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Revision 11271

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/CVS/taxonObservation_/map.csv: denorm_* terms _alt-ed with normalized terms: use DUPLICATE#of instead where possible. documented where and why _alt was necessary (this applies to a few rows for division, genus).

View differences:

inputs/CVS/taxonObservation_/map.csv
71 71 
plantConcept_entry_sppID,*plantConcept_entry_sppID,,
72 72 
USDAPlantsCode,*USDAPlantsCode,,
73 73 
VascularPlant,*VascularPlant,,
74 
denorm_kingdom,kingdom,/_alt/1,
75 
denorm_division,*division,/_alt/1,
74 
denorm_kingdom,kingdom,,
75 
denorm_division,*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"
76 76 
denorm_category,*category,,
77 
denorm_family,family,/_alt/1,
78 
denorm_genus,genus,/_alt/1,
77 
denorm_family,family,,
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 80 
denorm_triAbbr,*triAbbr,,
81 81 
denorm_triName,*triName,,
......
93 93 
exotic,*exotic,,
94 94 
usda_code,*usda_code,,
95 95 
usda_growthForm,*usda_growthForm,,
96 
Kingdom,kingdom,/_alt/2,
96 
Kingdom,DUPLICATE#of:denorm_kingdom#Kingdom,,
97 97 
Subkingdom,*Subkingdom,,
98 
Division,*Division,/_alt/2,
98 
Division,*division,/_alt/2,
99 99 
Class,class,,
100 100 
Subclass,*Subclass,,
101 101 
Order,order,,
102 102 
composite family,*composite family,,
103 
family,family,/_alt/2,
103 
family,DUPLICATE#of:denorm_family#family,,
104 104 
tribe,*tribe,,
105 105 
composite genus,*composite genus,,
106 106 
genus,genus,/_alt/2,
inputs/CVS/taxonObservation_/VegBIEN.csv
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 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"
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",
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",must be _alt-ed with genus because this is missing in 1 row that has genus
39 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",
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",
41 
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/2",
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",
42 41 
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",
43 42 
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",
44 
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/_alt/1",
45 
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/_alt/2",
43 
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",
46 44 
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
47 45 
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",
48 
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_alt/1,
49 
family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_alt/2,
46 
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
50 47 
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
51 48 
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,
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,
49 
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
53 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,
54 51 
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"
55 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,
56 53 
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",
57 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",
58 
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family/_alt/1,
59 
family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family/_alt/2,
60 
denorm_genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/1,
55 
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
56 
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
61 57 
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,
62 58 
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"
63 59 
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
......
70 66 
authorPlantName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname,
71 67 
museumAccessionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
72 68 
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
73 
Division,,** No join mapping for *Division/_alt/2 **
69 
Division,,** No join mapping for *division/_alt/2 **
70 
Kingdom,,** No non-empty join mapping for DUPLICATE#of:denorm_kingdom#Kingdom **
74 71 
PARTY_ID,,** No join mapping for *PARTY_ID **
75 72 
PLANTCONCEPT_ID,,** No join mapping for *PLANTCONCEPT_ID **
76 73 
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID **
......
100 97 
dba_src_ID,,** No join mapping for *dba_src_ID **
101 98 
dba_unsure,,** No join mapping for *dba_unsure **
102 99 
denorm_category,,** No join mapping for *category **
103 
denorm_division,,** No join mapping for *division/_alt/1 **
100 
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"
104 101 
denorm_hybridX,,** No join mapping for *hybridX **
105 102 
denorm_quadAbbr,,** No join mapping for *quadAbbr **
106 103 
denorm_quadName,,** No join mapping for *quadName **
......
113 110 
entry_unknownSp,,** No join mapping for *entry_unknownSp **
114 111 
entry_userInitials,,** No join mapping for *entry_userInitials **
115 112 
exotic,,** No join mapping for *exotic **
113 
family,,** No non-empty join mapping for DUPLICATE#of:denorm_family#family **
116 114 
groupType,,** No join mapping for *groupType **
117 115 
growthForm_short,,** No join mapping for *growthForm_short **
118 116 
lowestChildRank,,** No join mapping for *lowestChildRank **
inputs/CVS/taxonObservation_/test.xml.ref
74 74 
                                                                                                                <parent_id>
75 75 
                                                                                                                    <taxonlabel>
76 76 
                                                                                                                        <rank>family</rank>
77 
                                                                                                                        <taxonepithet>
78 
                                                                                                                            <_alt>
79 
                                                                                                                                <1>$denorm_family</1>
80 
                                                                                                                                <2>$family</2>
81 
                                                                                                                            </_alt>
