label_id>
80 58
                                                    <parent_id>
81 59
                                                        <taxonlabel>
82 60
                                                            <parent_id>
......
160 138
        </path>
161 139
    </_setDefault>
162 140
</VegBIEN>
163
Inserted 20 new rows into database
141
Inserted 18 new rows into database
inputs/CTFS/TaxonOccurrence/VegBIEN.csv
11 11
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
12 12
SpeciesInvID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
13 13
SpeciesInvID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,
14
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
15
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
16
SpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
17
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4",
18
SpeciesAuthority,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
19 14
SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet",
20 15
SpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
21 16
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
inputs/CTFS/TaxonOccurrence/test.xml.ref
17 17
                                        <taxonverbatim>
18 18
                                            <taxonlabel_id>
19 19
                                                <taxonlabel>
20
                                                    <matched_label_id>
21
                                                        <taxonlabel>
22
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
23
                                                            <taxonomicname>
24
                                                                <_merge_prefix>
25
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
26
                                                                    <value>
27
                                                                        <_join_words>
28
                                                                            <1>
29
                                                                                <_join_words>
30
                                                                                    <2>$Genus</2>
31
                                                                                    <3>$SpeciesName</3>
32
                                                                                    <4>$SubSpeciesName</4>
33
                                                                                </_join_words>
34
                                                                            </1>
35
                                                                            <2>$SpeciesAuthority</2>
36
                                                                        </_join_words>
37
                                                                    </value>
38
                                                                </_merge_prefix>
39
                                                            </taxonomicname>
40
                                                        </taxonlabel>
41
                                                    </matched_label_id>
42 20
                                                    <parent_id>
43 21
                                                        <taxonlabel>
44 22
                                                            <parent_id>
......
116 94
        </path>
117 95
    </_setDefault>
118 96
</VegBIEN>
119
Inserted 20 new rows into database
97
Inserted 17 new rows into database
inputs/SALVIAS/projects/test.xml.ref
21 21
        </path>
22 22
    </_setDefault>
23 23
</VegBIEN>
24
Inserted 3 new rows into database
24
Inserted 2 new rows into database
inputs/SALVIAS/stems/test.xml.ref
82 82
        </path>
83 83
    </_setDefault>
84 84
</VegBIEN>
85
Inserted 24 new rows into database
85
Inserted 14 new rows into database
inputs/SALVIAS/plotObservations/test.xml.ref
156 156
                                        <taxonverbatim>
157 157
                                            <taxonlabel_id>
158 158
                                                <taxonlabel>
159
                                                    <matched_label_id>
160
                                                        <taxonlabel>
161
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
162
                                                            <taxonomicname>
163
                                                                <_merge_prefix>
164
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
165
                                                                    <value>
166
                                                                        <_join_words>
167
                                                                            <1>
168
                                                                                <_join_words>
169
                                                                                    <2>$Genus</2>
170
                                                                                    <3>$Species</3>
171
                                                                                    <5>
172
                                                                                        <_join_words>
173
                                                                                            <1>
174
                                                                                                <_if name="if has infraspecificEpithet">
175
                                                                                                    <cond>$infra_ep_1</cond>
176
                                                                                                    <then>$infra_rank_1</then>
177
                                                                                                </_if>
178
                                                                                            </1>
179
                                                                                            <2>$infra_ep_1</2>
180
                                                                                        </_join_words>
181
                                                                                    </5>
182
                                                                                </_join_words>
183
                                                                            </1>
184
                                                                            <2>$auth</2>
185
                                                                        </_join_words>
186
                                                                    </value>
187
                                                                </_merge_prefix>
188
                                                            </taxonomicname>
189
                                                        </taxonlabel>
190
                                                    </matched_label_id>
191 159
                                                    <parent_id>
192 160
                                                        <taxonlabel>
193 161
                                                            <rank>$infra_rank_1</rank>
......
277 245
                                        <taxonverbatim>
278 246
                                            <taxonlabel_id>
279 247
                                                <taxonlabel>
280
                                                    <matched_label_id>
281
                                                        <taxonlabel>
282
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
283
                                                            <taxonomicname>
284
                                                                <_merge_prefix>
285
                                                                    <prefix><_taxon_family_require_std><family>$OrigFamily</family></_taxon_family_require_std></prefix>
286
                                                                    <value>
287
                                                                        <_join_words>
288
                                                                            <2>$OrigGenus</2>
289
                                                                            <3>$OrigSpecies</3>
290
                                                                        </_join_words>
291
                                                                    </value>
292
                                                                </_merge_prefix>
293
                                                            </taxonomicname>
294
                                                        </taxonlabel>
295
                                                    </matched_label_id>
296 248
                                                    <parent_id>
297 249
                                                        <taxonlabel>
298 250
                                                            <parent_id>
......
