Revision 6881
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/bien2_traits/TraitObservation/header.csv | ||
|---|---|---|
| 1 |
TraitObservationID,TaxonomyID,Family,Genus,SpecificEpithet,InfraspecificRank,InfraspecificEpithet,Taxon,AuthorOfScientificName,Habit,TraitName,TraitValue,Unit,Method,Region,Country,StateProvince,LowerPolitical,LocalityDescription,VerbatimLatitude,VerbatimLongitude,VerbatimElevation,Source,URLSource,SourceCitation,SourceID,VisitingDate,ReferenceID,Access,Project_PI,Project_PI_contact,Observation,Authorship,AuthorshipContact,TaxonomyID_index,Family_index,Taxon_index,TraitName_index,ReferenceID_index |
|
| inputs/bien2_traits/TraitObservation/map.csv | ||
|---|---|---|
| 1 |
bien2_traits,VegCore,Filter,Comments |
|
| 2 |
TraitObservationID,occurrenceID,, |
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| 3 |
TaxonomyID,UNUSED,,Always 0 |
|
| 4 |
Family,family,, |
|
| 5 |
Genus,genus,, |
|
| 6 |
SpecificEpithet,specificEpithet,, |
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| 7 |
InfraspecificRank,taxonRank,, |
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| 8 |
InfraspecificEpithet,infraspecificEpithet,, |
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| 9 |
Taxon,taxonName,, |
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| 10 |
AuthorOfScientificName,scientificNameAuthorship,, |
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| 11 |
Habit,growthForm,, |
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| 12 |
TraitName,measurementType,, |
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| 13 |
TraitValue,measurementValue,, |
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| 14 |
Unit,measurementUnit,, |
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| 15 |
Method,Method,, |
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| 16 |
Region,*Region,, |
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| 17 |
Country,country,, |
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| 18 |
StateProvince,stateProvince,, |
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| 19 |
LowerPolitical,*LowerPolitical,, |
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| 20 |
LocalityDescription,verbatimLocality,, |
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| 21 |
VerbatimLatitude,verbatimLatitude,, |
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| 22 |
VerbatimLongitude,verbatimLongitude,, |
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| 23 |
VerbatimElevation,verbatimElevation,, |
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| 24 |
Source,OMIT,,There isn't a mapping for this yet |
|
| 25 |
URLSource,*URLSource,, |
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| 26 |
SourceCitation,*SourceCitation,, |
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| 27 |
SourceID,*SourceID,, |
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| 28 |
VisitingDate,*VisitingDate,, |
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| 29 |
ReferenceID,*ReferenceID,, |
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| 30 |
Access,*Access,, |
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| 31 |
Project_PI,*Project_PI,, |
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| 32 |
Project_PI_contact,*Project_PI_contact,, |
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| 33 |
Observation,*Observation,, |
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| 34 |
Authorship,*Authorship,, |
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| 35 |
AuthorshipContact,*AuthorshipContact,, |
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| 36 |
TaxonomyID_index,OMIT,, |
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| 37 |
Family_index,OMIT,, |
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| 38 |
Taxon_index,OMIT,, |
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| 39 |
TraitName_index,OMIT,, |
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| 40 |
ReferenceID_index,OMIT,, |
