Revision 6742
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/CVS/Organism/postprocess.sql | ||
|---|---|---|
| 1 |
ALTER TABLE :table DROP COLUMN "realLatitude"; |
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| 2 |
ALTER TABLE :table DROP COLUMN "realLongitude"; |
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| inputs/CVS/Organism/map.csv | ||
|---|---|---|
| 1 |
CVS,VegCore,Filter,Comments |
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| 2 |
authorObsCode,fieldNumber,, |
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| 3 |
obsStartDate,startDate,, |
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| 4 |
locationAccuracy-m,coordinateUncertaintyInMeters,, |
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| 5 |
publicLatitude,decimalLatitude,, |
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| 6 |
publicLongitude,decimalLongitude,, |
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| 7 |
confidentialityStatus,*confidentialityStatus,, |
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| 8 |
state,stateProvince,, |
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| 9 |
county,county,, |
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| 10 |
currentTaxonName sec Weakley 2006,taxonName,, |
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| 11 |
%cover,coverPercent,, |
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| 12 |
:Weakley 2006,accordingTo,, |
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| inputs/CVS/Organism/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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| 2 |
<VegBIEN> |
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| 3 |
<_setDefault id="-1"> |
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| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
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| 5 |
<path> |
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| 6 |
<_simplifyPath> |
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| 7 |
<next>parent_id</next> |
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| 8 |
<path> |
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| 9 |
<location> |
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| 10 |
<authorlocationcode>$authorObsCode</authorlocationcode> |
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| 11 |
<locationevent> |
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| 12 |
<authoreventcode>$authorObsCode</authoreventcode> |
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| 13 |
<obsstartdate>$obsStartDate</obsstartdate> |
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| 14 |
<taxonoccurrence> |
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| 15 |
<aggregateoccurrence><cover_fraction><_percent_to_fraction><value>$%cover</value></_percent_to_fraction></cover_fraction></aggregateoccurrence> |
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| 16 |
<authortaxoncode>$currentTaxonName sec Weakley 2006</authortaxoncode> |
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| 17 |
<taxondetermination> |
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| 18 |
<taxonverbatim_id> |
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| 19 |
<taxonverbatim> |
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| 20 |
<taxonlabel_id> |
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| 21 |
<taxonlabel> |
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| 22 |
<matched_label_id> |
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| 23 |
<taxonlabel> |
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| 24 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
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| 25 |
<taxonomicname>$currentTaxonName sec Weakley 2006</taxonomicname> |
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| 26 |
</taxonlabel> |
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</matched_label_id> |
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| 28 |
<taxonconcept><concept_reference_id><source><shortname>Weakley 2006</shortname></source></concept_reference_id></taxonconcept> |
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<taxonomicname>$currentTaxonName sec Weakley 2006</taxonomicname> |
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| 30 |
</taxonlabel> |
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| 31 |
</taxonlabel_id> |
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<taxonname>$currentTaxonName sec Weakley 2006</taxonname> |
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</taxonverbatim> |
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| 34 |
</taxonverbatim_id> |
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| 35 |
</taxondetermination> |
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| 36 |
</taxonoccurrence> |
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| 37 |
</locationevent> |
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| 38 |
<locationplace> |
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| 39 |
<place_id> |
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| 40 |
<place> |
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| 41 |
<coordinates_id> |
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| 42 |
<coordinates> |
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<coordsaccuracy_m><_noCV><value>$locationAccuracy-m</value></_noCV></coordsaccuracy_m> |
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| 44 |
<latitude_deg> |
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| 45 |
<_nullIf> |
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| 46 |
<null>0</null> |
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<type>float</type> |
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<value>$publicLatitude</value> |
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</_nullIf> |
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| 50 |
</latitude_deg> |
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| 51 |
<longitude_deg> |
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| 52 |
<_nullIf> |
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<null>0</null> |
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<type>float</type> |
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<value>$publicLongitude</value> |
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</_nullIf> |
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</longitude_deg> |
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</coordinates> |
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| 59 |
</coordinates_id> |
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<county>$county</county> |
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| 61 |
<matched_place_id> |
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| 62 |
<place> |
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| 63 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
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| 64 |
<coordinates_id> |
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| 65 |
<coordinates> |
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| 66 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
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| 67 |
<latitude_deg> |
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| 68 |
<_nullIf> |
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| 69 |
<null>0</null> |
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| 70 |
<type>float</type> |
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<value>$publicLatitude</value> |
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| 72 |
</_nullIf> |
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| 73 |
</latitude_deg> |
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| 74 |
<longitude_deg> |
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| 75 |
<_nullIf> |
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| 76 |
<null>0</null> |
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| 77 |
<type>float</type> |
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| 78 |
<value>$publicLongitude</value> |
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| 79 |
</_nullIf> |
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| 80 |
</longitude_deg> |
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| 81 |
</coordinates> |
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| 82 |
</coordinates_id> |
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| 83 |
<county>$county</county> |
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| 84 |
<stateprovince>$state</stateprovince> |
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| 85 |
</place> |
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| 86 |
</matched_place_id> |
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| 87 |
<stateprovince>$state</stateprovince> |
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| 88 |
</place> |
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| 89 |
</place_id> |
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| 90 |
