Revision 5756
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/bien_web/observation/map.csv | ||
|---|---|---|
| 1 |
bien_web,VegCore,Filter,Comments |
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| 2 |
dataSourceName,institutionCode,, |
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| 3 |
family,family,, |
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| 4 |
genus,genus,, |
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| 5 |
species,specificEpithet,, |
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| 6 |
taxon,scientificName,, |
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| 7 |
taxonAuthor,scientificNameAuthorship,, |
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| 8 |
taxonMorphospecies,scientificNameWithMorphospecies,, |
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| 9 |
country,country,, |
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| 10 |
stateProvince,stateProvince,, |
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| 11 |
countyParish,county,, |
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| 12 |
collector,recordedBy,, |
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| 13 |
collectionNumber,recordNumber,, |
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| 14 |
identifiedBy,identifiedBy,, |
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| 15 |
observationDate,dateCollected,, |
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| 16 |
plotCode,plotName,, |
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| 17 |
plotAreaHa,plotArea_ha,, |
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| 18 |
plotMethod,samplingProtocol,, |
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| 19 |
latitude,decimalLatitude,, |
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| 20 |
longitude,decimalLongitude,, |
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| 21 |
elevation_m,elevationInMeters,, |
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| 22 |
isCultivated,cultivated,, |
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| 23 |
isCultivatedReason,cultivatedBasis,, |
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pctCover,coverPercent,, |
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| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 1 |
bien_web,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
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| 2 |
plotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
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| 3 |
dataSourceName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1", |
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| 4 |
plotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
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| 5 |
plotAreaHa,/location/area_m2/_ha_to_m2/value, |
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| 6 |
elevation_m,/location/elevation_m/_alt/1, |
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| 7 |
latitude,"/location/locationcoords/latitude_deg/_nullIf:[null=0,type=float]/value", |
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| 8 |
longitude,"/location/locationcoords/longitude_deg/_nullIf:[null=0,type=float]/value", |
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| 9 |
plotMethod,/location/locationevent/*_id/method/name, |
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plotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode", |
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| 11 |
observationDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1/_*/date, |
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| 12 |
pctCover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
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| 13 |
collectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
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| 14 |
dataSourceName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
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| 15 |
plotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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| 16 |
collectionNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
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| 17 |
taxon,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
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isCultivated,/location/locationevent/taxonoccurrence/iscultivated/_alt/1, |
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| 19 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
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| 20 |
taxon,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_alt/1", |
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| 21 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
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| 22 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
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| 23 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1", |
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| 24 |
taxonAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_alt/2/_join_words/2", |
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| 25 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creator_id/_simplifyPath:[next=creator_id]/path/party/fullname/_alt/2, |
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| 26 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if has verbatim name""]/then/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=NCBI]/taxonomicname", |
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| 28 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
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| 29 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if has verbatim name""]/then/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=NCBI]/taxonomicname", |
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| 30 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
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| 31 |
taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/1, |
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| 32 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1, |
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| 33 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2, |
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| 34 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
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| 35 |
taxonAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_alt/2/_join_words/2, |
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| 36 |
taxonAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
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| 37 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
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| 38 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
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| 39 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/species, |
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| 40 |
taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
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| 41 |
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
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| 42 |
country,/location/locationplace/*_id/placepath/country, |
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| 43 |
countyParish,/location/locationplace/*_id/placepath/county, |
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| 44 |
stateProvince,/location/locationplace/*_id/placepath/stateprovince, |
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| 45 |
isCultivatedReason,,** No join mapping for cultivatedBasis ** |
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| 46 |
taxonMorphospecies,,** No join mapping for scientificNameWithMorphospecies ** |
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| inputs/bien_web/observation/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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<VegBIEN> |
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<_simplifyPath id="-1"> |
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| 4 |
<next>parent_id</next> |
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<path> |
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<location> |
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<authorlocationcode>$plotCode</authorlocationcode> |
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| 8 |
<area_m2><_ha_to_m2><value>$plotAreaHa</value></_ha_to_m2></area_m2> |
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| 9 |
<elevation_m>$elevation_m</elevation_m> |
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| 10 |
<locationcoords> |
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| 11 |
<latitude_deg> |
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<_nullIf> |
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<null>0</null> |
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<type>float</type> |
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<value>$latitude</value> |
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</_nullIf> |
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</latitude_deg> |
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| 18 |
<longitude_deg> |
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<_nullIf> |
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<null>0</null> |
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<type>float</type> |
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<value>$longitude</value> |
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</_nullIf> |
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</longitude_deg> |
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| 25 |
</locationcoords> |
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| 26 |
<locationevent> |
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<method_id><method><name>$plotMethod</name></method></method_id> |
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<taxonoccurrence> |
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<aggregateoccurrence> |
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<collectiondate><_date><date>$observationDate</date></_date></collectiondate> |
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<cover_fraction><_percent_to_fraction><value>$pctCover</value></_percent_to_fraction></cover_fraction> |
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| 32 |
<plantobservation> |
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<collectionnumber>$collectionNumber</collectionnumber> |
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<specimenreplicate><institution_id><party><organizationname>$dataSourceName</organizationname></party></institution_id></specimenreplicate> |