390 342
        </path>
391 343
    </_setDefault>
392 344
</VegBIEN>
393
Inserted 50 new rows into database
345
Inserted 0 new rows into database
inputs/U/Specimen/VegBIEN.csv
28 28
Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
29 29
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
30 30
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
31
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
32
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
33 31
Detyy,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
34 32
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
35 33
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
inputs/GBIF/Specimen/VegBIEN.csv
19 19
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
20 20
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
21 21
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
22
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
23
ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
24
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
25
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
26
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
27
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
28
AuthorOfScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
29 22
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
30 23
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
31 24
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
......
44 37
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
45 38
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
46 39
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
47
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
48
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
49
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2,
50 40
GBIFGenusOriginal,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
51 41
GBIFFamilyOriginal,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
52 42
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
inputs/QFA/Specimen/VegBIEN.csv
39 39
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value",
40 40
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
41 41
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
42
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
43
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
44
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
45
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
46
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
47
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
48
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
49
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
50 42
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
51 43
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
52 44
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
inputs/JBM/Specimen/test.xml.ref
84 84
                                        <taxonverbatim>
85 85
                                            <taxonlabel_id>
86 86
                                                <taxonlabel>
87
                                                    <matched_label_id>
88
                                                        <taxonlabel>
89
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
90
                                                            <taxonomicname>
91
                                                                <_merge_prefix>
92
                                                                    <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
93
                                                                    <value>
94
                                                                        <_alt>
95
                                                                            <1>$scientificName</1>
96
                                                                            <2>
97
                                                                                <_join_words>
98
                                                                                    <2>$genus</2>
99
                                                                                    <3>$specificEpithet</3>
100
                                                                                </_join_words>
101
                                                                            </2>
102
                                                                        </_alt>
103
                                                                    </value>
104
                                                                </_merge_prefix>
105
                                                            </taxonomicname>
106
                                                        </taxonlabel>
107
                                                    </matched_label_id>
108 87
                                                    <parent_id>
109 88
                                                        <taxonlabel>
110 89
                                                            <parent_id>
......
270 249
        </path>
271 250
    </_setDefault>
272 251
</VegBIEN>
273
Inserted 38 new rows into database
252
Inserted 35 new rows into database
inputs/HIBG/Specimen/VegBIEN.csv
37 37
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
38 38
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
39 39
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
40
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
41
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
43
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
44
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
45
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
46
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
47
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
48 40
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
49 41
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
50 42
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
inputs/SpeciesLink/Specimen/test.xml.ref
218 218
                                        <taxonverbatim>
219 219
                                            <taxonlabel_id>
220 220
                                                <taxonlabel>
221
                                                    <matched_label_id>
222
                                                        <taxonlabel>
223
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
224
                                                            <taxonomicname>
225
                                                                <_merge_prefix>
226
                                                                    <prefix>
227
                                                                        <_taxon_family_require_std>
228
                                                                            <family>
229
                                                                                <_alt>
230
                                                                                    <0>$conceptual_darwin_2003_1_0_Family</0>
231
                                                                                    <1>$dwc_dwcore_Family</1>
232
                                                                                    <2>$dwc_terms_family</2>
233
                                                                                </_alt>
234
                                                                            </family>
235
                                                                        </_taxon_family_require_std>
236
                                                                    </prefix>
237
                                                                    <value>
238
                                                                        <_join_words>
239
                                                                            <1>
240
                                                                                <_alt>
241
                                                                                    <1>
242
                                                                                        <_alt>
243
                                                                                            <0>$conceptual_darwin_2003_1_0_ScientificName</0>
244
                                                                                            <1>$dwc_dwcore_ScientificName</1>
245
                                                                                            <2>$dwc_terms_scientificName</2>
246
                                                                                        </_alt>
247
                                                                                    </1>
248
                                                                                    <2>
249
                                                                                        <_join_words>
250
                                                                                            <2>
251
                                                                                                <_alt>
252
                                                                                                    <0>$conceptual_darwin_2003_1_0_Genus</0>
253
                                                                                                    <1>$dwc_dwcore_Genus</1>
254
                                                                                                    <2>$dwc_terms_genus</2>
255
                                                                                                </_alt>