</locationplace> |
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| 91 |
</location> |
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| 92 |
</path> |
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| 93 |
</_simplifyPath> |
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| 94 |
</path> |
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| 95 |
</_setDefault> |
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| 96 |
</VegBIEN> |
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| 97 |
Inserted 25 new rows into database |
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| inputs/CVS/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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| 2 |
authorObsCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
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| 3 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
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| 4 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
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| 5 |
obsStartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
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| 6 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authorlocationcode", |
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| 7 |
obsStartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
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| 8 |
obsStartDate,/location/locationevent/obsstartdate/_alt/1, |
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| 9 |
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
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| 10 |
authorObsCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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| 11 |
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
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| 12 |
currentTaxonName sec Weakley 2006,"/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/1/_taxon_family_require_std/family/_nullIf/null/_first/1", |
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| 13 |
currentTaxonName sec Weakley 2006,"/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/1", |
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| 14 |
:Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonconcept/concept_reference_id/source/shortname, |
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| 15 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1, |
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| 16 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
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| 17 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
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| 18 |
locationAccuracy-m,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value, |
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| 19 |
publicLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
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| 20 |
publicLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
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| 21 |
county,/location/locationplace/*_id/place/county, |
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| 22 |
publicLatitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
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| 23 |
publicLongitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
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| 24 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
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| 25 |
state,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
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| 26 |
state,/location/locationplace/*_id/place/stateprovince, |
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| 27 |
confidentialityStatus,,** No join mapping for *confidentialityStatus ** |
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| inputs/CVS/Organism/new_terms.csv | ||
|---|---|---|
| 1 |
obsStartDate,startDate,, |
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| 2 |
locationAccuracy-m,coordinateUncertaintyInMeters,, |
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| 3 |
publicLatitude,decimalLatitude,, |
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| 4 |
publicLongitude,decimalLongitude,, |
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| 5 |
currentTaxonName sec Weakley 2006,taxonName,, |
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| 6 |
%cover,coverPercent,, |
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| inputs/CVS/Organism/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*confidentialityStatus |
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| inputs/CVS/taxonObservation_/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*PLANTCONCEPT_ID |
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| 2 |
*taxonObservation_reference_ID |
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| 3 |
*currentTaxonInterpPlantConcept_ID |
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| 4 |
*taxonInferenceArea |
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| 5 |
*taxonObservation_accessionCode |
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| 6 |
*taxonObservation_dba_src_ID |
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| 7 |
*cust_cvs_corner1Presence |
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| 8 |
*cust_cvs_corner2Presence |
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| 9 |
*cust_cvs_corner3Presence |
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| 10 |
*cust_cvs_corner4Presence |
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| 11 |
*cust_cvs_corner5Presence |
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| 12 |
*entry_herbLineID |
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| 13 |
*entry_treeLineID |
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| 14 |
*taxonObservation_entry_sppID |
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| 15 |
*entry_unknownSp |
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| 16 |
*entry_sortOrder |
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| 17 |
*cust_cvs_collectionFlag |
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| 18 |
*taxonObservationNotes |
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| 19 |
*temp_taxonUpToDate |
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| 20 |
*TAXONINTERPRETATION_ID |
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| 21 |
*taxonInterpretation_PLANTNAME_ID |
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| 22 |
*taxonInterpretation_PARTY_ID |
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| 23 |
*ROLE_ID |
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| 24 |
*interpretationType |
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| 25 |
*reference_ID |
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| 26 |
*originalInterpretation |
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| 27 |
*currentInterpretation |
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| 28 |
*taxonConfidence |
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| 29 |
*collector_ID |
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| 30 |
*collectionNumber |
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| 31 |
*museum_ID |
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*groupType |
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*notesPublic |
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| 34 |
*notesMgt |
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| 35 |
*revisions |
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| 36 |
*taxonInterpretation_dba_src_ID |
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| 37 |
*taxonInterpretation_accessionCode |
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| 38 |
*PARTY_ID |
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| 39 |
*salutation |
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| 40 |
*middleName |
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| 41 |
*suffix |
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| 42 |
*entry_userInitials |
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| 43 |
*organizationName |
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| 44 |
*currentName_ID |
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| 45 |
*contactInstructions |
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| 46 |
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| 47 |
*accessionCode |
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| 48 |
*partyType |
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| 49 |
*dba_src_ID |
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| 50 |
*dba_unsure |
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| 51 |
*PLANTNAME_ID |
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| 52 |
*plantConcept_reference_ID |
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| 53 |
*plantname |
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| 54 |
*plantNameWithAuthority |
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| 55 |
*plantCode |
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| 56 |
*plantDescription |
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| 57 |
*plantConcept_accessionCode |
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| 58 |
*plantConcept_dba_src_ID |
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| 59 |
*plantConcept_entry_sppID |
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| 60 |
*USDAPlantsCode |
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| 61 |
*VascularPlant |
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| 62 |
*denorm_kingdom |
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| 63 |
*denorm_division |
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| 64 |
*denorm_category |
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| 65 |
*denorm_family |
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| 66 |
*denorm_genus |
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| 67 |
*denorm_species |
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| 68 |
*denorm_triAbbr |
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| 69 |
*denorm_triName |
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| 70 |
*denorm_quadAbbr |
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| 71 |
*denorm_quadName |
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| 72 |
*denorm_hybridX |
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| 73 |
*taxonLevel |
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| 74 |
*lowestParentName |
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| 75 |
*lowestParentConcept_ID |
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| 76 |
*lowestChildRank |
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| 77 |
*commonName |
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| 78 |
*growthForm_short |
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| 79 |
*woody |
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| 80 |
*exotic |
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| 81 |
*usda_code |
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| 82 |
*usda_growthForm |
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| 83 |
*Subkingdom |
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| 84 |
*Superdivision |
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| 85 |
*Division |
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| 86 |
*Subdivision |
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| 87 |
*Subclass |
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| inputs/CVS/taxonImportance/map.csv | ||
|---|---|---|
| 1 |
CVS,VegCore,Filter,Comments |
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| 2 |
taxonImportance_ID,aggregateOccurrenceID,, |
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| 3 |
taxonObservation_ID,taxonOccurrenceID,, |
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| 4 |
stratum_ID,*stratum_ID,, |
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| 5 |
cover,coverPercent,, |
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| 6 |
basalArea,*basalArea,, |
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| 7 |
biomass,*biomass,, |
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| 8 |
inferenceArea,*inferenceArea,, |
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| 9 |
cust_cvs_StemFrequency,*cust_cvs_StemFrequency,, |
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| 10 |
dba_src_ID,*dba_src_ID,, |
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| 11 |
entry_herbLineID,*entry_herbLineID,, |
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| 12 |
entry_treeLineID,*entry_treeLineID,, |
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| 13 |
cust_cvs_corner1Presence,*cust_cvs_corner1Presence,, |
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| 14 |
cust_cvs_corner2Presence,*cust_cvs_corner2Presence,, |
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| 15 |
cust_cvs_corner3Presence,*cust_cvs_corner3Presence,, |
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| 16 |
cust_cvs_corner4Presence,*cust_cvs_corner4Presence,, |
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| 17 |
cust_cvs_corner5Presence,*cust_cvs_corner5Presence,, |
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| 18 |
cust_cvs_originalCoverCode,*cust_cvs_originalCoverCode,, |
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| inputs/CVS/taxonImportance/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*stratum_ID |
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| 2 |
*basalArea |
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| 3 |
*biomass |
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| 4 |
*inferenceArea |
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| 5 |
*cust_cvs_StemFrequency |
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| 6 |
*dba_src_ID |
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| 7 |
*entry_herbLineID |
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| 8 |
*entry_treeLineID |
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| 9 |
*cust_cvs_corner1Presence |
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| 10 |
*cust_cvs_corner2Presence |
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| 11 |
*cust_cvs_corner3Presence |
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| 12 |
*cust_cvs_corner4Presence |
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| 13 |
*cust_cvs_corner5Presence |
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| 14 |
*cust_cvs_originalCoverCode |
|
| inputs/CVS/plot_/create.sql | ||
|---|---|---|
| 1 |
SELECT |
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| 2 |
* |
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| 3 |
, (SELECT "placeName" |
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| 4 |
FROM place |
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| 5 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
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| 6 |
WHERE |
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| 7 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 8 |
AND "placeSystem" = 'continent' |
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| 9 |
LIMIT 1 |
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| 10 |
) AS continent |
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| 11 |
, (SELECT "placeName" |
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| 12 |
FROM place |
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| 13 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
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| 14 |
WHERE |
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| 15 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 16 |
AND "placeSystem" = 'area|country|territory' |
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| 17 |
LIMIT 1 |
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| 18 |
) AS "area|country|territory" |
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| 19 |
, (SELECT "placeName" |
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| 20 |
FROM place |
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| 21 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
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| 22 |
WHERE |
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| 23 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 24 |
AND "placeSystem" = 'region|state|province' |
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| 25 |
LIMIT 1 |
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| 26 |
) AS "region|state|province" |
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| 27 |
, (SELECT "placeName" |
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| 28 |
FROM place |
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| 29 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
|
| 30 |
WHERE |
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| 31 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 32 |
AND "placeSystem" = 'county' |
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| 33 |
LIMIT 1 |
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| 34 |
) AS county_ |
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| 35 |
, (SELECT "placeName" |
|
| 36 |
FROM place |
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| 37 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
|
| 38 |
WHERE |
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| 39 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 40 |
AND "placeSystem" = 'quadrangle' |
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| 41 |
LIMIT 1 |
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| 42 |
) AS quadrangle |
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| 43 |
, (SELECT "placeName" |
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| 44 |
FROM place |
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| 45 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
