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Revision 11739

fix: inputs/CVS/taxonObservation_/header.csv, map.csv: updated for CVS refresh and addition of plantConcept_ derived columns

View differences:

inputs/CVS/taxonObservation_/header.csv
1
PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Division,Class,Subclass,Order,composite family,family,tribe,composite genus,genus,subgenus,section,composite species,species,subspecies,composite variety,variety
1
PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,sensitiveSpeciesFuzzPlot,Kingdom,Subkingdom,Division,Class,Subclass,Order,composite family,family,tribe,composite genus,*genus,subgenus,section,composite species,species,subspecies,composite variety,variety,division,genus
inputs/CVS/taxonObservation_/map.csv
61 61
USDAPlantsCode,*USDAPlantsCode,,
62 62
VascularPlant,*VascularPlant,,
63 63
denorm_kingdom,kingdom,,
64
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"
64
denorm_division,division_main,/_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"
65 65
denorm_category,*category,,
66 66
denorm_family,family,,
67
denorm_genus,genus,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
67
denorm_genus,genus_main,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
68 68
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
69 69
denorm_triAbbr,infraspecificRank,,
70 70
denorm_triName,infraspecificEpithet,,
......
82 82
exotic,*exotic,,
83 83
usda_code,*usda_code,,
84 84
usda_growthForm,*usda_growthForm,,
85
sensitiveSpeciesFuzzPlot,*sensitiveSpeciesFuzzPlot,,
85 86
Kingdom,DUPLICATE#of:denorm_kingdom#Kingdom,,
86 87
Subkingdom,*Subkingdom,,
87
Division,*division,/_alt/2,
88
Division,division_normalized,/_alt/2,
88 89
Class,class,,
89 90
Subclass,*Subclass,,
90 91
Order,order,,
......
92 93
family,DUPLICATE#of:denorm_family#family,,
93 94
tribe,*tribe,,
94 95
composite genus,*composite genus,,
95
genus,genus,/_alt/2,"unlike VegBank, does *not* include genus author"
96
genus,genus_normalized,/_alt/2,"unlike VegBank, does *not* include genus author"
96 97
subgenus,subgenus,,
97 98
section,*section,,
98 99
composite species,*composite species,,
......
101 102
composite variety,EQUIV#to:species#composite variety,,full taxonomic name at that rank
102 103
variety,EQUIV#to:species#variety,,full taxonomic name at that rank
103 104
:plot,observationGranularity,,
105
division,*division,,
106
genus,genus,,
inputs/CVS/taxonObservation_/VegBIEN.csv
31 31
TAXONOBSERVATION_ID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/sourceaccessioncode/_first/1,
32 32
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
33 33
denorm_species,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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"
34
denorm_genus,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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
35
genus,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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"
34
genus,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
36 35
denorm_family,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
37 36
Order,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
38 37
Class,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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 42
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
44 43
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
45 44
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
46
denorm_genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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
47
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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"
45
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,
48 46
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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"
49 47
denorm_triName,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
50 48
taxonLevel,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_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",
51 49
denorm_triName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
52 50
denorm_family,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/family,
53
denorm_genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/genus/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
54
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/genus/_alt/2,"unlike VegBank, does *not* include genus author"
51
genus,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/genus,
55 52
denorm_species,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/specific_epithet,"unlike VegBank, this is in fact the epithet, not the full name"
56 53
plantname,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/taxonname,
57 54
plantNameWithAuthority,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[!isoriginal=true]/*_id/taxonverbatim/taxonomicname,
......
65 62
authorPlantName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname,
66 63
museumAccessionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
67 64
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
68
Division,,** No join mapping for *division/_alt/2 ** 
65
Division,,** No join mapping for division_normalized/_alt/2 ** 
69 66
Kingdom,,** No non-empty join mapping for DUPLICATE#of:denorm_kingdom#Kingdom ** 
70 67
PLANTCONCEPT_ID,,** No join mapping for *PLANTCONCEPT_ID ** 
71 68
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID ** 
......
92 89
dba_src_ID,,** No join mapping for *dba_src_ID ** 
93 90
dba_unsure,,** No join mapping for *dba_unsure ** 
94 91
denorm_category,,** No join mapping for *category ** 
95
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"
92
denorm_division,,"** No join mapping for division_main/_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"
93
denorm_genus,,** No join mapping for genus_main/_alt/1 ** must be _alt-ed with genus because this is missing in 1 row that has genus
96 94
denorm_hybridX,,** No join mapping for *hybridX ** 
97 95
denorm_quadAbbr,,** No join mapping for infraspecificRank2 ** sometimes misparsed as the last + sign in the plantNameWithAuthority
98 96
denorm_quadName,,** No join mapping for infraspecificEpithet2 ** sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
99 97
denorm_triAbbr,,** No join mapping for infraspecificRank ** 
98
division,,** No join mapping for *division ** 
100 99
entry_herbLineID,,** No join mapping for *entry_herbLineID ** 
101 100
entry_sortOrder,,** No join mapping for *entry_sortOrder ** 
102 101
entry_treeLineID,,** No join mapping for *entry_treeLineID ** 
103 102
entry_unknownSp,,** No join mapping for *entry_unknownSp ** 
104 103
exotic,,** No join mapping for *exotic ** 
105 104
family,,** No non-empty join mapping for DUPLICATE#of:denorm_family#family ** 
105