256
                                                                                            </2>
257
                                                                                            <3>
258
                                                                                                <_alt>
259
                                                                                                    <0>$conceptual_darwin_2003_1_0_Species</0>
260
                                                                                                    <1>$dwc_dwcore_SpecificEpithet</1>
261
                                                                                                    <2>$dwc_terms_specificEpithet</2>
262
                                                                                                </_alt>
263
                                                                                            </3>
264
                                                                                            <4>$conceptual_darwin_2003_1_0_Subspecies</4>
265
                                                                                            <5>
266
                                                                                                <_alt>
267
                                                                                                    <0>$dwc_dwcore_InfraspecificEpithet</0>
268
                                                                                                    <1>$dwc_terms_infraspecificEpithet</1>
269
                                                                                                </_alt>
270
                                                                                            </5>
271
                                                                                        </_join_words>
272
                                                                                    </2>
273
                                                                                </_alt>
274
                                                                            </1>
275
                                                                            <2>
276
                                                                                <_alt>
277
                                                                                    <1>$dwc_terms_scientificNameAuthorship</1>
278
                                                                                    <2>$conceptual_darwin_2003_1_0_ScientificNameAuthor</2>
279
                                                                                    <3>$dwc_dwcore_AuthorYearOfScientificName</3>
280
                                                                                </_alt>
281
                                                                            </2>
282
                                                                        </_join_words>
283
                                                                    </value>
284
                                                                </_merge_prefix>
285
                                                            </taxonomicname>
286
                                                        </taxonlabel>
287
                                                    </matched_label_id>
288 221
                                                    <creationdate>
289 222
                                                        <_alt>
290 223
                                                            <1><_dateRangeStart><value>$dwc_terms_dateIdentified</value></_dateRangeStart></1>
......
731 664
        </path>
732 665
    </_setDefault>
733 666
</VegBIEN>
734
Inserted 47 new rows into database
667
Inserted 44 new rows into database
inputs/SALVIAS/plotObservations/VegBIEN.csv
97 97
PlotObsID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
98 98
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
99 99
det_by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
100
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
101
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
102
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
103
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
104
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
105
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
106
auth,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",Brad: This is the author of the scientificName.
107 100
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
108 101
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
109 102
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
......
126 119
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
127 120
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
128 121
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
129
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,Brad: OMIT
130
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2,
131
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3,Brad: OMIT
132 122
OrigSpecies,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",Brad: OMIT
133 123
OrigGenus,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
134 124
OrigFamily,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",Brad: OMIT
inputs/SALVIAS/plotMetadata_/test.xml.ref
189 189
        </path>
190 190
    </_setDefault>
191 191
</VegBIEN>
192
Inserted 16 new rows into database
192
Inserted 15 new rows into database
inputs/U/Specimen/test.xml.ref
92 92
                                        <taxonverbatim>
93 93
                                            <taxonlabel_id>
94 94
                                                <taxonlabel>
95
                                                    <matched_label_id>
96
                                                        <taxonlabel>
97
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
98
                                                            <taxonomicname>
99
                                                                <_merge_prefix>
100
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
101
                                                                    <value>$Genus</value>
102
                                                                </_merge_prefix>
103
                                                            </taxonomicname>
104
                                                        </taxonlabel>
105
                                                    </matched_label_id>
106 95
                                                    <creationdate>
107 96
                                                        <_date>
108 97
                                                            <year>
......
264 253
        </path>
265 254
    </_setDefault>
266 255
</VegBIEN>
267
Inserted 35 new rows into database
256
Inserted 32 new rows into database
inputs/GBIF/Specimen/test.xml.ref
52 52
                                        <taxonverbatim>
53 53
                                            <taxonlabel_id>
54 54
                                                <taxonlabel>
55
                                                    <matched_label_id>
56
                                                        <taxonlabel>
57
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
58
                                                            <taxonomicname>
59
                                                                <_merge_prefix>
60
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
61
                                                                    <value>
62
                                                                        <_join_words>
63
                                                                            <1>
64
                                                                                <_alt>
65
                                                                                    <1>$ScientificName</1>
66
                                                                                    <2>
67
                                                                                        <_join_words>
68
                                                                                            <2>$Genus</2>
69
                                                                                            <3>$SpecificEpithet</3>
70
                                                                                            <5>$InfraspecificEpithet</5>
71
                                                                                        </_join_words>
72
                                                                                    </2>
73
                                                                                </_alt>
74
                                                                            </1>
75
                                                                            <2>$AuthorOfScientificName</2>
76
                                                                        </_join_words>
77
                                                                    </value>
78
                                                                </_merge_prefix>
79
                                                            </taxonomicname>
80
                                                        </taxonlabel>
81
                                                    </matched_label_id>
82 55
                                                    <parent_id>
83 56
                                                        <taxonlabel>
84 57
                                                            <parent_id>
......
