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Revision 5264

Added by Aaron Marcuse-Kubitza over 12 years ago

mappings/VegCore-VegBIEN.csv: Also map *taxonRank to taxonconcept.rank, so that if it's in the taxonrank enum, it will automatically populate this field

View differences:

inputs/UNCC/Specimen/VegBIEN.csv
62 62 
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,
63 63 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,
64 64 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
65 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank/_alt/1,
66 
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank/_alt/2,
65 67 
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
66 68 
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_alt/1,
67 69 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
inputs/UNCC/Specimen/test.xml.ref
118 118 
                                    <author>$authors</author>
119 119 
                                    <family>$family</family>
120 120 
                                    <genus>$genus</genus>
121 
                                    <rank>
122 
                                        <_alt>
123 
                                            <1>$usdaRank</1>
124 
                                            <2>$infrarank</2>
125 
                                        </_alt>
126 
                                    </rank>
121 127 
                                    <species>$species</species>
122 128 
                                    <taxonname>$infraname</taxonname>
123 129 
                                    <taxonomicname>$SciName</taxonomicname>
inputs/ACAD/Specimen/VegBIEN.csv
51 51 
kingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/kingdom,
52 52 
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/order,
53 53 
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/phylum,
54 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
54 55 
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
55 56 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_alt/1,
56 57 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicnamewithauthor,
inputs/ACAD/Specimen/test.xml.ref
132 132 
                                    <kingdom>$kingdom</kingdom>
133 133 
                                    <order>$order</order>
134 134 
                                    <phylum>$phylum</phylum>
135 
                                    <rank>$taxonRank</rank>
135 136 
                                    <species>$specificEpithet</species>
136 137 
                                    <taxonname>$infraspecificEpithet</taxonname>
137 138 
                                    <taxonomicnamewithauthor>$scientificName</taxonomicnamewithauthor>
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
81 81 
specific_authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,Brad: This is the author of the scientificName.
82 82 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,
83 83 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
84 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
84 85 
specific_epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
85 86 
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_alt/1,
86 87 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
inputs/SALVIAS-CSV/Organism/test.xml.ref
183 183 
                                    <author>$specific_authority</author>
184 184 
                                    <family>$family</family>
185 185 
                                    <genus>$genus</genus>
186 
                                    <rank>$infra_rank_1</rank>
186 187 
                                    <species>$specific_epithet</species>
187 188 
                                    <taxonname>$infra_ep_1</taxonname>
188 189 
                                    <verbatimrank>$infra_rank_1</verbatimrank>
inputs/SALVIAS/plotObservations/VegBIEN.csv
74 74 
auth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,Brad: This is the author of the scientificName.
75 75 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,
76 76 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
77 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
77 78 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
78 79 
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_alt/1,
79 80 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
inputs/SALVIAS/plotObservations/test.xml.ref
154 154 
                                    <author>$auth</author>
155 155 
                                    <family>$Family</family>
156 156 
                                    <genus>$Genus</genus>
157 
                                    <rank>$infra_rank_1</rank>
157 158 
                                    <species>$Species</species>
158 159 
                                    <taxonname>$infra_ep_1</taxonname>
159 160 
                                    <verbatimrank>$infra_rank_1</verbatimrank>
inputs/.TNRS/tnrs/VegBIEN.csv
23 23 
Accepted_name_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,
24 24 
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
25 25 
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/identifyingtaxonomicname/_alt/2/_join_words/2,
26 
Accepted_name_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/rank,
26 27 
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/taxonomicname,
27 28 
Accepted_name_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/verbatimrank,
28 29 
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,Contains author based on matched name
29 30 
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,Contains family based on matched name
30 31 
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
32 
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
31 33 
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
32 34 
Author_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/author,Contains author in original string
33 35 
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/family,Contains family in original string (uncommon)
inputs/.TNRS/tnrs/test.xml.ref
104 104 
                                                        <2>$Accepted_name_author</2>
105 105 
                                                    </_join_words>
106 106 
                                                </identifyingtaxonomicname>
107 
                                                <rank>$Accepted_name_rank</rank>
107 108 
                                                <taxonomicname>$Accepted_name</taxonomicname>
108 109 
                                                <verbatimrank>$Accepted_name_rank</verbatimrank>
109 110 
                                            </taxonconcept>
......
112 113 
                                    <author>$Name_matched_author</author>
113 114 
                                    <family>$Name_matched_accepted_family</family>
114 115 
                                    <genus>$Genus_matched</genus>
116 
                                    <rank>$Name_matched_rank</rank>
115 117 
                                    <species>$Specific_epithet_matched</species>
116 118 
                                    <taxonconcept fkey="canon_taxonconcept_id">
117 119 
                                        <author>$Author_matched</author>
inputs/QMOR/Specimen/VegBIEN.csv
58 58 
kingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/kingdom,
59 59 
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/order,
60 60 
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/phylum,
61 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
61 62 
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
62 63 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_alt/1,
63 64 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
inputs/QMOR/Specimen/test.xml.ref
156 156 
                                    <kingdom>$kingdom</kingdom>
157 157 
                                    <order>$order</order>
158 158 
                                    <phylum>$phylum</phylum>
159 
                                    <rank>$taxonRank</rank>
159 160 
                                    <species>$specificEpithet</species>
160 161 
                                    <taxonname>$infraspecificEpithet</taxonname>
161 162 
                                    <taxonomicname>$scientificName</taxonomicname>
mappings/VegCore-VegBIEN.csv
182 182 
acceptedKingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/kingdom,
183 183 
acceptedOrder,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/order,
184 184 
acceptedPhylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/phylum,
185 
acceptedTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/rank,
185 186 
acceptedSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/species,
186 187 
acceptedSubspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/subspecies,
187 188 
acceptedInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/taxonname,
......
200 201 
kingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/kingdom,
201 202 
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/order,
202 203 
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/phylum,
204 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/rank,
203 205 
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
204 206 
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies,
205 207 
verbatimScientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/author,
......
256 258 
originalKingdom,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/kingdom,
257 259 
originalOrder,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/order,
258 260 
originalPhylum,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/phylum,
261 
originalTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/rank,
259 262 
originalSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/species,
260 263 
originalSubspecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/subspecies,
261 264 
originalInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/taxonname,
mappings/for_review/VegCore-VegBIEN.csv
182 182 
acceptedKingdom,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/kingdom,
183 183 
acceptedOrder,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/order,
184 184 
acceptedPhylum,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/phylum,
185 
acceptedTaxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/rank,
185 186 
acceptedSpecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/species,
186 187 
acceptedSubspecies,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/subspecies,
187 188 
acceptedInfraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/taxonname,
......
200 201 
kingdom,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/kingdom,
201 202 
order,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/order,
202 203 
phylum,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/phylum,
204 
taxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/rank,
203 205 
specificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/species,
204 206 
subspecies,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/subspecies,
205 207 
verbatimScientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/author,
......
256 258 
originalKingdom,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/kingdom,
257 259 
originalOrder,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/order,
258 260 
originalPhylum,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/phylum,
261 
originalTaxonRank,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/rank,
259 262 
originalSpecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/species,
260 263 
originalSubspecies,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/subspecies,
261 264 
originalInfraspecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/taxonname,

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