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Revision 6882

Added by Aaron Marcuse-Kubitza almost 12 years ago

schemas/vegbien.sql: Reattached trait to taxonoccurrence instead of taxonlabel, because the TraitObservation traits data is actually associated with a particular occurrence (plant observation complete with location, date, etc.), rather than just a taxon

View differences:

inputs/bien2_traits/TraitObservation/VegBIEN.csv
39 39 
InfraspecificRank,"/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",
40 40 
InfraspecificEpithet,/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/2,
41 41 
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,
42 
TraitName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/name,
43 
Unit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/units,
44 
TraitValue,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/value,
45 42 
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
46 43 
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
47 44 
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
48 45 
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
49 46 
Taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
50 47 
InfraspecificRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
48 
TraitName,/location/locationevent/taxonoccurrence/trait/name,
49 
Unit,/location/locationevent/taxonoccurrence/trait/units,
50 
TraitValue,/location/locationevent/taxonoccurrence/trait/value,
51 51 
LocalityDescription,/location/locationnarrative/_merge/2,
52 52 
VerbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude,
53 53 
VerbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude,
inputs/bien2_traits/TraitObservation/test.xml.ref
159 159 
                                                            </2>
160 160 
                                                        </_join_words>
161 161 
                                                    </taxonomicname>
162 
                                                    <trait>
163 
                                                        <name>$TraitName</name>
164 
                                                        <units>$Unit</units>
165 
                                                        <value>$TraitValue</value>
166 
                                                    </trait>
167 162 
                                                </taxonlabel>
168 163 
                                            </taxonlabel_id>
169 164 
                                            <author>$AuthorOfScientificName</author>
......
175 170 
                                        </taxonverbatim>
176 171 
                                    </taxonverbatim_id>
177 172 
                                </taxondetermination>
173 
                                <trait>
174 
                                    <name>$TraitName</name>
175 
                                    <units>$Unit</units>
176 
                                    <value>$TraitValue</value>
177 
                                </trait>
178 178 
                            </taxonoccurrence>
179 179 
                        </locationevent>
180 180 
                        <locationnarrative>$LocalityDescription</locationnarrative>
schemas/vegbien.my.sql
3374 3374 

  		




  3375
  3375
  
    
CREATE TABLE trait (


  		




  3376
  3376
  
    
    trait_id int(11) NOT NULL,


  		




  3377
  
  
    
    taxonlabel_id int(11) NOT NULL,


  		




  
  3377
  
    
    taxonoccurrence_id int(11) NOT NULL,


  		




  3378
  3378
  
    
    name varchar(255) NOT NULL,


  		




  3379
  3379
  
    
    value varchar(255),


  		




  3380
  3380
  
    
    units varchar(255)


  		




  ......




  6545
  6545
  
    

  		




  6546
  6546
  
    

  		




  6547
  6547
  
    
--


  		




  6548
  
  
    
-- Name: trait_taxonlabel_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  
  6548
  
    
-- Name: trait_taxonoccurrence_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  6549
  6549
  
    
--


  		




  6550
  6550
  
    

  		




  6551
  6551
  
    
ALTER TABLE trait


  		




  6552
  
  
    
    ADD CONSTRAINT trait_taxonlabel_id_fkey FOREIGN KEY (taxonlabel_id) REFERENCES taxonlabel(taxonlabel_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  
  6552
  
    
    ADD CONSTRAINT trait_taxonoccurrence_id_fkey FOREIGN KEY (taxonoccurrence_id) REFERENCES taxonoccurrence(taxonoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  6553
  6553
  
    

  		




  6554
  6554
  
    

  		




  6555
  6555
  
    
--


  		












  

    
      schemas/vegbien.sql
    
  





  4471
  4471
  
    

  		




  4472
  4472
  
    
CREATE TABLE trait (


  		




  4473
  4473
  
    
    trait_id integer NOT NULL,


  		




  4474
  
  
    
    taxonlabel_id integer NOT NULL,


  		




  
  4474
  
    
    taxonoccurrence_id integer NOT NULL,


  		




  4475
  4475
  
    
    name text NOT NULL,


  		




  4476
  4476
  
    
    value text,


  		




  4477
  4477
  
    
    units text


  		




  ......




