Revision 6746
Added by Aaron Marcuse-Kubitza about 12 years ago
inputs/VegBank/taxonimportance/map.csv | ||
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1 |
VegBank,VegCore,Filter,Comments |
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2 |
taxonimportance_id,aggregateOccurrenceID,, |
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3 |
taxonobservation_id,taxonOccurrenceID,,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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4 |
|
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5 |
[1] The following query returns rows: |
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6 |
----- |
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SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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FROM ""VegBank"".taxonimportance |
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GROUP BY taxonobservation_id |
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HAVING count(distinct taxonimportance_id) > 1 |
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-----" |
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stratum_id,*stratum_id,, |
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cover,coverPercent,, |
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basalarea,*basalarea,, |
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biomass,*biomass,, |
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inferencearea,*inferencearea,, |
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17 |
stratumbase,*stratumbase,, |
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stratumheight,*stratumheight,, |
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19 |
emb_taxonimportance,*emb_taxonimportance,, |
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20 |
covercode,*covercode,, |
inputs/VegBank/taxonimportance/test.xml.ref | ||
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1 |
Put template: |
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2 |
<VegBIEN> |
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3 |
<_setDefault id="-1"> |
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<source_id><source><shortname>VegBank</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<taxonoccurrence> |
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<aggregateoccurrence> |
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<cover_fraction><_percent_to_fraction><value>$cover</value></_percent_to_fraction></cover_fraction> |
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<sourceaccessioncode>$taxonimportance_id</sourceaccessioncode> |
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</aggregateoccurrence> |
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<sourceaccessioncode>$taxonobservation_id</sourceaccessioncode> |
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</taxonoccurrence> |
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</locationevent> |
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</location> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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25 |
Inserted 4 new rows into database |
inputs/VegBank/taxonimportance/VegBIEN.csv | ||
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1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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taxonobservation_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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3 |
|
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[1] The following query returns rows: |
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----- |
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SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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FROM ""VegBank"".taxonimportance |
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GROUP BY taxonobservation_id |
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HAVING count(distinct taxonimportance_id) > 1 |
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-----" |
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cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
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taxonimportance_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
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taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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|
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[1] The following query returns rows: |
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----- |
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SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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FROM ""VegBank"".taxonimportance |
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GROUP BY taxonobservation_id |
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HAVING count(distinct taxonimportance_id) > 1 |
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-----" |
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taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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23 |
|
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[1] The following query returns rows: |
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----- |
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SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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FROM ""VegBank"".taxonimportance |
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GROUP BY taxonobservation_id |
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HAVING count(distinct taxonimportance_id) > 1 |
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-----" |
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taxonimportance_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
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basalarea,,** No join mapping for *basalarea ** |
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33 |
biomass,,** No join mapping for *biomass ** |
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34 |
covercode,,** No join mapping for *covercode ** |
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35 |
emb_taxonimportance,,** No join mapping for *emb_taxonimportance ** |
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36 |
inferencearea,,** No join mapping for *inferencearea ** |
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stratum_id,,** No join mapping for *stratum_id ** |
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stratumbase,,** No join mapping for *stratumbase ** |
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stratumheight,,** No join mapping for *stratumheight ** |
inputs/VegBank/taxonimportance/new_terms.csv | ||
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1 |
taxonimportance_id,aggregateOccurrenceID,, |
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taxonobservation_id,taxonOccurrenceID,,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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3 |
|
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4 |
[1] The following query returns rows: |
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----- |
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SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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FROM ""VegBank"".taxonimportance |
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GROUP BY taxonobservation_id |
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HAVING count(distinct taxonimportance_id) > 1 |
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-----" |
