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Revision 5248

Added by Aaron Marcuse-Kubitza over 12 years ago

inputs/.TNRS/tnrs/map.csv: Remapped Name_submitted to new verbatimScientificNameWithAuthorship to create an additional level of taxonconcept for the concatenated (TNRS input) name separate from the parsed (TNRS output) name

View differences:

inputs/.TNRS/tnrs/map.csv
1 1 
TNRS,VegCore,Filter,Comments
2 2 
Name_number,OMIT,,
3 
Name_submitted,scientificNameWithAuthorship,,
3 
Name_submitted,verbatimScientificNameWithAuthorship,,
4 4 
Overall_score,OMIT,,
5 5 
Name_matched,scientificName,,
6 6 
Name_matched_rank,taxonRank,,
inputs/.TNRS/tnrs/VegBIEN.csv
1 1 
TNRS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 
Name_submitted,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",
3 2 
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
4 3 
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/cond/_exists",
5 4 
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/then/taxon_id/_forEach:[in:[cultivar,forma,variety,],do=""taxon[rank=_val]/parent_id""]/taxon[rank=infraspecies]/taxonname",
......
9 8 
Specific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/then/taxon_id/_forEach:[in:[cultivar,forma,variety,infraspecies,subspecies,],do=""taxon[rank=_val]/parent_id""]/taxon[rank=species]/taxonname",
10 9 
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/then/taxon_id/_forEach:[in:[cultivar,forma,variety,infraspecies,subspecies,species,],do=""taxon[rank=_val]/parent_id""]/taxon[rank=genus]/taxonname",
11 10 
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/then/taxon_id/_forEach:[in:[cultivar,forma,variety,infraspecies,subspecies,species,genus,],do=""taxon[rank=_val]/parent_id""]/taxon[rank=family]/taxonname",Contains family based on matched name
12 
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/1",
13 11 
Name_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1",
14 12 
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1",Contains family based on matched name
15 13 
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2",
......
35 33 
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
36 34 
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
37 35 
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2,
36 
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname,
38 37 
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
39 
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicnamewithauthor,
40 38 
Accepted_name_lsid,,** No non-empty join mapping for OMIT **
41 39 
Accepted_name_species,,** No non-empty join mapping for OMIT ** Also contains genus. Omitted because Accepted_name contains more info.
42 40 
Accepted_name_url,,** No non-empty join mapping for OMIT **
inputs/.TNRS/tnrs/test.xml.ref
61 61 
                                        </taxon>
62 62 
                                    </taxon_id>
63 63 
                                    <identifyingtaxonomicname>
64 
                                        <_alt>
65 
                                            <1>$Name_submitted</1>
66 
                                            <2>
67 
                                                <_join_words>
68 
                                                    <1>
69 
                                                        <_alt>
70 
                                                            <1>$Name_matched</1>
71 
                                                            <2>
64 
                                        <_join_words>
65 
                                            <1>
66 
                                                <_alt>
67 
                                                    <1>$Name_matched</1>
68 
                                                    <2>
69 
                                                        <_join_words>
70 
                                                            <1>$Name_matched_accepted_family</1>
71 
                                                            <2>$Genus_matched</2>
72 
                                                            <3>
72 73 
                                                                <_join_words>
73 
                                                                    <1>$Name_matched_accepted_family</1>
74 
                                                                    <2>$Genus_matched</2>
75 
                                                                    <3>
76 
                                                                        <_join_words>
77 
                                                                            <1>$Specific_epithet_matched</1>
78 
                                                                            <2>$Unmatched_terms</2>
79 
                                                                        </_join_words>
80 
                                                                    </3>
81 
                                                                    <5>
82 
                                                                        <_join_words>
83 
                                                                            <1>
84 
                                                                                <_if name="if has infraspecificEpithet">
85 
                                                                                    <cond>$Infraspecific_epithet_matched</cond>
86 
                                                                                    <then>$Name_matched_rank</then>
87 
                                                                                </_if>
88 
                                                                            </1>
89 
                                                                            <2>$Infraspecific_epithet_matched</2>
90 
                                                                        </_join_words>
91 
                                                                    </5>
74 
                                                                    <1>$Specific_epithet_matched</1>
75 
                                                                    <2>$Unmatched_terms</2>
92 76 
                                                                </_join_words>
93 
                                                            </2>
94 
                                                        </_alt>
95 
                                                    </1>
96 
                                                    <2>$Name_matched_author</2>
97 
                                                </_join_words>
98 
                                            </2>
99 
                                        </_alt>
77 
                                                            </3>
78 
                                                            <5>
79 
                                                                <_join_words>
80 
                                                                    <1>
81 
                                                                        <_if name="if has infraspecificEpithet">
82 
                                                                            <cond>$Infraspecific_epithet_matched</cond>
83 
                                                                            <then>$Name_matched_rank</then>
84 
                                                                        </_if>
85 
                                                                    </1>
86 
                                                                    <2>$Infraspecific_epithet_matched</2>
87 
                                                                </_join_words>
88 
                                                            </5>
89 
                                                        </_join_words>
90 
                                                    </2>
91 
                                                </_alt>
92 
                                            </1>
93 
                                            <2>$Name_matched_author</2>
94 
                                        </_join_words>
100 95 
                                    </identifyingtaxonomicname>
101 96 
                                    <_set_canon_taxonconcept>
102 97 
                                        <canon_taxonconcept_id>
......
134 129 
                                            <2>$Infraspecific_epithet_matched</2>
135 130 
                                        </_join_words>
136 131 
                                    </subspecies>
132 
                                    <taxonconcept fkey="canon_taxonconcept_id"><identifyingtaxonomicname>$Name_submitted</identifyingtaxonomicname></taxonconcept>
137 133 
                                    <taxonomicname>$Name_matched</taxonomicname>
138 
                                    <taxonomicnamewithauthor>$Name_submitted</taxonomicnamewithauthor>
139 134 
                                </taxonconcept>
140 135 
                            </taxonconcept_id>
141 136 
                        </taxondetermination>
inputs/.TNRS/tnrs/new_terms.csv
1 1 
Name_number,OMIT,,
2 
Name_submitted,scientificNameWithAuthorship,,
2 
Name_submitted,verbatimScientificNameWithAuthorship,,
3 3 
Overall_score,OMIT,,
4 4 
Name_matched,scientificName,,
5 5 
Name_matched_rank,taxonRank,,

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