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| 46 |
WHERE |
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| 47 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 48 |
AND "placeSystem" = 'Geographic Name' |
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| 49 |
LIMIT 1 |
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| 50 |
) AS "Geographic Name" |
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| 51 |
, (SELECT "placeName" |
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| 52 |
FROM place |
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| 53 |
JOIN "namedPlace" USING ("NAMEDPLACE_ID")
|
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| 54 |
WHERE |
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| 55 |
place."PLOTPLACE_ID" = plot."PLOT_ID" |
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| 56 |
AND "placeSystem" = 'River Basin' |
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| 57 |
LIMIT 1 |
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| 58 |
) AS "River Basin" |
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| 59 |
FROM plot |
|
| inputs/CVS/plot_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
authorPlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
|
| 5 |
authorPlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 6 |
PLOT_ID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 7 |
confidentialityStatus,"/location/accesslevel/_map:[./{0,1,2,3,4}=public,5=""data by request"",6=private]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
|
| 8 |
area,/location/area_m2,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 9 |
elevation,/location/elevation_m/_alt/1,"""The elevation of the plot origin in meters above sea level"" (elevation definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 10 |
locationNarrative,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 11 |
landform,/location/landform, |
|
| 12 |
authorPlotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 13 |
PLOT_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 14 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 15 |
authorPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 16 |
locationNarrative,/location/locationnarrative/_merge/1, |
|
| 17 |
confidentialityStatus,"/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value/_alt/1/_km_to_m/value/_map:[1=1,2=10,3=100,./{0,4,5,6}=]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
|
| 18 |
locationAccuracy,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value/_alt/2, |
|
| 19 |
shape,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc, |
|
| 20 |
latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 21 |
longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 22 |
continent,/location/locationplace/*_id/place/continent, |
|
| 23 |
COUNTRY,/location/locationplace/*_id/place/country, |
|
| 24 |
area|country|territory,/location/locationplace/*_id/place/country, |
|
| 25 |
county,/location/locationplace/*_id/place/county, |
|
| 26 |
county_,/location/locationplace/*_id/place/county, |
|
| 27 |
latitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 28 |
longitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 29 |
COUNTRY,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 30 |
area|country|territory,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 31 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 32 |
county_,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 33 |
region|state|province,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 34 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 35 |
region|state|province,/location/locationplace/*_id/place/stateprovince, |
|
| 36 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 37 |
PARENT_ID,/location/parent_id/location/sourceaccessioncode, |
|
| 38 |
slopeAspect,/location/slopeaspect_deg/_alt/1/_compass/value, |
|
| 39 |
maxSlopeAspect,/location/slopeaspect_deg/_alt/2/_avg/max, |
|
| 40 |
minSlopeAspect,/location/slopeaspect_deg/_alt/2/_avg/min, |
|
| 41 |
slopeGradient,/location/slopegradient_fraction/_alt/1, |
|
| 42 |
maxSlopeGradient,/location/slopegradient_fraction/_alt/2/_avg/max, |
|
| 43 |
minSlopeGradient,/location/slopegradient_fraction/_alt/2/_avg/min, |
|
| 44 |
PLOT_ID,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/1", |
|
| 45 |
authorPlotCode,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
|
| 46 |
Geographic Name,,** No join mapping for *Geographic Name ** |
|
| 47 |
REPLACEMENTPLOT_ID,,** No join mapping for *REPLACEMENTPLOT_ID ** |
|
| 48 |
River Basin,,** No join mapping for *River Basin ** |
|
| 49 |
accessionCode,,** No join mapping for *accessionCode ** |
|
| 50 |
authorCoordinateType,,** No join mapping for *authorCoordinateType ** |
|
| 51 |
authorCoordinateUnits,,** No join mapping for *authorCoordinateUnits ** |
|
| 52 |
authorDatum,,** No join mapping for *authorDatum ** |
|
| 53 |
authorE,,** No join mapping for *authorE ** |
|
| 54 |
authorLocation,,** No join mapping for *authorLocation ** |
|
| 55 |
authorN,,** No join mapping for *authorN ** |
|
| 56 |
authorZone,,** No join mapping for *authorZone ** |
|
| 57 |
azimuth,,** No join mapping for *azimuth ** |
|
| 58 |
confidentialityFieldsBlocked,,** No join mapping for *confidentialityFieldsBlocked ** |
|
| 59 |
confidentialityReason,,** No join mapping for *confidentialityReason ** |
|
| 60 |
cust_cvs_province,,** No join mapping for *cust_cvs_province ** |
|
| 61 |
cust_eep_reach,,** No join mapping for *cust_eep_reach ** |
|
| 62 |
dateentered,,** No join mapping for *dateentered ** |
|
| 63 |
dba_src_ID,,** No join mapping for *dba_src_ID ** |
|
| 64 |
dsgpoly,,** No join mapping for *dsgpoly ** |
|
| 65 |
elevationAccuracy,,** No join mapping for *elevationAccuracy ** |
|
| 66 |
elevationRange,,** No non-empty join mapping for UNUSED ** |
|
| 67 |
layoutNarrative,,** No join mapping for *layoutNarrative ** |
|
| 68 |
notesMgt,,** No join mapping for *notesMgt ** |
|
| 69 |
notesPublic,,** No join mapping for *notesPublic ** |
|
| 70 |
permanence,,** No join mapping for *permanence ** |
|
| 71 |
placementMethod,,** No join mapping for *placementMethod ** |
|
| 72 |
plotObsolete,,** No join mapping for *plotObsolete ** |
|
| 73 |
plotRationaleNarrative,,** No join mapping for *plotRationaleNarrative ** |
|
| 74 |
quadrangle,,** No join mapping for *quadrangle ** |
|
| 75 |
realLatitude,,** No non-empty join mapping for PRIVATE ** |
|
| 76 |
realLongitude,,** No non-empty join mapping for PRIVATE ** |
|
| 77 |
reference_ID,,** No join mapping for *reference_ID ** |
|
| 78 |
revisions,,** No join mapping for *revisions ** |
|
| 79 |
rockType,,** No join mapping for *rockType ** |
|
| 80 |
standSize,,** No join mapping for *standSize ** |
|
| 81 |
submitter_email,,** No join mapping for *submitter_email ** |
|
| 82 |
submitter_givenname,,** No join mapping for *submitter_givenname ** |
|
| 83 |
submitter_surname,,** No join mapping for *submitter_surname ** |
|
| 84 |
surficialDeposits,,** No join mapping for *surficialDeposits ** |
|
| 85 |
topoPosition,,** No join mapping for *topoPosition ** |
|
| inputs/CVS/plot_/new_terms.csv | ||
|---|---|---|
| 1 |
authorPlotCode,locationName,, |
|
| 2 |
PARENT_ID,parentLocationID,, |
|
| 3 |
locationAccuracy,coordinateUncertaintyInMeters,/_alt/2, |
|
| 4 |
confidentialityStatus,dcterms:accessRights,"/_map:[./{0,1,2,3,4}=public,5=""data by request"",6=private]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
|
| 5 |
confidentialityStatus,coordinateUncertaintyInMeters,"/_alt/1/_km_to_m/value/_map:[1=1,2=10,3=100,./{0,4,5,6}=]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
|
| 6 |
shape,footprintWKT,, |
|
| 7 |
area,plotArea_m2,,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 8 |
elevationRange,UNUSED,, |
|
| 9 |
area|country|territory,country,, |
|
| 10 |
region|state|province,stateProvince,, |
|
| inputs/CVS/stemCount/header.csv | ||
|---|---|---|
| 1 |
STEMCOUNT_ID,TAXONIMPORTANCE_ID,stemDiameter,stemDiameterAccuracy,stemHeight,stemHeightAccuracy,stemCount,stemTaxonArea,dba_src_ID,cust_cvs_ddh,cust_cvs_ddhAccuracy,cust_cvs_isPlanted,cust_cvs_subsamplingFactor,entry_herbLineID,entry_treeLineID,entry_recordCount,entry_sortOrder |
|
| inputs/CVS/stemCount/map.csv | ||
|---|---|---|
| 1 |
CVS,VegCore,Filter,Comments |
|
| 2 |
STEMCOUNT_ID,individualID,, |
|
| 3 |
TAXONIMPORTANCE_ID,aggregateOccurrenceID,, |
|
| 4 |
stemDiameter,diameterBreastHeight_cm,, |
|
| 5 |
stemDiameterAccuracy,*stemDiameterAccuracy,, |
|
| 6 |
stemHeight,height_m,, |
|
| 7 |
stemHeightAccuracy,*stemHeightAccuracy,, |
|
| 8 |
stemCount,stemCount,, |
|
| 9 |
stemTaxonArea,*stemTaxonArea,, |
|
| 10 |
dba_src_ID,*dba_src_ID,, |
|
| 11 |
cust_cvs_ddh,*cust_cvs_ddh,, |
|
| 12 |
cust_cvs_ddhAccuracy,*cust_cvs_ddhAccuracy,, |
|
| 13 |
cust_cvs_isPlanted,*cust_cvs_isPlanted,, |
|
| 14 |
cust_cvs_subsamplingFactor,*cust_cvs_subsamplingFactor,, |
|
| 15 |
entry_herbLineID,*entry_herbLineID,, |
|
| 16 |
entry_treeLineID,*entry_treeLineID,, |
|
| 17 |
entry_recordCount,*entry_recordCount,, |
|
| 18 |
