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Revision 11275

inputs/CVS/import_order.txt: added plantConcept_/ so it would get automapped after switching to new-style import

View differences:

inputs/CVS/import_order.txt
1 1
Source
2 2
plot_
3 3
observation_
4
plantConcept_
4 5
taxonObservation_
5 6
stemCount_
6 7
stemLocation_
inputs/CVS/plantConcept_/map.csv
1
CVS,VegCore,Filter,Comments
2
PLANTCONCEPT_ID,*PLANTCONCEPT_ID,,
3
PLANTNAME_ID,*PLANTNAME_ID,,
4
plantConcept_reference_ID,*plantConcept_reference_ID,,
5
plantname,taxonName,,
6
plantNameWithAuthority,scientificName,,
7
plantCode,*plantCode,,
8
plantDescription,*plantDescription,,
9
plantConcept_accessionCode,*plantConcept_accessionCode,,
10
plantConcept_dba_src_ID,*plantConcept_dba_src_ID,,
11
plantConcept_entry_sppID,*plantConcept_entry_sppID,,
12
USDAPlantsCode,*USDAPlantsCode,,
13
VascularPlant,*VascularPlant,,
14
denorm_kingdom,kingdom,,
15
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"
16
denorm_category,*category,,
17
denorm_family,family,,
18
denorm_genus,genus,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
19
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
20
denorm_triAbbr,infraspecificRank,,
21
denorm_triName,infraspecificEpithet,,
22
denorm_quadAbbr,infraspecificRank2,,sometimes misparsed as the last + sign in the plantNameWithAuthority
23
denorm_quadName,infraspecificEpithet2,,sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
24
denorm_hybridX,*hybridX,,
25
taxonLevel,taxonRank,,
26
taxonRank,OMIT#taxonRank,,Omitted because taxonLevel contains this information in text form
27
lowestParentName,*lowestParentName,,
28
lowestParentConcept_ID,*lowestParentConcept_ID,,
29
lowestChildRank,*lowestChildRank,,
30
commonName,vernacularName,,
31
growthForm_short,*growthForm_short,,
32
woody,*woody,,
33
exotic,*exotic,,
34
usda_code,*usda_code,,
35
usda_growthForm,*usda_growthForm,,
36
Kingdom,DUPLICATE#of:denorm_kingdom#Kingdom,,
37
Subkingdom,*Subkingdom,,
38
Division,*division,/_alt/2,
39
Class,class,,
40
Subclass,*Subclass,,
41
Order,order,,
42
composite family,*composite family,,
43
family,DUPLICATE#of:denorm_family#family,,
44
tribe,*tribe,,
45
composite genus,*composite genus,,
46
genus,genus,/_alt/2,"unlike VegBank, does *not* include genus author"
47
subgenus,subgenus,,
48
section,*section,,
49
composite species,*composite species,,
50
species,speciesBinomial,,full taxonomic name at that rank
51
subspecies,EQUIV#to:species#subspecies,,full taxonomic name at that rank
52
composite variety,EQUIV#to:species#composite variety,,full taxonomic name at that rank
53
variety,EQUIV#to:species#variety,,full taxonomic name at that rank
inputs/CVS/plantConcept_/VegBIEN.csv
1
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2
plantNameWithAuthority,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
3
plantname,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
4
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",
5
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"
6
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
7
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"
8
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",
9
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",
10
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",
11
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",
12
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
13
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
14
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",
15
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
16
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
17
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,
18
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
19
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"
20
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"
21
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",
22
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",
23
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,
24
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
25
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
26
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus/_alt/2,"unlike VegBank, does *not* include genus author"
27
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"
28
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
29
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
30
taxonLevel,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
31
Division,,** No join mapping for *division/_alt/2 ** 
32
Kingdom,,** No non-empty join mapping for DUPLICATE#of:denorm_kingdom#Kingdom ** 
33
PLANTCONCEPT_ID,,** No join mapping for *PLANTCONCEPT_ID ** 
34
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID ** 
35
Subclass,,** No join mapping for *Subclass ** 
36
Subkingdom,,** No join mapping for *Subkingdom ** 
37
USDAPlantsCode,,** No join mapping for *USDAPlantsCode ** 
38
VascularPlant,,** No join mapping for *VascularPlant ** 
39
commonName,,** No join mapping for vernacularName ** 
40
composite family,,** No join mapping for *composite family ** 
41
composite genus,,** No join mapping for *composite genus ** 
42
composite species,,** No join mapping for *composite species ** 
43
composite variety,,** No non-empty join mapping for EQUIV#to:species#composite variety ** full taxonomic name at that rank
44
denorm_category,,** No join mapping for *category ** 
45
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"
46
denorm_hybridX,,** No join mapping for *hybridX ** 
47
denorm_quadAbbr,,** No join mapping for infraspecificRank2 ** sometimes misparsed as the last + sign in the plantNameWithAuthority
48
denorm_quadName,,** No join mapping for infraspecificEpithet2 ** sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
49
denorm_triAbbr,,** No join mapping for infraspecificRank ** 
50
exotic,,** No join mapping for *exotic ** 
51
family,,** No non-empty join mapping for DUPLICATE#of:denorm_family#family ** 
52
growthForm_short,,** No join mapping for *growthForm_short ** 
53
lowestChildRank,,** No join mapping for *lowestChildRank ** 
54
lowestParentConcept_ID,,** No join mapping for *lowestParentConcept_ID ** 
55
lowestParentName,,** No join mapping for *lowestParentName ** 
56
plantCode,,** No join mapping for *plantCode ** 
57
plantConcept_accessionCode,,** No join mapping for *plantConcept_accessionCode ** 
58
plantConcept_dba_src_ID,,** No join mapping for *plantConcept_dba_src_ID ** 
59
plantConcept_entry_sppID,,** No join mapping for *plantConcept_entry_sppID ** 
60
plantConcept_reference_ID,,** No join mapping for *plantConcept_reference_ID ** 
61
plantDescription,,** No join mapping for *plantDescription ** 
62
section,,** No join mapping for *section ** 
63
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank
64
subgenus,,** No join mapping for subgenus ** 
65
subspecies,,** No non-empty join mapping for EQUIV#to:species#subspecies ** full taxonomic name at that rank
66
taxonRank,,** No non-empty join mapping for OMIT#taxonRank ** Omitted because taxonLevel contains this information in text form
67
tribe,,** No join mapping for *tribe ** 
68
usda_code,,** No join mapping for *usda_code ** 
69
usda_growthForm,,** No join mapping for *usda_growthForm ** 
70
variety,,** No non-empty join mapping for EQUIV#to:species#variety ** full taxonomic name at that rank
71
woody,,** No join mapping for *woody ** 
inputs/CVS/plantConcept_/test.xml.ref
1
Put template:
2
<VegBIEN>
3
    <_setDefault id="-1">
4
        <source_id><source><shortname>CVS.new</shortname></source></source_id>
5
        <path>
6
            <_simplifyPath>
7
                <next>parent_id</next>
8
                <path>
9
                    <location>
10
                        <locationevent>
11
                            <locationevent fkey="parent_id">
12
                                <taxonoccurrence>
13
                                    <taxondetermination>
14
                                        <taxonverbatim_id>
15
                                            <taxonverbatim>
16
                                                <taxonlabel_id>
17