|
| inputs/bien2_traits/TraitObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
bien2_traits,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
TraitObservationID,"/_if[@name=""if specimen""]/cond/_exists", |
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| 3 |
TraitObservationID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
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| 4 |
TraitObservationID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 5 |
VerbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
|
| 6 |
TraitObservationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 7 |
LocalityDescription,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2, |
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| 8 |
TraitObservationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 9 |
TraitObservationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
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| 10 |
Taxon,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
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| 11 |
Habit,/location/locationevent/taxonoccurrence/growthform, |
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| 12 |
TraitObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
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| 13 |
TraitObservationID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
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| 14 |
Taxon,"/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", |
|
| 15 |
Family,"/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/value", |
|
| 16 |
Taxon,"/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", |
|
| 17 |
Genus,"/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/2/_join_words/2", |
|
| 18 |
SpecificEpithet,"/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/2/_join_words/3/_join_words/1", |
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| 19 |
InfraspecificEpithet,"/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/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 20 |
InfraspecificRank,"/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/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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| 21 |
InfraspecificEpithet,"/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/2/_join_words/5/_join_words/2", |
|
| 22 |
AuthorOfScientificName,"/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/2", |
|
| 23 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
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| 24 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank", |
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| 25 |
SpecificEpithet,"/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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| 26 |
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 is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
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| 27 |
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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| 28 |
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 is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
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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]/taxonepithet", |
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| 30 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
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| 31 |
InfraspecificRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
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| 32 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 33 |
Taxon,/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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| 34 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value, |
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| 35 |
Taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
