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Revision 5262

schemas/vegbien.sql: taxonconcept: Renamed morphospecies to taxonname since it's used in the same way as taxon.taxonname: to store the lowest-rank portion of the taxonomic name, such as the morphospecies suffix

View differences:

inputs/.TNRS/tnrs/VegBIEN.csv
29 29
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,Contains author based on matched name
30 30
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,Contains family based on matched name
31 31
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
32
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists",
33
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/else",
34 32
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
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",
......
39 37
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/family,Contains family in original string (uncommon)
40 38
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/genus,
41 39
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname,
42
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists",
43
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/then",
44 40
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/species,
45 41
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
46 42
Infraspecific_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
47 43
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/subspecies/_alt/2/_join_words/2,
44
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/cond/_exists",
45
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/then",
48 46
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonomicname,
49 47
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonomicnamewithauthor,
50 48
Infraspecific_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/verbatimrank,
49
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_if[@name=""if has verbatim name""]/cond/_exists",
50
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_if[@name=""if has verbatim name""]/else",
51 51
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
52 52
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank,
53 53
Accepted_name_lsid,,** No non-empty join mapping for OMIT ** 
inputs/.TNRS/tnrs/test.xml.ref
129 129
                                        <family>$Family_matched</family>
130 130
                                        <genus>$Genus_matched</genus>
131 131
                                        <identifyingtaxonomicname>$Name_submitted</identifyingtaxonomicname>
132
                                        <morphospecies>$Unmatched_terms</morphospecies>
133 132
                                        <species>$Specific_epithet_matched</species>
134 133
                                        <subspecies>
135 134
                                            <_join_words>
......
142 141
                                                <2>$Infraspecific_epithet_matched</2>
143 142
                                            </_join_words>
144 143
                                        </subspecies>
144
                                        <taxonname>$Unmatched_terms</taxonname>
145 145
                                        <taxonomicname>$Name_matched</taxonomicname>
146 146
                                        <taxonomicnamewithauthor>$Name_submitted</taxonomicnamewithauthor>
147 147
                                        <verbatimrank>$Infraspecific_rank</verbatimrank>
schemas/vegbien.my.sql
783 783
    creator_id int(11) NOT NULL,
784 784
    identifyingtaxonomicname text,
785 785
    canon_taxonconcept_id int(11),
786
    taxonname text,
786 787
    rank text,
787 788
    verbatimrank text,
788 789
    taxon_id int(11),
......
801 802
    variety text,
802 803
    forma text,
803 804
    cultivar text,
804
    morphospecies text,
805 805
    otherranks text,
806 806
    accessioncode text
807 807
);
......
836 836

  
837 837

  
838 838
--
839
-- Name: COLUMN taxonconcept.taxonname; Type: COMMENT; Schema: public; Owner: -
840
--
841

  
842

  
843

  
844

  
845
--
839 846
-- Name: COLUMN taxonconcept.taxon_id; Type: COMMENT; Schema: public; Owner: -
840 847
--
841 848

  
......
948 955

  
949 956

  
950 957
--
951
-- Name: COLUMN taxonconcept.morphospecies; Type: COMMENT; Schema: public; Owner: -
952
--
953

  
954

  
955

  
956

  
957
--
958 958
-- Name: COLUMN taxonconcept.otherranks; Type: COMMENT; Schema: public; Owner: -
959 959
--
960 960

  
schemas/vegbien.sql
1116 1116
    creator_id integer NOT NULL,
1117 1117
    identifyingtaxonomicname text,
1118 1118
    canon_taxonconcept_id integer,
1119
    taxonname text,
1119 1120
    rank taxonrank,
1120 1121
    verbatimrank text,
1121 1122
    taxon_id integer,
......
1134 1135
    variety text,
1135 1136
    forma text,
1136 1137
    cultivar text,
1137
    morphospecies text,
1138 1138
    otherranks rankedtaxonname[],
1139 1139
    accessioncode text,
1140 1140
    CONSTRAINT taxonconcept_required_key CHECK (((((((identifyingtaxonomicname IS NOT NULL) OR (taxonomicname IS NOT NULL)) OR (taxonomicnamewithauthor IS NOT NULL)) OR (family IS NOT NULL)) OR (genus IS NOT NULL)) OR (otherranks IS NOT NULL)))
......
1176 1176

  
1177 1177

  
1178 1178
--
1179
-- Name: COLUMN taxonconcept.taxonname; Type: COMMENT; Schema: public; Owner: -
1180
--
1181

  
1182
COMMENT ON COLUMN taxonconcept.taxonname IS 'The lowest-rank portion of the taxonomic name.
1183

  
1184
The morphospecies suffix goes in this field.';
1185

  
1186

  
1187
--
1179 1188
-- Name: COLUMN taxonconcept.taxon_id; Type: COMMENT; Schema: public; Owner: -
1180 1189
--
1181 1190

  
......
1295 1304

  
1296 1305

  
1297 1306
--
1298
-- Name: COLUMN taxonconcept.morphospecies; Type: COMMENT; Schema: public; Owner: -
1299
--
1300

  
1301
COMMENT ON COLUMN taxonconcept.morphospecies IS 'The morphospecies portion of the taxonomic name.';
1302

  
1303

  
1304
--
1305 1307
-- Name: COLUMN taxonconcept.otherranks; Type: COMMENT; Schema: public; Owner: -
1306 1308
--
1307 1309

