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Revision 10678

inputs/VegBank/taxonobservation_/map.csv: mapped int_origplant*, int_currplant* to *scientificName/*taxonName/etc.

View differences:

inputs/VegBank/taxonobservation_/map.csv
7 7
taxoninferencearea,*taxoninferencearea,,
8 8
emb_taxonobservation,*emb_taxonobservation,,
9 9
int_origplantconcept_id,*int_origplantconcept_id,,
10
int_origplantscifull,*int_origplantscifull,,
11
int_origplantscinamenoauth,*int_origplantscinamenoauth,,
12
int_origplantcommon,*int_origplantcommon,,
10
int_origplantscifull,originalScientificName,,
11
int_origplantscinamenoauth,originalTaxonName,,
12
int_origplantcommon,originalVernacularName,,
13 13
int_origplantcode,*int_origplantcode,,
14 14
int_currplantconcept_id,*int_currplantconcept_id,,
15
int_currplantscifull,*int_currplantscifull,,
16
int_currplantscinamenoauth,*int_currplantscinamenoauth,,
15
int_currplantscifull,scientificName,,
16
int_currplantscinamenoauth,taxonName,,
17 17
int_currplantcommon,vernacularName,,
18 18
int_currplantcode,*int_currplantcode,,
19 19
taxonobservation_accessioncode,*taxonobservation_accessioncode,,
inputs/VegBank/taxonobservation_/VegBIEN.csv
21 21
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
22 22
collectionnumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
23 23
authorplantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1",
24
int_origplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1",
25
int_currplantscifull,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
26
int_currplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
24 27
givenname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/1,
25 28
surname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/2,
26 29
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
......
36 39
Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet",
37 40
Kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",
38 41
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
42
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
43
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
39 44
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,
40 45
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
41 46
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4,
......
44 49
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
45 50
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
46 51
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
52
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
53
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
47 54
taxonobservation_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists",
48 55
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
49 56
interpretationtype,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationtype,
50 57
taxonfit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
51 58
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname,
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int_origplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname,
60
int_origplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname,
52 61
museumaccessionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
53 62
collectionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
54 63
Division,,** No join mapping for *Division ** 
......
70 79
int_currplantcode,,** No join mapping for *int_currplantcode ** 
71 80
int_currplantcommon,,** No join mapping for vernacularName ** 
72 81
int_currplantconcept_id,,** No join mapping for *int_currplantconcept_id ** 
73
int_currplantscifull,,** No join mapping for *int_currplantscifull ** 
74
int_currplantscinamenoauth,,** No join mapping for *int_currplantscinamenoauth ** 
75 82
int_origplantcode,,** No join mapping for *int_origplantcode ** 
76
int_origplantcommon,,** No join mapping for *int_origplantcommon ** 
83
int_origplantcommon,,** No join mapping for originalVernacularName ** 
77 84
int_origplantconcept_id,,** No join mapping for *int_origplantconcept_id ** 
78
int_origplantscifull,,** No join mapping for *int_origplantscifull ** 
79
int_origplantscinamenoauth,,** No join mapping for *int_origplantscinamenoauth ** 
80 85
middlename,,** No join mapping for *middlename ** 
81 86
museum_id,,** No join mapping for *museum_id ** 
82 87
notesmgt,,** No join mapping for *notesmgt ** 
inputs/VegBank/taxonobservation_/test.xml.ref
110 110
                                                        <_merge_prefix>
111 111
                                                            <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
112 112
                                                            <value>
113
                                                                <_join_words>
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                                                                    <2><_filter_genus><value>$Genus</value></_filter_genus></2>
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                                                                    <3>$Species</3>
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                                                                    <4>$Subspecies</4>
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                                                                    <6>
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                                                                        <_join_words>
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                                                                            <1>var. </1>
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                                                                            <2>$Variety</2>
121
                                                                        </_join_words>
122
                                                                    </6>
123
                                                                    <7>
124
                                                                        <_join_words>
125
                                                                            <1>fm. </1>
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                                                                            <2>$Forma</2>