|
| 36 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2, |
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| 37 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
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| 38 |
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 39 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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| 40 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
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| 41 |
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
|
| 42 |
TraitName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/name, |
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| 43 |
Unit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/units, |
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| 44 |
TraitValue,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/trait/value, |
|
| 45 |
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 46 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 47 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 48 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 49 |
Taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 50 |
InfraspecificRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 51 |
LocalityDescription,/location/locationnarrative/_merge/2, |
|
| 52 |
VerbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude, |
|
| 53 |
VerbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude, |
|
| 54 |
Country,/location/locationplace/*_id/place/country, |
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| 55 |
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 56 |
StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 57 |
StateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 58 |
VerbatimElevation,/location/verbatimelevation, |
|
| 59 |
Access,,** No join mapping for *Access ** |
|
| 60 |
Authorship,,** No join mapping for *Authorship ** |
|
| 61 |
AuthorshipContact,,** No join mapping for *AuthorshipContact ** |
|
| 62 |
Family_index,,** No non-empty join mapping for OMIT ** |
|
| 63 |
LowerPolitical,,** No join mapping for *LowerPolitical ** |
|
| 64 |
Method,,** No join mapping for Method ** |
|
| 65 |
Observation,,** No join mapping for *Observation ** |
|
| 66 |
Project_PI,,** No join mapping for *Project_PI ** |
|
| 67 |
Project_PI_contact,,** No join mapping for *Project_PI_contact ** |
|
| 68 |
ReferenceID,,** No join mapping for *ReferenceID ** |
|
| 69 |
ReferenceID_index,,** No non-empty join mapping for OMIT ** |
|
| 70 |
Region,,** No join mapping for *Region ** |
|
| 71 |
Source,,** No non-empty join mapping for OMIT ** There isn't a mapping for this yet |
|
| 72 |
SourceCitation,,** No join mapping for *SourceCitation ** |
|
| 73 |
SourceID,,** No join mapping for *SourceID ** |
|
| 74 |
Taxon_index,,** No non-empty join mapping for OMIT ** |
|
| 75 |
TaxonomyID,,** No non-empty join mapping for UNUSED ** Always 0 |
|
| 76 |
TaxonomyID_index,,** No non-empty join mapping for OMIT ** |
|
| 77 |
TraitName_index,,** No non-empty join mapping for OMIT ** |
|
| 78 |
URLSource,,** No join mapping for *URLSource ** |
|
| 79 |
VisitingDate,,** No join mapping for *VisitingDate ** |
|
| inputs/bien2_traits/TraitObservation/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>bien2_traits</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<authorlocationcode>$TraitObservationID</authorlocationcode> |
|
| 11 |
<elevation_m> |
|
| 12 |
<_units> |
|
| 13 |
<to>m</to> |
|
| 14 |
<to></to> |
|
| 15 |
<value>$VerbatimElevation</value> |
|
| 16 |
</_units> |
|
| 17 |
</elevation_m> |
|
| 18 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$LocalityDescription</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
|
| 19 |
<locationevent> |
|
| 20 |
<taxonoccurrence> |
|
| 21 |
<aggregateoccurrence><plantobservation><specimenreplicate><sourceaccessioncode>$TraitObservationID</sourceaccessioncode></specimenreplicate></plantobservation></aggregateoccurrence> |
