Revision 10260
Added by Aaron Marcuse-Kubitza almost 11 years ago
| inputs/JBM/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
JBM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
catalogNumber,"/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", |
|
| 8 |
id,"/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", |
|
| 9 |
institutionCode,"/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""]/then/_first/2", |
|
| 10 |
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
|
| 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 13 |
rights,/location/accessconditions, |
|
| 14 |
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/1, |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
|
| 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
|
| 21 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
|
| 22 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
|
| 23 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 24 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
|
| 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/2, |
|
| 28 |
recordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 29 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 34 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 35 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 36 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 37 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 38 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 39 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 40 |
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", |
|
| 41 |
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", |
|
| 42 |
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", |
|
| 43 |
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 44 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 45 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 46 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 47 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 48 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 49 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 50 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 51 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 52 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 53 |
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 54 |
recordNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 55 |
locality,/location/locationnarrative/_merge/1, |
|
| 56 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 57 |
coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value, |
|
| 58 |
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 59 |
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 60 |
verbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude, |
|
| 61 |
verbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude, |
|
| 62 |
country,/location/locationplace/*_id/place/country, |
|
| 63 |
county,/location/locationplace/*_id/place/county, |
|
| 64 |
decimalLatitude,"/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" |
|
| 65 |
decimalLongitude,"/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" |
|
| 66 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 67 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 68 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 69 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 70 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 71 |
countryCode,,** No join mapping for countryCode ** |
|
| 72 |
datasetID,,** No join mapping for datasetURL ** |
|
| 73 |
datasetName,,** No join mapping for dataset ** |
|
| 74 |
dynamicProperties,,** No join mapping for dynamicProperties ** |
|
| 75 |
geodeticDatum,,** No join mapping for geodeticDatum ** |
|
| 76 |
language,,** No join mapping for language ** |
|
| 77 |
modified,,** No join mapping for modified ** |
|
| 78 |
nomenclaturalCode,,** No join mapping for nomenclaturalCode ** |
|
| 79 |
ownerInstitutionCode,,** No join mapping for specimenOwner ** |
|
| 80 |
rightsHolder,,** No join mapping for dataOwners ** |
|
| 81 |
row_num,,** No join mapping for *row_num ** |
|
| 82 |
type,,** No join mapping for type ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 83 | 2 | |
| inputs/HIBG/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
HIBG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
catalogNumber,"/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", |
|
| 8 |
id,"/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", |
|
| 9 |
institutionCode,"/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""]/then/_first/2", |
|
| 10 |
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
|
| 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 13 |
rights,/location/accessconditions, |
|
| 14 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
|
| 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 16 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 17 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 18 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 19 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
|
| 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
|
| 21 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
|
| 22 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
|
| 23 |
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 24 |
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 25 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 26 |
reproductiveCondition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 27 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 28 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 29 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/2, |
|
| 30 |
recordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 31 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 32 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 33 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 34 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 35 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 36 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 37 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 38 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 39 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 40 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 41 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 42 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 43 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 44 |
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", |
|
| 45 |
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", |
|
| 46 |
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", |
|
| 47 |
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 48 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 49 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 50 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 51 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 52 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 53 |
taxonRank,"/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", |
|