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cover,coverPercent,, |
inputs/VegBank/taxonimportance/unmapped_terms.csv | ||
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1 |
*stratum_id |
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2 |
*basalarea |
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*biomass |
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*inferencearea |
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*stratumbase |
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*stratumheight |
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*emb_taxonimportance |
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*covercode |
inputs/VegBank/taxonimportance/header.csv | ||
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1 |
taxonimportance_id,taxonobservation_id,stratum_id,cover,basalarea,biomass,inferencearea,stratumbase,stratumheight,emb_taxonimportance,covercode |
inputs/VegBank/stemcount/header.csv | ||
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1 |
stemcount_id,taxonimportance_id,stemdiameter,stemdiameteraccuracy,stemheight,stemheightaccuracy,stemcount,stemtaxonarea,emb_stemcount |
inputs/VegBank/stemcount/map.csv | ||
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1 |
VegBank,VegCore,Filter,Comments |
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2 |
stemcount_id,individualID,, |
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3 |
taxonimportance_id,aggregateOccurrenceID,, |
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4 |
stemdiameter,diameterBreastHeight_cm,,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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stemdiameteraccuracy,*stemdiameteraccuracy,, |
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stemheight,height_m,,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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stemheightaccuracy,*stemheightaccuracy,, |
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stemcount,stemCount,, |
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stemtaxonarea,*stemtaxonarea,, |
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emb_stemcount,*emb_stemcount,, |
inputs/VegBank/stemcount/test.xml.ref | ||
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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>VegBank</shortname></source></source_id> |
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5 |
<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<taxonoccurrence> |
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<aggregateoccurrence> |
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<plantobservation> |
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<sourceaccessioncode>$stemcount_id</sourceaccessioncode> |
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<stemcount>$stemcount</stemcount> |
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<stemobservation> |
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<diameterbreastheight_m><_cm_to_m><value>$stemdiameter</value></_cm_to_m></diameterbreastheight_m> |
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<height_m>$stemheight</height_m> |
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</stemobservation> |
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</plantobservation> |
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<sourceaccessioncode>$taxonimportance_id</sourceaccessioncode> |
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</aggregateoccurrence> |
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</taxonoccurrence> |
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</locationevent> |
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</location> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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31 |
Inserted 4 new rows into database |
inputs/VegBank/stemcount/VegBIEN.csv | ||
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1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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2 |
stemcount_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
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stemcount_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
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stemcount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
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stemdiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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stemheight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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taxonimportance_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
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stemcount_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
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taxonimportance_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
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stemcount_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
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emb_stemcount,,** No join mapping for *emb_stemcount ** |
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stemdiameteraccuracy,,** No join mapping for *stemdiameteraccuracy ** |
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stemheightaccuracy,,** No join mapping for *stemheightaccuracy ** |
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stemtaxonarea,,** No join mapping for *stemtaxonarea ** |
inputs/VegBank/stemcount/new_terms.csv | ||
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1 |
stemcount_id,individualID,, |
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2 |
taxonimportance_id,aggregateOccurrenceID,, |
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3 |
stemdiameter,diameterBreastHeight_cm,,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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4 |
stemheight,height_m,,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
inputs/VegBank/stemcount/unmapped_terms.csv | ||
---|---|---|
1 |
*stemdiameteraccuracy |
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*stemheightaccuracy |
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*stemtaxonarea |
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4 |
*emb_stemcount |
inputs/VegBank/stemcount_/create.sql | ||
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1 |
SELECT * |
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FROM taxonimportance |
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LEFT JOIN stemcount USING (taxonimportance_id) |
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; |
inputs/VegBank/stemcount_/header.csv | ||
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1 |
taxonimportance_id,taxonobservation_id,stratum_id,cover,basalarea,biomass,inferencearea,stratumbase,stratumheight,emb_taxonimportance,covercode,stemcount_id,stemdiameter,stemdiameteraccuracy,stemheight,stemheightaccuracy,stemcount,stemtaxonarea,emb_stemcount |
inputs/VegBank/stemcount_/map.csv | ||
---|---|---|
1 |
VegBank,VegCore,Filter,Comments |
|
2 |
taxonimportance_id,OMIT,,Omitted because stemcount_id is more specific |
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3 |
taxonobservation_id,taxonOccurrenceID,,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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4 |
|
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5 |
[1] The following query returns rows: |
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6 |
----- |
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SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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FROM ""VegBank"".taxonimportance |
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GROUP BY taxonobservation_id |