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</plantobservation> |
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</aggregateoccurrence> |
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<authortaxoncode>$collectionNumber</authortaxoncode> |
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<iscultivated>$isCultivated</iscultivated> |
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| 39 |
<taxondetermination> |
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<party_id><party><fullname>$identifiedBy</fullname></party></party_id> |
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| 41 |
<taxonverbatim_id> |
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<taxonverbatim> |
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| 43 |
<taxonlabel_id> |
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<taxonlabel> |
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<matched_label_id> |
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<taxonlabel> |
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<creator_id> |
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<party> |
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<creator_id>0</creator_id> |
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<organizationname>TNRS</organizationname> |
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</party> |
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</creator_id> |
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<taxonomicname> |
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<_alt> |
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<1>$taxon</1> |
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<2> |
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<_join_words> |
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<1> |
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<_join_words> |
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<1>$family</1> |
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<2>$genus</2> |
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<3>$species</3> |
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</_join_words> |
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</1> |
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<2>$taxonAuthor</2> |
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</_join_words> |
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</2> |
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</_alt> |
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</taxonomicname> |
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</taxonlabel> |
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</matched_label_id> |
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<creator_id> |
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<_simplifyPath> |
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<next>creator_id</next> |
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<path><party><fullname>$identifiedBy</fullname></party></path> |
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</_simplifyPath> |
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</creator_id> |
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<parent_id> |
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| 79 |
<taxonlabel> |
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| 80 |
<parent_id> |
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| 81 |
<taxonlabel> |
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| 82 |
<rank>cultivar</rank> |
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| 83 |
<parent_id> |
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| 84 |
<taxonlabel> |
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<rank>forma</rank> |
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| 86 |
<parent_id> |
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| 87 |
<taxonlabel> |
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| 88 |
<rank>variety</rank> |
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| 89 |
<parent_id> |
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| 90 |
<taxonlabel> |
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| 91 |
<rank>subspecies</rank> |
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| 92 |
<parent_id> |
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| 93 |
<taxonlabel> |
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| 94 |
<rank>species</rank> |
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<taxonepithet>$species</taxonepithet> |
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| 96 |
<parent_id> |
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| 97 |
<taxonlabel> |
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| 98 |
<rank>genus</rank> |
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| 99 |
<taxonepithet>$genus</taxonepithet> |
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| 100 |
<parent_id> |
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| 101 |
<taxonlabel> |
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| 102 |
<rank>family</rank> |
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| 103 |
<taxonepithet>$family</taxonepithet> |
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</taxonlabel> |
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</parent_id> |
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| 106 |
</taxonlabel> |
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| 107 |
</parent_id> |
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| 108 |
</taxonlabel> |
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| 109 |
</parent_id> |
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| 110 |
</taxonlabel> |
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| 111 |
</parent_id> |
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| 112 |
</taxonlabel> |
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| 113 |
</parent_id> |
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| 114 |
</taxonlabel> |
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| 115 |
</parent_id> |
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| 116 |
</taxonlabel> |
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| 117 |
</parent_id> |
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| 118 |
</taxonlabel> |
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| 119 |
</parent_id> |
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| 120 |
<taxonomicname> |
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| 121 |
<_alt> |
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| 122 |
<1>$taxon</1> |
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| 123 |
<2> |
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| 124 |
<_join_words> |
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| 125 |
<1> |
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| 126 |
<_join_words> |
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| 127 |
<1>$family</1> |
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| 128 |
<2>$genus</2> |
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| 129 |
<3>$species</3> |
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| 130 |
</_join_words> |
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| 131 |
</1> |
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| 132 |
<2>$taxonAuthor</2> |
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| 133 |
</_join_words> |
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</2> |
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| 135 |
</_alt> |
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| 136 |
</taxonomicname> |
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| 137 |
</taxonlabel> |
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| 138 |
</taxonlabel_id> |
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| 139 |
<author>$taxonAuthor</author> |
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| 140 |
<family>$family</family> |
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| 141 |
<genus>$genus</genus> |
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| 142 |
<species>$species</species> |
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| 143 |
<taxonomicname>$taxon</taxonomicname> |
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| 144 |
</taxonverbatim> |
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| 145 |
</taxonverbatim_id> |
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| 146 |
</taxondetermination> |
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| 147 |
<verbatimcollectorname>$collector</verbatimcollectorname> |
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| 148 |
</taxonoccurrence> |
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| 149 |
</locationevent> |
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| 150 |
<locationplace> |
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| 151 |
<placepath_id> |
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| 152 |
<placepath> |
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| 153 |
<country>$country</country> |
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| 154 |
<county>$countyParish</county> |
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| 155 |
<stateprovince>$stateProvince</stateprovince> |
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| 156 |
</placepath> |
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| 157 |
</placepath_id> |
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| 158 |
</locationplace> |
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| 159 |
</location> |
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| 160 |
</path> |
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| 161 |
</_simplifyPath> |
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| 162 |
</VegBIEN> |
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| 163 |
Inserted 1 new rows into database |
|
| inputs/bien_web/observation/new_terms.csv | ||
|---|---|---|
| 1 |
dataSourceName,institutionCode,, |
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| 2 |
taxon,scientificName,, |
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| 3 |
taxonAuthor,scientificNameAuthorship,, |
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| 4 |
taxonMorphospecies,scientificNameWithMorphospecies,, |
|
| 5 |
countyParish,county,, |
|
| 6 |
collectionNumber,recordNumber,, |
|
| 7 |
observationDate,dateCollected,, |
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| 8 |
plotCode,plotName,, |
|
| 9 |
plotMethod,samplingProtocol,, |
|
| 10 |
elevation_m,elevationInMeters,, |
|
| 11 |
isCultivated,cultivated,, |
|
| 12 |
isCultivatedReason,cultivatedBasis,, |
|
| 13 |
pctCover,coverPercent,, |
|
| inputs/bien_web/observation/unmapped_terms.csv | ||
|---|---|---|
| 1 |
scientificNameWithMorphospecies |
|
| 2 |
cultivatedBasis |
|
Also available in: Unified diff
Added inputs/bien_web/