| 54 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 55 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 56 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 57 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 58 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 59 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 60 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 61 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 62 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 63 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 64 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 65 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 66 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 67 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 68 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 69 |
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 70 |
recordNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 71 |
locality,/location/locationnarrative/_merge/1, |
|
| 72 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 73 |
locationRemarks,/location/locationnarrative/_merge/4, |
|
| 74 |
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 75 |
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 76 |
verbatimCoordinates,/location/locationplace/*_id/place/*_id/coordinates/verbatimcoordinates, |
|
| 77 |
continent,/location/locationplace/*_id/place/continent, |
|
| 78 |
country,/location/locationplace/*_id/place/country, |
|
| 79 |
county,/location/locationplace/*_id/place/county, |
|
| 80 |
decimalLatitude,"/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" |
|
| 81 |
decimalLongitude,"/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" |
|
| 82 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 83 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 84 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 85 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 86 |
verbatimElevation,/location/verbatimelevation, |
|
| 87 |
associatedMedia,,** No join mapping for associatedMedia ** |
|
| 88 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 89 |
bibliographicCitation,,** No join mapping for bibliographicCitation ** |
|
| 90 |
datasetID,,** No join mapping for datasetURL ** |
|
| 91 |
datasetName,,** No join mapping for dataset ** |
|
| 92 |
dynamicProperties,,** No join mapping for dynamicProperties ** |
|
| 93 |
geodeticDatum,,** No join mapping for geodeticDatum ** |
|
| 94 |
georeferenceSources,,** No join mapping for georeferenceSources ** |
|
| 95 |
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus ** |
|
| 96 |
identificationRemarks,,** No join mapping for identificationRemarks ** |
|
| 97 |
informationWithheld,,** No join mapping for informationWithheld ** |
|
| 98 |
institutionID,,** No non-empty join mapping for UNUSED#institutionID ** |
|
| 99 |
language,,** No join mapping for language ** |
|
| 100 |
modified,,** No join mapping for modified ** |
|
| 101 |
municipality,,** No join mapping for municipality ** |
|
| 102 |
nomenclaturalCode,,** No join mapping for nomenclaturalCode ** |
|
| 103 |
ownerInstitutionCode,,** No join mapping for specimenOwner ** |
|
| 104 |
references,,** No join mapping for distributors ** |
|
| 105 |
rightsHolder,,** No join mapping for dataOwners ** |
|
| 106 |
row_num,,** No join mapping for *row_num ** |
|
| 107 |
type,,** No join mapping for type ** |
|
| 108 |
verbatimCoordinateSystem,,** No join mapping for coordinateUnits ** |
|
| 109 |
verbatimDepth,,** No join mapping for verbatimDepth ** |
|
| 110 |
verbatimSRS,,** No join mapping for verbatimSRS ** |
|
| 111 |
waterBody,,** No join mapping for waterBody ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 112 | 2 | |
| inputs/IUCN/European_Red_List_Plants/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/IUCN/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/IUCN/European_Red_List_Plants/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
<parent_id> |
| 32 | 32 |
<taxonlabel> |
| 33 | 33 |
<rank>species</rank> |
| 34 |
<taxonepithet>$Species</taxonepithet>
|
|
| 34 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 35 | 35 |
<parent_id> |
| 36 | 36 |
<taxonlabel> |
| 37 | 37 |
<rank>genus</rank> |
| 38 | 38 |
<parent_id> |
| 39 | 39 |
<taxonlabel> |
| 40 | 40 |
<rank>family</rank> |
| 41 |
<taxonepithet>$Family</taxonepithet>
|
|
| 41 |
<taxonepithet>$family</taxonepithet>
|
|
| 42 | 42 |
</taxonlabel> |
| 43 | 43 |
</parent_id> |
| 44 | 44 |
</taxonlabel> |
| ... | ... | |
| 57 | 57 |
</parent_id> |
| 58 | 58 |
<taxonomicname> |
| 59 | 59 |
<_merge_prefix> |
| 60 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
|
|
| 61 |
<value>$Species</value>
|
|
| 60 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 61 |
<value>$specificEpithet</value>
|
|
| 62 | 62 |
</_merge_prefix> |
| 63 | 63 |
</taxonomicname> |
| 64 | 64 |
</taxonlabel> |
| 65 | 65 |
</taxonlabel_id> |
| 66 |
<family>$Family</family>
|
|
| 67 |
<specific_epithet>$Species</specific_epithet>
|
|
| 66 |
<family>$family</family>
|
|
| 67 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 68 | 68 |
</taxonverbatim> |
| 69 | 69 |
</taxonverbatim_id> |
| 70 | 70 |
</taxondetermination> |
| inputs/TRT/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/TRT/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
MO,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
specimenid,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
acronyms,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 4 |
specimenid,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 5 |
specimenid,"/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", |
|
| 6 |
acronyms,"/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""]/then/_first/2", |
|
| 7 |
minimumelevation,/location/elevation_m/_alt/2/_avg/1,Setting units to m for now because only 4% of rows have valid elevationunits other than Meters (these rows all have units of Feet) |
|
| 8 |
maximumelevation,/location/elevation_m/_alt/2/_avg/2,Setting units to m for now because only 4% of rows have valid elevationunits other than Meters (these rows all have units of Feet) |
|
| 9 |
collectionnumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 10 |
iscultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1", |
|
| 11 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 12 |
determinationyear,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 13 |
qualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
|
| 14 |
collectionnumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 15 |
ecologicalcondition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 16 |
collectionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 17 |
specimenid,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 18 |
acronyms,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 19 |
acronyms,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 20 |
specimenid,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 21 |
collectionnumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 22 |
fullname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 23 |
name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 24 |
collectorstring,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 25 |
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 26 |
specimenid,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 27 |
iscultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1", |
|
| 28 |
specimenid,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 29 |