                                                    <taxonlabel>
18
                                                        <parent_id>
19
                                                            <taxonlabel>
20
                                                                <rank>$taxonLevel</rank>
21
                                                                <parent_id>
22
                                                                    <taxonlabel>
23
                                                                        <rank>cultivar</rank>
24
                                                                        <parent_id>
25
                                                                            <taxonlabel>
26
                                                                                <rank>forma</rank>
27
                                                                                <parent_id>
28
                                                                                    <taxonlabel>
29
                                                                                        <rank>variety</rank>
30
                                                                                        <parent_id>
31
                                                                                            <taxonlabel>
32
                                                                                                <rank>subspecies</rank>
33
                                                                                                <parent_id>
34
                                                                                                    <taxonlabel>
35
                                                                                                        <rank>species</rank>
36
                                                                                                        <taxonepithet>$denorm_species</taxonepithet>
37
                                                                                                        <parent_id>
38
                                                                                                            <taxonlabel>
39
                                                                                                                <rank>genus</rank>
40
                                                                                                                <taxonepithet>
41
                                                                                                                    <_alt>
42
                                                                                                                        <1>$denorm_genus</1>
43
                                                                                                                        <2>$genus</2>
44
                                                                                                                    </_alt>
45
                                                                                                                </taxonepithet>
46
                                                                                                                <parent_id>
47
                                                                                                                    <taxonlabel>
48
                                                                                                                        <rank>family</rank>
49
                                                                                                                        <taxonepithet>$denorm_family</taxonepithet>
50
                                                                                                                        <parent_id>
51
                                                                                                                            <taxonlabel>
52
                                                                                                                                <rank>order</rank>
53
                                                                                                                                <taxonepithet>$Order</taxonepithet>
54
                                                                                                                                <parent_id>
55
                                                                                                                                    <taxonlabel>
56
                                                                                                                                        <rank>class</rank>
57
                                                                                                                                        <taxonepithet>$Class</taxonepithet>
58
                                                                                                                                        <parent_id>
59
                                                                                                                                            <taxonlabel>
60
                                                                                                                                                <rank>phylum</rank>
61
                                                                                                                                                <parent_id>
62
                                                                                                                                                    <taxonlabel>
63
                                                                                                                                                        <rank>kingdom</rank>
64
                                                                                                                                                        <taxonepithet>$denorm_kingdom</taxonepithet>
65
                                                                                                                                                    </taxonlabel>
66
                                                                                                                                                </parent_id>
67
                                                                                                                                            </taxonlabel>
68
                                                                                                                                        </parent_id>
69
                                                                                                                                    </taxonlabel>
70
                                                                                                                                </parent_id>
71
                                                                                                                            </taxonlabel>
72
                                                                                                                        </parent_id>
73
                                                                                                                    </taxonlabel>
74
                                                                                                                </parent_id>
75
                                                                                                            </taxonlabel>
76
                                                                                                        </parent_id>
77
                                                                                                    </taxonlabel>
78
                                                                                                </parent_id>
79
                                                                                            </taxonlabel>
80
                                                                                        </parent_id>
