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Revision 3594

Added by Aaron Marcuse-Kubitza over 12 years ago

Added inputs/CVS/

View differences:

inputs/CVS/test/VegX.organisms.xml.ref
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<?xml version="1.0" ?>
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<VegX xmlns:tcs="http://www.tdwg.org/schemas/tcs/1.01">
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    <individualOrganismObservations>
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        <individualOrganismObservation id="0">
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            <individualOrganismID>0</individualOrganismID>
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            <plotObservationID>0</plotObservationID>
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            <volumeCanopy><attributeID>0</attributeID></volumeCanopy>
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        </individualOrganismObservation>
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        <individualOrganismObservation id="1">
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            <individualOrganismID>1</individualOrganismID>
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            <plotObservationID>1</plotObservationID>
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            <volumeCanopy><attributeID>1</attributeID></volumeCanopy>
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        </individualOrganismObservation>
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    </individualOrganismObservations>
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    <individualOrganisms>
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        <individualOrganism id="0"><taxonNameUsageConceptID>0</taxonNameUsageConceptID></individualOrganism>
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        <individualOrganism id="1"><taxonNameUsageConceptID>1</taxonNameUsageConceptID></individualOrganism>
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    </individualOrganisms>
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    <taxonNameUsageConcepts>
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        <taxonNameUsageConcept id="0"/>
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        <taxonNameUsageConcept id="1"/>
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    </taxonNameUsageConcepts>
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    <taxonDeterminations>
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        <taxonDetermination>
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            <taxonNameUsageConceptID>0</taxonNameUsageConceptID>
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            <taxonRelationshipAssertions><taxonRelationshipAssertion><assertion><taxonConceptID>0</taxonConceptID></assertion></taxonRelationshipAssertion></taxonRelationshipAssertions>
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        </taxonDetermination>
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        <taxonDetermination>
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            <taxonNameUsageConceptID>1</taxonNameUsageConceptID>
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            <taxonRelationshipAssertions><taxonRelationshipAssertion><assertion><taxonConceptID>1</taxonConceptID></assertion></taxonRelationshipAssertion></taxonRelationshipAssertions>
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        </taxonDetermination>
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    </taxonDeterminations>
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    <taxonConcepts>
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        <taxonConcept id="0">
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            <tcs:Rank code="binom"/>
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            <tcs:Name>Acer rubrum</tcs:Name>
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        </taxonConcept>
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        <taxonConcept id="1">
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            <tcs:Rank code="binom"/>
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            <tcs:Name>Aralia spinosa</tcs:Name>
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        </taxonConcept>
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    </taxonConcepts>
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    <plotObservations>
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        <plotObservation id="0">
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            <plotUniqueIdentifierID>0</plotUniqueIdentifierID>
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            <obsStartDate>1988-05-17</obsStartDate>
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            <partyWithRole><partyID>0</partyID></partyWithRole>
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        </plotObservation>
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        <plotObservation id="1">
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            <plotUniqueIdentifierID>1</plotUniqueIdentifierID>
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            <obsStartDate>1988-05-17</obsStartDate>
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            <partyWithRole><partyID>1</partyID></partyWithRole>
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        </plotObservation>
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    </plotObservations>
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    <plots>
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        <plot id="0">
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            <geospatial>
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                <CoordinateUncertaintyInMeters>10</CoordinateUncertaintyInMeters>
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                <DecimalLatitude>34.69908082</DecimalLatitude>
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                <DecimalLongitude>-76.82808905</DecimalLongitude>
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            </geospatial>
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            <location>
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                <placeType>county</placeType>
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                <placeName>Carteret</placeName>
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            </location>
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            <location>
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                <placeType>state</placeType>
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                <placeName>North Carolina</placeName>
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            </location>
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            <plotName>001-00-0201</plotName>
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        </plot>
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        <plot id="1">
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            <geospatial>
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                <CoordinateUncertaintyInMeters>10</CoordinateUncertaintyInMeters>
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                <DecimalLatitude>34.69908082</DecimalLatitude>
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                <DecimalLongitude>-76.82808905</DecimalLongitude>
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            </geospatial>
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            <location>
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                <placeType>county</placeType>
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                <placeName>Carteret</placeName>
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            </location>
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            <location>
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                <placeType>state</placeType>
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                <placeName>North Carolina</placeName>
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            </location>
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            <plotName>001-00-0201</plotName>
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        </plot>
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    </plots>
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    <parties>
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        <party id="0"><organizationName>CVS</organizationName></party>
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        <party id="1"><organizationName>CVS</organizationName></party>
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    </parties>