entry_sortOrder,*entry_sortOrder,, |
|
| inputs/CVS/stemCount/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
STEMCOUNT_ID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 3 |
STEMCOUNT_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 4 |
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
|
| 5 |
stemDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value, |
|
| 6 |
stemHeight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
|
| 7 |
TAXONIMPORTANCE_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
|
| 8 |
STEMCOUNT_ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
TAXONIMPORTANCE_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
|
| 10 |
STEMCOUNT_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
|
| 11 |
cust_cvs_ddh,,** No join mapping for *cust_cvs_ddh ** |
|
| 12 |
cust_cvs_ddhAccuracy,,** No join mapping for *cust_cvs_ddhAccuracy ** |
|
| 13 |
cust_cvs_isPlanted,,** No join mapping for *cust_cvs_isPlanted ** |
|
| 14 |
cust_cvs_subsamplingFactor,,** No join mapping for *cust_cvs_subsamplingFactor ** |
|
| 15 |
dba_src_ID,,** No join mapping for *dba_src_ID ** |
|
| 16 |
entry_herbLineID,,** No join mapping for *entry_herbLineID ** |
|
| 17 |
entry_recordCount,,** No join mapping for *entry_recordCount ** |
|
| 18 |
entry_sortOrder,,** No join mapping for *entry_sortOrder ** |
|
| 19 |
entry_treeLineID,,** No join mapping for *entry_treeLineID ** |
|
| 20 |
stemDiameterAccuracy,,** No join mapping for *stemDiameterAccuracy ** |
|
| 21 |
stemHeightAccuracy,,** No join mapping for *stemHeightAccuracy ** |
|
| 22 |
stemTaxonArea,,** No join mapping for *stemTaxonArea ** |
|
| inputs/CVS/stemCount/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<locationevent> |
|
| 11 |
<taxonoccurrence> |
|
| 12 |
<aggregateoccurrence> |
|
| 13 |
<plantobservation> |
|
| 14 |
<sourceaccessioncode>$STEMCOUNT_ID</sourceaccessioncode> |
|
| 15 |
<stemcount>$stemCount</stemcount> |
|
| 16 |
<stemobservation> |
|
| 17 |
<diameterbreastheight_m><_cm_to_m><value>$stemDiameter</value></_cm_to_m></diameterbreastheight_m> |
|
| 18 |
<height_m>$stemHeight</height_m> |
|
| 19 |
</stemobservation> |
|
| 20 |
</plantobservation> |
|
| 21 |
<sourceaccessioncode>$TAXONIMPORTANCE_ID</sourceaccessioncode> |
|
| 22 |
</aggregateoccurrence> |
|
| 23 |
</taxonoccurrence> |
|
| 24 |
</locationevent> |
|
| 25 |
</location> |
|
| 26 |
</path> |
|
| 27 |
</_simplifyPath> |
|
| 28 |
</path> |
|
| 29 |
</_setDefault> |
|
| 30 |
</VegBIEN> |
|
| 31 |
Inserted 4 new rows into database |
|
| inputs/CVS/stemCount/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*stemDiameterAccuracy |
|
| 2 |
*stemHeightAccuracy |
|
| 3 |
*stemTaxonArea |
|
| 4 |
*dba_src_ID |
|
| 5 |
*cust_cvs_ddh |
|
| 6 |
*cust_cvs_ddhAccuracy |
|
| 7 |
*cust_cvs_isPlanted |
|
| 8 |
*cust_cvs_subsamplingFactor |
|
| 9 |
*entry_herbLineID |
|
| 10 |
*entry_treeLineID |
|
| 11 |
*entry_recordCount |
|
| 12 |
*entry_sortOrder |
|
| inputs/CVS/stemCount/new_terms.csv | ||
|---|---|---|
| 1 |
STEMCOUNT_ID,individualID,, |
|
| 2 |
TAXONIMPORTANCE_ID,aggregateOccurrenceID,, |
|
| 3 |
stemDiameter,diameterBreastHeight_cm,, |
|
| 4 |
stemHeight,height_m,, |
|
| inputs/CVS/stemLocation/new_terms.csv | ||
|---|---|---|
| 1 |
STEMLOCATION_ID,stemID,, |
|
| 2 |
STEMCOUNT_ID,individualID,, |
|
| 3 |
stemCode,authorStemCode,, |
|
| 4 |
stemXPosition,organismX_m,, |
|
| 5 |
stemYPosition,organismY_m,, |
|
| inputs/CVS/cvs.~.utils.sql | ||
|---|---|---|
| 1 |
-- Function: plantconcept_ancestors(integer) |
|
| 2 |
|
|
| 3 |
-- DROP FUNCTION plantconcept_ancestors(integer); |
|
| 4 |
|
|
| 5 |
CREATE OR REPLACE FUNCTION plantconcept_ancestors(IN "PLANTCONCEPT_ID_" integer, OUT "PLANTCONCEPT_ID" integer, OUT "plantLevel" character varying) |
|
| 6 |
RETURNS SETOF record AS |
|
| 7 |
$BODY$ |
|
| 8 |
DECLARE |
|
| 9 |
"plantParent_ID" "plantStatus"."plantParent_ID"%TYPE; |
|
| 10 |
BEGIN |
|
| 11 |
-- Get "plantParent_ID". Remove "PLANTCONCEPT_ID" if no match or no "plantStatus". |
|
| 12 |
SELECT |
|
| 13 |
"plantStatus"."PLANTCONCEPT_ID" |
|
| 14 |
, "plantStatus"."plantLevel" |
|
| 15 |
, "plantStatus"."plantParent_ID" |
|
| 16 |
INTO "PLANTCONCEPT_ID", "plantLevel", "plantParent_ID" |
|
| 17 |
FROM "plantStatus" |
|
| 18 |
WHERE "plantStatus"."PLANTCONCEPT_ID" = "PLANTCONCEPT_ID_" |
|
| 19 |
; |
|
| 20 |
-- Add this level to the list (output params' current values) |
|
| 21 |
RETURN NEXT; |
|
| 22 |
-- Recurse |
|
| 23 |
IF "plantParent_ID" IS NOT NULL THEN |
|
| 24 |
RETURN QUERY ( |
|
| 25 |
SELECT * FROM "plantconcept_ancestors"("plantParent_ID")
|
|
| 26 |
); |
|
| 27 |
END IF; |
|
| 28 |
END; |
|
| 29 |
$BODY$ |
|
| 30 |
LANGUAGE plpgsql STABLE STRICT |
|
| 31 |
COST 100 |
|
| 32 |
ROWS 10; |
|
| 33 |
|
|
| 34 |
-- Function: plantconcept_plantnames(integer) |
|
| 35 |
|
|
| 36 |
-- DROP FUNCTION plantconcept_plantnames(integer); |
|
| 37 |
|
|
| 38 |
CREATE OR REPLACE FUNCTION plantconcept_plantnames(IN "PLANTCONCEPT_ID" integer, OUT "Kingdom" text, OUT "Subkingdom" text, OUT "Superdivision" text, OUT "Division" text, OUT "Subdivision" text, OUT "Class" text, OUT "Subclass" text, OUT "Order" text, OUT "Family" text, OUT "Genus" text, OUT "Species" text, OUT "Subspecies" text, OUT "Variety" text, OUT "Forma" text) |
|
| 39 |
RETURNS record AS |
|
| 40 |
$BODY$ |
|
| 41 |
WITH "level_plantName" AS ( |
|
| 42 |
SELECT "plantLevel", "plantName"."plantName" |
|
| 43 |
FROM plantconcept_ancestors($1) |
|
| 44 |
JOIN "plantConcept" USING ("PLANTCONCEPT_ID")
|
|
| 45 |
JOIN "plantName" USING ("PLANTNAME_ID")
|
|
| 46 |
) |
|
| 47 |
SELECT |
|
| 48 |
(SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Kingdom') |
|
| 49 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Subkingdom') |
|
| 50 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Superdivision') |
|
| 51 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Division') |
|
| 52 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Subdivision') |
|
| 53 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Class') |
|
| 54 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Subclass') |
|
| 55 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Order') |
|
| 56 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Family') |
|
| 57 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Genus') |
|
| 58 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Species') |
|
| 59 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Subspecies') |
|
| 60 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Variety') |
|
| 61 |
, (SELECT "plantName" FROM "level_plantName" WHERE "plantLevel" = 'Forma') |
|
| 62 |
$BODY$ |
|
| 63 |
LANGUAGE sql VOLATILE STRICT |
|
| 64 |
COST 100; |
|
| inputs/CVS/taxonObservation_/header.csv | ||
|---|---|---|
| 1 |
PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PARTY_ID,salutation,givenName,middleName,surName,suffix,entry_userInitials,organizationName,currentName_ID,contactInstructions,email,accessionCode,partyType,dba_src_ID,dba_unsure,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma |
|
| inputs/CVS/taxonObservation_/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<authorlocationcode>$museumAccessionNumber</authorlocationcode> |
|
| 11 |
<locationevent> |
|
| 12 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
|
| 13 |
<taxonoccurrence> |
|
| 14 |
<aggregateoccurrence> |
|
| 15 |
<collectiondate>$collectionDate</collectiondate> |
|
| 16 |
<notes>$notes</notes> |
|
| 17 |
<plantobservation> |
|
| 18 |
<specimenreplicate><catalognumber_dwc>$museumAccessionNumber</catalognumber_dwc></specimenreplicate> |
|
| 19 |
<stemobservation><sourceaccessioncode>$stemLocation_ID</sourceaccessioncode></stemobservation> |
|
| 20 |
</plantobservation> |
|
| 21 |
</aggregateoccurrence> |
|
| 22 |
<authortaxoncode>$authorPlantName</authortaxoncode> |
|
| 23 |
<collector_id> |
|
| 24 |
<party> |
|
| 25 |
<fullname> |
|
| 26 |
<_join_words> |
|
| 27 |
<1>$givenName</1> |
|
| 28 |
<2>$surName</2> |
|
| 29 |
</_join_words> |
|
| 30 |
</fullname> |
|
| 31 |
</party> |
|
| 32 |
</collector_id> |
|
| 33 |
<sourceaccessioncode>$TAXONOBSERVATION_ID</sourceaccessioncode> |
|
| 34 |
<taxondetermination> |
|
| 35 |
<taxonverbatim_id> |
|
| 36 |
<taxonverbatim> |
|
| 37 |
<taxonlabel_id> |
|
| 38 |
<taxonlabel> |
|
| 39 |
<matched_label_id> |
|
| 40 |
<taxonlabel> |
|
| 41 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 42 |
<taxonomicname> |
|
| 43 |
<_join_words> |
|
| 44 |
<1><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></1> |
|
| 45 |
<2> |
|
| 46 |
<_join_words> |
|
| 47 |
<2>$Genus</2> |
|
| 48 |
<3>$Species</3> |
|
| 49 |
<4>$Subspecies</4> |
|
| 50 |
<7> |
|
| 51 |
<_join_words> |
|
| 52 |
<1>var. </1> |
|
| 53 |
<2>$Variety</2> |
|
| 54 |
</_join_words> |
|
| 55 |
</7> |
|
| 56 |
<8> |
|
| 57 |
<_join_words> |
|
| 58 |
<1>fm. </1> |
|
| 59 |
<2>$Forma</2> |
|
| 60 |
</_join_words> |
|
| 61 |
</8> |
|
| 62 |
</_join_words> |
|
| 63 |
</2> |
|
| 64 |
</_join_words> |
|
| 65 |
</taxonomicname> |
|
| 66 |
</taxonlabel> |
|
| 67 |
</matched_label_id> |
|
| 68 |
<creationdate><_dateRangeStart><value>$interpretationDate</value></_dateRangeStart></creationdate> |
