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Revision 11274

inputs/CVS/taxonObservation_/map.csv: denorm_{tri,quad}*: mapped to infraspecificRank*, infraspecificEpithet*

View differences:

inputs/CVS/taxonObservation_/map.csv
77 77
denorm_family,family,,
78 78
denorm_genus,genus,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
79 79
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
80
denorm_triAbbr,*triAbbr,,
81
denorm_triName,*triName,,
82
denorm_quadAbbr,*quadAbbr,,
83
denorm_quadName,*quadName,,
80
denorm_triAbbr,infraspecificRank,,
81
denorm_triName,infraspecificEpithet,,
82
denorm_quadAbbr,infraspecificRank2,,sometimes misparsed as the last + sign in the plantNameWithAuthority
83
denorm_quadName,infraspecificEpithet2,,sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
84 84
denorm_hybridX,*hybridX,,
85 85
taxonLevel,taxonRank,,
86 86
taxonRank,OMIT#taxonRank,,Omitted because taxonLevel contains this information in text form
inputs/CVS/taxonObservation_/VegBIEN.csv
32 32
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
33 33
TAXONOBSERVATION_ID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/sourceaccessioncode/_first/1,
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
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
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 35
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"
38 36
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",must be _alt-ed with genus because this is missing in 1 row that has genus
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",
37
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","unlike VegBank, does *not* include genus author"
40 38
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",
41 39
Order,"/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,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet",
42 40
Class,"/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,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet",
43 41
denorm_kingdom,"/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,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",
42
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
44 43
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
45 44
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
46 45
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
47 46
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
48 47
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,
49 48
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,must be _alt-ed with genus because this is missing in 1 row that has genus
50
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,
49
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,"unlike VegBank, does *not* include genus author"
51 50
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"
52
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,
51
denorm_triName,"/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""]/cond",
53 52
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",
54
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",
53
denorm_triName,/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/2,
55 54
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
56 55
denorm_genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
57
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,
56
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,"unlike VegBank, does *not* include genus author"
58 57
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"
59 58
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
60 59
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
......
83 82
composite family,,** No join mapping for *composite family ** 
84 83
composite genus,,** No join mapping for *composite genus ** 
85 84
composite species,,** No join mapping for *composite species ** 
86
composite variety,,** No join mapping for *composite variety ** 
85
composite variety,,** No non-empty join mapping for EQUIV#to:species#composite variety ** full taxonomic name at that rank
87 86
contactInstructions,,** No join mapping for *contactInstructions ** 
88 87
currentInterpretation,,** No join mapping for *currentInterpretation ** 
89 88
currentName_ID,,** No join mapping for *currentName_ID ** 
......
99 98
denorm_category,,** No join mapping for *category ** 
100 99
denorm_division,,"** No join mapping for *division/_alt/1 ** must be _alt-ed with Division because this is missing in 2 rows that have Division, and different from Division in 1 row"
101 100
denorm_hybridX,,** No join mapping for *hybridX ** 
102
denorm_quadAbbr,,** No join mapping for *quadAbbr ** 
103
denorm_quadName,,** No join mapping for *quadName ** 
104
denorm_triAbbr,,** No join mapping for *triAbbr ** 
105
denorm_triName,,** No join mapping for *triName ** 
101
denorm_quadAbbr,,** No join mapping for infraspecificRank2 ** sometimes misparsed as the last + sign in the plantNameWithAuthority
102
denorm_quadName,,** No join mapping for infraspecificEpithet2 ** sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
103
denorm_triAbbr,,** No join mapping for infraspecificRank ** 
106 104
email,,** No join mapping for *email ** 
107 105
entry_herbLineID,,** No join mapping for *entry_herbLineID ** 
108 106
entry_sortOrder,,** No join mapping for *entry_sortOrder ** 
......
135 133
section,,** No join mapping for *section ** 
136 134
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank
137 135
subgenus,,** No join mapping for subgenus ** 
136
subspecies,,** No non-empty join mapping for EQUIV#to:species#subspecies ** full taxonomic name at that rank
138 137
suffix,,** No join mapping for *suffix ** 
139 138
taxonConfidence,,** No join mapping for identificationVerificationStatus ** 
140 139
taxonInferenceArea,,** No join mapping for *taxonInferenceArea ** 
