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Revision 11270

Added by Aaron Marcuse-Kubitza almost 11 years ago

bugfix: inputs/CVS/taxonObservation_/map.csv: species: remapped to speciesBinomial, not specificEpithet (like for VegBank). however, note that denorm_species is in fact the epithet, unlike VegBank.

View differences:

inputs/CVS/taxonObservation_/map.csv
76 76 
denorm_category,*category,,
77 77 
denorm_family,family,/_alt/1,
78 78 
denorm_genus,genus,/_alt/1,
79 
denorm_species,specificEpithet,/_alt/1,
79 
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
80 80 
denorm_triAbbr,*triAbbr,,
81 81 
denorm_triName,*triName,,
82 82 
denorm_quadAbbr,*quadAbbr,,
......
107 107 
subgenus,subgenus,,
108 108 
section,*section,,
109 109 
composite species,*composite species,,
110 
species,specificEpithet,/_alt/2,
110 
species,speciesBinomial,,full taxonomic name at that rank
111 111 
subspecies,subspecies,,
112 112 
composite variety,*composite variety,,
113 113 
variety,variety,,
inputs/CVS/taxonObservation_/VegBIEN.csv
34 34 
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
35 35 
variety,"/location/locationevent/locationevent:[@fkey=parent_id]/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",
36 36 
subspecies,"/location/locationevent/locationevent:[@fkey=parent_id]/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",
37 
denorm_species,"/location/locationevent/locationevent:[@fkey=parent_id]/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/_alt/1",
38 
species,"/location/locationevent/locationevent:[@fkey=parent_id]/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/_alt/2",
37 
denorm_species,"/location/locationevent/locationevent:[@fkey=parent_id]/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","unlike VegBank, this is in fact the epithet, not the full name"
39 38 
denorm_genus,"/location/locationevent/locationevent:[@fkey=parent_id]/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/_alt/1",
40 39 
genus,"/location/locationevent/locationevent:[@fkey=parent_id]/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/_alt/2",
41 40 
denorm_family,"/location/locationevent/locationevent:[@fkey=parent_id]/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/_alt/1",
......
52 51 
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
53 52 
denorm_genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value/_alt/1,
54 53 
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value/_alt/2,
55 
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/1,
56 
species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1/_alt/2,
54 
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,"unlike VegBank, this is in fact the epithet, not the full name"
57 55 
subspecies,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4,
58 56 
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
59 57 
variety,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2",
......
61 59 
family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family/_alt/2,
62 60 
denorm_genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/1,
63 61 
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,
64 
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet/_alt/1,
65 
species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet/_alt/2,
62 
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,"unlike VegBank, this is in fact the epithet, not the full name"
66 63 
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
67 64 
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
68 65 
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
......
138 135 
revisions,,** No join mapping for *revisions **
139 136 
salutation,,** No join mapping for *salutation **
140 137 
section,,** No join mapping for *section **
138 
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank
141 139 
subgenus,,** No join mapping for subgenus **
142 140 
suffix,,** No join mapping for *suffix **
143 141 
taxonConfidence,,** No join mapping for identificationVerificationStatus **
inputs/CVS/taxonObservation_/test.xml.ref
61 61 
                                                                                                <parent_id>
62 62 
                                                                                                    <taxonlabel>
63 63 
                                                                                                        <rank>species</rank>
64 
                                                                                                        <taxonepithet>
65 
                                                                                                            <_alt>
66 
                                                                                                                <1>$denorm_species</1>
67 
                                                                                                                <2>$species</2>
68 
                                                                                                            </_alt>
69 
                                                                                                        </taxonepithet>
64 
                                                                                                        <taxonepithet>$denorm_species</taxonepithet>
70 65 
                                                                                                        <parent_id>
71 66 
                                                                                                            <taxonlabel>
72 67 
                                                                                                                <rank>genus</rank>
......
160 155 
                                                                                                </value>
161 156 
                                                                                            </_filter_genus>
162 157 
                                                                                        </2>
163 
                                                                                        <3>
164 
                                                                                            <_alt>
165 
                                                                                                <1>$denorm_species</1>
166 
                                                                                                <2>$species</2>
167 
                                                                                            </_alt>
168 
                                                                                        </3>
158 
                                                                                        <3>$denorm_species</3>
169 159 
                                                                                        <4>$subspecies</4>
170 160 
                                                                                        <6>
171 161 
                                                                                            <_join_words>
......
195 185 
                                                        <2>$genus</2>
196 186 
                                                    </_alt>
197 187 
                                                </genus>
198 
                                                <specific_epithet>
199 
                                                    <_alt>
200 
                                                        <1>$denorm_species</1>
201 
                                                        <2>$species</2>
202 
                                                    </_alt>
203 
                                                </specific_epithet>
188 
                                                <specific_epithet>$denorm_species</specific_epithet>
204 189 
                                                <taxonname>$plantname</taxonname>
205 190 
                                                <taxonomicname>$plantNameWithAuthority</taxonomicname>
206 191 
                                                <verbatimrank>$taxonLevel</verbatimrank>
inputs/CVS/taxonObservation_/new_terms.csv
11 11 
denorm_category,*category,,
12 12 
denorm_family,family,/_alt/1,
13 13 
denorm_genus,genus,/_alt/1,
14 
denorm_species,specificEpithet,/_alt/1,
14 
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
15 15 
denorm_triAbbr,*triAbbr,,
16 16 
denorm_triName,*triName,,
17 17 
denorm_quadAbbr,*quadAbbr,,
inputs/CVS/taxonObservation_/unmapped_terms.csv
80 80 
subgenus
81 81 
*section
82 82 
*composite species
83 
speciesBinomial
83 84 
*composite variety

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