|
| 69 |
<parent_id> |
|
| 70 |
<taxonlabel> |
|
| 71 |
<rank>$taxonRank</rank> |
|
| 72 |
<taxonverbatim><verbatimrank>$taxonRank</verbatimrank></taxonverbatim> |
|
| 73 |
<parent_id> |
|
| 74 |
<taxonlabel> |
|
| 75 |
<rank>cultivar</rank> |
|
| 76 |
<parent_id> |
|
| 77 |
<taxonlabel> |
|
| 78 |
<rank>forma</rank> |
|
| 79 |
<taxonepithet>$Forma</taxonepithet> |
|
| 80 |
<parent_id> |
|
| 81 |
<taxonlabel> |
|
| 82 |
<rank>variety</rank> |
|
| 83 |
<taxonepithet>$Variety</taxonepithet> |
|
| 84 |
<parent_id> |
|
| 85 |
<taxonlabel> |
|
| 86 |
<rank>subspecies</rank> |
|
| 87 |
<taxonepithet>$Subspecies</taxonepithet> |
|
| 88 |
<parent_id> |
|
| 89 |
<taxonlabel> |
|
| 90 |
<rank>species</rank> |
|
| 91 |
<taxonepithet>$Species</taxonepithet> |
|
| 92 |
<parent_id> |
|
| 93 |
<taxonlabel> |
|
| 94 |
<rank>genus</rank> |
|
| 95 |
<taxonepithet>$Genus</taxonepithet> |
|
| 96 |
<parent_id> |
|
| 97 |
<taxonlabel> |
|
| 98 |
<rank>family</rank> |
|
| 99 |
<taxonepithet>$Family</taxonepithet> |
|
| 100 |
<parent_id> |
|
| 101 |
<taxonlabel> |
|
| 102 |
<rank>order</rank> |
|
| 103 |
<taxonepithet>$Order</taxonepithet> |
|
| 104 |
<parent_id> |
|
| 105 |
<taxonlabel> |
|
| 106 |
<rank>class</rank> |
|
| 107 |
<taxonepithet>$Class</taxonepithet> |
|
| 108 |
<parent_id> |
|
| 109 |
<taxonlabel> |
|
| 110 |
<rank>phylum</rank> |
|
| 111 |
<parent_id> |
|
| 112 |
<taxonlabel> |
|
| 113 |
<rank>kingdom</rank> |
|
| 114 |
<taxonepithet>$Kingdom</taxonepithet> |
|
| 115 |
</taxonlabel> |
|
| 116 |
</parent_id> |
|
| 117 |
</taxonlabel> |
|
| 118 |
</parent_id> |
|
| 119 |
</taxonlabel> |
|
| 120 |
</parent_id> |
|
| 121 |
</taxonlabel> |
|
| 122 |
</parent_id> |
|
| 123 |
</taxonlabel> |
|
| 124 |
</parent_id> |
|
| 125 |
</taxonlabel> |
|
| 126 |
</parent_id> |
|
| 127 |
</taxonlabel> |
|
| 128 |
</parent_id> |
|
| 129 |
</taxonlabel> |
|
| 130 |
</parent_id> |
|
| 131 |
</taxonlabel> |
|
| 132 |
</parent_id> |
|
| 133 |
</taxonlabel> |
|
| 134 |
</parent_id> |
|
| 135 |
</taxonlabel> |
|
| 136 |
</parent_id> |
|
| 137 |
</taxonlabel> |
|
| 138 |
</parent_id> |
|
| 139 |
<rank>$taxonRank</rank> |
|
| 140 |
<taxonomicname> |
|
| 141 |
<_join_words> |
|
| 142 |
<1><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></1> |
|
| 143 |
<2> |
|
| 144 |
<_join_words> |
|
| 145 |
<2>$Genus</2> |
|
| 146 |
<3>$Species</3> |
|
| 147 |
<4>$Subspecies</4> |
|
| 148 |
<6> |
|
| 149 |
<_join_words> |
|
| 150 |
<1>var. </1> |
|
| 151 |
<2>$Variety</2> |
|
| 152 |
</_join_words> |
|
| 153 |
</6> |
|
| 154 |
<7> |
|
| 155 |
<_join_words> |
|
| 156 |
<1>fm. </1> |
|
| 157 |
<2>$Forma</2> |
|
| 158 |
</_join_words> |
|
| 159 |
</7> |
|
| 160 |
</_join_words> |
|
| 161 |
</2> |
|
| 162 |
</_join_words> |
|
| 163 |
</taxonomicname> |
|
| 164 |
</taxonlabel> |
|
| 165 |
</taxonlabel_id> |
|
| 166 |
<family>$Family</family> |
|
| 167 |
<genus>$Genus</genus> |
|
| 168 |
<specific_epithet>$Species</specific_epithet> |
|
| 169 |
<verbatimrank>$taxonRank</verbatimrank> |
|
| 170 |
</taxonverbatim> |
|
| 171 |
</taxonverbatim_id> |
|
| 172 |
<determinationdate><_dateRangeStart><value>$interpretationDate</value></_dateRangeStart></determinationdate> |
|
| 173 |
<taxonfit>$taxonFit</taxonfit> |
|
| 174 |
</taxondetermination> |
|
| 175 |
<taxondetermination> |
|
| 176 |
<isoriginal>true</isoriginal> |
|
| 177 |
<taxonverbatim_id> |
|
| 178 |
<taxonverbatim> |
|
| 179 |
<taxonlabel_id> |
|
| 180 |
<taxonlabel> |
|
| 181 |
<matched_label_id> |
|
| 182 |
<taxonlabel> |
|
| 183 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 184 |
<taxonomicname>$authorPlantName</taxonomicname> |
|
| 185 |
</taxonlabel> |
|
| 186 |
</matched_label_id> |
|
| 187 |
<taxonomicname>$authorPlantName</taxonomicname> |
|
| 188 |
</taxonlabel> |
|
| 189 |
</taxonlabel_id> |
|
| 190 |
<taxonname>$authorPlantName</taxonname> |
|
| 191 |
</taxonverbatim> |
|
| 192 |
</taxonverbatim_id> |
|
| 193 |
</taxondetermination> |
|
| 194 |
</taxonoccurrence> |
|
| 195 |
</locationevent> |
|
| 196 |
</location> |
|
| 197 |
</path> |
|
| 198 |
</_simplifyPath> |
|
| 199 |
</path> |
|
| 200 |
</_setDefault> |
|
| 201 |
</VegBIEN> |
|
| 202 |
Inserted 24 new rows into database |
|
| inputs/CVS/taxonObservation_/new_terms.csv | ||
|---|---|---|
| 1 |
TAXONOBSERVATION_ID,taxonOccurrenceID,, |
|
| 2 |
OBSERVATION_ID,eventID,, |
|
| 3 |
authorPlantName,originalTaxonName,, |
|
| 4 |
stemLocation_ID,stemID,, |
|
| 5 |
interpretationDate,dateIdentified,, |
|
| 6 |
collectionDate,dateCollected,, |
|
| 7 |
museumAccessionNumber,catalogNumber,, |
|
| 8 |
givenName,recordedBy.givenName,, |
|
| 9 |
surName,recordedBy.surName,, |
|
| inputs/CVS/taxonImportance/header.csv | ||
|---|---|---|
| 1 |
taxonImportance_ID,taxonObservation_ID,stratum_ID,cover,basalArea,biomass,inferenceArea,cust_cvs_StemFrequency,dba_src_ID,entry_herbLineID,entry_treeLineID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,cust_cvs_originalCoverCode |
|
| inputs/CVS/taxonImportance/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<locationevent> |
|
| 11 |
<taxonoccurrence> |
|
| 12 |
<aggregateoccurrence> |
|
| 13 |
<cover_fraction><_percent_to_fraction><value>$cover</value></_percent_to_fraction></cover_fraction> |
|
| 14 |
<sourceaccessioncode>$taxonImportance_ID</sourceaccessioncode> |
|
| 15 |
</aggregateoccurrence> |
|
| 16 |
<sourceaccessioncode>$taxonObservation_ID</sourceaccessioncode> |
|
| 17 |
</taxonoccurrence> |
|
| 18 |
</locationevent> |
|
| 19 |
</location> |
|
| 20 |
</path> |
|
| 21 |
</_simplifyPath> |
|
| 22 |
</path> |
|
| 23 |
</_setDefault> |
|
| 24 |
</VegBIEN> |
|
| 25 |
Inserted 4 new rows into database |
|
| inputs/CVS/plot_/map.csv | ||
|---|---|---|
| 1 |
CVS,VegCore,Filter,Comments |
|
| 2 |
PLOT_ID,locationID,, |
|
| 3 |
authorPlotCode,locationName,, |
|
| 4 |
reference_ID,*reference_ID,, |
|
| 5 |
PARENT_ID,parentLocationID,, |
|
| 6 |
plotObsolete,*plotObsolete,, |
|
| 7 |
REPLACEMENTPLOT_ID,*REPLACEMENTPLOT_ID,, |
|
| 8 |
realLatitude,PRIVATE,, |
|
| 9 |
realLongitude,PRIVATE,, |
|
| 10 |
locationAccuracy,coordinateUncertaintyInMeters,/_alt/2, |
|
| 11 |
confidentialityStatus,dcterms:accessRights,"/_map:[./{0,1,2,3,4}=public,5=""data by request"",6=private]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
|
| 12 |
confidentialityStatus,coordinateUncertaintyInMeters,"/_alt/1/_km_to_m/value/_map:[1=1,2=10,3=100,./{0,4,5,6}=]/value",Values defined at <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1581&entity=dba_fielddescription¶ms=1581>
|
|
| 13 |
confidentialityFieldsBlocked,*confidentialityFieldsBlocked,, |
|
| 14 |
confidentialityReason,*confidentialityReason,, |
|
| 15 |
latitude,decimalLatitude,, |
|
| 16 |
longitude,decimalLongitude,, |
|
| 17 |
authorCoordinateType,*authorCoordinateType,, |
|
| 18 |
authorCoordinateUnits,*authorCoordinateUnits,, |
|
| 19 |
authorE,*authorE,, |
|
| 20 |
authorN,*authorN,, |
|
| 21 |
authorZone,*authorZone,, |
|
| 22 |
authorDatum,*authorDatum,, |
|
| 23 |
authorLocation,*authorLocation,, |
|
| 24 |
locationNarrative,locality,, |
|
| 25 |
plotRationaleNarrative,*plotRationaleNarrative,, |
|
| 26 |
azimuth,*azimuth,, |
|
| 27 |
dsgpoly,*dsgpoly,, |
|
| 28 |
shape,footprintWKT,, |
|
| 29 |
area,plotArea_m2,,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 30 |
standSize,*standSize,, |
|
| 31 |
placementMethod,*placementMethod,, |
|
| 32 |
permanence,*permanence,, |
|
| 33 |
layoutNarrative,*layoutNarrative,, |
|
| 34 |
elevation,elevationInMeters,,"""The elevation of the plot origin in meters above sea level"" (elevation definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 35 |
elevationAccuracy,*elevationAccuracy,, |
|
| 36 |
elevationRange,UNUSED,, |
|
| 37 |
slopeAspect,slopeAspect,, |
|
| 38 |
minSlopeAspect,minSlopeAspect,, |
|
| 39 |
maxSlopeAspect,maxSlopeAspect,, |
|
| 40 |
slopeGradient,slopeGradient,, |
|
| 41 |
minSlopeGradient,minSlopeGradient,, |
|
| 42 |
maxSlopeGradient,maxSlopeGradient,, |
|
| 43 |
topoPosition,*topoPosition,, |
|
| 44 |
landform,landform,, |
|
| 45 |
surficialDeposits,*surficialDeposits,, |
|
| 46 |
rockType,*rockType,, |
|
| 47 |
county,county,, |
|
| 48 |
cust_cvs_province,*cust_cvs_province,, |
|
| 49 |
stateProvince,stateProvince,, |
|
| 50 |
COUNTRY,country,, |
|
| 51 |
dateentered,*dateentered,, |
|
| 52 |
submitter_surname,*submitter_surname,, |
|
| 53 |
submitter_givenname,*submitter_givenname,, |
|
| 54 |
submitter_email,*submitter_email,, |
|
| 55 |
accessionCode,*accessionCode,, |
|
| 56 |
notesPublic,*notesPublic,, |
|
| 57 |
notesMgt,*notesMgt,, |
|
| 58 |
revisions,*revisions,, |
|
| 59 |
cust_eep_reach,*cust_eep_reach,, |
|
| 60 |
dba_src_ID,*dba_src_ID,, |
|
| 61 |
continent,continent,, |
|
| 62 |
area|country|territory,country,, |
|
| 63 |
region|state|province,stateProvince,, |
|
| 64 |
county_,county,, |
|
| 65 |
quadrangle,*quadrangle,, |
|
| 66 |
Geographic Name,*Geographic Name,, |
|
| 67 |
River Basin,*River Basin,, |
|
| inputs/CVS/plot_/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*reference_ID |
|
| 2 |
*plotObsolete |
|
| 3 |
*REPLACEMENTPLOT_ID |
|
| 4 |
*confidentialityFieldsBlocked |
|