  6589
  6589
  
    
-- Name: trait_unique; Type: INDEX; Schema: public; Owner: -; Tablespace: 


  		




  6590
  6590
  
    
--


  		




  6591
  6591
  
    

  		




  6592
  
  
    
CREATE UNIQUE INDEX trait_unique ON trait USING btree (taxonlabel_id, name, (COALESCE(value, '\N'::text)), (COALESCE(units, '\N'::text)));


  		




  
  6592
  
    
CREATE UNIQUE INDEX trait_unique ON trait USING btree (taxonoccurrence_id, name, (COALESCE(value, '\N'::text)), (COALESCE(units, '\N'::text)));


  		




  6593
  6593
  
    

  		




  6594
  6594
  
    

  		




  6595
  6595
  
    
--


  		




  ......




  7705
  7705
  
    

  		




  7706
  7706
  
    

  		




  7707
  7707
  
    
--


  		




  7708
  
  
    
-- Name: trait_taxonlabel_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  
  7708
  
    
-- Name: trait_taxonoccurrence_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -


  		




  7709
  7709
  
    
--


  		




  7710
  7710
  
    

  		




  7711
  7711
  
    
ALTER TABLE ONLY trait


  		




  7712
  
  
    
    ADD CONSTRAINT trait_taxonlabel_id_fkey FOREIGN KEY (taxonlabel_id) REFERENCES taxonlabel(taxonlabel_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  
  7712
  
    
    ADD CONSTRAINT trait_taxonoccurrence_id_fkey FOREIGN KEY (taxonoccurrence_id) REFERENCES taxonoccurrence(taxonoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;


  		




  7713
  7713
  
    

  		




  7714
  7714
  
    

  		




  7715
  7715
  
    
--


  		












  

    
      mappings/VegCore-VegBIEN.csv
    
  





  275
  275
  
    
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,


  		




  276
  276
  
    
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3,


  		




  277
  277
  
    
taxonomicStatus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus,


  		




  278
  
  
    
measurementType,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/name,


  		




  279
  
  
    
measurementUnit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/units,


  		




  280
  
  
    
measurementValue,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/value,


  		




  281
  278
  
    
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,


  		




  282
  279
  
    
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,


  		




  283
  280
  
    
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,


  		




  ......




  346
  343
  
    
originalScientificName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname,


  		




  347
  344
  
    
originalTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/verbatimrank,


  		




  348
  345
  
    
originalIdentificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,


  		




  
  346
  
    
measurementType,/location/locationevent/taxonoccurrence/trait/name,


  		




  
  347
  
    
measurementUnit,/location/locationevent/taxonoccurrence/trait/units,


  		




  
  348
  
    
measurementValue,/location/locationevent/taxonoccurrence/trait/value,


  		




  349
  349
  
    
voucherType,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left",


  		




  350
  350
  
    
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",


  		




  351
  351
  
    
temperature,/location/locationevent/temperature_c,


  		












  

    
      mappings/for_review/VegCore-VegBIEN.csv
    
  





  275
  275
  
    
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,


  		




  276
  276
  
    
taxonNameOrEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname,


  		




  277
  277
  
    
taxonomicStatus,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus,


  		




  278
  
  
    
measurementType,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/trait/name,


  		




  279
  
  
    
measurementUnit,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/trait/units,


  		




  280
  
  
    
measurementValue,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/trait/value,


  		




  281
  278
  
    
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/author,


  		




  282
  279
  
    
family,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/family,


  		




  283
  280
  
    
genus,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/genus,


  		




  ......




  346
  343
  
    
originalScientificName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname,


  		




  347
  344
  
    
originalTaxonRank,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/verbatimrank,


  		




  348
  345
  
    
originalIdentificationQualifier,//taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,


  		




  
  346
  
    
measurementType,//trait/name,


  		




  
  347
  
    
measurementUnit,//trait/units,


  		




  
  348
  
    
measurementValue,//trait/value,


  		




  349
  349
  
    
voucherType,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond",


  		




  350
  350
  
    
catalogNumber,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",


  		




  351
  351
  
    
temperature,//locationevent/temperature_c,


  		












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