Revision 10174
Added by Aaron Marcuse-Kubitza almost 11 years ago
| inputs/.NCBI/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 3 | 2 | |
| inputs/.NCBI/nodes/VegBIEN.csv | ||
|---|---|---|
| 1 |
NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
parentTaxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode, |
|
| 3 |
parentTaxonID,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists", |
|
| 4 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 5 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 6 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 7 |
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", |
|
| 8 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 9 |
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", |
|
| 10 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 11 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 12 |
*4,,** No join mapping for *4 ** |
|
| 13 |
*5,,** No join mapping for *5 ** |
|
| 14 |
*6,,** No join mapping for *6 ** |
|
| 15 |
*7,,** No join mapping for *7 ** |
|
| 16 |
*8,,** No join mapping for *8 ** |
|
| 17 |
*9,,** No join mapping for *9 ** |
|
| 18 |
*embl code,,** No join mapping for *embl code ** |
|
| 19 |
*name class,,** No join mapping for *name class ** |
|
| 20 |
*names.src.row_num,,** No join mapping for *names.src.row_num ** |
|
| 21 |
*nodes.src.row_num,,** No join mapping for *nodes.src.row_num ** |
|
| 22 |
*unique name,,** No join mapping for *unique name ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 23 | 2 | |
| inputs/GBIF/raw_occurrence_record_plants/VegBIEN.csv | ||
|---|---|---|
| 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
accessionNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
dataProviderRecordID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
specimenHolderInstitutions,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
dataProviderRecordID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
accessionNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 7 |
accessionNumber,"/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 |
dataProviderRecordID,"/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 |
specimenHolderInstitutions,"/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 |
collection,"/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 |
accessionNumber,"/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", |
|
| 12 |
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/1, |
|
| 13 |
maximumElevationInMeters,/location/elevation_m/_alt/2/_avg/2, |
|
| 14 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 15 |
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 16 |
accessionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 17 |
collection,/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 |
|
| 18 |
accessionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 19 |
dataProviderRecordID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 20 |
specimenHolderInstitutions,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
|
| 21 |
specimenHolderInstitutions,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
|
| 22 |
dataProviderRecordID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 23 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 24 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 25 |
dataProviderRecordID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 26 |
dataProviderRecordID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 27 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 28 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 29 |
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", |
|
| 30 |
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", |
|
| 31 |
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", |
|
| 32 |
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", |
|
| 33 |
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", |
|
| 34 |
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", |
|
| 35 |
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", |
|
| 36 |
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", |
|
| 37 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 38 |