determinedby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 30 |
rankabbreviation,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 31 |
speciesnamepart,"/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", |
|
| 32 |
genusnamepart,"/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", |
|
| 33 |
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", |
|
| 34 |
epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 35 |
rankabbreviation,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 36 |
determinationnameid,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 37 |
rankabbreviation,"/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", |
|
| 38 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 39 |
fullname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 40 |
name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 41 |
genusnamepart,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 42 |
speciesnamepart,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 43 |
epithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 44 |
rankabbreviation,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 45 |
epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 46 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 47 |
genusnamepart,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 48 |
speciesnamepart,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 49 |
name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 50 |
fullname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 51 |
rankabbreviation,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 52 |
determinationyear,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 53 |
qualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
|
| 54 |
collectionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 55 |
locality,/location/locationnarrative/_merge/1, |
|
| 56 |
notes,/location/locationnarrative/_merge/4, |
|
| 57 |
minlatdecdeg,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 58 |
minlongdecdeg,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 59 |
continent,/location/locationplace/*_id/place/continent, |
|
| 60 |
country,/location/locationplace/*_id/place/country, |
|
| 61 |
lower,/location/locationplace/*_id/place/county, |
|
| 62 |
minlatdecdeg,"/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" |
|
| 63 |
minlongdecdeg,"/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" |
|
| 64 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 65 |
lower,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 66 |
upper,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 67 |
upper,/location/locationplace/*_id/place/stateprovince, |
|
| 68 |
coord_method,,** No join mapping for georeferenceProtocol ** |
|
| 69 |
description,,** No join mapping for specimenDescription ** |
|
| 70 |
elev_method,,** No join mapping for *elev_method ** |
|
| 71 |
elevationunits,,** No join mapping for *elevationunits ** |
|
| 72 |
minimumday,,** No join mapping for day ** |
|
| 73 |
minimummonth,,** No join mapping for month ** |
|
| 74 |
minimumyear,,** No join mapping for year ** |
|
| 75 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 76 | 2 | |
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
TRT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
catalogNumber,"/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", |
|
| 8 |
id,"/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", |
|
| 9 |
institutionCode,"/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""]/then/_first/2", |
|
| 10 |
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 11 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
|
| 12 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 13 |
rights,/location/accessconditions, |
|
| 14 |
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
|
| 15 |
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/1, |
|
| 16 |
maximumElevationInMeters,/location/elevation_m/_alt/2/_avg/2, |
|
| 17 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 18 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 19 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 20 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value", |
|
| 22 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
|
| 23 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
|
| 24 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
|
| 25 |
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 26 |
identificationQualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
|
| 27 |
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 28 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 29 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
|
| 30 |
reproductiveCondition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 31 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 32 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 33 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/2, |
|
| 34 |
recordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 35 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 36 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 37 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 38 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 39 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 40 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 41 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 42 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 43 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 44 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 45 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
|
| 46 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
|
| 47 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 48 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 49 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 50 |
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", |
|
| 51 |
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", |
|
| 52 |
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", |
|
| 53 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 54 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 55 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 56 |
taxonRank,"/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", |
|
| 57 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 58 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 59 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 60 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 61 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 62 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 63 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 64 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 65 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 66 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 67 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 68 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 69 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 70 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 71 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 72 |
identificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
|
| 73 |
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 74 |
recordNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 75 |