82 
                                                                                                                        </taxonepithet>
77 
                                                                                                                        <taxonepithet>$denorm_family</taxonepithet>
83 78 
                                                                                                                        <parent_id>
84 79 
                                                                                                                            <taxonlabel>
85 80 
                                                                                                                                <rank>order</rank>
......
94 89 
                                                                                                                                                <parent_id>
95 90 
                                                                                                                                                    <taxonlabel>
96 91 
                                                                                                                                                        <rank>kingdom</rank>
97 
                                                                                                                                                        <taxonepithet>
98 
                                                                                                                                                            <_alt>
99 
                                                                                                                                                                <1>$denorm_kingdom</1>
100 
                                                                                                                                                                <2>$Kingdom</2>
101 
                                                                                                                                                            </_alt>
102 
                                                                                                                                                        </taxonepithet>
92 
                                                                                                                                                        <taxonepithet>$denorm_kingdom</taxonepithet>
103 93 
                                                                                                                                                    </taxonlabel>
104 94 
                                                                                                                                                </parent_id>
105 95 
                                                                                                                                            </taxonlabel>
......
127 117 
                                                        <rank>$taxonLevel</rank>
128 118 
                                                        <taxonomicname>
129 119 
                                                            <_merge_prefix>
130 
                                                                <prefix>
131 
                                                                    <_taxon_family_require_std>
132 
                                                                        <family>
133 
                                                                            <_alt>
134 
                                                                                <1>$denorm_family</1>
135 
                                                                                <2>$family</2>
136 
                                                                            </_alt>
137 
                                                                        </family>
138 
                                                                    </_taxon_family_require_std>
139 
                                                                </prefix>
120 
                                                                <prefix><_taxon_family_require_std><family>$denorm_family</family></_taxon_family_require_std></prefix>
140 121 
                                                                <value>
141 122 
                                                                    <_alt>
142 123 
                                                                        <1>$plantNameWithAuthority</1>
......
173 154 
                                                        </taxonomicname>
174 155 
                                                    </taxonlabel>
175 156 
                                                </taxonlabel_id>
176 
                                                <family>
177 
                                                    <_alt>
178 
                                                        <1>$denorm_family</1>
179 
                                                        <2>$family</2>
180 
                                                    </_alt>
181 
                                                </family>
157 
                                                <family>$denorm_family</family>
182 158 
                                                <genus>
183 159 
                                                    <_alt>
184 160 
                                                        <1>$denorm_genus</1>
inputs/CVS/taxonObservation_/new_terms.csv
6 6 
surName,recordedBy_surName,,
7 7 
plantname,taxonName,,
8 8 
plantNameWithAuthority,scientificName,,
9 
denorm_kingdom,kingdom,/_alt/1,
10 
denorm_division,*division,/_alt/1,
9 
denorm_kingdom,kingdom,,
10 
denorm_division,*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"
11 11 
denorm_category,*category,,
12 
denorm_family,family,/_alt/1,
13 
denorm_genus,genus,/_alt/1,
12 
denorm_family,family,,
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 15 
denorm_triAbbr,*triAbbr,,
16 16 
denorm_triName,*triName,,
inputs/CVS/taxonObservation_/unmapped_terms.csv
72 72 
*usda_code
73 73 
*usda_growthForm
74 74 
*Subkingdom
75 
*Division
75 
*division
76 76 
*Subclass
77 77 
*composite family
78 78 
*tribe

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