|
| 22 |
<growthform>$Habit</growthform> |
|
| 23 |
<sourceaccessioncode>$TraitObservationID</sourceaccessioncode> |
|
| 24 |
<taxondetermination> |
|
| 25 |
<taxonverbatim_id> |
|
| 26 |
<taxonverbatim> |
|
| 27 |
<taxonlabel_id> |
|
| 28 |
<taxonlabel> |
|
| 29 |
<matched_label_id> |
|
| 30 |
<taxonlabel> |
|
| 31 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 32 |
<taxonomicname> |
|
| 33 |
<_join_words> |
|
| 34 |
<1> |
|
| 35 |
<_taxon_family_require_std> |
|
| 36 |
<family> |
|
| 37 |
<_nullIf> |
|
| 38 |
<null>$Taxon</null> |
|
| 39 |
<value>$Family</value> |
|
| 40 |
</_nullIf> |
|
| 41 |
</family> |
|
| 42 |
</_taxon_family_require_std> |
|
| 43 |
</1> |
|
| 44 |
<2> |
|
| 45 |
<_join_words> |
|
| 46 |
<1> |
|
| 47 |
<_alt> |
|
| 48 |
<1>$Taxon</1> |
|
| 49 |
<2> |
|
| 50 |
<_join_words> |
|
| 51 |
<2>$Genus</2> |
|
| 52 |
<3>$SpecificEpithet</3> |
|
| 53 |
<5> |
|
| 54 |
<_join_words> |
|
| 55 |
<1> |
|
| 56 |
<_if name="if has infraspecificEpithet"> |
|
| 57 |
<cond>$InfraspecificEpithet</cond> |
|
| 58 |
<then>$InfraspecificRank</then> |
|
| 59 |
</_if> |
|
| 60 |
</1> |
|
| 61 |
<2>$InfraspecificEpithet</2> |
|
| 62 |
</_join_words> |
|
| 63 |
</5> |
|
| 64 |
</_join_words> |
|
| 65 |
</2> |
|
| 66 |
</_alt> |
|
| 67 |
</1> |
|
| 68 |
<2>$AuthorOfScientificName</2> |
|
| 69 |
</_join_words> |
|
| 70 |
</2> |
|
| 71 |
</_join_words> |
|
| 72 |
</taxonomicname> |
|
| 73 |
</taxonlabel> |
|
| 74 |
</matched_label_id> |
|
| 75 |
<parent_id> |
|
| 76 |
<taxonlabel> |
|
| 77 |
<rank>$InfraspecificRank</rank> |
|
| 78 |
<taxonverbatim><verbatimrank>$InfraspecificRank</verbatimrank></taxonverbatim> |
|
| 79 |
<parent_id> |
|
| 80 |
<taxonlabel> |
|
| 81 |
<rank>cultivar</rank> |
|
| 82 |
<parent_id> |
|
| 83 |
<taxonlabel> |
|
| 84 |
<rank>forma</rank> |
|
| 85 |
<parent_id> |
|
| 86 |
<taxonlabel> |
|
| 87 |
<rank>variety</rank> |
|
| 88 |
<parent_id> |
|
| 89 |
<taxonlabel> |
|
| 90 |
<rank>subspecies</rank> |
|
| 91 |
<parent_id> |
|
| 92 |
<taxonlabel> |
|
| 93 |
<rank>species</rank> |
|
| 94 |
<taxonepithet>$SpecificEpithet</taxonepithet> |
|
| 95 |
<parent_id> |
|
| 96 |
<taxonlabel> |
|
| 97 |
<rank>genus</rank> |
|
| 98 |
<taxonepithet>$Genus</taxonepithet> |
|
| 99 |
<parent_id> |
|
| 100 |
<taxonlabel> |
|
| 101 |
<rank>family</rank> |
|
| 102 |
<taxonepithet>$Family</taxonepithet> |
|
| 103 |
</taxonlabel> |
|
| 104 |
</parent_id> |
|
| 105 |
</taxonlabel> |
|
| 106 |
</parent_id> |
|
| 107 |
</taxonlabel> |
|
| 108 |
</parent_id> |
|
| 109 |
</taxonlabel> |
|
| 110 |
</parent_id> |
|
| 111 |
</taxonlabel> |
|
| 112 |
</parent_id> |
|
| 113 |
</taxonlabel> |
|
| 114 |
</parent_id> |
|
| 115 |
</taxonlabel> |
|
| 116 |
</parent_id> |
|
| 117 |
<taxonepithet>$InfraspecificEpithet</taxonepithet> |
|
| 118 |
</taxonlabel> |
|
| 119 |
</parent_id> |
|
| 120 |
<rank>$InfraspecificRank</rank> |
|
| 121 |
<taxonomicname> |
|
| 122 |
<_join_words> |
|
| 123 |
<1> |
|
| 124 |
<_taxon_family_require_std> |
|
| 125 |
<family> |
|
| 126 |
<_nullIf> |
|
| 127 |
<null>$Taxon</null> |
|
| 128 |
<value>$Family</value> |
|
| 129 |
</_nullIf> |
|
| 130 |
</family> |
|
| 131 |
</_taxon_family_require_std> |
|
| 132 |
</1> |
|
| 133 |
<2> |
|
| 134 |
<_join_words> |
|
| 135 |
<1> |
|
| 136 |
<_alt> |
|
| 137 |
<1>$Taxon</1> |
|
| 138 |
<2> |
|
| 139 |
<_join_words> |
|
| 140 |
<2>$Genus</2> |
|
| 141 |
<3>$SpecificEpithet</3> |
|
| 142 |
<5> |
|
| 143 |
<_join_words> |
|
| 144 |
<1> |
|
| 145 |
<_if name="if has infraspecificEpithet"> |
|
| 146 |
<cond>$InfraspecificEpithet</cond> |
|
| 147 |
<then>$InfraspecificRank</then> |
|
| 148 |
</_if> |
|
| 149 |
</1> |
|
| 150 |
<2>$InfraspecificEpithet</2> |
|
| 151 |
</_join_words> |
|
| 152 |
</5> |
|
| 153 |
</_join_words> |
|
| 154 |
</2> |
|
| 155 |
</_alt> |
|
| 156 |
</1> |
|
| 157 |
<2>$AuthorOfScientificName</2> |
|
| 158 |
</_join_words> |
|
| 159 |
</2> |
|
| 160 |
</_join_words> |
|
| 161 |
</taxonomicname> |
|
| 162 |
<trait> |
|
