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Revision 5252

Added by Aaron Marcuse-Kubitza about 12 years ago

mappings/VegCore-VegBIEN.csv: Mapped *taxonRank to new taxonconcept.verbatimrank

View differences:

inputs/UNCC/Specimen/VegBIEN.csv
68 68 
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then/_alt/2",
69 69 
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
70 70 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
71 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank/_alt/1,
72 
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank/_alt/2,
71 73 
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
72 74 
collector1,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/2,
73 75 
collector2,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/3,
inputs/UNCC/Specimen/test.xml.ref
136 136 
                                        </_join_words>
137 137 
                                    </subspecies>
138 138 
                                    <taxonomicname>$SciName</taxonomicname>
139 
                                    <verbatimrank>
140 
                                        <_alt>
141 
                                            <1>$usdaRank</1>
142 
                                            <2>$infrarank</2>
143 
                                        </_alt>
144 
                                    </verbatimrank>
139 145 
                                </taxonconcept>
140 146 
                            </taxonconcept_id>
141 147 
                        </taxondetermination>
inputs/ACAD/Specimen/VegBIEN.csv
56 56 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
57 57 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
58 58 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicnamewithauthor,
59 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
59 60 
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
60 61 
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
61 62 
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
inputs/ACAD/Specimen/test.xml.ref
145 145 
                                        </_join_words>
146 146 
                                    </subspecies>
147 147 
                                    <taxonomicnamewithauthor>$scientificName</taxonomicnamewithauthor>
148 
                                    <verbatimrank>$taxonRank</verbatimrank>
148 149 
                                </taxonconcept>
149 150 
                            </taxonconcept_id>
150 151 
                            <determinationdate><_date><date><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></date></_date></determinationdate>
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
85 85 
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
86 86 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
87 87 
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
88 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
88 89 
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
89 90 
orig_family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,Brad: OMIT
90 91 
orig_species,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3,Brad: OMIT
inputs/SALVIAS-CSV/Organism/test.xml.ref
195 195 
                                            <2>$infra_ep_1</2>
196 196 
                                        </_join_words>
197 197 
                                    </subspecies>
198 
                                    <verbatimrank>$infra_rank_1</verbatimrank>
198 199 
                                </taxonconcept>
199 200 
                            </taxonconcept_id>
200 201 
                            <taxonfit>$cf_aff</taxonfit>
inputs/SALVIAS/plotObservations/VegBIEN.csv
78 78 
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
79 79 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
80 80 
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
81 
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
81 82 
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
82 83 
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1,Brad: OMIT
83 84 
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2,
inputs/SALVIAS/plotObservations/test.xml.ref
166 166 
                                            <2>$infra_ep_1</2>
167 167 
                                        </_join_words>
168 168 
                                    </subspecies>
169 
                                    <verbatimrank>$infra_rank_1</verbatimrank>
169 170 
                                </taxonconcept>
170 171 
                            </taxonconcept_id>
171 172 
                            <taxonfit>$cfaff</taxonfit>
inputs/.TNRS/tnrs/VegBIEN.csv
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 26 
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
27 27 
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/taxonomicname,
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,
......
35 36 
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
36 37 
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname,
37 38 
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
39 
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
38 40 
Accepted_name_lsid,,** No non-empty join mapping for OMIT **
39 41 
Accepted_name_species,,** No non-empty join mapping for OMIT ** Also contains genus. Omitted because Accepted_name contains more info.
40 42 
Accepted_name_url,,** No non-empty join mapping for OMIT **
inputs/.TNRS/tnrs/test.xml.ref
110 110 
                                                    </_join_words>
111 111 
                                                </identifyingtaxonomicname>
112 112 
                                                <taxonomicname>$Accepted_name</taxonomicname>
113 
                                                <verbatimrank>$Accepted_name_rank</verbatimrank>
113 114 
                                            </taxonconcept>
114 115 
                                        </canon_taxonconcept_id>
115 116 
                                    </_set_canon_taxonconcept>
......
131 132 
                                    </subspecies>
132 133 
                                    <taxonconcept fkey="canon_taxonconcept_id"><identifyingtaxonomicname>$Name_submitted</identifyingtaxonomicname></taxonconcept>
133 134 
                                    <taxonomicname>$Name_matched</taxonomicname>
135 
                                    <verbatimrank>$Name_matched_rank</verbatimrank>
134 136 
                                </taxonconcept>
135 137 
                            </taxonconcept_id>
136 138 
                        </taxondetermination>
inputs/QMOR/Specimen/VegBIEN.csv
63 63 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
64 64 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
65 65 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
66 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
66 67 
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
67 68 
identificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
68 69 
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
inputs/QMOR/Specimen/test.xml.ref
169 169 
                                        </_join_words>
170 170 
                                    </subspecies>
171 171 
                                    <taxonomicname>$scientificName</taxonomicname>
172 
                                    <verbatimrank>$taxonRank</verbatimrank>
172 173 
                                </taxonconcept>
173 174 
                            </taxonconcept_id>
174 175 
                            <determinationdate><_date><date><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></date></_date></determinationdate>
mappings/VegCore-VegBIEN.csv
190 190 
acceptedInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/subspecies/_alt/2/_join_words/2,
191 191 
acceptedScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/taxonomicname,
192 192 
acceptedVariety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/variety,
193 
acceptedTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/verbatimrank,
193 194 
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,
194 195 
class,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/class,
195 196 
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/creator_id/_simplifyPath:[next=creator_id]/path/party/givenname/_namePart/first,
......
212 213 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
213 214 
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicnamewithauthor,
214 215 
variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/variety,
216 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
215 217 
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
216 218 
dayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
217 219 
monthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
......
248 250 
originalScientificName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/taxonomicname,
249 251 
originalScientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/taxonomicnamewithauthor,
250 252 
originalVariety,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/variety,
253 
originalTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/verbatimrank,
251 254 
originalIdentificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,
252 255 
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
253 256 
recordedBy.givenName,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,
mappings/for_review/VegCore-VegBIEN.csv
190 190 
acceptedInfraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/subspecies,
191 191 
acceptedScientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/taxonomicname,
192 192 
acceptedVariety,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/variety,
193 
acceptedTaxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/verbatimrank,
193 194 
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/author,
194 195 
class,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/class,
195 196 
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/creator_id/party/givenname,
......
212 213 
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonomicname,
213 214 
scientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonomicnamewithauthor,
214 215 
variety,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/variety,
216 
taxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/verbatimrank,
215 217 
dateIdentified,//taxonoccurrence/taxondetermination[]/determinationdate/_*/date,
216 218 
dayIdentified,//taxonoccurrence/taxondetermination[]/determinationdate,
217 219 
monthIdentified,//taxonoccurrence/taxondetermination[]/determinationdate,
......
248 250 
originalScientificName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/taxonomicname,
249 251 
originalScientificNameWithAuthorship,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/taxonomicnamewithauthor,
250 252 
originalVariety,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/variety,
253 
originalTaxonRank,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonconcept/verbatimrank,
251 254 
originalIdentificationQualifier,//taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,
252 255 
recordedBy,//taxonoccurrence/verbatimcollectorname,
253 256 
recordedBy.givenName,//taxonoccurrence/verbatimcollectorname,

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