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    <attributes>
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        <attribute id="0"><ordinal><coverPercent>0.05</coverPercent></ordinal></attribute>
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        <attribute id="1"><ordinal><coverPercent>0.505</coverPercent></ordinal></attribute>
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    </attributes>
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</VegX>
inputs/CVS/test/VegBIEN.organisms.xml.ref
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<?xml version="1.0" ?>
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<VegBIEN>
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    <plantobservation id="0">
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        <aggregateoccurrence>
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            <taxonoccurrence_id>
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                <taxonoccurrence>
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                    <locationevent_id>
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                        <locationevent>
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                            <location_id>
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                                <location>
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                                    <locationdetermination>
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                                        <coordsaccuracy>10</coordsaccuracy>
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                                        <namedplace_id>
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                                            <namedplace>
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                                                <rank>county</rank>
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                                                <placename>Carteret</placename>
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                                                <parent_id>
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                                                    <namedplace>
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                                                        <rank>stateProvince</rank>
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                                                        <placename>North Carolina</placename>
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                                                    </namedplace>
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                                                </parent_id>
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                                            </namedplace>
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                                        </namedplace_id>
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                                        <latitude>34.69908082</latitude>
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                                        <longitude>-76.82808905</longitude>
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                                    </locationdetermination>
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                                    <centerlatitude>34.69908082</centerlatitude>
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                                    <centerlongitude>-76.82808905</centerlongitude>
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                                    <datasource_id><party><organizationname>CVS</organizationname></party></datasource_id>
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                                    <sourceaccessioncode>001-00-0201</sourceaccessioncode>
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                                </location>
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                            </location_id>
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                            <obsstartdate>1988-05-17</obsstartdate>
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                            <authorlocationcode>001-00-0201</authorlocationcode>
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                        </locationevent>
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                    </locationevent_id>
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                    <taxondetermination>
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                        <isoriginal>true</isoriginal>
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                        <iscurrent>true</iscurrent>
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                        <role>identifier</role>
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                        <plantconcept_id>
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                            <plantconcept>
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                                <plantname_id>
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                                    <plantname>
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                                        <rank>binomial</rank>
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                                        <plantname>Acer rubrum</plantname>
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                                    </plantname>
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                                </plantname_id>
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                            </plantconcept>
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                        </plantconcept_id>
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                    </taxondetermination>
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                </taxonoccurrence>
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            </taxonoccurrence_id>
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            <cover>0.05</cover>
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        </aggregateoccurrence>
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    </plantobservation>
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    <plantobservation id="1">
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        <aggregateoccurrence>
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            <taxonoccurrence_id>
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                <taxonoccurrence>
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                    <locationevent_id>
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                        <locationevent>
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                            <location_id>
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                                <location>
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                                    <locationdetermination>
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                                        <coordsaccuracy>10</coordsaccuracy>
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                                        <namedplace_id>
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                                            <namedplace>
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                                                <rank>county</rank>
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                                                <placename>Carteret</placename>
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                                                <parent_id>
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                                                    <namedplace>
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                                                        <rank>stateProvince</rank>
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                                                        <placename>North Carolina</placename>
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                                                    </namedplace>
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                                                </parent_id>
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                                            </namedplace>
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                                        </namedplace_id>
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                                        <latitude>34.69908082</latitude>