| 163 |
<name>$TraitName</name> |
|
| 164 |
<units>$Unit</units> |
|
| 165 |
<value>$TraitValue</value> |
|
| 166 |
</trait> |
|
| 167 |
</taxonlabel> |
|
| 168 |
</taxonlabel_id> |
|
| 169 |
<author>$AuthorOfScientificName</author> |
|
| 170 |
<family>$Family</family> |
|
| 171 |
<genus>$Genus</genus> |
|
| 172 |
<specific_epithet>$SpecificEpithet</specific_epithet> |
|
| 173 |
<taxonname>$Taxon</taxonname> |
|
| 174 |
<verbatimrank>$InfraspecificRank</verbatimrank> |
|
| 175 |
</taxonverbatim> |
|
| 176 |
</taxonverbatim_id> |
|
| 177 |
</taxondetermination> |
|
| 178 |
</taxonoccurrence> |
|
| 179 |
</locationevent> |
|
| 180 |
<locationnarrative>$LocalityDescription</locationnarrative> |
|
| 181 |
<locationplace> |
|
| 182 |
<place_id> |
|
| 183 |
<place> |
|
| 184 |
<coordinates_id> |
|
| 185 |
<coordinates> |
|
| 186 |
<verbatimlatitude>$VerbatimLatitude</verbatimlatitude> |
|
| 187 |
<verbatimlongitude>$VerbatimLongitude</verbatimlongitude> |
|
| 188 |
</coordinates> |
|
| 189 |
</coordinates_id> |
|
| 190 |
<country>$Country</country> |
|
| 191 |
<matched_place_id> |
|
| 192 |
<place> |
|
| 193 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 194 |
<country>$Country</country> |
|
| 195 |
<stateprovince>$StateProvince</stateprovince> |
|
| 196 |
</place> |
|
| 197 |
</matched_place_id> |
|
| 198 |
<stateprovince>$StateProvince</stateprovince> |
|
| 199 |
</place> |
|
| 200 |
</place_id> |
|
| 201 |
</locationplace> |
|
| 202 |
<verbatimelevation>$VerbatimElevation</verbatimelevation> |
|
| 203 |
</location> |
|
| 204 |
</path> |
|
| 205 |
</_simplifyPath> |
|
| 206 |
</path> |
|
| 207 |
</_setDefault> |
|
| 208 |
</VegBIEN> |
|
| 209 |
Inserted 35 new rows into database |
|
| inputs/bien2_traits/TraitObservation/new_terms.csv | ||
|---|---|---|
| 1 |
TraitObservationID,occurrenceID,, |
|
| 2 |
TaxonomyID,UNUSED,,Always 0 |
|
| 3 |
InfraspecificRank,taxonRank,, |
|
| 4 |
AuthorOfScientificName,scientificNameAuthorship,, |
|
| 5 |
TraitName,measurementType,, |
|
| 6 |
TraitValue,measurementValue,, |
|
| 7 |
Unit,measurementUnit,, |
|
| 8 |
LocalityDescription,verbatimLocality,, |
|
| 9 |
TaxonomyID_index,OMIT,, |
|
| 10 |
Family_index,OMIT,, |
|
| 11 |
Taxon_index,OMIT,, |
|
| 12 |
TraitName_index,OMIT,, |
|
| 13 |
ReferenceID_index,OMIT,, |
|
| inputs/bien2_traits/TraitObservation/unmapped_terms.csv | ||
|---|---|---|
| 1 |
Method |
|
| 2 |
*Region |
|
| 3 |
*LowerPolitical |
|
| 4 |
*URLSource |
|
| 5 |
*SourceCitation |
|
| 6 |
*SourceID |
|
| 7 |
*VisitingDate |
|
| 8 |
*ReferenceID |
|
| 9 |
*Access |
|
| 10 |
*Project_PI |
|
| 11 |
*Project_PI_contact |
|
| 12 |
*Observation |
|
| 13 |
*Authorship |
|
| 14 |
*AuthorshipContact |
|
| inputs/bien2_traits/Source/map.csv | ||
|---|---|---|
| 1 |
bien2_traits,VegCore,Filter,Comments |
|
| 2 |
:primary database,referenceType,, |
|
| inputs/bien2_traits/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
bien2_traits,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/bien2_traits/Source/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>bien2_traits</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>bien2_traits</shortname> |
|
| 11 |
<sourcetype>primary database</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 14 |
</_simplifyPath> |
|
| 15 |
</path> |
|
| 16 |
</_setDefault> |
|
| 17 |
</VegBIEN> |
|
| 18 |
Inserted 0 new rows into database |
|
| inputs/bien2_traits/import_order.txt | ||
|---|---|---|
| 1 |
Source |
|
| 2 |
TraitObservation |
|
| inputs/bien2_traits/_MySQL/bien2_staging.schema.sql.make | ||
|---|---|---|
| 1 |
#!/bin/sh |
|
| 2 |
env server=nimoy schema=1 my2pg_export bien2_staging TraitObservation |
|
| 0 | 3 | |
| inputs/bien2_traits/_MySQL/bien2_staging.schema.sql | ||
|---|---|---|
| 1 |
-- MySQL dump 10.13 Distrib 5.5.28, for debian-linux-gnu (x86_64) |
|
| 2 |
-- |
|
| 3 |
-- Host: localhost Database: bien2_staging |
|
| 4 |
-- ------------------------------------------------------ |
|
| 5 |
-- Server version 5.5.28-0ubuntu0.12.04.3 |