locality,/location/locationnarrative/_merge/1, |
|
| 76 |
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 77 |
locationRemarks,/location/locationnarrative/_merge/4, |
|
| 78 |
coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value, |
|
| 79 |
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 80 |
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 81 |
verbatimCoordinates,/location/locationplace/*_id/place/*_id/coordinates/verbatimcoordinates, |
|
| 82 |
verbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude, |
|
| 83 |
verbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude, |
|
| 84 |
continent,/location/locationplace/*_id/place/continent, |
|
| 85 |
country,/location/locationplace/*_id/place/country, |
|
| 86 |
county,/location/locationplace/*_id/place/county, |
|
| 87 |
decimalLatitude,"/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" |
|
| 88 |
decimalLongitude,"/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" |
|
| 89 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 90 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 91 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 92 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 93 |
verbatimElevation,/location/verbatimelevation, |
|
| 94 |
associatedMedia,,** No join mapping for associatedMedia ** |
|
| 95 |
associatedReferences,,** No join mapping for associatedReferences ** |
|
| 96 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 97 |
bibliographicCitation,,** No join mapping for bibliographicCitation ** |
|
| 98 |
datasetID,,** No join mapping for datasetURL ** |
|
| 99 |
datasetName,,** No join mapping for dataset ** |
|
| 100 |
geodeticDatum,,** No join mapping for geodeticDatum ** |
|
| 101 |
georeferenceProtocol,,** No join mapping for georeferenceProtocol ** |
|
| 102 |
georeferenceRemarks,,** No join mapping for georeferenceRemarks ** |
|
| 103 |
georeferenceSources,,** No join mapping for georeferenceSources ** |
|
| 104 |
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus ** |
|
| 105 |
georeferencedBy,,** No join mapping for georeferencedBy ** |
|
| 106 |
georeferencedDate,,** No join mapping for georeferencedDate ** |
|
| 107 |
higherClassification,,** No join mapping for higherClassification ** |
|
| 108 |
institutionID,,** No non-empty join mapping for UNUSED#institutionID ** |
|
| 109 |
language,,** No join mapping for language ** |
|
| 110 |
municipality,,** No join mapping for municipality ** |
|
| 111 |
nomenclaturalCode,,** No join mapping for nomenclaturalCode ** |
|
| 112 |
otherCatalogNumbers,,** No join mapping for otherCatalogNumbers ** |
|
| 113 |
ownerInstitutionCode,,** No join mapping for specimenOwner ** |
|
| 114 |
previousIdentifications,,** No join mapping for previousIdentifications ** |
|
| 115 |
rightsHolder,,** No join mapping for dataOwners ** |
|
| 116 |
row_num,,** No join mapping for *row_num ** |
|
| 117 |
type,,** No join mapping for type ** |
|
| 118 |
typeStatus,,** No join mapping for typeStatus ** |
|
| 119 |
verbatimCoordinateSystem,,** No join mapping for coordinateUnits ** |
|
| 120 |
verbatimEventDate,,** No join mapping for verbatimEventDate ** |
|
| 121 |
verbatimSRS,,** No join mapping for verbatimSRS ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 122 | 2 | |
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$specimenid</authorlocationcode>
|
|
| 10 |
<authorlocationcode>$dataProviderRecordID</authorlocationcode>
|
|
| 11 | 11 |
<elevation_m> |
| 12 | 12 |
<_avg> |
| 13 |
<1>$minimumelevation</1>
|
|
| 14 |
<2>$maximumelevation</2>
|
|
| 13 |
<1>$minimumElevationInMeters</1>
|
|
| 14 |
<2>$maximumElevationInMeters</2>
|
|
| 15 | 15 |
</_avg> |
| 16 | 16 |
</elevation_m> |
| 17 | 17 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
| ... | ... | |
| 19 | 19 |
<taxonoccurrence> |
| 20 | 20 |
<aggregateoccurrence> |
| 21 | 21 |
<plantobservation> |
| 22 |
<authorplantcode>$collectionnumber</authorplantcode>
|
|
| 23 |
<reproductivecondition>$ecologicalcondition</reproductivecondition>
|
|
| 22 |
<authorplantcode>$collectorNumber</authorplantcode>
|
|
| 23 |
<reproductivecondition>$reproductiveCondition</reproductivecondition>
|
|
| 24 | 24 |
<specimenreplicate> |
| 25 |
<collectionnumber>$collectionnumber</collectionnumber>
|
|
| 25 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 26 | 26 |
<institution_id> |
| 27 | 27 |
<sourcelist> |
| 28 |
<name>$acronyms</name>
|
|
| 28 |
<name>$specimenHolderInstitutions</name>
|
|
| 29 | 29 |
<sourcename> |
| 30 | 30 |
<name> |
| 31 | 31 |
<_split> |
| 32 | 32 |
<separator>[,;] *</separator> |
| 33 |
<value>$acronyms</value>
|
|
| 33 |
<value>$specimenHolderInstitutions</value>
|
|
| 34 | 34 |
</_split> |
| 35 | 35 |
</name> |
| 36 | 36 |
</sourcename> |
| 37 | 37 |
</sourcelist> |
| 38 | 38 |
</institution_id> |
| 39 |
<sourceaccessioncode>$specimenid</sourceaccessioncode>
|
|
| 39 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 40 | 40 |
</specimenreplicate> |
| 41 | 41 |
</plantobservation> |
| 42 | 42 |
</aggregateoccurrence> |
| 43 |
<collector_id><party><fullname>$collectorstring</fullname></party></collector_id>
|
|
| 44 |
<iscultivated>$iscultivated</iscultivated>
|
|
| 45 |
<sourceaccessioncode>$specimenid</sourceaccessioncode>
|
|
| 43 |
<collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
|
|
| 44 |
<iscultivated>$cultivated</iscultivated> |
|
| 45 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 46 | 46 |
<taxondetermination> |
| 47 |
<party_id><party><fullname>$determinedby</fullname></party></party_id>
|
|
| 47 |
<party_id><party><fullname>$identifiedBy</fullname></party></party_id>
|
|
| 48 | 48 |
<taxonverbatim_id> |
| 49 | 49 |
<taxonverbatim> |
| 50 | 50 |
<taxonlabel_id> |
| 51 | 51 |
<taxonlabel> |
| 52 | 52 |
<parent_id> |
| 53 | 53 |
<taxonlabel> |
| 54 |
<rank>$rankabbreviation</rank>
|
|
| 54 |
<rank>$taxonRank</rank>
|
|
| 55 | 55 |
<parent_id> |
| 56 | 56 |
<taxonlabel> |
| 57 | 57 |
<rank>cultivar</rank> |
| ... | ... | |
| 67 | 67 |
<parent_id> |
| 68 | 68 |
<taxonlabel> |
| 69 | 69 |
<rank>species</rank> |
| 70 |
<taxonepithet>$speciesnamepart</taxonepithet>
|
|
| 70 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 71 | 71 |
<parent_id> |
| 72 | 72 |
<taxonlabel> |
| 73 | 73 |
<rank>genus</rank> |
| 74 |
<taxonepithet>$genusnamepart</taxonepithet>
|
|
| 74 |
<taxonepithet>$genus</taxonepithet> |
|
| 75 | 75 |
<parent_id> |
| 76 | 76 |
<taxonlabel> |
| 77 | 77 |
<rank>family</rank> |
| ... | ... | |
| 90 | 90 |
</parent_id> |
| 91 | 91 |
</taxonlabel> |
| 92 | 92 |
</parent_id> |
| 93 |
<taxonepithet>$epithet</taxonepithet>
|
|
| 93 |
<taxonepithet>$infraspecificEpithet</taxonepithet>
|
|
| 94 | 94 |
</taxonlabel> |
| 95 | 95 |
</parent_id> |
| 96 |
<rank>$rankabbreviation</rank>
|
|
| 97 |
<sourceaccessioncode>$determinationnameid</sourceaccessioncode>
|
|
| 96 |
<rank>$taxonRank</rank>
|
|
| 97 |
<sourceaccessioncode>$scientificNameID</sourceaccessioncode>
|
|
| 98 | 98 |
<taxonomicname> |
| 99 | 99 |
<_merge_prefix> |
| 100 | 100 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
| 101 | 101 |
<value> |
| 102 | 102 |
<_alt> |
| 103 |
<1>$fullname</1>
|
|
| 103 |
<1>$scientificName</1>
|
|
| 104 | 104 |
<2> |
| 105 | 105 |
<_alt> |
| 106 |
<1>$name</1>
|
|
| 106 |
<1>$taxonName</1>
|
|
| 107 | 107 |
<2> |
| 108 | 108 |
<_join_words> |
| 109 |
<2><_filter_genus><value>$genusnamepart</value></_filter_genus></2>