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                                        <longitude>-76.82808905</longitude>
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                                    </locationdetermination>
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                                    <centerlatitude>34.69908082</centerlatitude>
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                                    <centerlongitude>-76.82808905</centerlongitude>
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                                    <datasource_id><party><organizationname>CVS</organizationname></party></datasource_id>
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                                    <sourceaccessioncode>001-00-0201</sourceaccessioncode>
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                                </location>
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                            </location_id>
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                            <obsstartdate>1988-05-17</obsstartdate>
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                            <authorlocationcode>001-00-0201</authorlocationcode>
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                        </locationevent>
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                    </locationevent_id>
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                    <taxondetermination>
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                        <isoriginal>true</isoriginal>
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                        <iscurrent>true</iscurrent>
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                        <role>identifier</role>
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                        <plantconcept_id>
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                            <plantconcept>
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                                <plantname_id>
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                                    <plantname>
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                                        <rank>binomial</rank>
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                                        <plantname>Aralia spinosa</plantname>
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                                    </plantname>
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                                </plantname_id>
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                            </plantconcept>
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                        </plantconcept_id>
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                    </taxondetermination>
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                </taxonoccurrence>
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            </taxonoccurrence_id>
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            <cover>0.505</cover>
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        </aggregateoccurrence>
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    </plantobservation>
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</VegBIEN>
inputs/CVS/test/import.organisms.out.ref
1 
Inserted 18 new rows into database
inputs/CVS/maps/src.organisms.csv
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CVS,VegX:/*s/individualOrganismObservation,Comments
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authorObsCode,,
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obsStartDate,,
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realLatitude,,
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realLongitude,,
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locationAccuracy-m,,
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publicLatitude,,
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publicLongitude,,
9 
confidentialityStatus,,
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state,,
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county,,
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currentTaxonName sec Weakley 2006,,
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%cover,,
inputs/CVS/maps/VegX.organisms.csv
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CVS,VegX:/*s/individualOrganismObservation,Comments
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authorObsCode,/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,
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obsStartDate,/*ID->/*s/plotObservation/obsStartDate/_*/date,
4 
realLatitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude/_alt/1,
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realLongitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude/_alt/1,
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locationAccuracy-m,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/CoordinateUncertaintyInMeters,
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publicLatitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude/_alt/2,
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publicLongitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude/_alt/2,
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confidentialityStatus,,
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state,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/location[placeType=state]/placeName,
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county,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/location[placeType=county]/placeName,
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currentTaxonName sec Weakley 2006,"/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name",
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%cover,/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent,
inputs/CVS/maps/VegX.organisms.full.csv
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CVS,"VegX::[@xmlns:tcs=""http://www.tdwg.org/schemas/tcs/1.01""]/*s/individualOrganismObservation",Comments
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currentTaxonName sec Weakley 2006,"/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name",
3 
locationAccuracy-m,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/CoordinateUncertaintyInMeters,
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realLatitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude/_alt/1,
5 
publicLatitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude/_alt/2,
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realLongitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude/_alt/1,
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publicLongitude,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude/_alt/2,
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county,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/location[placeType=county]/placeName,
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state,/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/location[placeType=state]/placeName,
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obsStartDate,/*ID->/*s/plotObservation/obsStartDate/_*/date,
11 
authorObsCode,/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,
12 
%cover,/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent,
13 
confidentialityStatus,,
inputs/CVS/maps/VegBIEN.organisms.csv
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CVS,VegBIEN:/plantobservation,Comments
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locationAccuracy-m,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy,
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county,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
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state,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",
5 
realLatitude,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/latitude,centerlatitude}/_alt/1",
6 
publicLatitude,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/latitude,centerlatitude}/_alt/2",
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realLongitude,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1",
8 
publicLongitude,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/2",
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obsStartDate,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_*/date,
10 
authorObsCode,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{./authorlocationcode,*_id/location:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode/_merge/2/_alt/2}","""{./"" sorts it before the location.datasource_id mapping with ""{.}"""
11 
currentTaxonName sec Weakley 2006,"/aggregateoccurrence/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/first",
12 
%cover,/aggregateoccurrence/cover,
13 
confidentialityStatus,,** No input mapping for confidentialityStatus **

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