|
| 6 |
|
|
| 7 |
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; |
|
| 8 |
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; |
|
| 9 |
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; |
|
| 10 |
/*!40101 SET NAMES latin1 */; |
|
| 11 |
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; |
|
| 12 |
/*!40103 SET TIME_ZONE='+00:00' */; |
|
| 13 |
/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; |
|
| 14 |
/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; |
|
| 15 |
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO,POSTGRESQL' */; |
|
| 16 |
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; |
|
| 17 |
|
|
| 18 |
-- |
|
| 19 |
-- Table structure for table "TraitObservation" |
|
| 20 |
-- |
|
| 21 |
|
|
| 22 |
DROP TABLE IF EXISTS "TraitObservation"; |
|
| 23 |
/*!40101 SET @saved_cs_client = @@character_set_client */; |
|
| 24 |
/*!40101 SET character_set_client = utf8 */; |
|
| 25 |
CREATE TABLE "TraitObservation" ( |
|
| 26 |
"TraitObservationID" int(11) unsigned NOT NULL, |
|
| 27 |
"TaxonomyID" int(11) unsigned NOT NULL, |
|
| 28 |
"Family" varchar(100) DEFAULT NULL, |
|
| 29 |
"Genus" varchar(100) DEFAULT NULL, |
|
| 30 |
"SpecificEpithet" varchar(100) DEFAULT NULL, |
|
| 31 |
"InfraspecificRank" varchar(25) DEFAULT NULL, |
|
| 32 |
"InfraspecificEpithet" varchar(100) DEFAULT NULL, |
|
| 33 |
"Taxon" varchar(255) DEFAULT NULL, |
|
| 34 |
"AuthorOfScientificName" varchar(255) DEFAULT NULL, |
|
| 35 |
"Habit" varchar(50) DEFAULT NULL, |
|
| 36 |
"TraitName" varchar(200) DEFAULT NULL, |
|
| 37 |
"TraitValue" varchar(100) DEFAULT NULL, |
|
| 38 |
"Unit" varchar(100) DEFAULT NULL, |
|
| 39 |
"Method" varchar(255) DEFAULT NULL, |
|
| 40 |
"Region" varchar(100) DEFAULT NULL, |
|
| 41 |
"Country" varchar(100) DEFAULT NULL, |
|
| 42 |
"StateProvince" varchar(100) DEFAULT NULL, |
|
| 43 |
"LowerPolitical" varchar(100) DEFAULT NULL, |
|
| 44 |
"LocalityDescription" varchar(100) DEFAULT NULL, |
|
| 45 |
"VerbatimLatitude" varchar(150) DEFAULT NULL, |
|
| 46 |
"VerbatimLongitude" varchar(150) DEFAULT NULL, |
|
| 47 |
"VerbatimElevation" varchar(150) DEFAULT NULL, |
|
| 48 |
"Source" varchar(100) DEFAULT NULL, |
|
| 49 |
"URLSource" varchar(100) DEFAULT NULL, |
|
| 50 |
"SourceCitation" varchar(1000) DEFAULT NULL, |
|
| 51 |
"SourceID" varchar(255) DEFAULT NULL, |
|
| 52 |
"VisitingDate" varchar(100) DEFAULT NULL, |
|
| 53 |
"ReferenceID" int(11) unsigned DEFAULT NULL, |
|
| 54 |
"Access" varchar(100) DEFAULT NULL, |
|
| 55 |
"Project_PI" varchar(255) DEFAULT NULL, |
|
| 56 |
"Project_PI_contact" varchar(100) DEFAULT NULL, |
|
| 57 |
"Observation" varchar(255) DEFAULT NULL, |
|
| 58 |
"Authorship" varchar(255) DEFAULT NULL, |
|
| 59 |
"AuthorshipContact" varchar(100) DEFAULT NULL, |
|
| 60 |
PRIMARY KEY ("TraitObservationID"),
|
|
| 61 |
KEY "TaxonomyID" ("TaxonomyID"),
|
|
| 62 |
KEY "Family" ("Family"),
|
|
| 63 |
KEY "Taxon" ("Taxon"),
|
|
| 64 |
KEY "TraitName" ("TraitName"),
|
|
| 65 |
KEY "ReferenceID" ("ReferenceID")
|
|
| 66 |
); |
|
| 67 |
/*!40101 SET character_set_client = @saved_cs_client */; |
|
| 68 |
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; |
|
| 69 |
|
|
| 70 |
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; |
|
| 71 |
/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; |
|
| 72 |
/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; |
|
| 73 |
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; |
|
| 74 |
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; |
|
| 75 |
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; |
|
| 76 |
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; |
|
| 77 |
|
|
| 78 |
-- Dump completed on 2012-12-17 12:45:51 |
|
| inputs/bien2_traits/_MySQL/bien2_staging.data.sql.make | ||
|---|---|---|
| 1 |
#!/bin/sh |
|
| 2 |
env server=nimoy data=1 my2pg_export bien2_staging TraitObservation |
|
| 0 | 3 | |
| inputs/bien2_traits/bien2_staging.schema.sql | ||
|---|---|---|
| 1 |
SET standard_conforming_strings = off; |
|
| 2 |