81
                                                                                    </taxonlabel>
82
                                                                                </parent_id>
83
                                                                            </taxonlabel>
84
                                                                        </parent_id>
85
                                                                    </taxonlabel>
86
                                                                </parent_id>
87
                                                                <taxonepithet>$denorm_triName</taxonepithet>
88
                                                            </taxonlabel>
89
                                                        </parent_id>
90
                                                        <rank>$taxonLevel</rank>
91
                                                        <taxonomicname>
92
                                                            <_merge_prefix>
93
                                                                <prefix><_taxon_family_require_std><family>$denorm_family</family></_taxon_family_require_std></prefix>
94
                                                                <value>
95
                                                                    <_alt>
96
                                                                        <1>$plantNameWithAuthority</1>
97
                                                                        <2>
98
                                                                            <_alt>
99
                                                                                <1>$plantname</1>
100
                                                                                <2>
101
                                                                                    <_join_words>
102
                                                                                        <2>
103
                                                                                            <_filter_genus>
104
                                                                                                <value>
105
                                                                                                    <_alt>
106
                                                                                                        <1>$denorm_genus</1>
107
                                                                                                        <2>$genus</2>
108
                                                                                                    </_alt>
109
                                                                                                </value>
110
                                                                                            </_filter_genus>
111
                                                                                        </2>
112
                                                                                        <3>$denorm_species</3>
113
                                                                                        <5>
114
                                                                                            <_join_words>
115
                                                                                                <1>
116
                                                                                                    <_if name="if has infraspecificEpithet">
117
                                                                                                        <cond>$denorm_triName</cond>
118
                                                                                                        <then>$taxonLevel</then>
119
                                                                                                    </_if>
120
                                                                                                </1>
121
                                                                                                <2>$denorm_triName</2>
122
                                                                                            </_join_words>
123
                                                                                        </5>
124
                                                                                    </_join_words>
125
                                                                                </2>
126
                                                                            </_alt>
127
                                                                        </2>
128
                                                                    </_alt>
129
                                                                </value>
130
                                                            </_merge_prefix>
131
                                                        </taxonomicname>
132
                                                    </taxonlabel>
133
                                                </taxonlabel_id>
134
                                                <family>$denorm_family</family>
135
                                                <genus>
136
                                                    <_alt>
137
                                                        <1>$denorm_genus</1>
138
                                                        <2>$genus</2>
139
                                                    </_alt>
140
                                                </genus>
141
                                                <specific_epithet>$denorm_species</specific_epithet>
142
                                                <taxonname>$plantname</taxonname>
143
                                                <taxonomicname>$plantNameWithAuthority</taxonomicname>
144
                                                <verbatimrank>$taxonLevel</verbatimrank>
145
                                            </taxonverbatim>
146
                                        </taxonverbatim_id>
147
                                    </taxondetermination>
148
                                </taxonoccurrence>
149
                            </locationevent>
150
                        </locationevent>
151
                    </location>
152
                </path>
153
            </_simplifyPath>
154
        </path>
155
    </_setDefault>
156
</VegBIEN>
157
Inserted 14 new rows into database
inputs/CVS/plantConcept_/new_terms.csv
1
plantname,taxonName,,
2
plantNameWithAuthority,scientificName,,
3
denorm_kingdom,kingdom,,
4
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"
5
denorm_category,*category,,
6
denorm_family,family,,
7
denorm_genus,genus,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
8
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
9
denorm_triAbbr,infraspecificRank,,
10
denorm_triName,infraspecificEpithet,,
11
denorm_quadAbbr,infraspecificRank2,,sometimes misparsed as the last + sign in the plantNameWithAuthority
12
denorm_quadName,infraspecificEpithet2,,sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
13
denorm_hybridX,*hybridX,,
14
taxonLevel,taxonRank,,
15
composite variety,EQUIV#to:species#composite variety,,full taxonomic name at that rank
inputs/CVS/plantConcept_/unmapped_terms.csv
1
*PLANTCONCEPT_ID
2
*PLANTNAME_ID
3
*plantConcept_reference_ID
4
*plantCode
5
*plantDescription
6
*plantConcept_accessionCode
7
*plantConcept_dba_src_ID
8
*plantConcept_entry_sppID
9
*USDAPlantsCode
10
*VascularPlant
11
*division
12
*category
13
infraspecificRank
14
infraspecificRank2
15
infraspecificEpithet2
16
*hybridX
17
*lowestParentName
18
*lowestParentConcept_ID
19
*lowestChildRank
20
vernacularName
21
*growthForm_short
22
*woody
23
*exotic
24
*usda_code
25
*usda_growthForm
26
*Subkingdom
27
*division
28
*Subclass
29
*composite family
30
*tribe
31
*composite genus
32
subgenus
33
*section
34
*composite species
35
speciesBinomial

Also available in: Unified diff