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Revision 10685

fix: inputs/VegBank/taxonobservation_/map.csv: also mapped plantname to scientificName, since int_currplantscifull is not always provided when this is. (it cannot replace int_currplantscifull, because when int_currplantscifull also provided, this often leaves out lower ranks.) this should fill in taxonomic information for taxonobservations that are currently missing it.

View differences:

inputs/VegBank/taxonobservation_/map.csv
12 12
int_origplantcommon,originalVernacularName,,
13 13
int_origplantcode,*int_origplantcode,,
14 14
int_currplantconcept_id,*int_currplantconcept_id,,
15
int_currplantscifull,scientificName,,
15
int_currplantscifull,scientificName,/_alt/1,
16 16
int_currplantscinamenoauth,taxonName,,
17 17
int_currplantcommon,vernacularName,,
18 18
int_currplantcode,*int_currplantcode,,
......
43 43
taxoninterpretation_accessioncode,*taxoninterpretation_accessioncode,,
44 44
plantname_id,*plantname_id,,
45 45
plantconcept_reference_id,*plantconcept_reference_id,,
46
plantname,*plantname,,
46
plantname,scientificName,/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
47 47
plantcode,*plantcode,,
48 48
plantdescription,*plantdescription,,
49 49
d_obscount,*d_obscount,,
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
int_origplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1",
24
int_currplantscifull,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
24
int_currplantscifull,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/1",
25
plantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/2","when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
25 26
int_currplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
26 27
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
27 28
taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
......
36 37
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 38
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 39
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
39
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
40
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/1,
41
plantname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
40 42
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
41 43
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,
42 44
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,
......
47 49
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
48 50
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
49 51
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
50
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
52
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/1,
53
plantname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
51 54
taxonobservation_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists",
52 55
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
53 56
interpretationtype,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationtype,
......
84 87
plantconcept_id,,** No join mapping for *plantconcept_id ** 
85 88
plantconcept_reference_id,,** No join mapping for *plantconcept_reference_id ** 
86 89
plantdescription,,** No join mapping for *plantdescription ** 
87
plantname,,** No join mapping for *plantname ** 
88 90
plantname_id,,** No join mapping for *plantname_id ** 
89 91
reference_id,,** No join mapping for *reference_id ** 
90 92
revisions,,** No join mapping for *revisions ** 
inputs/VegBank/taxonobservation_/test.xml.ref
101 101
                                                            <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
102 102
                                                            <value>
103 103
                                                                <_alt>
104
                                                                    <1>$int_currplantscifull</1>
104
                                                                    <1>
105
                                                                        <_alt>
106
                                                                            <1>$int_currplantscifull</1>
107
                                                                            <2>$plantname</2>
108
                                                                        </_alt>
109
                                                                    </1>
105 110
                                                                    <2>
106 111
                                                                        <_alt>
107 112
                                                                            <1>$int_currplantscinamenoauth</1>
......
136 141
                                            <genus>$Genus</genus>
137 142
                                            <specific_epithet>$Species</specific_epithet>
138 143
                                            <taxonname>$int_currplantscinamenoauth</taxonname>
139
                                            <taxonomicname>$int_currplantscifull</taxonomicname>
144
                                            <taxonomicname>
145
                                                <_alt>
146
                                                    <1>$int_currplantscifull</1>
147
                                                    <2>$plantname</2>
148
                                                </_alt>
149
                                            </taxonomicname>
140 150
                                        </taxonverbatim>
141 151
                                    </taxonverbatim_id>
142 152
                                    <determinationdate><_dateRangeStart><value>$interpretationdate</value></_dateRangeStart></determinationdate>
......
160 170
        </path>
161 171
    </_setDefault>
162 172
</VegBIEN>
163
Inserted 14 new rows into database
173
Inserted 16 new rows into database
inputs/VegBank/taxonobservation_/new_terms.csv
2 2
int_origplantscifull,EQUIV#to:authorplantname#int_origplantscifull,, = originalScientificName_scrubbed
3 3
int_origplantscinamenoauth,originalTaxonName,,
4 4
int_origplantcommon,originalVernacularName,,
5
int_currplantscifull,scientificName,,
5
int_currplantscifull,scientificName,/_alt/1,
6 6
int_currplantscinamenoauth,taxonName,,
7 7
int_currplantcommon,vernacularName,,
8 8
interpretationdate,dateIdentified,,
9 9
collectiondate,dateCollected,,
10
plantname,scientificName,/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
inputs/VegBank/taxonobservation_/unmapped_terms.csv
27 27
*taxoninterpretation_accessioncode
28 28
*plantname_id
29 29
*plantconcept_reference_id
30
*plantname
31 30
*plantcode
32 31
*plantdescription
33 32
*d_obscount

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