SET escape_string_warning = off; |
|
| 3 |
-- MySQL dump 10.13 Distrib 5.5.28, for debian-linux-gnu (x86_64) |
|
| 4 |
-- |
|
| 5 |
-- Host: localhost Database: bien2_staging |
|
| 6 |
-- ------------------------------------------------------ |
|
| 7 |
-- Server version 5.5.28-0ubuntu0.12.04.3 |
|
| 8 |
|
|
| 9 |
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; |
|
| 10 |
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; |
|
| 11 |
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; |
|
| 12 |
SET NAMES 'latin1'; |
|
| 13 |
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; |
|
| 14 |
/*!40103 SET TIME_ZONE='+00:00' */; |
|
| 15 |
/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; |
|
| 16 |
/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; |
|
| 17 |
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO,POSTGRESQL' */; |
|
| 18 |
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; |
|
| 19 |
|
|
| 20 |
-- |
|
| 21 |
-- Table structure for table "TraitObservation" |
|
| 22 |
-- |
|
| 23 |
|
|
| 24 |
DROP TABLE IF EXISTS "TraitObservation"; |
|
| 25 |
/*!40101 SET @saved_cs_client = @@character_set_client */; |
|
| 26 |
/*!40101 SET character_set_client = utf8 */; |
|
| 27 |
CREATE TABLE "TraitObservation" ( |
|
| 28 |
"TraitObservationID" integer NOT NULL, |
|
| 29 |
"TaxonomyID" integer NOT NULL, |
|
| 30 |
"Family" varchar(100) DEFAULT NULL, |
|
| 31 |
"Genus" varchar(100) DEFAULT NULL, |
|
| 32 |
"SpecificEpithet" varchar(100) DEFAULT NULL, |
|
| 33 |
"InfraspecificRank" varchar(25) DEFAULT NULL, |
|
| 34 |
"InfraspecificEpithet" varchar(100) DEFAULT NULL, |
|
| 35 |
"Taxon" varchar(255) DEFAULT NULL, |
|
| 36 |
"AuthorOfScientificName" varchar(255) DEFAULT NULL, |
|
| 37 |
"Habit" varchar(50) DEFAULT NULL, |
|
| 38 |
"TraitName" varchar(200) DEFAULT NULL, |
|
| 39 |
"TraitValue" varchar(100) DEFAULT NULL, |
|
| 40 |
"Unit" varchar(100) DEFAULT NULL, |
|
| 41 |
"Method" varchar(255) DEFAULT NULL, |
|
| 42 |
"Region" varchar(100) DEFAULT NULL, |
|
| 43 |
"Country" varchar(100) DEFAULT NULL, |
|
| 44 |
"StateProvince" varchar(100) DEFAULT NULL, |
|
| 45 |
"LowerPolitical" varchar(100) DEFAULT NULL, |
|
| 46 |
"LocalityDescription" varchar(100) DEFAULT NULL, |
|
| 47 |
"VerbatimLatitude" varchar(150) DEFAULT NULL, |
|
| 48 |
"VerbatimLongitude" varchar(150) DEFAULT NULL, |
|
| 49 |
"VerbatimElevation" varchar(150) DEFAULT NULL, |
|
| 50 |
"Source" varchar(100) DEFAULT NULL, |
|
| 51 |
"URLSource" varchar(100) DEFAULT NULL, |
|
| 52 |
"SourceCitation" varchar(1000) DEFAULT NULL, |
|
| 53 |
"SourceID" varchar(255) DEFAULT NULL, |
|
| 54 |
"VisitingDate" varchar(100) DEFAULT NULL, |
|
| 55 |
"ReferenceID" integer DEFAULT NULL, |
|
| 56 |
"Access" varchar(100) DEFAULT NULL, |
|
| 57 |
"Project_PI" varchar(255) DEFAULT NULL, |
|
| 58 |
"Project_PI_contact" varchar(100) DEFAULT NULL, |
|
| 59 |
"Observation" varchar(255) DEFAULT NULL, |
|
| 60 |
"Authorship" varchar(255) DEFAULT NULL, |
|
| 61 |
"AuthorshipContact" varchar(100) DEFAULT NULL, |
|
| 62 |
PRIMARY KEY ("TraitObservationID"),
|
|
| 63 |
"TaxonomyID_index" boolean, |
|
| 64 |
"Family_index" boolean, |
|
| 65 |
"Taxon_index" boolean, |
|
| 66 |
"TraitName_index" boolean, |
|
| 67 |
"ReferenceID_index" boolean |
|
| 68 |
); |
|
| 69 |
/*!40101 SET character_set_client = @saved_cs_client */; |
|
| 70 |
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; |
|
| 71 |
|
|
| 72 |
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; |
|
| 73 |
/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; |
|
| 74 |
/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; |
|
| 75 |
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; |
|
| 76 |
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; |
|
| 77 |
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; |
|
| 78 |
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; |
|
| 79 |
|
|
| 80 |
-- Dump completed on 2012-12-17 12:45:51 |
|
Also available in: Unified diff
Added inputs/bien2_traits/