160 133
                                        <taxonverbatim>
161 134
                                            <taxonlabel_id>
162 135
                                                <taxonlabel>
163
                                                    <matched_label_id>
164
                                                        <taxonlabel>
165
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
166
                                                            <taxonomicname>
167
                                                                <_merge_prefix>
168
                                                                    <prefix><_taxon_family_require_std><family>$GBIFFamilyOriginal</family></_taxon_family_require_std></prefix>
169
                                                                    <value>
170
                                                                        <_alt>
171
                                                                            <1>$ScientificNameOriginal</1>
172
                                                                            <2>$GBIFGenusOriginal</2>
173
                                                                        </_alt>
174
                                                                    </value>
175
                                                                </_merge_prefix>
176
                                                            </taxonomicname>
177
                                                        </taxonlabel>
178
                                                    </matched_label_id>
179 136
                                                    <parent_id>
180 137
                                                        <taxonlabel>
181 138
                                                            <parent_id>
......
299 256
        </path>
300 257
    </_setDefault>
301 258
</VegBIEN>
302
Inserted 47 new rows into database
259
Inserted 42 new rows into database
inputs/QFA/Specimen/test.xml.ref
98 98
                                        <taxonverbatim>
99 99
                                            <taxonlabel_id>
100 100
                                                <taxonlabel>
101
                                                    <matched_label_id>
102
                                                        <taxonlabel>
103
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
104
                                                            <taxonomicname>
105
                                                                <_merge_prefix>
106
                                                                    <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
107
                                                                    <value>
108
                                                                        <_alt>
109
                                                                            <1>$scientificName</1>
110
                                                                            <2>
111
                                                                                <_join_words>
112
                                                                                    <1>
113
                                                                                        <_join_words>
114
                                                                                            <2>$genus</2>
115
                                                                                            <3>$specificEpithet</3>
116
                                                                                            <5>
117
                                                                                                <_join_words>
118
                                                                                                    <1>
119
                                                                                                        <_if name="if has infraspecificEpithet">
120
                                                                                                            <cond>$infraspecificEpithet</cond>
121
                                                                                                            <then>$taxonRank</then>
122
                                                                                                        </_if>
123
                                                                                                    </1>
124
                                                                                                    <2>$infraspecificEpithet</2>
125
                                                                                                </_join_words>
126
                                                                                            </5>
127
                                                                                        </_join_words>
128
                                                                                    </1>
129
                                                                                    <2>$scientificNameAuthorship</2>
130
                                                                                </_join_words>
131
                                                                            </2>
132
                                                                        </_alt>
133
                                                                    </value>
134
                                                                </_merge_prefix>
135
                                                            </taxonomicname>
136
                                                        </taxonlabel>
137
                                                    </matched_label_id>
138 101
                                                    <creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate>
139 102
                                                    <parent_id>
140 103
                                                        <taxonlabel>
......
322 285
        </path>
323 286
    </_setDefault>
324 287
</VegBIEN>
325
Inserted 45 new rows into database
288
Inserted 42 new rows into database
inputs/UBC/Specimen/VegBIEN.csv
37 37
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
38 38
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
39 39
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
40
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
41
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
43
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
44
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
45
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
46
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
47
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
48 40
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
49 41
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
50 42
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
inputs/NY/Specimen/VegBIEN.csv
31 31
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
32 32
FieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",Usage inconsistent with DwC definition
33 33
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
34
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
35
ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
36
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
37
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
38
Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4",
39
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
40 34
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
41 35
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
42 36
YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
inputs/UNCC/Specimen/VegBIEN.csv
98 98
GROUP BY herbarium, accession
99 99
HAVING count(*) > 1
100 100
-----"
101
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
102
SciName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
103
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
104
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
105
infraname,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
106
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then/_alt/1",
107
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then/_alt/2",
108
infraname,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
109
authors,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2",
110 101
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank/_alt/1",
111 102
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank/_alt/2",
112 103
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
inputs/CVS/taxonObservation_/VegBIEN.csv
23 23
surName,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/2,
24 24
TAXONOBSERVATION_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
25 25
TAXONOBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,
26
denorm_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_alt/1",
27
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_alt/2",
28
plantNameWithAuthority,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/1",
29
plantname,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
30
denorm_genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/1",
31
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_alt/2",
32
denorm_species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/1",
33
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/2",
34
subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4/_alt/2",
35
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
36
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""var. ""]/2",
37 26
interpretationDate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
38 27
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
39 28
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet",
......