127
                                                                        </_join_words>
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                                                                    </7>
129
                                                                </_join_words>
113
                                                                <_alt>
114
                                                                    <1>$int_currplantscifull</1>
115
                                                                    <2>
116
                                                                        <_alt>
117
                                                                            <1>$int_currplantscinamenoauth</1>
118
                                                                            <2>
119
                                                                                <_join_words>
120
                                                                                    <2><_filter_genus><value>$Genus</value></_filter_genus></2>
121
                                                                                    <3>$Species</3>
122
                                                                                    <4>$Subspecies</4>
123
                                                                                    <6>
124
                                                                                        <_join_words>
125
                                                                                            <1>var. </1>
126
                                                                                            <2>$Variety</2>
127
                                                                                        </_join_words>
128
                                                                                    </6>
129
                                                                                    <7>
130
                                                                                        <_join_words>
131
                                                                                            <1>fm. </1>
132
                                                                                            <2>$Forma</2>
133
                                                                                        </_join_words>
134
                                                                                    </7>
135
                                                                                </_join_words>
136
                                                                            </2>
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                                                                        </_alt>
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                                                                    </2>
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                                                                </_alt>
130 140
                                                            </value>
131 141
                                                        </_merge_prefix>
132 142
                                                    </taxonomicname>
......
135 145
                                            <family>$Family</family>
136 146
                                            <genus>$Genus</genus>
137 147
                                            <specific_epithet>$Species</specific_epithet>
148
                                            <taxonname>$int_currplantscinamenoauth</taxonname>
149
                                            <taxonomicname>$int_currplantscifull</taxonomicname>
138 150
                                        </taxonverbatim>
139 151
                                    </taxonverbatim_id>
140 152
                                    <determinationdate><_dateRangeStart><value>$interpretationdate</value></_dateRangeStart></determinationdate>
......
143 155
                                </taxondetermination>
144 156
                                <taxondetermination>
145 157
                                    <isoriginal>true</isoriginal>
146
                                    <taxonverbatim_id><taxonverbatim><taxonname>$authorplantname</taxonname></taxonverbatim></taxonverbatim_id>
158
                                    <taxonverbatim_id>
159
                                        <taxonverbatim>
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                                            <taxonname>
161
                                                <_alt>
162
                                                    <0>$authorplantname</0>
163
                                                    <1>$int_origplantscinamenoauth</1>
164
                                                </_alt>
165
                                            </taxonname>
166
                                            <taxonomicname>$int_origplantscifull</taxonomicname>
167
                                        </taxonverbatim>
168
                                    </taxonverbatim_id>
147 169
                                </taxondetermination>
148 170
                            </taxonoccurrence>
149 171
                        </locationevent>
inputs/VegBank/taxonobservation_/new_terms.csv
1 1
observation_id,eventID,,
2
int_origplantscifull,originalScientificName,,
3
int_origplantscinamenoauth,originalTaxonName,,
4
int_origplantcommon,originalVernacularName,,
5
int_currplantscifull,scientificName,,
6
int_currplantscinamenoauth,taxonName,,
2 7
int_currplantcommon,vernacularName,,
3 8
interpretationdate,dateIdentified,,
4 9
collectiondate,dateCollected,,
inputs/VegBank/taxonobservation_/unmapped_terms.csv
3 3
*taxoninferencearea
4 4
*emb_taxonobservation
5 5
*int_origplantconcept_id
6
*int_origplantscifull
7
*int_origplantscinamenoauth
8
*int_origplantcommon
6
originalVernacularName
9 7
*int_origplantcode
10 8
*int_currplantconcept_id
11
*int_currplantscifull
12
*int_currplantscinamenoauth
13 9
vernacularName
14 10
*int_currplantcode
15 11
*taxonobservation_accessioncode

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