|
|
| 110 |
<3>$speciesnamepart</3>
|
|
| 109 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 110 |
<3>$specificEpithet</3>
|
|
| 111 | 111 |
<5> |
| 112 | 112 |
<_join_words> |
| 113 | 113 |
<1> |
| 114 | 114 |
<_if name="if has infraspecificEpithet"> |
| 115 |
<cond>$epithet</cond>
|
|
| 116 |
<then>$rankabbreviation</then>
|
|
| 115 |
<cond>$infraspecificEpithet</cond>
|
|
| 116 |
<then>$taxonRank</then>
|
|
| 117 | 117 |
</_if> |
| 118 | 118 |
</1> |
| 119 |
<2>$epithet</2>
|
|
| 119 |
<2>$infraspecificEpithet</2>
|
|
| 120 | 120 |
</_join_words> |
| 121 | 121 |
</5> |
| 122 | 122 |
</_join_words> |
| ... | ... | |
| 130 | 130 |
</taxonlabel> |
| 131 | 131 |
</taxonlabel_id> |
| 132 | 132 |
<family>$family</family> |
| 133 |
<genus>$genusnamepart</genus>
|
|
| 134 |
<specific_epithet>$speciesnamepart</specific_epithet>
|
|
| 135 |
<taxonname>$name</taxonname>
|
|
| 136 |
<taxonomicname>$fullname</taxonomicname>
|
|
| 137 |
<verbatimrank>$rankabbreviation</verbatimrank>
|
|
| 133 |
<genus>$genus</genus> |
|
| 134 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 135 |
<taxonname>$taxonName</taxonname>
|
|
| 136 |
<taxonomicname>$scientificName</taxonomicname>
|
|
| 137 |
<verbatimrank>$taxonRank</verbatimrank>
|
|
| 138 | 138 |
</taxonverbatim> |
| 139 | 139 |
</taxonverbatim_id> |
| 140 | 140 |
<determinationdate> |
| ... | ... | |
| 143 | 143 |
<_nullIf> |
| 144 | 144 |
<null>0</null> |
| 145 | 145 |
<type>float</type> |
| 146 |
<value>$determinationyear</value>
|
|
| 146 |
<value>$yearIdentified</value>
|
|
| 147 | 147 |
</_nullIf> |
| 148 | 148 |
</year> |
| 149 | 149 |
</_date> |
| 150 | 150 |
</determinationdate> |
| 151 |
<taxonfit>$qualifier</taxonfit>
|
|
| 151 |
<taxonfit>$identificationQualifier</taxonfit>
|
|
| 152 | 152 |
</taxondetermination> |
| 153 | 153 |
</taxonoccurrence> |
| 154 | 154 |
</locationevent> |
| 155 | 155 |
<locationnarrative> |
| 156 | 156 |
<_merge> |
| 157 | 157 |
<1>$locality</1> |
| 158 |
<4>$notes</4>
|
|
| 158 |
<4>$locationRemarks</4>
|
|
| 159 | 159 |
</_merge> |
| 160 | 160 |
</locationnarrative> |
| 161 | 161 |
<locationplace> |
| ... | ... | |
| 167 | 167 |
<_nullIf> |
| 168 | 168 |
<null>0</null> |
| 169 | 169 |
<type>float</type> |
| 170 |
<value>$minlatdecdeg</value>
|
|
| 170 |
<value>$decimalLatitude</value>
|
|
| 171 | 171 |
</_nullIf> |
| 172 | 172 |
</latitude_deg> |
| 173 | 173 |
<longitude_deg> |
| 174 | 174 |
<_nullIf> |
| 175 | 175 |
<null>0</null> |
| 176 | 176 |
<type>float</type> |
| 177 |
<value>$minlongdecdeg</value>
|
|
| 177 |
<value>$decimalLongitude</value>
|
|
| 178 | 178 |
</_nullIf> |
| 179 | 179 |
</longitude_deg> |
| 180 | 180 |
</coordinates> |
| 181 | 181 |
</coordinates_id> |
| 182 | 182 |
<continent>$continent</continent> |
| 183 | 183 |
<country>$country</country> |
| 184 |
<county>$lower</county>
|
|
| 184 |
<county>$county</county>
|
|
| 185 | 185 |
<matched_place_id> |
| 186 | 186 |
<place> |
| 187 | 187 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| ... | ... | |
| 192 | 192 |
<_nullIf> |
| 193 | 193 |
<null>0</null> |
| 194 | 194 |
<type>float</type> |
| 195 |
<value>$minlatdecdeg</value>
|
|
| 195 |
<value>$decimalLatitude</value>
|
|
| 196 | 196 |
</_nullIf> |
| 197 | 197 |
</latitude_deg> |
| 198 | 198 |
<longitude_deg> |
| 199 | 199 |
<_nullIf> |
| 200 | 200 |
<null>0</null> |
| 201 | 201 |
<type>float</type> |
| 202 |
<value>$minlongdecdeg</value>
|
|
| 202 |
<value>$decimalLongitude</value>
|
|
| 203 | 203 |
</_nullIf> |
| 204 | 204 |
</longitude_deg> |
| 205 | 205 |
</coordinates> |
| 206 | 206 |
</coordinates_id> |
| 207 | 207 |
<country>$country</country> |
| 208 |
<county>$lower</county>
|
|
| 209 |
<stateprovince>$upper</stateprovince>
|
|
| 208 |
<county>$county</county>
|
|
| 209 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 210 | 210 |
</place> |
| 211 | 211 |
</matched_place_id> |
| 212 |
<stateprovince>$upper</stateprovince>
|
|
| 212 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 213 | 213 |
</place> |
| 214 | 214 |
</place_id> |
| 215 | 215 |
</locationplace> |
| inputs/MT/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$id</authorlocationcode>
|
|
| 10 |
<authorlocationcode>$dataProviderRecordID</authorlocationcode>
|
|
| 11 | 11 |
<accessconditions>$rights</accessconditions> |
| 12 | 12 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated> |
| 13 | 13 |
<locationevent> |
| ... | ... | |
| 19 | 19 |
<specimenreplicate> |
| 20 | 20 |
<collectioncode_dwc> |
| 21 | 21 |
<_alt> |
| 22 |
<1>$collectionCode</1>
|
|
| 23 |
<2>$collectionID</2>
|
|
| 22 |
<1>$collection</1> |
|
| 23 |
<2>$collectionURL</2>
|
|
| 24 | 24 |
</_alt> |
| 25 | 25 |
</collectioncode_dwc> |
| 26 | 26 |
<institution_id> |
| 27 | 27 |
<sourcelist> |
| 28 |
<name>$institutionCode</name>
|
|
| 28 |
<name>$specimenHolderInstitutions</name>
|
|
| 29 | 29 |
<sourcename> |
| 30 | 30 |
<name> |
| 31 | 31 |
<_split> |
| 32 | 32 |
<separator>[,;] *</separator> |
| 33 |
<value>$institutionCode</value>
|
|
| 33 |
<value>$specimenHolderInstitutions</value>
|
|
| 34 | 34 |
</_split> |
| 35 | 35 |
</name> |
| 36 | 36 |
</sourcename> |
| 37 | 37 |
</sourcelist> |
| 38 | 38 |
</institution_id> |
| 39 |
<sourceaccessioncode>$id</sourceaccessioncode>
|
|
| 39 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 40 | 40 |
</specimenreplicate> |
| 41 | 41 |
</plantobservation> |
| 42 | 42 |
</aggregateoccurrence> |
| ... | ... | |
| 56 | 56 |
<value>$establishmentMeans</value> |
| 57 | 57 |
</_map> |
| 58 | 58 |
</isnative> |
| 59 |
<sourceaccessioncode>$id</sourceaccessioncode>
|
|
| 59 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 60 | 60 |
<taxondetermination> |
| 61 | 61 |
<taxonverbatim_id> |
| 62 | 62 |
<taxonverbatim> |
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
MT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 4 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 5 |
id,"/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", |
|
| 6 |
institutionCode,"/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""]/then/_first/2", |
|
| 7 |
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 8 |
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
|
| 9 |
rights,/location/accessconditions, |
|
| 10 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 11 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
|
| 12 |
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 13 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 14 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/2, |
|
| 15 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 17 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 18 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 19 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 20 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
|
| 21 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
|
| 22 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 23 |
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", |
|
| 24 |
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", |
|
| 25 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 26 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 27 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 28 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 29 |
locality,/location/locationnarrative/_merge/1, |
|
| 30 |