  
......
4738 4740
-- Name: taxonconcept_unique_within_creator_by_name; Type: INDEX; Schema: public; Owner: -; Tablespace: 
4739 4741
--
4740 4742

  
4741
CREATE UNIQUE INDEX taxonconcept_unique_within_creator_by_name ON taxonconcept USING btree (creator_id, (COALESCE(creator_id, 2147483647)), (COALESCE(taxonomicname, '\\N'::text)), (COALESCE(author, '\\N'::text)), (COALESCE(taxonomicnamewithauthor, '\\N'::text)), (COALESCE(domain, '\\N'::text)), (COALESCE(kingdom, '\\N'::text)), (COALESCE(phylum, '\\N'::text)), (COALESCE(class, '\\N'::text)), (COALESCE("order", '\\N'::text)), (COALESCE(family, '\\N'::text)), (COALESCE(genus, '\\N'::text)), (COALESCE(species, '\\N'::text)), (COALESCE(subspecies, '\\N'::text)), (COALESCE(variety, '\\N'::text)), (COALESCE(forma, '\\N'::text)), (COALESCE(cultivar, '\\N'::text)), (COALESCE(morphospecies, '\\N'::text)), (COALESCE(otherranks, ARRAY[]::rankedtaxonname[]))) WHERE (identifyingtaxonomicname IS NULL);
4743
CREATE UNIQUE INDEX taxonconcept_unique_within_creator_by_name ON taxonconcept USING btree (creator_id, (COALESCE(creator_id, 2147483647)), (COALESCE(taxonomicname, '\\N'::text)), (COALESCE(author, '\\N'::text)), (COALESCE(taxonomicnamewithauthor, '\\N'::text)), (COALESCE(domain, '\\N'::text)), (COALESCE(kingdom, '\\N'::text)), (COALESCE(phylum, '\\N'::text)), (COALESCE(class, '\\N'::text)), (COALESCE("order", '\\N'::text)), (COALESCE(family, '\\N'::text)), (COALESCE(genus, '\\N'::text)), (COALESCE(species, '\\N'::text)), (COALESCE(subspecies, '\\N'::text)), (COALESCE(variety, '\\N'::text)), (COALESCE(forma, '\\N'::text)), (COALESCE(cultivar, '\\N'::text)), (COALESCE(taxonname, '\\N'::text)), (COALESCE(otherranks, ARRAY[]::rankedtaxonname[]))) WHERE (identifyingtaxonomicname IS NULL);
4742 4744

  
4743 4745

  
4744 4746
--
mappings/VegCore-VegBIEN.csv
200 200
forma,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/forma,
201 201
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus,
202 202
kingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/kingdom,
203
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists",
204
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/else",
205 203
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/order,
206 204
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/phylum,
207 205
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species,
......
217 215
verbatimGenus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/genus,
218 216
verbatimScientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname,
219 217
verbatimKingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/kingdom,
220
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists",
221
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/then",
222 218
verbatimOrder,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/order,
223 219
verbatimPhylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/phylum,
224 220
verbatimSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/species,
......
226 222
verbatimInfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
227 223
verbatimTaxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
228 224
verbatimInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/subspecies/_alt/2/_join_words/2,
225
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/cond/_exists",
226
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/then",
229 227
verbatimScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonomicname,
230 228
verbatimScientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonomicnamewithauthor,
231 229
verbatimVariety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/variety,
232 230
verbatimTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/verbatimrank,
231
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_if[@name=""if has verbatim name""]/cond/_exists",
232
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonname/_if[@name=""if has verbatim name""]/else",
233 233
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname,
234 234
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicnamewithauthor,
235 235
variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/variety,
mappings/for_review/VegCore-VegBIEN.csv
200 200
forma,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/forma,
201 201
genus,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/genus,
202 202
kingdom,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/kingdom,
203
verbatimScientificNameWithAuthorship,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists",
204
morphospecies,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/else",
205 203
order,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/order,
206 204
phylum,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/phylum,
207 205
specificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/species,
......
217 215
verbatimGenus,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/genus,
218 216
verbatimScientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/identifyingtaxonomicname,
219 217
verbatimKingdom,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/kingdom,
220
verbatimScientificNameWithAuthorship,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists",
221
morphospecies,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/then",
222 218
verbatimOrder,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/order,
223 219
verbatimPhylum,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/phylum,
224 220
verbatimSpecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/species,
......
226 222
verbatimInfraspecificEpithet,"//taxonconcept/subspecies/_if[@name=""if has infraspecificEpithet""]/cond",
227 223
verbatimTaxonRank,"//taxonconcept/subspecies/_if[@name=""if has infraspecificEpithet""]/then",
228 224
verbatimInfraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/subspecies,
225
verbatimScientificNameWithAuthorship,"//taxonconcept/taxonname/_if[@name=""if has verbatim name""]/cond/_exists",
226
morphospecies,"//taxonconcept/taxonname/_if[@name=""if has verbatim name""]/then",
229 227
verbatimScientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/taxonomicname,
230 228
verbatimScientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/taxonomicnamewithauthor,
231 229
verbatimVariety,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/variety,
232 230
verbatimTaxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/verbatimrank,
231
verbatimScientificNameWithAuthorship,"//taxonconcept/taxonname/_if[@name=""if has verbatim name""]/cond/_exists",
232
morphospecies,"//taxonconcept/taxonname/_if[@name=""if has verbatim name""]/else",
233 233
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonomicname,
234 234
scientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonomicnamewithauthor,
235 235
variety,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/variety,

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