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", |
|
| 39 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 40 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 41 |
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, |
|
| 42 |
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, |
|
| 43 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 44 |
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", |
|
| 45 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 46 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 47 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 48 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 49 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 50 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 51 |
accessionNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 52 |
minimumDepthInMeters,/location/locationevent/waterdepth_m/_avg/1, |
|
| 53 |
maximumDepthInMeters,/location/locationevent/waterdepth_m/_avg/2, |
|
| 54 |
locality,/location/locationnarrative/_merge/1, |
|
| 55 |
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 56 |
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 57 |
continent,/location/locationplace/*_id/place/continent, |
|
| 58 |
country,/location/locationplace/*_id/place/country, |
|
| 59 |
county,/location/locationplace/*_id/place/county, |
|
| 60 |
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" |
|
| 61 |
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" |
|
| 62 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 63 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 64 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 65 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
|
| 66 |
*altitude_precision,,** No join mapping for *altitude_precision ** |
|
| 67 |
*created,,** No join mapping for *created ** |
|
| 68 |
*data_provider_id,,** No join mapping for *data_provider_id ** |
|
| 69 |
*data_resource_id,,** No join mapping for *data_resource_id ** |
|
| 70 |
*deleted,,** No join mapping for *deleted ** |
|
| 71 |
*depth_precision,,** No join mapping for *depth_precision ** |
|
| 72 |
*resource_access_point_id,,** No join mapping for *resource_access_point_id ** |
|
| 73 |
*unit_qualifier,,** No join mapping for *unit_qualifier ** |
|
| 74 |
authors,,** No join mapping for authors ** |
|
| 75 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 76 |
coordinatePrecision_deg,,** No join mapping for coordinatePrecision_deg ** |
|
| 77 |
day,,** No join mapping for day ** |
|
| 78 |
modified,,** No join mapping for modified ** |
|
| 79 |
month,,** No join mapping for month ** |
|
| 80 |
raw_occurrence_record-row_num,,** No join mapping for raw_occurrence_record-row_num ** |
|
| 81 |
year,,** No join mapping for year ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 82 | 2 | |
| inputs/GBIF/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
:specimen,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype", |
|
| 3 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 4 |
:specimen,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left", |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 5 | 2 | |
| inputs/input.Makefile | ||
|---|---|---|
| 366 | 366 |
endif |
| 367 | 367 |
|
| 368 | 368 |
%/VegBIEN.csv: %/map.csv $(coreMap) |
| 369 |
<$< $(bin)/cat_cols 1 2$(if $(wildcard\
|
|
| 370 |
$*/run),|$(bin)/cols 1 1 3|(head -1 $<; tail -n +2)\
|
|
| 371 |
)|$(bin)/join $(coreMap)|$(bin)/sort_map >$@
|
|
| 369 |
$(if $(wildcard $*/run),-ln -s ../$(coreMap) $@\
|
|
| 370 |
,<$< $(bin)/cat_cols 1 2|$(bin)/join $(coreMap)|$(bin)/sort_map >$@)
|
|
| 371 |
# ignore errors if symlink exists
|
|
| 372 | 372 |
maps += $(autogenMaps) |
| 373 | 373 |
|
| 374 | 374 |
maps: $(maps) _always ; |
| inputs/FIA/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
:plot,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype", |
|
| 3 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 4 |
:plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left", |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 5 | 2 | |
| inputs/FIA/PLOT/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
locationName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
