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Revision 10678

Added by Aaron Marcuse-Kubitza over 11 years ago

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,
59 
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>$Family</family></_taxon_family_require_std></prefix>
112 112 
                                                            <value>
113 
                                                                <_join_words>
114 
                                                                    <2><_filter_genus><value>$Genus</value></_filter_genus></2>
115 
                                                                    <3>$Species</3>
116 
                                                                    <4>$Subspecies</4>
117 
                                                                    <6>
118 
                                                                        <_join_words>
119 
                                                                            <1>var. </1>
120 
                                                                            <2>$Variety</2>
121 
                                                                        </_join_words>
122 
                                                                    </6>
123 
                                                                    <7>
124 
                                                                        <_join_words>
125 
                                                                            <1>fm. </1>
126 
                                                                            <2>$Forma</2>
127 
                                                                        </_join_words>
128 
                                                                    </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>$Forma</2>
133 
                                                                                        </_join_words>
134 
                                                                                    </7>
135 
                                                                                </_join_words>
136 
                                                                            </2>
137 
                                                                        </_alt>
138 
                                                                    </2>
139 
                                                                </_alt>
130 140 
                                                            </value>
131 141 
                                                        </_merge_prefix>
132 142 
                                                    </taxonomicname>
......
135 145 
                                            <family>$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>
160 
                                            <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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