continent,/location/locationplace/*_id/place/continent, |
|
| 31 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 32 |
countryCode,,** No join mapping for countryCode ** |
|
| 33 |
datasetName,,** No join mapping for dataset ** |
|
| 34 |
language,,** No join mapping for language ** |
|
| 35 |
rightsHolder,,** No join mapping for dataOwners ** |
|
| 36 |
row_num,,** No join mapping for *row_num ** |
|
| 37 |
type,,** No join mapping for type ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 38 | 2 | |
| inputs/MT/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/test_taxonomic_names/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/test_taxonomic_names/Taxon/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/test_taxonomic_names/Taxon/test.xml.ref | ||
|---|---|---|
| 15 | 15 |
<taxonlabel_id> |
| 16 | 16 |
<taxonlabel> |
| 17 | 17 |
<sourceaccessioncode>$scientificNameID</sourceaccessioncode> |
| 18 |
<taxonomicname>$scientificName</taxonomicname>
|
|
| 18 |
<taxonomicname>$taxonName</taxonomicname>
|
|
| 19 | 19 |
</taxonlabel> |
| 20 | 20 |
</taxonlabel_id> |
| 21 |
<taxonname>$scientificName</taxonname>
|
|
| 21 |
<taxonname>$taxonName</taxonname>
|
|
| 22 | 22 |
</taxonverbatim> |
| 23 | 23 |
</taxonverbatim_id> |
| 24 | 24 |
</taxondetermination> |
| inputs/test_taxonomic_names/Taxon/VegBIEN.csv | ||
|---|---|---|
| 1 |
test_taxonomic_names,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 3 |
scientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 4 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 5 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 6 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 7 | 2 | |
| inputs/XAL/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
XAL:/content/record/,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
darwin:CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
darwin:InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 4 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 5 |
darwin:CatalogNumber,"/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", |
|
| 6 |
darwin:InstitutionCode,"/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""]/then/_first/2", |
|
| 7 |
darwin:CollectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 8 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 9 |
darwin:MinimumElevation,/location/elevation_m/_alt/2/_avg/1, |
|
| 10 |
darwin:MaximumElevation,/location/elevation_m/_alt/2/_avg/2, |
|
| 11 |
darwin:CollectorNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 12 |
darwin:Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 13 |
darwin:DayIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 14 |
darwin:MonthIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 15 |
darwin:YearIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 16 |
darwin:DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 17 |
darwin:MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 18 |
darwin:YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 19 |
darwin:IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
|
| 20 |
darwin:Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 21 |
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 22 |
darwin:Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
|
| 23 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 24 |
darwin:CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 25 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 26 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 27 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 28 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 29 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 30 |
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 31 |
darwin:Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 32 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 33 |
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 34 |
darwin:Subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
|
| 35 |
darwin: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", |
|
| 36 |
darwin: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", |
|
| 37 |
darwin: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", |
|
| 38 |
darwin:Order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 39 |
darwin:Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 40 |
darwin:Phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 41 |
darwin:Kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 42 |
darwin:Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 43 |
darwin:ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 44 |
darwin:Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 45 |
darwin:Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 46 |
darwin:Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 47 |
darwin:ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 48 |
darwin:ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 49 |
darwin:Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 50 |
darwin:Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 51 |
darwin:Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 52 |
darwin:ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 53 |
darwin:DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
|
| 54 |
darwin:MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
|
| 55 |
darwin:YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
|
| 56 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 57 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 58 |
darwin:MinimumDepth,/location/locationevent/waterdepth_m/_avg/1, |
|
| 59 |
darwin:MaximumDepth,/location/locationevent/waterdepth_m/_avg/2, |
|
| 60 |
darwin:Locality,/location/locationnarrative/_merge/1, |
|
| 61 |
darwin:Latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 62 |
darwin:Longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 63 |
darwin:ContinentOcean,/location/locationplace/*_id/place/continent, |
|
| 64 |
darwin:Country,/location/locationplace/*_id/place/country, |
|
| 65 |
darwin:County,/location/locationplace/*_id/place/county, |
|
| 66 |
darwin: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" |
|
| 67 |
darwin: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" |
|
| 68 |
darwin:Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 69 |
darwin:County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 70 |
darwin:StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 71 |
darwin:StateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 72 |
darwin:BasisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 73 |
darwin:CoordinatePrecision,,** No non-empty join mapping for UNUSED#darwin:CoordinatePrecision ** |
|
| 74 |
darwin:DateLastModified,,** No join mapping for modified ** |
|
| 75 |
darwin:FieldNumber,,** No non-empty join mapping for UNUSED#darwin:FieldNumber ** This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). |
|
| 76 |
darwin:JulianDay,,** No join mapping for day ** |
|
| 77 |
darwin:PreparationType,,** No join mapping for preparations ** |
|
| 78 |
darwin:PreviousCatalogNumber,,** No join mapping for otherCatalogNumbers ** |
|
| 79 |
darwin:RelatedCatalogItem,,** No join mapping for relatedResourceID ** |
|
| 80 |
darwin:RelationshipType,,** No join mapping for relationshipOfResource ** |
|
| 81 |
darwin:TimeOfDay,,** No join mapping for eventTime ** |
|