| 5 |
*confidentialityReason |
|
| 6 |
*authorCoordinateType |
|
| 7 |
*authorCoordinateUnits |
|
| 8 |
*authorE |
|
| 9 |
*authorN |
|
| 10 |
*authorZone |
|
| 11 |
*authorDatum |
|
| 12 |
*authorLocation |
|
| 13 |
*plotRationaleNarrative |
|
| 14 |
*azimuth |
|
| 15 |
*dsgpoly |
|
| 16 |
*standSize |
|
| 17 |
*placementMethod |
|
| 18 |
*permanence |
|
| 19 |
*layoutNarrative |
|
| 20 |
*elevationAccuracy |
|
| 21 |
*topoPosition |
|
| 22 |
*surficialDeposits |
|
| 23 |
*rockType |
|
| 24 |
*cust_cvs_province |
|
| 25 |
*dateentered |
|
| 26 |
*submitter_surname |
|
| 27 |
*submitter_givenname |
|
| 28 |
*submitter_email |
|
| 29 |
*accessionCode |
|
| 30 |
*notesPublic |
|
| 31 |
*notesMgt |
|
| 32 |
*revisions |
|
| 33 |
*cust_eep_reach |
|
| 34 |
*dba_src_ID |
|
| 35 |
*quadrangle |
|
| 36 |
*Geographic Name |
|
| 37 |
*River Basin |
|
| inputs/CVS/import_order.txt | ||
|---|---|---|
| 1 | 1 |
Source |
| 2 |
Organism |
|
| 2 |
plot_ |
|
| 3 |
observation_ |
|
| 4 |
taxonObservation_ |
|
| 5 |
taxonImportance |
|
| 6 |
stemCount |
|
| 7 |
stemLocation |
|
| inputs/CVS/plantConcept_/create.sql | ||
|---|---|---|
| 1 |
SELECT |
|
| 2 |
* |
|
| 3 |
, (plantconcept_plantnames("PLANTCONCEPT_ID")).*
|
|
| 4 |
FROM "plantConcept" |
|
| inputs/CVS/plantConcept_/header.csv | ||
|---|---|---|
| 1 |
PLANTCONCEPT_ID,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma |
|
| inputs/CVS/cvs.~.clean_up.sql | ||
|---|---|---|
| 1 |
-- Prevent "column name specified more than once" errors when tables are joined |
|
| 2 |
ALTER TABLE "soilObs" RENAME "dba_src_ID" TO "soilObs_dba_src_ID"; |
|
| 3 |
ALTER TABLE "taxonObservation" RENAME "reference_ID" TO "taxonObservation_reference_ID"; |
|
| 4 |
ALTER TABLE "taxonObservation" RENAME "accessionCode" TO "taxonObservation_accessionCode"; |
|
| 5 |
ALTER TABLE "taxonObservation" RENAME "dba_src_ID" TO "taxonObservation_dba_src_ID"; |
|
| 6 |
ALTER TABLE "taxonObservation" RENAME "entry_sppID" TO "taxonObservation_entry_sppID"; |
|
| 7 |
ALTER TABLE "taxonInterpretation" RENAME "PARTY_ID" TO "taxonInterpretation_PARTY_ID"; |
|
| 8 |
ALTER TABLE "taxonInterpretation" RENAME "PLANTNAME_ID" TO "taxonInterpretation_PLANTNAME_ID"; |
|
| 9 |
ALTER TABLE "taxonInterpretation" RENAME "dba_src_ID" TO "taxonInterpretation_dba_src_ID"; |
|
| 10 |
ALTER TABLE "taxonInterpretation" RENAME "accessionCode" TO "taxonInterpretation_accessionCode"; |
|
| 11 |
ALTER TABLE "plantConcept" RENAME "reference_ID" TO "plantConcept_reference_ID"; |
|
| 12 |
ALTER TABLE "plantConcept" RENAME "accessionCode" TO "plantConcept_accessionCode"; |
|
| 13 |
ALTER TABLE "plantConcept" RENAME "dba_src_ID" TO "plantConcept_dba_src_ID"; |
|
| 14 |
ALTER TABLE "plantConcept" RENAME "entry_sppID" TO "plantConcept_entry_sppID"; |
|
| inputs/CVS/observation_/create.sql | ||
|---|---|---|
| 1 |
SELECT * |
|
| 2 |
FROM observation |
|
| 3 |
LEFT JOIN "soilObs" USING ("OBSERVATION_ID")
|
|
| inputs/CVS/observation_/header.csv | ||
|---|---|---|
| 1 |
OBSERVATION_ID,PREVIOUSOBS_ID,PLOT_ID,PROJECT_ID,authorObsCode,obsStartDate,obsEndDate,dateAccuracy,dateEntered,COVERMETHOD_ID,coverDispersion,autoTaxonCover,STRATUMMETHOD_ID,methodNarrative,taxonObservationArea,stemSizeLimit,stemObservationArea,stemSampleMethod,originalData,effortLevel,plotValidationLevel,floristicQuality,bryophyteQuality,lichenQuality,observationNarrative,landscapeNarrative,homogeneity,phenologicAspect,representativeness,standMaturity,successionalStatus,basalArea,hydrologicRegime,soilMoistureRegime,soilDrainage,waterSalinity,waterDepth,shoreDistance,soilDepth,organicDepth,SOILTAXON_ID,soilTaxonSrc,soilTaxonComplex,soilMapUnit,percentBedRock,percentRockGravel,percentWood,percentLitter,percentBareSoil,percentWater,percentOther,nameOther,treeHt,shrubHt,fieldHt,nonvascularHt,submergedHt,treeCover,shrubCover,fieldCover,nonvascularCover,floatingCover,submergedCover,dominantStratum,growthform1Type,growthform2Type,growthform3Type,growthform1Cover,growthform2Cover,growthform3Cover,totalCover,accessionCode,notesPublic,notesMgt,revisions,cust_cvs_CowardinSystem,cust_cvs_mcnab_LFI_asp,cust_cvs_mcnab_LFI_45,cust_cvs_mcnab_LFI_90,cust_cvs_mcnab_LFI_135,cust_cvs_mcnab_LFI_180,cust_cvs_mcnab_LFI_225,cust_cvs_mcnab_LFI_270,cust_cvs_mcnab_LFI_315,cust_cvs_mcnab_TSI_asp,cust_cvs_mcnab_TSI_45,cust_cvs_mcnab_TSI_90,cust_cvs_mcnab_TSI_135,cust_cvs_mcnab_TSI_180,cust_cvs_mcnab_TSI_225,cust_cvs_mcnab_TSI_270,cust_cvs_mcnab_TSI_315,cust_cvs_mcnab_LFI,cust_cvs_mcnab_TSI,cust_cvs_LeafType,cust_cvs_LeafPhenology,cust_cvs_CanopyHeight,cust_cvs_compassType,cust_cvs_LocationSource,cust_cvs_GPSLocationX,cust_cvs_GPSLocationY,cust_cvs_Ownership,cust_cvs_taxaRichness,cust_cvs_lengthSoilProbe,cust_cvs_percentHistosol,cust_cvs_percentBedrock,cust_cvs_percentBoulder,cust_cvs_percentGravelCobble,cust_cvs_percentMineralSoil,cust_cvs_percentCWD,cust_cvs_percentFWD,cust_cvs_percentDuff,cust_cvs_percentLitter,cust_cvs_percentNonVasc,cust_cvs_percentWater,cust_cvs_percentOther,cust_cvs_percentOtherName,cust_cvs_samplingLevel,cust_cvs_postDsgPoly,cust_cvs_stemsSampled,cust_cvs_stemSamplingNarrative,cust_eep_plotLastPlantedDate,cust_eep_plotNotSampled,cust_eep_plotNotSampledReason,entry_ares_herbs,entry_ares_trees,entry_currentLandUse,entry_depth,entry_elevationUnits,entry_formerLandUse,entry_identificationNarrative,entry_IntensiveModuleList,entry_moduleSize_Overall,entry_moduleSizeX,entry_moduleSizeY,entry_photosTaken,entry_physClass,entry_plot_X,entry_plot_Y,entry_soilModulesSampled,entry_subsequentObsNum,entry_taxonomicAuthority_ID,entry_taxonomicAuthorityDate,entry_team,entry_plot,entry_numberOfModules,errors,dba_src_ID,dba_notes,numberOfTaxa,SOILOBS_ID,soilHorizon,soilDepthTop,soilDepthBottom,soilColor,soilOrganic,soilTexture,soilSand,soilSilt,soilClay,soilCoarse,soilPH,exchangeCapacity,baseSaturation,soilDescription,cust_cvs_collectionName,cust_cvs_Lab,cust_cvs_N,cust_cvs_S,cust_cvs_P,cust_cvs_Ca_ppm,cust_cvs_Mg_ppm,cust_cvs_K_ppm,cust_cvs_Na_ppm,cust_cvs_percent_Ca,cust_cvs_percent_Mg,cust_cvs_percent_K,cust_cvs_percent_Na,cust_cvs_percent_Othr,cust_cvs_percent_H,cust_cvs_B_ppm,cust_cvs_Fe_ppm,cust_cvs_Mn_ppm,cust_cvs_Cu_ppm,cust_cvs_Zn_ppm,cust_cvs_Al_ppm,cust_cvs_Density,cust_cvs_Ca_over_Mg_ppm,soilObs_dba_src_ID |
|
| inputs/CVS/observation_/map.csv | ||
|---|---|---|
| 1 |
CVS,VegCore,Filter,Comments |
|
| 2 |
OBSERVATION_ID,eventID,, |
|
| 3 |
PREVIOUSOBS_ID,*PREVIOUSOBS_ID,, |
|
| 4 |
PLOT_ID,locationID,, |
|
| 5 |
PROJECT_ID,projectID,, |
|
| 6 |
authorObsCode,fieldNumber,, |
|
| 7 |
obsStartDate,startDate,, |
|
| 8 |
obsEndDate,endDate,, |
|
| 9 |
dateAccuracy,*dateAccuracy,, |
|
| 10 |
dateEntered,*dateEntered,, |
|
| 11 |
COVERMETHOD_ID,*COVERMETHOD_ID,, |
|
| 12 |
coverDispersion,*coverDispersion,, |
|
| 13 |
autoTaxonCover,*autoTaxonCover,, |
|
| 14 |
STRATUMMETHOD_ID,*STRATUMMETHOD_ID,, |
|
| 15 |
methodNarrative,samplingProtocol,, |
|
| 16 |
taxonObservationArea,*taxonObservationArea,, |
|
| 17 |
stemSizeLimit,*stemSizeLimit,, |
|
| 18 |
stemObservationArea,*stemObservationArea,, |
|
| 19 |
stemSampleMethod,*stemSampleMethod,, |
|
| 20 |
originalData,*originalData,, |
|
| 21 |
effortLevel,*effortLevel,, |
|
| 22 |
plotValidationLevel,*plotValidationLevel,, |
|
| 23 |
floristicQuality,*floristicQuality,, |
|
| 24 |
bryophyteQuality,*bryophyteQuality,, |
|
| 25 |
lichenQuality,*lichenQuality,, |
|
| 26 |
observationNarrative,*observationNarrative,, |
|
| 27 |
landscapeNarrative,*landscapeNarrative,, |
|
| 28 |
homogeneity,*homogeneity,, |
|
| 29 |
phenologicAspect,*phenologicAspect,, |
|
| 30 |
representativeness,*representativeness,, |
|
| 31 |
standMaturity,*standMaturity,, |
|
| 32 |
successionalStatus,*successionalStatus,, |
|
| 33 |
basalArea,*basalArea,, |
|
| 34 |
hydrologicRegime,*hydrologicRegime,, |
|
| 35 |
soilMoistureRegime,*soilMoistureRegime,, |
|
| 36 |
soilDrainage,*soilDrainage,, |
|
| 37 |
waterSalinity,*waterSalinity,, |
|
| 38 |
waterDepth,*waterDepth,, |
|
| 39 |
shoreDistance,*shoreDistance,, |
|
| 40 |
soilDepth,*soilDepth,, |
|
| 41 |
organicDepth,*organicDepth,, |
|
| 42 |
SOILTAXON_ID,*SOILTAXON_ID,, |
|
| 43 |
soilTaxonSrc,*soilTaxonSrc,, |
|
| 44 |
soilTaxonComplex,*soilTaxonComplex,, |
|
| 45 |
soilMapUnit,*soilMapUnit,, |
|
| 46 |
percentBedRock,*percentBedRock,, |
|
| 47 |
percentRockGravel,*percentRockGravel,, |
|
| 48 |
percentWood,*percentWood,, |
|
| 49 |
percentLitter,*percentLitter,, |
|
| 50 |
percentBareSoil,*percentBareSoil,, |
|
| 51 |
percentWater,*percentWater,, |
|
| 52 |
percentOther,*percentOther,, |
|
| 53 |
nameOther,*nameOther,, |
|
| 54 |
treeHt,*treeHt,, |
|
| 55 |
shrubHt,*shrubHt,, |
|
| 56 |
fieldHt,*fieldHt,, |
|
| 57 |
nonvascularHt,*nonvascularHt,, |
|
| 58 |
submergedHt,*submergedHt,, |
|
| 59 |
treeCover,*treeCover,, |
|
| 60 |
shrubCover,*shrubCover,, |
|
| 61 |
fieldCover,*fieldCover,, |
|
| 62 |
nonvascularCover,*nonvascularCover,, |
|
| 63 |
floatingCover,*floatingCover,, |
|
| 64 |
submergedCover,*submergedCover,, |
|
| 65 |
dominantStratum,*dominantStratum,, |
|
| 66 |
growthform1Type,*growthform1Type,, |
|
| 67 |
growthform2Type,*growthform2Type,, |
|
| 68 |
growthform3Type,*growthform3Type,, |