locationID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
locationID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
locationName,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 6 |
locationID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 7 |
locationName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 8 |
locationID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 9 |
locationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 10 |
locationName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 11 |
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 12 |
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 13 |
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" |
|
| 14 |
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" |
|
| 15 |
locationID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 16 |
locationID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 17 |
*COUNTYCD,,** No join mapping for *COUNTYCD ** |
|
| 18 |
*INVYR,,** No join mapping for *INVYR ** |
|
| 19 |
*PLOT-CONGCD,,** No join mapping for *PLOT-CONGCD ** |
|
| 20 |
*PLOT-CREATED_BY,,** No join mapping for *PLOT-CREATED_BY ** |
|
| 21 |
*PLOT-CREATED_DATE,,** No join mapping for *PLOT-CREATED_DATE ** |
|
| 22 |
*PLOT-CREATED_IN_INSTANCE,,** No join mapping for *PLOT-CREATED_IN_INSTANCE ** |
|
| 23 |
*PLOT-CTY_CN,,** No join mapping for *PLOT-CTY_CN ** |
|
| 24 |
*PLOT-CYCLE,,** No join mapping for *PLOT-CYCLE ** |
|
| 25 |
*PLOT-DECLINATION,,** No join mapping for *PLOT-DECLINATION ** |
|
| 26 |
*PLOT-DESIGNCD,,** No join mapping for *PLOT-DESIGNCD ** |
|
| 27 |
*PLOT-DESIGNCD_P2A,,** No join mapping for *PLOT-DESIGNCD_P2A ** |
|
| 28 |
*PLOT-ECOSUBCD,,** No join mapping for *PLOT-ECOSUBCD ** |
|
| 29 |
*PLOT-ECO_UNIT_PNW,,** No join mapping for *PLOT-ECO_UNIT_PNW ** |
|
| 30 |
*PLOT-EMAP_HEX,,** No join mapping for *PLOT-EMAP_HEX ** |
|
| 31 |
*PLOT-GROW_TYP_CD,,** No join mapping for *PLOT-GROW_TYP_CD ** |
|
| 32 |
*PLOT-INTENSITY,,** No join mapping for *PLOT-INTENSITY ** |
|
| 33 |
*PLOT-INVASIVE_SAMPLING_STATUS_CD,,** No join mapping for *PLOT-INVASIVE_SAMPLING_STATUS_CD ** |
|
| 34 |
*PLOT-INVASIVE_SPECIMEN_RULE_CD,,** No join mapping for *PLOT-INVASIVE_SPECIMEN_RULE_CD ** |
|
| 35 |
*PLOT-KINDCD,,** No join mapping for *PLOT-KINDCD ** |
|
| 36 |
*PLOT-KINDCD_NC,,** No join mapping for *PLOT-KINDCD_NC ** |
|
| 37 |
*PLOT-MACRO_BREAKPOINT_DIA,,** No join mapping for *PLOT-MACRO_BREAKPOINT_DIA ** |
|
| 38 |
*PLOT-MANUAL,,** No join mapping for *PLOT-MANUAL ** |
|
| 39 |
*PLOT-MICROPLOT_LOC,,** No join mapping for *PLOT-MICROPLOT_LOC ** |
|
| 40 |
*PLOT-MODIFIED_BY,,** No join mapping for *PLOT-MODIFIED_BY ** |
|
| 41 |
*PLOT-MODIFIED_DATE,,** No join mapping for *PLOT-MODIFIED_DATE ** |
|
| 42 |
*PLOT-MODIFIED_IN_INSTANCE,,** No join mapping for *PLOT-MODIFIED_IN_INSTANCE ** |
|
| 43 |
*PLOT-MORT_TYP_CD,,** No join mapping for *PLOT-MORT_TYP_CD ** |
|
| 44 |
*PLOT-NF_PLOT_NONSAMPLE_REASN_CD,,** No join mapping for *PLOT-NF_PLOT_NONSAMPLE_REASN_CD ** |
|
| 45 |
*PLOT-NF_PLOT_STATUS_CD,,** No join mapping for *PLOT-NF_PLOT_STATUS_CD ** |
|
| 46 |
*PLOT-NF_SAMPLING_STATUS_CD,,** No join mapping for *PLOT-NF_SAMPLING_STATUS_CD ** |
|
| 47 |
*PLOT-P2PANEL,,** No join mapping for *PLOT-P2PANEL ** |
|
| 48 |
*PLOT-P2VEG_SAMPLING_LEVEL_DETAIL_CD,,** No join mapping for *PLOT-P2VEG_SAMPLING_LEVEL_DETAIL_CD ** |
|
| 49 |
*PLOT-P2VEG_SAMPLING_STATUS_CD,,** No join mapping for *PLOT-P2VEG_SAMPLING_STATUS_CD ** |
|
| 50 |
*PLOT-P3PANEL,,** No join mapping for *PLOT-P3PANEL ** |
|
| 51 |
*PLOT-PLOT_NONSAMPLE_REASN_CD,,** No join mapping for *PLOT-PLOT_NONSAMPLE_REASN_CD ** |
|
| 52 |
*PLOT-PLOT_STATUS_CD,,** No join mapping for *PLOT-PLOT_STATUS_CD ** |
|
| 53 |
*PLOT-PREV_PLT_CN,,** No join mapping for *PLOT-PREV_PLT_CN ** |
|
| 54 |
*PLOT-QA_STATUS,,** No join mapping for *PLOT-QA_STATUS ** |
|
| 55 |
*PLOT-RDDISTCD,,** No join mapping for *PLOT-RDDISTCD ** |
|
| 56 |
*PLOT-REMPER,,** No join mapping for *PLOT-REMPER ** |
|
| 57 |
*PLOT-SAMP_METHOD_CD,,** No join mapping for *PLOT-SAMP_METHOD_CD ** |
|
| 58 |
*PLOT-SRV_CN,,** No join mapping for *PLOT-SRV_CN ** |
|
| 59 |
*PLOT-SUBCYCLE,,** No join mapping for *PLOT-SUBCYCLE ** |
|
| 60 |
*PLOT-SUBPANEL,,** No join mapping for *PLOT-SUBPANEL ** |