78 67
TAXONOBSERVATION_ID,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists",
79 68
interpretationDate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
80 69
taxonFit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
81
authorPlantName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
82 70
authorPlantName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
83 71
authorPlantName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname,
84 72
museumAccessionNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
inputs/IUCN/European_Red_List_Plants/VegBIEN.csv
1 1
IUCN,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family",
3
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
4 2
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
5 3
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
6 4
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
inputs/.TNRS/public.unscrubbed_taxondetermination_view/VegBIEN.csv
4 4
:0,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",Enables the taxonoccurrence CHECK constraint to pass
5 5
:0,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,Enables the taxonoccurrence CHECK constraint to pass
6 6
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists","This table contains only canonicalized names. (Not all names are accepted, but those that aren’t don’t (yet) have an accepted match.)"
7
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_first/1",Contains family based on matched name
8
Family_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_first/2",Contains family in original string (uncommon)
9
Name_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1",
10
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2",
11
Specific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
12
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/2",
13
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
14
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
15
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
16
Name_matched_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_first/1",Contains author based on matched name
17
Author_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2/_first/2",Contains author in original string
18 7
:_,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value/_now,
19 8
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/morphospecies/_if[@name=""if has accepted name""]/then",
20 9
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]:[then=0]/cond","This table contains only canonicalized names. (Not all names are accepted, but those that aren’t don’t (yet) have an accepted match.)"
inputs/.TNRS/tnrs_accepted/test.xml.ref
145 145
        </path>
146 146
    </_setDefault>
147 147
</VegBIEN>
148
Inserted 16 new rows into database
148
Inserted 14 new rows into database
inputs/NVS/AggregateOccurrence/test.xml.ref
32 32
                                        <taxonverbatim>
33 33
                                            <taxonlabel_id>
34 34
                                                <taxonlabel>
35
                                                    <matched_label_id>
36
                                                        <taxonlabel>
37
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
38
                                                            <taxonomicname>$Species Name</taxonomicname>
39
                                                        </taxonlabel>
40
                                                    </matched_label_id>
41 35
                                                    <parent_id>
42 36
                                                        <taxonlabel>
43 37
                                                            <parent_id>
......
84 78
        </path>
85 79
    </_setDefault>
86 80
</VegBIEN>
87
Inserted 17 new rows into database
81
Inserted 14 new rows into database
inputs/NVS/TaxonOccurrence/test.xml.ref
32 32
                                        <taxonverbatim>
33 33
                                            <taxonlabel_id>
34 34
                                                <taxonlabel>
35
                                                    <matched_label_id>
36
                                                        <taxonlabel>
37
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
38
                                                            <taxonomicname>$Species Name</taxonomicname>
39
                                                        </taxonlabel>
40
                                                    </matched_label_id>
41 35
                                                    <parent_id>
42 36
                                                        <taxonlabel>
43 37
                                                            <parent_id>
......
84 78
        </path>
85 79
    </_setDefault>
86 80
</VegBIEN>
87
Inserted 17 new rows into database
81
Inserted 14 new rows into database
inputs/NY/Specimen/test.xml.ref
128 128
                                        <taxonverbatim>
129 129
                                            <taxonlabel_id>
130 130
                                                <taxonlabel>
131
                                                    <matched_label_id>
132
                                                        <taxonlabel>
133
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
134
                                                            <taxonomicname>
135
                                                                <_merge_prefix>
136
                                                                    <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
137
                                                                    <value>
138
                                                                        <_join_words>
139
                                                                            <1>
140
                                                                                <_alt>
141
                                                                                    <1>$ScientificName</1>
142
                                                                                    <2>
143
                                                                                        <_join_words>
144
                                                                                            <2>$Genus</2>
145
                                                                                            <3>$Species</3>
146
                                                                                            <4>$Subspecies</4>
147
                                                                                        </_join_words>
148
                                                                                    </2>
149
                                                                                </_alt>
150
                                                                            </1>
151
                                                                            <2>$ScientificNameAuthor</2>
152
                                                                        </_join_words>
153
                                                                    </value>
154
                                                                </_merge_prefix>
155
                                                            </taxonomicname>
156
                                                        </taxonlabel>
157
                                                    </matched_label_id>
158 131
                                                    <creationdate>
159 132
                                                        <_date>
160 133
                                                            <day>
......