......
152 151
tribe,,** No join mapping for *tribe ** 
153 152
usda_code,,** No join mapping for *usda_code ** 
154 153
usda_growthForm,,** No join mapping for *usda_growthForm ** 
154
variety,,** No non-empty join mapping for EQUIV#to:species#variety ** full taxonomic name at that rank
155 155
woody,,** No join mapping for *woody ** 
inputs/CVS/taxonObservation_/test.xml.ref
53 53
                                                                                <parent_id>
54 54
                                                                                    <taxonlabel>
55 55
                                                                                        <rank>variety</rank>
56
                                                                                        <taxonepithet>$variety</taxonepithet>
57 56
                                                                                        <parent_id>
58 57
                                                                                            <taxonlabel>
59 58
                                                                                                <rank>subspecies</rank>
60
                                                                                                <taxonepithet>$subspecies</taxonepithet>
61 59
                                                                                                <parent_id>
62 60
                                                                                                    <taxonlabel>
63 61
                                                                                                        <rank>species</rank>
......
112 110
                                                                        </parent_id>
113 111
                                                                    </taxonlabel>
114 112
                                                                </parent_id>
113
                                                                <taxonepithet>$denorm_triName</taxonepithet>
115 114
                                                            </taxonlabel>
116 115
                                                        </parent_id>
117 116
                                                        <rank>$taxonLevel</rank>
......
137 136
                                                                                            </_filter_genus>
138 137
                                                                                        </2>
139 138
                                                                                        <3>$denorm_species</3>
140
                                                                                        <4>$subspecies</4>
141
                                                                                        <6>
139
                                                                                        <5>
142 140
                                                                                            <_join_words>
143
                                                                                                <1>var. </1>
144
                                                                                                <2>$variety</2>
141
                                                                                                <1>
142
                                                                                                    <_if name="if has infraspecificEpithet">
143
                                                                                                        <cond>$denorm_triName</cond>
144
                                                                                                        <then>$taxonLevel</then>
145
                                                                                                    </_if>
146
                                                                                                </1>
147
                                                                                                <2>$denorm_triName</2>
145 148
                                                                                            </_join_words>
146
                                                                                        </6>
149
                                                                                        </5>
147 150
                                                                                    </_join_words>
148 151
                                                                                </2>
149 152
                                                                            </_alt>
inputs/CVS/taxonObservation_/new_terms.csv
12 12
denorm_family,family,,
13 13
denorm_genus,genus,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
14 14
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
15
denorm_triAbbr,*triAbbr,,
16
denorm_triName,*triName,,
17
denorm_quadAbbr,*quadAbbr,,
18
denorm_quadName,*quadName,,
15
denorm_triAbbr,infraspecificRank,,
16
denorm_triName,infraspecificEpithet,,
17
denorm_quadAbbr,infraspecificRank2,,sometimes misparsed as the last + sign in the plantNameWithAuthority
18
denorm_quadName,infraspecificEpithet2,,sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
19 19
denorm_hybridX,*hybridX,,
20 20
taxonLevel,taxonRank,,
21 21
composite variety,EQUIV#to:species#composite variety,,full taxonomic name at that rank
inputs/CVS/taxonObservation_/unmapped_terms.csv
57 57
*VascularPlant
58 58
*division
59 59
*category
60
*triAbbr
61
*triName
62
*quadAbbr
63
*quadName
60
infraspecificRank
61
infraspecificRank2
62
infraspecificEpithet2
64 63
*hybridX
65 64
*lowestParentName
66 65
*lowestParentConcept_ID

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