|
| 61 |
*PLOT-SUBP_EXAMINE_CD,,** No join mapping for *PLOT-SUBP_EXAMINE_CD ** |
|
| 62 |
*PLOT-TOPO_POSITION_PNW,,** No join mapping for *PLOT-TOPO_POSITION_PNW ** |
|
| 63 |
*PLOT-WATERCD,,** No join mapping for *PLOT-WATERCD ** |
|
| 64 |
*PLOT-row_num,,** No join mapping for *PLOT-row_num ** |
|
| 65 |
*STATECD,,** No join mapping for *STATECD ** |
|
| 66 |
*UNITCD,,** No join mapping for *UNITCD ** |
|
| 67 |
day,,** No join mapping for day ** |
|
| 68 |
elevation_ft,,** No join mapping for elevation_ft ** |
|
| 69 |
month,,** No join mapping for month ** |
|
| 70 |
year,,** No join mapping for year ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 71 | 2 | |
| inputs/FIA/COUNTY/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
county,/location/locationplace/*_id/place/county, |
|
| 3 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 4 |
*COUNTY-CN,,** No join mapping for *COUNTY-CN ** |
|
| 5 |
*COUNTY-CREATED_BY,,** No join mapping for *COUNTY-CREATED_BY ** |
|
| 6 |
*COUNTY-CREATED_DATE,,** No join mapping for *COUNTY-CREATED_DATE ** |
|
| 7 |
*COUNTY-CREATED_IN_INSTANCE,,** No join mapping for *COUNTY-CREATED_IN_INSTANCE ** |
|
| 8 |
*COUNTY-MODIFIED_BY,,** No join mapping for *COUNTY-MODIFIED_BY ** |
|
| 9 |
*COUNTY-MODIFIED_DATE,,** No join mapping for *COUNTY-MODIFIED_DATE ** |
|
| 10 |
*COUNTY-MODIFIED_IN_INSTANCE,,** No join mapping for *COUNTY-MODIFIED_IN_INSTANCE ** |
|
| 11 |
*COUNTY-row_num,,** No join mapping for *COUNTY-row_num ** |
|
| 12 |
*COUNTYCD,,** No join mapping for *COUNTYCD ** |
|
| 13 |
*STATECD,,** No join mapping for *STATECD ** |
|
| 14 |
*UNITCD,,** No join mapping for *UNITCD ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 15 | 2 | |
| inputs/FIA/REF_PLANT_DICTIONARY/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 3 |
taxonName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 4 |
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=forma]/taxonepithet", |
|
| 5 |
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet", |
|
| 6 |
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", |
|
| 7 |
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", |
|
| 8 |
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", |
|
| 9 |
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", |
|
| 10 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 11 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 12 |
taxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 13 |
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, |
|
| 14 |
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, |
|
| 15 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 16 |
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2", |
|
| 17 |
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2", |
|
| 18 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 19 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 20 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 21 |
taxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 22 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 23 |
*F_PREFIX,,** No join mapping for *F_PREFIX ** |
|
| 24 |
*GENERA_BINOMIAL_AUTHOR,,** No join mapping for *GENERA_BINOMIAL_AUTHOR ** |
|
| 25 |
*PLANT_SYMBOL,,** No join mapping for *PLANT_SYMBOL ** |
|
| 26 |
*PLANT_SYMBOL_TYPE,,** No join mapping for *PLANT_SYMBOL_TYPE ** |
|
| 27 |
*QUADRINOMIAL_AUTHOR,,** No join mapping for *QUADRINOMIAL_AUTHOR ** |
|
| 28 |
*REF_PLANT_DICTIONARY-CATEGORY,,** No join mapping for *REF_PLANT_DICTIONARY-CATEGORY ** |
|
| 29 |
*REF_PLANT_DICTIONARY-CN,,** No join mapping for *REF_PLANT_DICTIONARY-CN ** |
|
| 30 |
*REF_PLANT_DICTIONARY-CREATED_BY,,** No join mapping for *REF_PLANT_DICTIONARY-CREATED_BY ** |
|
| 31 |
*REF_PLANT_DICTIONARY-CREATED_DATE,,** No join mapping for *REF_PLANT_DICTIONARY-CREATED_DATE ** |
|
| 32 |
*REF_PLANT_DICTIONARY-CREATED_IN_INSTANCE,,** No join mapping for *REF_PLANT_DICTIONARY-CREATED_IN_INSTANCE ** |
|
| 33 |
*REF_PLANT_DICTIONARY-DURATION,,** No join mapping for *REF_PLANT_DICTIONARY-DURATION ** |
|
| 34 |
*REF_PLANT_DICTIONARY-MODIFIED_BY,,** No join mapping for *REF_PLANT_DICTIONARY-MODIFIED_BY ** |
|
| 35 |