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HAVING count(distinct taxonimportance_id) > 1 |
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11 |
-----" |
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12 |
stratum_id,*stratum_id,, |
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13 |
cover,coverPercent,, |
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14 |
basalarea,*basalarea,, |
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15 |
biomass,*biomass,, |
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16 |
inferencearea,*inferencearea,, |
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17 |
stratumbase,*stratumbase,, |
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18 |
stratumheight,*stratumheight,, |
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19 |
emb_taxonimportance,*emb_taxonimportance,, |
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20 |
covercode,*covercode,, |
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21 |
stemcount_id,aggregateOccurrenceID,, |
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22 |
stemdiameter,diameterBreastHeight_cm,,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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stemdiameteraccuracy,*stemdiameteraccuracy,, |
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24 |
stemheight,height_m,,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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25 |
stemheightaccuracy,*stemheightaccuracy,, |
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stemcount,individualCount,, |
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stemtaxonarea,*stemtaxonarea,, |
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emb_stemcount,*emb_stemcount,, |
inputs/VegBank/stemcount_/VegBIEN.csv | ||
---|---|---|
1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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2 |
taxonobservation_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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3 |
|
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4 |
[1] The following query returns rows: |
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5 |
----- |
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6 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
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7 |
FROM ""VegBank"".taxonimportance |
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8 |
GROUP BY taxonobservation_id |
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9 |
HAVING count(distinct taxonimportance_id) > 1 |
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10 |
-----" |
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11 |
stemcount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
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12 |
cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
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13 |
stemdiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
|
14 |
stemheight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
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15 |
stemcount_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
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16 |
taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
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17 |
|
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18 |
[1] The following query returns rows: |
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19 |
----- |
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20 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
21 |
FROM ""VegBank"".taxonimportance |
|
22 |
GROUP BY taxonobservation_id |
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23 |
HAVING count(distinct taxonimportance_id) > 1 |
|
24 |
-----" |
|
25 |
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
26 |
|
|
27 |
[1] The following query returns rows: |
|
28 |
----- |
|
29 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
30 |
FROM ""VegBank"".taxonimportance |
|
31 |
GROUP BY taxonobservation_id |
|
32 |
HAVING count(distinct taxonimportance_id) > 1 |
|
33 |
-----" |
|
34 |
stemcount_id,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
|
35 |
basalarea,,** No join mapping for *basalarea ** |
|
36 |
biomass,,** No join mapping for *biomass ** |
|
37 |
covercode,,** No join mapping for *covercode ** |
|
38 |
emb_stemcount,,** No join mapping for *emb_stemcount ** |
|
39 |
emb_taxonimportance,,** No join mapping for *emb_taxonimportance ** |
|
40 |
inferencearea,,** No join mapping for *inferencearea ** |
|
41 |
stemdiameteraccuracy,,** No join mapping for *stemdiameteraccuracy ** |
|
42 |
stemheightaccuracy,,** No join mapping for *stemheightaccuracy ** |
|
43 |
stemtaxonarea,,** No join mapping for *stemtaxonarea ** |
|
44 |
stratum_id,,** No join mapping for *stratum_id ** |
|
45 |
stratumbase,,** No join mapping for *stratumbase ** |
|
46 |
stratumheight,,** No join mapping for *stratumheight ** |
|
47 |
taxonimportance_id,,** No non-empty join mapping for OMIT ** Omitted because stemcount_id is more specific |
inputs/VegBank/stemcount_/test.xml.ref | ||
---|---|---|
1 |
Put template: |
|
2 |
<VegBIEN> |
|
3 |
<_setDefault id="-1"> |
|
4 |
<source_id><source><shortname>VegBank</shortname></source></source_id> |
|
5 |
<path> |
|
6 |
<_simplifyPath> |
|
7 |
<next>parent_id</next> |
|
8 |
<path> |
|
9 |
<location> |
|
10 |
<locationevent> |
|
11 |
<taxonoccurrence> |
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12 |
<aggregateoccurrence> |
|
13 |
<count>$stemcount</count> |
|
14 |
<cover_fraction><_percent_to_fraction><value>$cover</value></_percent_to_fraction></cover_fraction> |
|
15 |
<plantobservation> |
|
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>$stemcount_id</sourceaccessioncode> |
|
22 |
</aggregateoccurrence> |
|
23 |
<sourceaccessioncode>$taxonobservation_id</sourceaccessioncode> |
|
24 |
</taxonoccurrence> |
|
25 |
</locationevent> |
|
26 |
</location> |
|
27 |
</path> |
|
28 |
</_simplifyPath> |
|
29 |
</path> |
|
30 |
</_setDefault> |
|
31 |
</VegBIEN> |
|
32 |
Inserted 8 new rows into database |
inputs/VegBank/stemcount_/new_terms.csv | ||
---|---|---|
1 |
taxonimportance_id,OMIT,,Omitted because stemcount_id is more specific |
|
2 |
taxonobservation_id,taxonOccurrenceID,,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
3 |
|
|
4 |
[1] The following query returns rows: |
|
5 |
----- |
|
6 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
7 |
FROM ""VegBank"".taxonimportance |
|
8 |
GROUP BY taxonobservation_id |
|
9 |
HAVING count(distinct taxonimportance_id) > 1 |
|
10 |
-----" |
|
11 |
cover,coverPercent,, |
|
12 |
stemcount_id,aggregateOccurrenceID,, |
|
13 |
stemdiameter,diameterBreastHeight_cm,,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
|
14 |
stemheight,height_m,,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
inputs/VegBank/stemcount_/unmapped_terms.csv | ||
---|---|---|
1 |
*stratum_id |
|
2 |
*basalarea |
|
3 |
*biomass |
|
4 |
*inferencearea |
|
5 |
*stratumbase |
|
6 |
*stratumheight |
|
7 |
*emb_taxonimportance |
|
8 |
*covercode |
|
9 |
*stemdiameteraccuracy |
|
10 |
*stemheightaccuracy |
|
11 |
*stemtaxonarea |
|
12 |
*emb_stemcount |
inputs/VegBank/import_order.txt | ||
---|---|---|
2 | 2 |
plot_ |
3 | 3 |
observation_ |
4 | 4 |
taxonobservation_ |
5 |
taxonimportance |
|
6 |
stemcount |
|
5 |
stemcount_ |
|
7 | 6 |
stemlocation |
Also available in: Unified diff
inputs/VegBank/: Joined together taxonimportance and stemcount tables to create stemcount_, because stemcount actually stores stem abundance by size, rather than grouping stems by organism (http://vegbankdev.nceas.ucsb.edu/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename)