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Revision 6803

Added by Aaron Marcuse-Kubitza about 12 years ago

inputs/CVS/taxonObservation_/map.csv: Fixed bug where taxonLevel, not taxonRank, needs to be mapped to taxonRank, because CVS's taxonRank is actually a number, while taxonLevel contains the corresponding text string

View differences:

inputs/CVS/taxonObservation_/map.csv
82 82 
denorm_quadAbbr,*denorm_quadAbbr,,
83 83 
denorm_quadName,*denorm_quadName,,
84 84 
denorm_hybridX,*denorm_hybridX,,
85 
taxonLevel,*taxonLevel,,
86 
taxonRank,taxonRank,,
85 
taxonLevel,taxonRank,,
86 
taxonRank,OMIT,,Omitted because taxonLevel contains this information in text form
87 87 
lowestParentName,*lowestParentName,,
88 88 
lowestParentConcept_ID,*lowestParentConcept_ID,,
89 89 
lowestChildRank,*lowestChildRank,,
inputs/CVS/taxonObservation_/VegBIEN.csv
24 24 
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2",
25 25 
Species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
26 26 
Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4",
27 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
27 
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
28 28 
Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""var. ""]/2",
29 29 
Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""fm. ""]/2",
30 30 
interpretationDate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
31 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
32 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank",
31 
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
32 
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank",
33 33 
Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=forma]/taxonepithet",
34 34 
Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet",
35 35 
Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet",
......
41 41 
Order,"/location/locationevent/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",
42 42 
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",
43 43 
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",
44 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
45 
taxonRank,"/location/locationevent/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",
44 
taxonLevel,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
45 
taxonLevel,"/location/locationevent/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",
46 46 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value,
47 47 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2,
48 48 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
49 49 
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4,
50 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
50 
taxonLevel,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
51 51 
Variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2",
52 52 
Forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2",
53 53 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
54 54 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
55 55 
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
56 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
56 
taxonLevel,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
57 57 
interpretationDate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
58 58 
taxonFit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
59 59 
authorPlantName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1,
......
139 139 
taxonInterpretation_PLANTNAME_ID,,** No join mapping for *taxonInterpretation_PLANTNAME_ID **
140 140 
taxonInterpretation_accessionCode,,** No join mapping for *taxonInterpretation_accessionCode **
141 141 
taxonInterpretation_dba_src_ID,,** No join mapping for *taxonInterpretation_dba_src_ID **
142 
taxonLevel,,** No join mapping for *taxonLevel **
143 142 
taxonObservationNotes,,** No join mapping for *taxonObservationNotes **
144 143 
taxonObservation_accessionCode,,** No join mapping for *taxonObservation_accessionCode **
145 144 
taxonObservation_dba_src_ID,,** No join mapping for *taxonObservation_dba_src_ID **
146 145 
taxonObservation_entry_sppID,,** No join mapping for *taxonObservation_entry_sppID **
147 146 
taxonObservation_reference_ID,,** No join mapping for *taxonObservation_reference_ID **
147 
taxonRank,,** No non-empty join mapping for OMIT ** Omitted because taxonLevel contains this information in text form
148 148 
temp_taxonUpToDate,,** No join mapping for *temp_taxonUpToDate **
149 149 
usda_code,,** No join mapping for *usda_code **
150 150 
usda_growthForm,,** No join mapping for *usda_growthForm **
inputs/CVS/taxonObservation_/test.xml.ref
67 67 
                                                    <creationdate><_dateRangeStart><value>$interpretationDate</value></_dateRangeStart></creationdate>
68 68 
                                                    <parent_id>
69 69 
                                                        <taxonlabel>
70 
                                                            <rank>$taxonRank</rank>
71 
                                                            <taxonverbatim><verbatimrank>$taxonRank</verbatimrank></taxonverbatim>
70 
                                                            <rank>$taxonLevel</rank>
71 
                                                            <taxonverbatim><verbatimrank>$taxonLevel</verbatimrank></taxonverbatim>
72 72 
                                                            <parent_id>
73 73 
                                                                <taxonlabel>
74 74 
                                                                    <rank>cultivar</rank>
......
135 135 
                                                            </parent_id>
136 136 
                                                        </taxonlabel>
137 137 
                                                    </parent_id>
138 
                                                    <rank>$taxonRank</rank>
138 
                                                    <rank>$taxonLevel</rank>
139 139 
                                                    <taxonomicname>
140 140 
                                                        <_join_words>
141 141 
                                                            <1><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></1>
......
165 165 
                                            <family>$Family</family>
166 166 
                                            <genus>$Genus</genus>
167 167 
                                            <specific_epithet>$Species</specific_epithet>
168 
                                            <verbatimrank>$taxonRank</verbatimrank>
168 
                                            <verbatimrank>$taxonLevel</verbatimrank>
169 169 
                                        </taxonverbatim>
170 170 
                                    </taxonverbatim_id>
171 171 
                                    <determinationdate><_dateRangeStart><value>$interpretationDate</value></_dateRangeStart></determinationdate>
inputs/CVS/taxonObservation_/new_terms.csv
7 7 
museumAccessionNumber,catalogNumber,,
8 8 
givenName,recordedBy.givenName,,
9 9 
surName,recordedBy.surName,,
10 
taxonLevel,taxonRank,,
inputs/CVS/taxonObservation_/unmapped_terms.csv
70 70 
*denorm_quadAbbr
71 71 
*denorm_quadName
72 72 
*denorm_hybridX
73 
*taxonLevel
74 73 
*lowestParentName
75 74 
*lowestParentConcept_ID
76 75 
*lowestChildRank

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