| 82 |
darwin:TypeStatus,,** No join mapping for typeStatus ** |
|
| 83 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 84 | 2 | |
| inputs/XAL/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/bien2_traits/TraitObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/bien2_traits/TraitObservation/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$TraitObservationID</authorlocationcode>
|
|
| 10 |
<authorlocationcode>$occurrenceID</authorlocationcode>
|
|
| 11 | 11 |
<elevation_m> |
| 12 | 12 |
<_units> |
| 13 | 13 |
<to>m</to> |
| 14 | 14 |
<to></to> |
| 15 |
<value>$VerbatimElevation</value>
|
|
| 15 |
<value>$verbatimElevation</value>
|
|
| 16 | 16 |
</_units> |
| 17 | 17 |
</elevation_m> |
| 18 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$LocalityDescription</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 18 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$verbatimLocality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 19 | 19 |
<locationevent> |
| 20 |
<method_id><method><name>$Method</name></method></method_id>
|
|
| 20 |
<method_id><method><name>$samplingProtocol</name></method></method_id>
|
|
| 21 | 21 |
<taxonoccurrence> |
| 22 |
<aggregateoccurrence><plantobservation><specimenreplicate><sourceaccessioncode>$TraitObservationID</sourceaccessioncode></specimenreplicate></plantobservation></aggregateoccurrence>
|
|
| 23 |
<growthform>$Habit</growthform>
|
|
| 24 |
<sourceaccessioncode>$TraitObservationID</sourceaccessioncode>
|
|
| 22 |
<aggregateoccurrence><plantobservation><specimenreplicate><sourceaccessioncode>$occurrenceID</sourceaccessioncode></specimenreplicate></plantobservation></aggregateoccurrence>
|
|
| 23 |
<growthform>$growthForm</growthform>
|
|
| 24 |
<sourceaccessioncode>$occurrenceID</sourceaccessioncode>
|
|
| 25 | 25 |
<taxondetermination> |
| 26 | 26 |
<taxonverbatim_id> |
| 27 | 27 |
<taxonverbatim> |
| ... | ... | |
| 29 | 29 |
<taxonlabel> |
| 30 | 30 |
<parent_id> |
| 31 | 31 |
<taxonlabel> |
| 32 |
<rank>$InfraspecificRank</rank>
|
|
| 32 |
<rank>$taxonRank</rank>
|
|
| 33 | 33 |
<parent_id> |
| 34 | 34 |
<taxonlabel> |
| 35 | 35 |
<rank>cultivar</rank> |
| ... | ... | |
| 45 | 45 |
<parent_id> |
| 46 | 46 |
<taxonlabel> |
| 47 | 47 |
<rank>species</rank> |
| 48 |
<taxonepithet>$SpecificEpithet</taxonepithet>
|
|
| 48 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 49 | 49 |
<parent_id> |
| 50 | 50 |
<taxonlabel> |
| 51 | 51 |
<rank>genus</rank> |
| 52 |
<taxonepithet>$Genus</taxonepithet>
|
|
| 52 |
<taxonepithet>$genus</taxonepithet>
|
|
| 53 | 53 |
<parent_id> |
| 54 | 54 |
<taxonlabel> |
| 55 | 55 |
<rank>family</rank> |
| 56 |
<taxonepithet>$Family</taxonepithet>
|
|
| 56 |
<taxonepithet>$family</taxonepithet>
|
|
| 57 | 57 |
</taxonlabel> |
| 58 | 58 |
</parent_id> |
| 59 | 59 |
</taxonlabel> |
| ... | ... | |
| 68 | 68 |
</parent_id> |
| 69 | 69 |
</taxonlabel> |
| 70 | 70 |
</parent_id> |
| 71 |
<taxonepithet>$InfraspecificEpithet</taxonepithet>
|
|
| 71 |
<taxonepithet>$infraspecificEpithet</taxonepithet>
|
|
| 72 | 72 |
</taxonlabel> |
| 73 | 73 |
</parent_id> |
| 74 |
<rank>$InfraspecificRank</rank>
|
|
| 74 |
<rank>$taxonRank</rank>
|
|
| 75 | 75 |
<taxonomicname> |
| 76 | 76 |
<_merge_prefix> |
| 77 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
|
|
| 77 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 78 | 78 |
<value> |
| 79 | 79 |
<_join_words> |
| 80 | 80 |
<1> |
| 81 | 81 |
<_alt> |
| 82 |
<1>$Taxon</1>
|
|
| 82 |
<1>$taxonName</1>
|
|
| 83 | 83 |
<2> |
| 84 | 84 |
<_join_words> |
| 85 |
<2><_filter_genus><value>$Genus</value></_filter_genus></2>
|
|
| 86 |
<3>$SpecificEpithet</3>
|
|
| 85 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 86 |
<3>$specificEpithet</3>
|
|
| 87 | 87 |
<5> |
| 88 | 88 |
<_join_words> |
| 89 | 89 |
<1> |
| 90 | 90 |
<_if name="if has infraspecificEpithet"> |
| 91 |
<cond>$InfraspecificEpithet</cond>
|
|
| 92 |
<then>$InfraspecificRank</then>
|
|
| 91 |
<cond>$infraspecificEpithet</cond>
|
|
| 92 |
<then>$taxonRank</then>
|
|
| 93 | 93 |
</_if> |
| 94 | 94 |
</1> |
| 95 |
<2>$InfraspecificEpithet</2>
|
|
| 95 |
<2>$infraspecificEpithet</2>
|
|
| 96 | 96 |
</_join_words> |
| 97 | 97 |
</5> |
| 98 | 98 |
</_join_words> |
| 99 | 99 |
</2> |
| 100 | 100 |
</_alt> |
| 101 | 101 |
</1> |
| 102 |
<2>$AuthorOfScientificName</2>
|
|
| 102 |
<2>$scientificNameAuthorship</2>
|
|
| 103 | 103 |
</_join_words> |
| 104 | 104 |
</value> |
| 105 | 105 |
</_merge_prefix> |
| 106 | 106 |
</taxonomicname> |
| 107 | 107 |
</taxonlabel> |
| 108 | 108 |
</taxonlabel_id> |
| 109 |
<author>$AuthorOfScientificName</author>
|
|
| 110 |
<family>$Family</family>
|
|
| 111 |
<genus>$Genus</genus>
|
|
| 112 |
<specific_epithet>$SpecificEpithet</specific_epithet>
|
|
| 113 |
<taxonname>$Taxon</taxonname>
|
|
| 114 |
<verbatimrank>$InfraspecificRank</verbatimrank>
|
|
| 109 |
<author>$scientificNameAuthorship</author>
|
|
| 110 |
<family>$family</family>
|
|
| 111 |
<genus>$genus</genus>
|
|
| 112 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 113 |
<taxonname>$taxonName</taxonname>
|
|
| 114 |
<verbatimrank>$taxonRank</verbatimrank>
|
|
| 115 | 115 |
</taxonverbatim> |
| 116 | 116 |
</taxonverbatim_id> |
| 117 | 117 |
</taxondetermination> |
| 118 | 118 |
<trait> |
| 119 |
<name>$TraitName</name>
|
|
| 120 |
<units>$Unit</units> |
|
| 121 |
<value>$TraitValue</value>
|
|
| 119 |
<name>$measurementName</name>
|
|
| 120 |
<units>$measurementUnit</units>
|
|
| 121 |
<value>$measurementValue</value>
|
|
| 122 | 122 |
</trait> |
| 123 | 123 |
</taxonoccurrence> |
| 124 | 124 |
</locationevent> |
| 125 |
<locationnarrative>$LocalityDescription</locationnarrative>
|
|
| 125 |
<locationnarrative>$verbatimLocality</locationnarrative>
|
|
| 126 | 126 |
<locationplace> |
| 127 | 127 |
<place_id> |
| 128 | 128 |
<place> |
| 129 | 129 |
<coordinates_id> |
| 130 | 130 |
<coordinates> |
| 131 |
<verbatimlatitude>$VerbatimLatitude</verbatimlatitude>
|
|
| 132 |
<verbatimlongitude>$VerbatimLongitude</verbatimlongitude>
|
|
| 131 |
<verbatimlatitude>$verbatimLatitude</verbatimlatitude>
|
|
| 132 |
<verbatimlongitude>$verbatimLongitude</verbatimlongitude>
|
|
| 133 | 133 |
</coordinates> |
| 134 | 134 |
</coordinates_id> |
| 135 |
<country>$Country</country>
|
|
| 135 |
<country>$country</country>
|
|
| 136 | 136 |
<matched_place_id> |
| 137 | 137 |
<place> |
| 138 | 138 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| 139 |
<country>$Country</country>
|
|
| 140 |
<stateprovince>$StateProvince</stateprovince>
|
|
| 139 |
<country>$country</country>
|
|
| 140 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 141 | 141 |
</place> |
| 142 | 142 |
</matched_place_id> |
| 143 |
<stateprovince>$StateProvince</stateprovince>
|
|
| 143 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 144 | 144 |
</place> |
| 145 | 145 |
</place_id> |
| 146 | 146 |
</locationplace> |
| 147 |
<verbatimelevation>$VerbatimElevation</verbatimelevation>
|
|
| 147 |
<verbatimelevation>$verbatimElevation</verbatimelevation>
|
|
| 148 | 148 |
</location> |
| 149 | 149 |
</path> |
| 150 | 150 |
</_simplifyPath> |
| 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", |
|
| 3 |
Source,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 4 |
TraitObservationID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 5 |
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", |
|
| 6 |
VerbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
|
| 7 |
TraitObservationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 8 |
LocalityDescription,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2, |
|
| 9 |
Method,/location/locationevent/*_id/method/name, |
|
| 10 |
TraitObservationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 11 |
TraitObservationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 12 |
Taxon,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 13 |
Habit,/location/locationevent/taxonoccurrence/growthform, |
|
| 14 |
TraitObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 15 |
TraitObservationID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 16 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 17 |
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", |
|
| 18 |
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", |
|
| 19 |
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", |
|
| 20 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 21 |
InfraspecificRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 22 |
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", |
|
| 23 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 24 |
Taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 25 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 26 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 27 |
InfraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 28 |
InfraspecificRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 29 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 30 |
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 31 |
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 32 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 33 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 34 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 35 |
Taxon,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 36 |
InfraspecificRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 37 |
TraitName,/location/locationevent/taxonoccurrence/trait/name, |
|
| 38 |
Unit,/location/locationevent/taxonoccurrence/trait/units, |
|
| 39 |
TraitValue,/location/locationevent/taxonoccurrence/trait/value, |
|
| 40 |
LocalityDescription,/location/locationnarrative/_merge/2, |
|
| 41 |
VerbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude, |
|
| 42 |
VerbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude, |
|
| 43 |
Country,/location/locationplace/*_id/place/country, |
|
| 44 |
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 45 |
StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 46 |
StateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 47 |
VerbatimElevation,/location/verbatimelevation, |
|
| 48 |
Access,,** No join mapping for *Access ** |
|
| 49 |
Authorship,,** No join mapping for *Authorship ** |
|
| 50 |
AuthorshipContact,,** No join mapping for *AuthorshipContact ** |
|
| 51 |
LowerPolitical,,** No join mapping for *LowerPolitical ** |
|
| 52 |
Observation,,** No join mapping for *Observation ** |
|
| 53 |
Project_PI,,** No join mapping for *Project_PI ** |
|
| 54 |
Project_PI_contact,,** No join mapping for *Project_PI_contact ** |
|
| 55 |
ReferenceID,,** No join mapping for *ReferenceID ** |
|
| 56 |
Region,,** No join mapping for *Region ** |
|
| 57 |
SourceCitation,,** No join mapping for *SourceCitation ** |
|
| 58 |
SourceID,,** No join mapping for *SourceID ** |
|
| 59 |
TaxonomyID,,** No non-empty join mapping for UNUSED#TaxonomyID ** Always 0 |
|
| 60 |
URLSource,,** No join mapping for *URLSource ** |
|
| 61 |
VisitingDate,,** No join mapping for *VisitingDate ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 62 | 2 | |
| inputs/bien2_traits/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/WIN/Specimen/header.csv | ||
|---|---|---|
| 1 |
row_num,id,municipality,verbatimLongitude,rightsHolder,scientificNameAuthorship,associatedMedia,verbatimSRS,dateIdentified,datasetID,bibliographicCitation,taxonRank,rights,occurrenceRemarks,verbatimElevation,eventDate,recordNumber,county,type,stateProvince,locality,scientificName,country,specificEpithet,coordinateUncertaintyInMeters,verbatimEventDate,habitat,identifiedBy,minimumElevationInMeters,datasetName,basisOfRecord,collectionID,collectionCode,verbatimCoordinates,decimalLatitude,institutionCode,catalogNumber,verbatimLatitude,identificationRemarks,nomenclaturalCode,recordedBy,infraspecificEpithet,kingdom,decimalLongitude,genus,verbatimCoordinateSystem,language,geodeticDatum,ownerInstitutionCode |
|
| inputs/WIN/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode> |
| 11 | 11 |
<_alt> |
| 12 |
<1>$id</1>
|
|
| 12 |
<1>$dataProviderRecordID</1>
|
|
| 13 | 13 |
<2> |
| 14 | 14 |
<_join> |
| 15 |
<1>$institutionCode</1>
|
|
| 15 |
<1>$specimenHolderInstitutions</1>
|
|
| 16 | 16 |
<2> |
| 17 | 17 |
<_join> |
| 18 |
<1>$collectionCode</1>
|
|
| 19 |
<2>$collectionID</2>
|
|
| 18 |
<1>$collection</1> |
|
| 19 |
<2>$collectionURL</2>
|
|
| 20 | 20 |
</_join> |
| 21 | 21 |
</2> |
| 22 |
<3>$catalogNumber</3>
|
|
| 22 |
<3>$accessionNumber</3>
|
|
| 23 | 23 |
</_join> |
| 24 | 24 |
</2> |
| 25 | 25 |
</_alt> |
| ... | ... | |
| 54 | 54 |
<aggregateoccurrence> |
| 55 | 55 |
<notes>$occurrenceRemarks</notes> |
| 56 | 56 |
<plantobservation> |
| 57 |
<authorplantcode>$recordNumber</authorplantcode>
|
|
| 57 |
<authorplantcode>$collectorNumber</authorplantcode>
|
|
| 58 | 58 |
<specimenreplicate> |
| 59 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc>
|
|
| 59 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
|
|
| 60 | 60 |
<collectioncode_dwc> |
| 61 | 61 |
<_alt> |
| 62 |
<1>$collectionCode</1>
|
|
| 63 |
<2>$collectionID</2>
|
|
| 62 |
<1>$collection</1> |
|
| 63 |
<2>$collectionURL</2>
|
|
| 64 | 64 |
</_alt> |
| 65 | 65 |
</collectioncode_dwc> |
| 66 |
<collectionnumber>$recordNumber</collectionnumber>
|
|
| 66 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 67 | 67 |
<institution_id> |
| 68 | 68 |
<sourcelist> |
| 69 |
<name>$institutionCode</name>
|
|
| 69 |
<name>$specimenHolderInstitutions</name>
|
|
| 70 | 70 |
<sourcename> |
| 71 | 71 |
<name> |
| 72 | 72 |
<_split> |
| 73 | 73 |
<separator>[,;] *</separator> |
| 74 |
<value>$institutionCode</value>
|
|
| 74 |
<value>$specimenHolderInstitutions</value>
|
|
| 75 | 75 |
</_split> |
| 76 | 76 |
</name> |
| 77 | 77 |
</sourcename> |
| 78 | 78 |
</sourcelist> |
| 79 | 79 |
</institution_id> |
| 80 |
<sourceaccessioncode>$id</sourceaccessioncode>
|
|
| 80 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 81 | 81 |
</specimenreplicate> |
| 82 | 82 |
</plantobservation> |
| 83 | 83 |
</aggregateoccurrence> |
| 84 | 84 |
<collector_id><party><fullname>$recordedBy</fullname></party></collector_id> |
| 85 |
<sourceaccessioncode>$id</sourceaccessioncode>
|
|
| 85 |
<sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
|
|
| 86 | 86 |
<taxondetermination> |
| 87 | 87 |
<party_id><party><fullname>$identifiedBy</fullname></party></party_id> |
| 88 | 88 |
<taxonverbatim_id> |
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
WIN,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
Also available in: Unified diff
inputs/*/ which do not contain any explicit collisions (wiki.vegpath.org/2013-06-27_conference_call#To-do-for-Aaron > #3.2 > the following datasources ...): switched to new-style import, which adds the staging table column renaming