402 375
        </path>
403 376
    </_setDefault>
404 377
</VegBIEN>
405
Inserted 46 new rows into database
378
Inserted 43 new rows into database
inputs/UNCC/Specimen/test.xml.ref
111 111
                                        <taxonverbatim>
112 112
                                            <taxonlabel_id>
113 113
                                                <taxonlabel>
114
                                                    <matched_label_id>
115
                                                        <taxonlabel>
116
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
117
                                                            <taxonomicname>
118
                                                                <_merge_prefix>
119
                                                                    <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
120
                                                                    <value>
121
                                                                        <_join_words>
122
                                                                            <1>
123
                                                                                <_alt>
124
                                                                                    <1>$SciName</1>
125
                                                                                    <2>
126
                                                                                        <_join_words>
127
                                                                                            <2>$genus</2>
128
                                                                                            <3>$species</3>
129
                                                                                            <5>
130
                                                                                                <_join_words>
131
                                                                                                    <1>
132
                                                                                                        <_if name="if has infraspecificEpithet">
133
                                                                                                            <cond>$infraname</cond>
134
                                                                                                            <then>
135
                                                                                                                <_alt>
136
                                                                                                                    <1>$usdaRank</1>
137
                                                                                                                    <2>$infrarank</2>
138
                                                                                                                </_alt>
139
                                                                                                            </then>
140
                                                                                                        </_if>
141
                                                                                                    </1>
142
                                                                                                    <2>$infraname</2>
143
                                                                                                </_join_words>
144
                                                                                            </5>
145
                                                                                        </_join_words>
146
                                                                                    </2>
147
                                                                                </_alt>
148
                                                                            </1>
149
                                                                            <2>$authors</2>
150
                                                                        </_join_words>
151
                                                                    </value>
152
                                                                </_merge_prefix>
153
                                                            </taxonomicname>
154
                                                        </taxonlabel>
155
                                                    </matched_label_id>
156 114
                                                    <parent_id>
157 115
                                                        <taxonlabel>
158 116
                                                            <rank>
......
297 255
        </path>
298 256
    </_setDefault>
299 257
</VegBIEN>
300
Inserted 28 new rows into database
258
Inserted 26 new rows into database
inputs/CVS/taxonObservation_/test.xml.ref
35 35
                                        <taxonverbatim>
36 36
                                            <taxonlabel_id>
37 37
                                                <taxonlabel>
38
                                                    <matched_label_id>
39
                                                        <taxonlabel>
40
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
41
                                                            <taxonomicname>
42
                                                                <_merge_prefix>
43
                                                                    <prefix>
44
                                                                        <_taxon_family_require_std>
45
                                                                            <family>
46
                                                                                <_alt>
47
                                                                                    <1>$denorm_family</1>
48
                                                                                    <2>$family</2>
49
                                                                                </_alt>
50
                                                                            </family>
51
                                                                        </_taxon_family_require_std>
52
                                                                    </prefix>
53
                                                                    <value>
54
                                                                        <_alt>
55
                                                                            <1>$plantNameWithAuthority</1>
56
                                                                            <2>
57
                                                                                <_alt>
58
                                                                                    <1>$plantname</1>
59
                                                                                    <2>
60
                                                                                        <_join_words>
61
                                                                                            <2>
62
                                                                                                <_alt>
63
                                                                                                    <1>$denorm_genus</1>
64
                                                                                                    <2>$genus</2>
65
                                                                                                </_alt>
66
                                                                                            </2>
67
                                                                                            <3>
68
                                                                                                <_alt>
69
                                                                                                    <1>$denorm_species</1>
70
                                                                                                    <2>$species</2>
71
                                                                                                </_alt>
72
                                                                                            </3>
73
                                                                                            <4>$subspecies</4>
74
                                                                                            <7>
75
                                                                                                <_join_words>
76
                                                                                                    <1>var. </1>
77
                                                                                                    <2>$variety</2>
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