genus,,"** No join mapping for genus_normalized/_alt/2 ** unlike VegBank, does *not* include genus author"
106 106
groupType,,** No join mapping for *groupType ** 
107 107
growthForm_short,,** No join mapping for *growthForm_short ** 
108 108
lowestChildRank,,** No join mapping for *lowestChildRank ** 
......
121 121
reference_ID,,** No join mapping for *reference_ID ** 
122 122
revisions,,** No join mapping for *revisions ** 
123 123
section,,** No join mapping for *section ** 
124
sensitiveSpeciesFuzzPlot,,** No join mapping for *sensitiveSpeciesFuzzPlot ** 
124 125
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank
125 126
subgenus,,** No join mapping for subgenus ** 
126 127
subspecies,,** No non-empty join mapping for EQUIV#to:species#subspecies ** full taxonomic name at that rank
inputs/CVS/taxonObservation_/test.xml.ref
53 53
                                                                                                        <parent_id>
54 54
                                                                                                            <taxonlabel>
55 55
                                                                                                                <rank>genus</rank>
56
                                                                                                                <taxonepithet>
57
                                                                                                                    <_alt>
58
                                                                                                                        <1>$denorm_genus</1>
59
                                                                                                                        <2>$genus</2>
60
                                                                                                                    </_alt>
61
                                                                                                                </taxonepithet>
56
                                                                                                                <taxonepithet>$genus</taxonepithet>
62 57
                                                                                                                <parent_id>
63 58
                                                                                                                    <taxonlabel>
64 59
                                                                                                                        <rank>family</rank>
......
115 110
                                                                                <1>$plantname</1>
116 111
                                                                                <2>
117 112
                                                                                    <_join_words>
118
                                                                                        <2>
119
                                                                                            <_filter_genus>
120
                                                                                                <value>
121
                                                                                                    <_alt>
122
                                                                                                        <1>$denorm_genus</1>
123
                                                                                                        <2>$genus</2>
124
                                                                                                    </_alt>
125
                                                                                                </value>
126
                                                                                            </_filter_genus>
127
                                                                                        </2>
113
                                                                                        <2><_filter_genus><value>$genus</value></_filter_genus></2>
128 114
                                                                                        <3>$denorm_species</3>
129 115
                                                                                        <5>
130 116
                                                                                            <_join_words>
......
148 134
                                                    </taxonlabel>
149 135
                                                </taxonlabel_id>
150 136
                                                <family>$denorm_family</family>
151
                                                <genus>
152
                                                    <_alt>
153
                                                        <1>$denorm_genus</1>
154
                                                        <2>$genus</2>
155
                                                    </_alt>
156
                                                </genus>
137
                                                <genus>$genus</genus>
157 138
                                                <specific_epithet>$denorm_species</specific_epithet>
158 139
                                                <taxonname>$plantname</taxonname>
159 140
                                                <taxonomicname>$plantNameWithAuthority</taxonomicname>
inputs/CVS/taxonObservation_/new_terms.csv
5 5
plantname,taxonName,,
6 6
plantNameWithAuthority,scientificName,,
7 7
denorm_kingdom,kingdom,,
8
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"
8
denorm_division,division_main,/_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"
9 9
denorm_category,*category,,
10 10
denorm_family,family,,
11
denorm_genus,genus,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
11
denorm_genus,genus_main,/_alt/1,must be _alt-ed with genus because this is missing in 1 row that has genus
12 12
denorm_species,specificEpithet,,"unlike VegBank, this is in fact the epithet, not the full name"
13 13
denorm_triAbbr,infraspecificRank,,
14 14
denorm_triName,infraspecificEpithet,,
inputs/CVS/taxonObservation_/unmapped_terms.csv
43 43
*plantConcept_entry_sppID
44 44
*USDAPlantsCode
45 45
*VascularPlant
46
*division
46
division_main
47 47
*category
48
genus_main
48 49
infraspecificRank
49 50
infraspecificRank2
50 51
infraspecificEpithet2
......
58 59
*exotic
59 60
*usda_code
60 61
*usda_growthForm
62
*sensitiveSpeciesFuzzPlot
61 63
*Subkingdom
62
*division
64
division_normalized
63 65
*Subclass
64 66
*composite family
65 67
*tribe
66 68
*composite genus
69
genus_normalized
67 70
subgenus
68 71
*section
69 72
*composite species
70 73
speciesBinomial
74
*division

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