*REF_PLANT_DICTIONARY-MODIFIED_DATE,,** No join mapping for *REF_PLANT_DICTIONARY-MODIFIED_DATE ** |
|
| 36 |
*REF_PLANT_DICTIONARY-MODIFIED_IN_INSTANCE,,** No join mapping for *REF_PLANT_DICTIONARY-MODIFIED_IN_INSTANCE ** |
|
| 37 |
*REF_PLANT_DICTIONARY-NEW_SCIENTIFIC_NAME,,** No join mapping for *REF_PLANT_DICTIONARY-NEW_SCIENTIFIC_NAME ** |
|
| 38 |
*REF_PLANT_DICTIONARY-NEW_SYMBOL,,** No join mapping for *REF_PLANT_DICTIONARY-NEW_SYMBOL ** |
|
| 39 |
*REF_PLANT_DICTIONARY-NOTES,,** No join mapping for *REF_PLANT_DICTIONARY-NOTES ** |
|
| 40 |
*REF_PLANT_DICTIONARY-STATE_AND_PROVINCE,,** No join mapping for *REF_PLANT_DICTIONARY-STATE_AND_PROVINCE ** |
|
| 41 |
*REF_PLANT_DICTIONARY-STATE_DISTRIBUTION,,** No join mapping for *REF_PLANT_DICTIONARY-STATE_DISTRIBUTION ** |
|
| 42 |
*REF_PLANT_DICTIONARY-US_NATIVITY,,** No join mapping for *REF_PLANT_DICTIONARY-US_NATIVITY ** |
|
| 43 |
*REF_PLANT_DICTIONARY-row_num,,** No join mapping for *REF_PLANT_DICTIONARY-row_num ** |
|
| 44 |
*SSP_PREFIX,,** No join mapping for *SSP_PREFIX ** |
|
| 45 |
*SUBVAR,,** No join mapping for *SUBVAR ** |
|
| 46 |
*SUBVARIETY,,** No join mapping for *SUBVARIETY ** |
|
| 47 |
*TRINOMIAL_AUTHOR,,** No join mapping for *TRINOMIAL_AUTHOR ** |
|
| 48 |
*VAR_PREFIX,,** No join mapping for *VAR_PREFIX ** |
|
| 49 |
*XGENUS,,** No join mapping for *XGENUS ** |
|
| 50 |
*XSPECIES,,** No join mapping for *XSPECIES ** |
|
| 51 |
*XSUBSPECIES,,** No join mapping for *XSUBSPECIES ** |
|
| 52 |
*XVARIETY,,** No join mapping for *XVARIETY ** |
|
| 53 |
taxonGrowthForm,,** No join mapping for taxonGrowthForm ** |
|
| 54 |
vernacularName,,** No join mapping for vernacularName ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 55 | 2 | |
| inputs/FIA/REF_UNIT/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
*REF_UNIT-CREATED_BY,,** No join mapping for *REF_UNIT-CREATED_BY ** |
|
| 3 |
*REF_UNIT-CREATED_DATE,,** No join mapping for *REF_UNIT-CREATED_DATE ** |
|
| 4 |
*REF_UNIT-CREATED_IN_INSTANCE,,** No join mapping for *REF_UNIT-CREATED_IN_INSTANCE ** |
|
| 5 |
*REF_UNIT-MEANING,,** No join mapping for *REF_UNIT-MEANING ** |
|
| 6 |
*REF_UNIT-MODIFIED_BY,,** No join mapping for *REF_UNIT-MODIFIED_BY ** |
|
| 7 |
*REF_UNIT-MODIFIED_DATE,,** No join mapping for *REF_UNIT-MODIFIED_DATE ** |
|
| 8 |
*REF_UNIT-MODIFIED_IN_INSTANCE,,** No join mapping for *REF_UNIT-MODIFIED_IN_INSTANCE ** |
|
| 9 |
*REF_UNIT-row_num,,** No join mapping for *REF_UNIT-row_num ** |
|
| 10 |
*STATECD,,** No join mapping for *STATECD ** |
|
| 11 |
*UNITCD,,** No join mapping for *UNITCD ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 12 | 2 | |
| inputs/FIA/COND/test.xml.ref | ||
|---|---|---|
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode>$locationName</authorlocationcode> |
| 11 |
<iscultivated>$cultivated</iscultivated> |
|
| 11 | 12 |
<locationevent><authoreventcode>$authorEventCode</authoreventcode></locationevent> |
| 12 | 13 |
<slopeaspect_deg><_compass><value>$slopeAspect</value></_compass></slopeaspect_deg> |
| 13 | 14 |
<slopegradient_fraction>$slopeGradient</slopegradient_fraction> |
| inputs/FIA/COND/VegBIEN.csv | ||
|---|---|---|
| 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
locationName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
authorEventCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 4 |
locationName,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 5 |
authorEventCode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 6 |
authorEventCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 7 |
locationName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 8 |
authorEventCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 9 |
authorEventCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 10 |
locationName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 11 |
slopeAspect,/location/slopeaspect_deg/_alt/1/_compass/value, |
|
| 12 |
slopeGradient,/location/slopegradient_fraction/_alt/1, |
|
| 13 |
*COND-ADFORCD,,** No join mapping for *COND-ADFORCD ** |
|
| 14 |
*COND-ADMIN_WITHDRAWN_CD,,** No join mapping for *COND-ADMIN_WITHDRAWN_CD ** |
|
| 15 |
*COND-ALSTK,,** No join mapping for *COND-ALSTK ** |
|
| 16 |
*COND-ALSTKCD,,** No join mapping for *COND-ALSTKCD ** |
|
| 17 |