|
| 69 |
growthform1Cover,*growthform1Cover,, |
|
| 70 |
growthform2Cover,*growthform2Cover,, |
|
| 71 |
growthform3Cover,*growthform3Cover,, |
|
| 72 |
totalCover,*totalCover,, |
|
| 73 |
accessionCode,*accessionCode,, |
|
| 74 |
notesPublic,*notesPublic,, |
|
| 75 |
notesMgt,*notesMgt,, |
|
| 76 |
revisions,*revisions,, |
|
| 77 |
cust_cvs_CowardinSystem,*cust_cvs_CowardinSystem,, |
|
| 78 |
cust_cvs_mcnab_LFI_asp,*cust_cvs_mcnab_LFI_asp,, |
|
| 79 |
cust_cvs_mcnab_LFI_45,*cust_cvs_mcnab_LFI_45,, |
|
| 80 |
cust_cvs_mcnab_LFI_90,*cust_cvs_mcnab_LFI_90,, |
|
| 81 |
cust_cvs_mcnab_LFI_135,*cust_cvs_mcnab_LFI_135,, |
|
| 82 |
cust_cvs_mcnab_LFI_180,*cust_cvs_mcnab_LFI_180,, |
|
| 83 |
cust_cvs_mcnab_LFI_225,*cust_cvs_mcnab_LFI_225,, |
|
| 84 |
cust_cvs_mcnab_LFI_270,*cust_cvs_mcnab_LFI_270,, |
|
| 85 |
cust_cvs_mcnab_LFI_315,*cust_cvs_mcnab_LFI_315,, |
|
| 86 |
cust_cvs_mcnab_TSI_asp,*cust_cvs_mcnab_TSI_asp,, |
|
| 87 |
cust_cvs_mcnab_TSI_45,*cust_cvs_mcnab_TSI_45,, |
|
| 88 |
cust_cvs_mcnab_TSI_90,*cust_cvs_mcnab_TSI_90,, |
|
| 89 |
cust_cvs_mcnab_TSI_135,*cust_cvs_mcnab_TSI_135,, |
|
| 90 |
cust_cvs_mcnab_TSI_180,*cust_cvs_mcnab_TSI_180,, |
|
| 91 |
cust_cvs_mcnab_TSI_225,*cust_cvs_mcnab_TSI_225,, |
|
| 92 |
cust_cvs_mcnab_TSI_270,*cust_cvs_mcnab_TSI_270,, |
|
| 93 |
cust_cvs_mcnab_TSI_315,*cust_cvs_mcnab_TSI_315,, |
|
| 94 |
cust_cvs_mcnab_LFI,*cust_cvs_mcnab_LFI,, |
|
| 95 |
cust_cvs_mcnab_TSI,*cust_cvs_mcnab_TSI,, |
|
| 96 |
cust_cvs_LeafType,*cust_cvs_LeafType,, |
|
| 97 |
cust_cvs_LeafPhenology,*cust_cvs_LeafPhenology,, |
|
| 98 |
cust_cvs_CanopyHeight,*cust_cvs_CanopyHeight,, |
|
| 99 |
cust_cvs_compassType,*cust_cvs_compassType,, |
|
| 100 |
cust_cvs_LocationSource,*cust_cvs_LocationSource,, |
|
| 101 |
cust_cvs_GPSLocationX,*cust_cvs_GPSLocationX,, |
|
| 102 |
cust_cvs_GPSLocationY,*cust_cvs_GPSLocationY,, |
|
| 103 |
cust_cvs_Ownership,*cust_cvs_Ownership,, |
|
| 104 |
cust_cvs_taxaRichness,*cust_cvs_taxaRichness,, |
|
| 105 |
cust_cvs_lengthSoilProbe,*cust_cvs_lengthSoilProbe,, |
|
| 106 |
cust_cvs_percentHistosol,*cust_cvs_percentHistosol,, |
|
| 107 |
cust_cvs_percentBedrock,*cust_cvs_percentBedrock,, |
|
| 108 |
cust_cvs_percentBoulder,*cust_cvs_percentBoulder,, |
|
| 109 |
cust_cvs_percentGravelCobble,*cust_cvs_percentGravelCobble,, |
|
| 110 |
cust_cvs_percentMineralSoil,*cust_cvs_percentMineralSoil,, |
|
| 111 |
cust_cvs_percentCWD,*cust_cvs_percentCWD,, |
|
| 112 |
cust_cvs_percentFWD,*cust_cvs_percentFWD,, |
|
| 113 |
cust_cvs_percentDuff,*cust_cvs_percentDuff,, |
|
| 114 |
cust_cvs_percentLitter,*cust_cvs_percentLitter,, |
|
| 115 |
cust_cvs_percentNonVasc,*cust_cvs_percentNonVasc,, |
|
| 116 |
cust_cvs_percentWater,*cust_cvs_percentWater,, |
|
| 117 |
cust_cvs_percentOther,*cust_cvs_percentOther,, |
|
| 118 |
cust_cvs_percentOtherName,*cust_cvs_percentOtherName,, |
|
| 119 |
cust_cvs_samplingLevel,*cust_cvs_samplingLevel,, |
|
| 120 |
cust_cvs_postDsgPoly,*cust_cvs_postDsgPoly,, |
|
| 121 |
cust_cvs_stemsSampled,*cust_cvs_stemsSampled,, |
|
| 122 |
cust_cvs_stemSamplingNarrative,*cust_cvs_stemSamplingNarrative,, |
|
| 123 |
cust_eep_plotLastPlantedDate,*cust_eep_plotLastPlantedDate,, |
|
| 124 |
cust_eep_plotNotSampled,*cust_eep_plotNotSampled,, |
|
| 125 |
cust_eep_plotNotSampledReason,*cust_eep_plotNotSampledReason,, |
|
| 126 |
entry_ares_herbs,*entry_ares_herbs,, |
|
| 127 |
entry_ares_trees,*entry_ares_trees,, |
|
| 128 |
entry_currentLandUse,*entry_currentLandUse,, |
|
| 129 |
entry_depth,*entry_depth,, |
|
| 130 |
entry_elevationUnits,*entry_elevationUnits,, |
|
| 131 |
entry_formerLandUse,*entry_formerLandUse,, |
|
| 132 |
entry_identificationNarrative,*entry_identificationNarrative,, |
|
| 133 |
entry_IntensiveModuleList,*entry_IntensiveModuleList,, |
|
| 134 |
entry_moduleSize_Overall,*entry_moduleSize_Overall,, |
|
| 135 |
entry_moduleSizeX,*entry_moduleSizeX,, |
|
| 136 |
entry_moduleSizeY,*entry_moduleSizeY,, |
|
| 137 |
entry_photosTaken,*entry_photosTaken,, |
|
| 138 |
entry_physClass,*entry_physClass,, |
|
| 139 |
entry_plot_X,*entry_plot_X,, |
|
| 140 |
entry_plot_Y,*entry_plot_Y,, |
|
| 141 |
entry_soilModulesSampled,*entry_soilModulesSampled,, |
|
| 142 |
entry_subsequentObsNum,*entry_subsequentObsNum,, |
|
| 143 |
entry_taxonomicAuthority_ID,*entry_taxonomicAuthority_ID,, |
|
| 144 |
entry_taxonomicAuthorityDate,*entry_taxonomicAuthorityDate,, |
|
| 145 |
entry_team,*entry_team,, |
|
| 146 |
entry_plot,*entry_plot,, |
|
| 147 |
entry_numberOfModules,*entry_numberOfModules,, |
|
| 148 |
errors,*errors,, |
|
| 149 |
dba_src_ID,*dba_src_ID,, |
|
| 150 |
dba_notes,*dba_notes,, |
|
| 151 |
numberOfTaxa,*numberOfTaxa,, |
|
| 152 |
SOILOBS_ID,*SOILOBS_ID,, |
|
| 153 |
soilHorizon,*soilHorizon,, |
|
| 154 |
soilDepthTop,*soilDepthTop,, |
|
| 155 |
soilDepthBottom,*soilDepthBottom,, |
|
| 156 |
soilColor,*soilColor,, |
|
| 157 |
soilOrganic,organic_percent,, |
|
| 158 |
soilTexture,texture,, |
|
| 159 |
soilSand,sand_percent,, |
|
| 160 |
soilSilt,silt_percent,, |
|
| 161 |
soilClay,clay_percent,, |
|
| 162 |
soilCoarse,*soilCoarse,, |
|
| 163 |
soilPH,ph,, |
|
| 164 |
exchangeCapacity,cationExchangeCapacity_cmol_kg,, |
|
| 165 |
baseSaturation,"?baseSaturation_percent, baseSaturation_fraction",, |
|
| 166 |
soilDescription,*soilDescription,, |
|
| 167 |
cust_cvs_collectionName,*cust_cvs_collectionName,, |
|
| 168 |
cust_cvs_Lab,*cust_cvs_Lab,, |
|
| 169 |
cust_cvs_N,*cust_cvs_N,, |
|
| 170 |
cust_cvs_S,*cust_cvs_S,, |
|
| 171 |
cust_cvs_P,*cust_cvs_P,, |
|
| 172 |
cust_cvs_Ca_ppm,*cust_cvs_Ca_ppm,, |
|
| 173 |
cust_cvs_Mg_ppm,*cust_cvs_Mg_ppm,, |
|
| 174 |
cust_cvs_K_ppm,*cust_cvs_K_ppm,, |
|
| 175 |
cust_cvs_Na_ppm,*cust_cvs_Na_ppm,, |
|
| 176 |
cust_cvs_percent_Ca,*cust_cvs_percent_Ca,, |
|
| 177 |
cust_cvs_percent_Mg,*cust_cvs_percent_Mg,, |
|
| 178 |
cust_cvs_percent_K,*cust_cvs_percent_K,, |
|
| 179 |
cust_cvs_percent_Na,*cust_cvs_percent_Na,, |
|
| 180 |
cust_cvs_percent_Othr,*cust_cvs_percent_Othr,, |
|
| 181 |
cust_cvs_percent_H,*cust_cvs_percent_H,, |
|
| 182 |
cust_cvs_B_ppm,*cust_cvs_B_ppm,, |
|
| 183 |
cust_cvs_Fe_ppm,*cust_cvs_Fe_ppm,, |
|
| 184 |
cust_cvs_Mn_ppm,*cust_cvs_Mn_ppm,, |
|
| 185 |
cust_cvs_Cu_ppm,*cust_cvs_Cu_ppm,, |
|
| 186 |
cust_cvs_Zn_ppm,*cust_cvs_Zn_ppm,, |
|
| 187 |
cust_cvs_Al_ppm,*cust_cvs_Al_ppm,, |
|
| 188 |
cust_cvs_Density,*cust_cvs_Density,, |
|
| 189 |
cust_cvs_Ca_over_Mg_ppm,*cust_cvs_Ca_over_Mg_ppm,, |
|
| 190 |
soilObs_dba_src_ID,*soilObs_dba_src_ID,, |
|
| inputs/CVS/observation_/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>CVS</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<sourceaccessioncode>$PLOT_ID</sourceaccessioncode> |
|
| 11 |
<locationevent> |
|
| 12 |
<method_id><method><name>$methodNarrative</name></method></method_id> |
|
| 13 |
<project_id><project><sourceaccessioncode>$PROJECT_ID</sourceaccessioncode></project></project_id> |
|
| 14 |
<authoreventcode>$authorObsCode</authoreventcode> |
|
| 15 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
|
| 16 |
<obsenddate>$obsEndDate</obsenddate> |
|
| 17 |
<obsstartdate>$obsStartDate</obsstartdate> |
|
| 18 |
<soilsample> |
|
| 19 |
<cationexchangecapacity_cmol_kg>$exchangeCapacity</cationexchangecapacity_cmol_kg> |
|
| 20 |
<clay_fraction><_percent_to_fraction><value>$soilClay</value></_percent_to_fraction></clay_fraction> |
|
| 21 |
<organic_fraction><_percent_to_fraction><value>$soilOrganic</value></_percent_to_fraction></organic_fraction> |
|
| 22 |
<ph>$soilPH</ph> |
|
| 23 |
<sand_fraction><_percent_to_fraction><value>$soilSand</value></_percent_to_fraction></sand_fraction> |
|
| 24 |
<silt_fraction><_percent_to_fraction><value>$soilSilt</value></_percent_to_fraction></silt_fraction> |
|
| 25 |
<texture>$soilTexture</texture> |
|
| 26 |
</soilsample> |
|
| 27 |
</locationevent> |
|
| 28 |
</location> |
|
| 29 |
</path> |
|
| 30 |
</_simplifyPath> |
|
| 31 |
</path> |
|
| 32 |
</_setDefault> |
|
| 33 |
</VegBIEN> |
|
| 34 |
Inserted 9 new rows into database |
|
| inputs/CVS/observation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 3 |
authorObsCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 4 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else", |
|
| 5 |
PLOT_ID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
methodNarrative,/location/locationevent/*_id/method/name, |
|
| 7 |
PROJECT_ID,/location/locationevent/*_id/project/sourceaccessioncode, |
|
| 8 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 9 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 10 |
OBSERVATION_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 11 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 12 |
obsEndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 13 |
obsStartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 14 |
PLOT_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 15 |
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authorlocationcode", |
|
| 16 |
obsEndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/1", |
|
| 17 |
obsStartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
|
Also available in: Unified diff
inputs/CVS/: Refreshed data with new export from Bob