*COND-BALIVE,,** No join mapping for *COND-BALIVE ** |
|
| 18 |
*COND-CANOPY_CVR_SAMPLE_METHOD_CD,,** No join mapping for *COND-CANOPY_CVR_SAMPLE_METHOD_CD ** |
|
| 19 |
*COND-CARBON_DOWN_DEAD,,** No join mapping for *COND-CARBON_DOWN_DEAD ** |
|
| 20 |
*COND-CARBON_LITTER,,** No join mapping for *COND-CARBON_LITTER ** |
|
| 21 |
*COND-CARBON_SOIL_ORG,,** No join mapping for *COND-CARBON_SOIL_ORG ** |
|
| 22 |
*COND-CARBON_STANDING_DEAD,,** No join mapping for *COND-CARBON_STANDING_DEAD ** |
|
| 23 |
*COND-CARBON_UNDERSTORY_AG,,** No join mapping for *COND-CARBON_UNDERSTORY_AG ** |
|
| 24 |
*COND-CARBON_UNDERSTORY_BG,,** No join mapping for *COND-CARBON_UNDERSTORY_BG ** |
|
| 25 |
*COND-CN,,** No join mapping for *COND-CN ** |
|
| 26 |
*COND-CONDPROP_UNADJ,,** No join mapping for *COND-CONDPROP_UNADJ ** |
|
| 27 |
*COND-COND_NONSAMPLE_REASN_CD,,** No join mapping for *COND-COND_NONSAMPLE_REASN_CD ** |
|
| 28 |
*COND-COND_STATUS_CD,,** No join mapping for *COND-COND_STATUS_CD ** |
|
| 29 |
*COND-CREATED_BY,,** No join mapping for *COND-CREATED_BY ** |
|
| 30 |
*COND-CREATED_DATE,,** No join mapping for *COND-CREATED_DATE ** |
|
| 31 |
*COND-CREATED_IN_INSTANCE,,** No join mapping for *COND-CREATED_IN_INSTANCE ** |
|
| 32 |
*COND-CYCLE,,** No join mapping for *COND-CYCLE ** |
|
| 33 |
*COND-DSTRBCD1,,** No join mapping for *COND-DSTRBCD1 ** |
|
| 34 |
*COND-DSTRBCD2,,** No join mapping for *COND-DSTRBCD2 ** |
|
| 35 |
*COND-DSTRBCD3,,** No join mapping for *COND-DSTRBCD3 ** |
|
| 36 |
*COND-DSTRBYR1,,** No join mapping for *COND-DSTRBYR1 ** |
|
| 37 |
*COND-DSTRBYR2,,** No join mapping for *COND-DSTRBYR2 ** |
|
| 38 |
*COND-DSTRBYR3,,** No join mapping for *COND-DSTRBYR3 ** |
|
| 39 |
*COND-FIRE_SRS,,** No join mapping for *COND-FIRE_SRS ** |
|
| 40 |
*COND-FLDAGE,,** No join mapping for *COND-FLDAGE ** |
|
| 41 |
*COND-FLDSZCD,,** No join mapping for *COND-FLDSZCD ** |
|
| 42 |
*COND-FLDTYPCD,,** No join mapping for *COND-FLDTYPCD ** |
|
| 43 |
*COND-FORINDCD,,** No join mapping for *COND-FORINDCD ** |
|
| 44 |
*COND-FORTYPCD,,** No join mapping for *COND-FORTYPCD ** |
|
| 45 |
*COND-FORTYPCDCALC,,** No join mapping for *COND-FORTYPCDCALC ** |
|
| 46 |
*COND-GRAZING_SRS,,** No join mapping for *COND-GRAZING_SRS ** |
|
| 47 |
*COND-GROUND_LAND_CLASS_PNW,,** No join mapping for *COND-GROUND_LAND_CLASS_PNW ** |
|
| 48 |
*COND-GSSTK,,** No join mapping for *COND-GSSTK ** |
|
| 49 |
*COND-GSSTKCD,,** No join mapping for *COND-GSSTKCD ** |
|
| 50 |
*COND-HABTYPCD1_DESCR_PUB_CD,,** No join mapping for *COND-HABTYPCD1_DESCR_PUB_CD ** |
|
| 51 |
*COND-HABTYPCD2,,** No join mapping for *COND-HABTYPCD2 ** |
|
| 52 |
*COND-HABTYPCD2_DESCR_PUB_CD,,** No join mapping for *COND-HABTYPCD2_DESCR_PUB_CD ** |
|
| 53 |
*COND-HABTYPCD2_PUB_CD,,** No join mapping for *COND-HABTYPCD2_PUB_CD ** |
|
| 54 |
*COND-HARVEST_TYPE1_SRS,,** No join mapping for *COND-HARVEST_TYPE1_SRS ** |
|
| 55 |
*COND-HARVEST_TYPE2_SRS,,** No join mapping for *COND-HARVEST_TYPE2_SRS ** |
|
| 56 |
*COND-HARVEST_TYPE3_SRS,,** No join mapping for *COND-HARVEST_TYPE3_SRS ** |
|
| 57 |
*COND-INDUSTRIALCD_FIADB,,** No join mapping for *COND-INDUSTRIALCD_FIADB ** |
|
| 58 |
*COND-LAND_USE_SRS,,** No join mapping for *COND-LAND_USE_SRS ** |
|
| 59 |
*COND-LIVE_CANOPY_CVR_PCT,,** No join mapping for *COND-LIVE_CANOPY_CVR_PCT ** |
|
| 60 |
*COND-LIVE_MISSING_CANOPY_CVR_PCT,,** No join mapping for *COND-LIVE_MISSING_CANOPY_CVR_PCT ** |
|
| 61 |
*COND-MACRPROP_UNADJ,,** No join mapping for *COND-MACRPROP_UNADJ ** |
|
| 62 |
*COND-MAPDEN,,** No join mapping for *COND-MAPDEN ** |
|
| 63 |
*COND-MICRPROP_UNADJ,,** No join mapping for *COND-MICRPROP_UNADJ ** |
|
| 64 |
*COND-MIXEDCONFCD,,** No join mapping for *COND-MIXEDCONFCD ** |
|
| 65 |
*COND-MODIFIED_BY,,** No join mapping for *COND-MODIFIED_BY ** |
|
| 66 |
*COND-MODIFIED_DATE,,** No join mapping for *COND-MODIFIED_DATE ** |
|
| 67 |
*COND-MODIFIED_IN_INSTANCE,,** No join mapping for *COND-MODIFIED_IN_INSTANCE ** |
|
| 68 |
*COND-NBR_LIVE_STEMS,,** No join mapping for *COND-NBR_LIVE_STEMS ** |
|
| 69 |
*COND-NF_COND_NONSAMPLE_REASN_CD,,** No join mapping for *COND-NF_COND_NONSAMPLE_REASN_CD ** |
|
| 70 |
*COND-NF_COND_STATUS_CD,,** No join mapping for *COND-NF_COND_STATUS_CD ** |
|
| 71 |
*COND-OPERABILITY_SRS,,** No join mapping for *COND-OPERABILITY_SRS ** |
|
| 72 |
*COND-OWNCD,,** No join mapping for *COND-OWNCD ** |
|
| 73 |
*COND-OWNGRPCD,,** No join mapping for *COND-OWNGRPCD ** |
|
| 74 |
*COND-OWNSUBCD,,** No join mapping for *COND-OWNSUBCD ** |
|
| 75 |
*COND-PHYSCLCD,,** No join mapping for *COND-PHYSCLCD ** |
|
| 76 |
*COND-PLANT_STOCKABILITY_FACTOR_PNW,,** No join mapping for *COND-PLANT_STOCKABILITY_FACTOR_PNW ** |
|
| 77 |
*COND-PLT_CN,,** No join mapping for *COND-PLT_CN ** |
|
| 78 |
*COND-PRESNFCD,,** No join mapping for *COND-PRESNFCD ** |
|
| 79 |
*COND-PROP_BASIS,,** No join mapping for *COND-PROP_BASIS ** |
|
| 80 |
*COND-RESERVCD,,** No join mapping for *COND-RESERVCD ** |
|
| 81 |
*COND-RESERVCD_FLD,,** No join mapping for *COND-RESERVCD_FLD ** |
|
| 82 |
*COND-SIBASE,,** No join mapping for *COND-SIBASE ** |
|
| 83 |
*COND-SICOND,,** No join mapping for *COND-SICOND ** |
|
| 84 |
*COND-SISP,,** No join mapping for *COND-SISP ** |
|
| 85 |
*COND-SITECLCD,,** No join mapping for *COND-SITECLCD ** |
|
| 86 |
*COND-SITECLCDEST,,** No join mapping for *COND-SITECLCDEST ** |
|
| 87 |
*COND-SITECL_METHOD,,** No join mapping for *COND-SITECL_METHOD ** |
|
| 88 |
*COND-SITETREE_TREE,,** No join mapping for *COND-SITETREE_TREE ** |
|
| 89 |
*COND-SOIL_ROOTING_DEPTH_PNW,,** No join mapping for *COND-SOIL_ROOTING_DEPTH_PNW ** |
|
| 90 |
*COND-STAND_STRUCTURE_SRS,,** No join mapping for *COND-STAND_STRUCTURE_SRS ** |
|
| 91 |
*COND-STDAGE,,** No join mapping for *COND-STDAGE ** |
|
| 92 |
*COND-STDORGCD,,** No join mapping for *COND-STDORGCD ** |
|
| 93 |
*COND-STDORGSP,,** No join mapping for *COND-STDORGSP ** |
|
| 94 |
*COND-STDSZCD,,** No join mapping for *COND-STDSZCD ** |
|
| 95 |
*COND-STND_COND_CD_PNWRS,,** No join mapping for *COND-STND_COND_CD_PNWRS ** |
|
| 96 |
*COND-STND_STRUC_CD_PNWRS,,** No join mapping for *COND-STND_STRUC_CD_PNWRS ** |
|
| 97 |
*COND-STUMP_CD_PNWRS,,** No join mapping for *COND-STUMP_CD_PNWRS ** |
|
| 98 |
*COND-SUBCYCLE,,** No join mapping for *COND-SUBCYCLE ** |
|
| 99 |
*COND-SUBPPROP_UNADJ,,** No join mapping for *COND-SUBPPROP_UNADJ ** |
|
| 100 |
*COND-TRTCD1,,** No join mapping for *COND-TRTCD1 ** |
|
| 101 |
*COND-TRTCD2,,** No join mapping for *COND-TRTCD2 ** |
|
| 102 |
*COND-TRTCD3,,** No join mapping for *COND-TRTCD3 ** |
|
| 103 |
*COND-TRTYR1,,** No join mapping for *COND-TRTYR1 ** |
|
| 104 |
*COND-TRTYR2,,** No join mapping for *COND-TRTYR2 ** |
|
| 105 |
*COND-TRTYR3,,** No join mapping for *COND-TRTYR3 ** |
|
| 106 |
*COND-VOL_LOC_GRP,,** No join mapping for *COND-VOL_LOC_GRP ** |
|
| 107 |
*COND-row_num,,** No join mapping for *COND-row_num ** |
|
| 108 |
*COUNTYCD,,** No join mapping for *COUNTYCD ** |
|
| 109 |
*HABTYPCD,,** No join mapping for *HABTYPCD ** |
|
| 110 |
*HABTYP_PUB_CD,,** No join mapping for *HABTYP_PUB_CD ** |
|
| 111 |
*INVYR,,** No join mapping for *INVYR ** |
|
| 112 |
*STATECD,,** No join mapping for *STATECD ** |
|
| 113 |
*UNITCD,,** No join mapping for *UNITCD ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 114 | 2 | |
| inputs/IRMNG/Source/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 3 | 2 | |
| inputs/IRMNG/species_homonyms/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 3 |
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", |
|
| 4 |
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", |
|
| 5 |
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", |
|
| 6 |
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", |
|
| 7 |
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", |
|
| 8 |
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", |
|
| 9 |
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", |
|
| 10 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 11 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 12 |
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", |
|
| 13 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
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, |
|
| 16 |
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, |
|
| 17 |
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", |
|
| 18 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 19 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 20 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 21 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 22 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 23 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 24 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 25 |
*row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 26 | 2 | |
| inputs/IRMNG/family_homonym_epithet/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 3 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 4 | 2 | |
| inputs/IRMNG/genus_homonym_epithet/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 3 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 4 | 2 | |
| inputs/IRMNG/family_homonyms/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 3 |
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", |
|
| 4 |
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", |
|
| 5 |
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", |
|
| 6 |
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", |
|
| 7 |
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", |
|
| 8 |
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", |
|
| 9 |
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", |
|
| 10 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 11 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 12 |
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", |
|
| 13 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
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, |
|
| 16 |
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, |
|
| 17 |
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", |
|
| 18 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 19 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 20 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 21 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 22 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 23 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 24 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 25 |
*row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 26 | 2 | |
| inputs/IRMNG/genus_homonyms/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 3 |
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", |
|
| 4 |
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", |
|
| 5 |
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", |
|
| 6 |
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", |
|
| 7 |
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", |
|
| 8 |
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", |
|
| 9 |
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", |
|
| 10 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 11 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 12 |
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", |
|
| 13 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
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, |
|
| 16 |
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, |
|
| 17 |
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", |
|
| 18 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 19 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 20 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 21 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 22 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 23 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 24 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 25 |
*row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 26 | 2 | |
Also available in: Unified diff
bugfix: inputs/input.Makefile: %/VegBIEN.csv: for new-style datasources, use a symlink to mappings/VegCore-VegBIEN.csv directly instead of prefiltering VegCore-VegBIEN.csv to include only the columns in map.csv. prefiltering used to be performed as part of mapping the map.csv VegCore output terms to VegBIEN using bin/join, but is no longer needed because the staging table columns are now VegCore terms. instead, the full VegCore-VegBIEN.csv is needed so that derived columns added in stage I or II validations are detected by bin/map (rather than just the original source columns in map.csv).