Revision 10419
Added by Aaron Marcuse-Kubitza almost 11 years ago
| inputs/CTFS/Plot/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
PlotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
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| 5 |
PlotName,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 6 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 7 |
SizeOfSite,/location/area_m2/_ha_to_m2/value,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)" |
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| 8 |
Elevation,/location/elevation_m/_alt/1,"Assuming units are m based on the range of values [1] and the country the data is from (Panama). Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>. |
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| 9 |
|
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| 10 |
[1] Using the following query: |
|
| 11 |
----- |
|
| 12 |
SELECT ""Elevation""::real, ""LocationName"" |
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| 13 |
FROM ""CTFS"".""Plot"" |
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GROUP BY ""Elevation""::real , ""LocationName"" |
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| 15 |
ORDER BY ""Elevation""::real DESC |
|
| 16 |
-----" |
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| 17 |
LocationName,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
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| 18 |
PlotName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 19 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 20 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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| 21 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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| 22 |
LocationName,/location/locationnarrative/_merge/1, |
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| 23 |
DescriptionOfSite,/location/locationnarrative/_merge/4, |
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| 24 |
ShapeOfSite,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc, |
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| 25 |
Latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
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| 26 |
Longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
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| 27 |
CountryName,/location/locationplace/*_id/place/country, |
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| 28 |
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" |
|
| 29 |
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" |
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| 30 |
CountryName,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
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| 31 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
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| 32 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
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| 33 |
Country.src.row_num,,** No join mapping for *Country.src.row_num ** |
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| 34 |
CountryID,,** No join mapping for *CountryID ** |
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| 35 |
Plot.src.row_num,,** No join mapping for *Plot.src.row_num ** |
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| 36 |
ReferenceX,,** No join mapping for *ReferenceX ** Rarely used |
|
| 37 |
ReferenceY,,** No join mapping for *ReferenceY ** Rarely used |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
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| 38 | 2 | |
| inputs/CTFS/StemObservation/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 | 3 |
SELECT mk_derived_col((:table_str, 'stemTag'), |
| 4 |
$$concat_ws('.', "Tag", "StemTag")$$); -- runtime: 30 s ("Time: 29390.121 ms") @starscream
|
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| 4 |
$$concat_ws('.', "individual_tag", "stem_subtag")$$); -- runtime: 30 s ("Time: 29390.121 ms") @starscream
|
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| 5 | 5 |
SELECT mk_derived_col((:table_str, 'tag'), $$"stemTag"$$); -- runtime: 25 s ("Time: 25010.752 ms") @starscream
|
| inputs/CTFS/StemObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
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| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| 0 | 3 | |
| inputs/CTFS/StemObservation/map.csv | ||
|---|---|---|
| 45 | 45 |
Family.src.row_num,*Family.src.row_num,, |
| 46 | 46 |
Family,family,, |
| 47 | 47 |
ReferenceID,*ReferenceID,, |
| 48 |
stemTag,stemTag,, |
|
| 49 |
tag,tag,, |
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| inputs/CTFS/StemObservation/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<parent_id><location><sourceaccessioncode>$PlotID</sourceaccessioncode></location></parent_id>
|
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| 11 |
<authorlocationcode>$QuadratID</authorlocationcode>
|
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| 10 |
<parent_id><location><sourceaccessioncode>$locationID</sourceaccessioncode></location></parent_id>
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| 11 |
<authorlocationcode>$subplot</authorlocationcode>
|
|
| 12 | 12 |
<locationevent> |
| 13 | 13 |
<parent_id> |
| 14 | 14 |
<locationevent> |
| ... | ... | |
| 16 | 16 |
<location> |
| 17 | 17 |
<sourceaccessioncode> |
| 18 | 18 |
<_if name="if subplot"> |
| 19 |
<cond>$QuadratID</cond>
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| 20 |
<then>$PlotID</then>
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| 19 |
<cond>$subplot</cond>
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| 20 |
<then>$locationID</then>
|
|
| 21 | 21 |
</_if> |
| 22 | 22 |
</sourceaccessioncode> |
| 23 | 23 |
</location> |
| 24 | 24 |
</location_id> |
| 25 |
<sourceaccessioncode>$CensusID</sourceaccessioncode>
|
|
| 25 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 26 | 26 |
</locationevent> |
| 27 | 27 |
</parent_id> |
| 28 | 28 |
<taxonoccurrence> |
| 29 | 29 |
<aggregateoccurrence> |
| 30 | 30 |
<plantobservation> |
| 31 |
<sourceaccessioncode>$MeasureID</sourceaccessioncode>
|
|
| 31 |
<sourceaccessioncode>$individualID</sourceaccessioncode>
|
|
| 32 | 32 |
<stemobservation> |
| 33 |
<authorstemcode>$StemID</authorstemcode>
|
|
| 34 |
<diameterbreastheight_m><_cm_to_m><value>$DBH</value></_cm_to_m></diameterbreastheight_m>
|
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| 33 |
<authorstemcode>$authorStemCode</authorstemcode>
|
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| 34 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
|
|
| 35 | 35 |
<tag>$tag</tag> |
| 36 |
<xposition_m>$x</xposition_m>
|
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| 37 |
<yposition_m>$y</yposition_m>
|
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| 36 |
<xposition_m>$organismX_m</xposition_m>
|
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| 37 |
<yposition_m>$organismY_m</yposition_m>
|
|
| 38 | 38 |
</stemobservation> |
| 39 | 39 |
</plantobservation> |
| 40 | 40 |
</aggregateoccurrence> |
| 41 | 41 |
<authortaxoncode>$tag</authortaxoncode> |
| 42 |
<sourceaccessioncode>$MeasureID</sourceaccessioncode>
|
|
| 42 |
<sourceaccessioncode>$individualID</sourceaccessioncode>
|
|
| 43 | 43 |
<taxondetermination> |
| 44 | 44 |
<taxonverbatim_id> |
| 45 | 45 |
<taxonverbatim> |
| ... | ... | |
| 59 | 59 |
<parent_id> |
| 60 | 60 |
<taxonlabel> |
| 61 | 61 |
<rank>subspecies</rank> |
| 62 |
<taxonepithet>$SubSpeciesName</taxonepithet>
|
|
| 62 |
<taxonepithet>$subspecies</taxonepithet>
|
|
| 63 | 63 |
<parent_id> |
| 64 | 64 |
<taxonlabel> |
| 65 | 65 |
<rank>species</rank> |
| 66 |
<taxonepithet>$SpeciesName</taxonepithet>
|
|
| 66 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 67 | 67 |
<parent_id> |
| 68 | 68 |
<taxonlabel> |
| 69 | 69 |
<rank>genus</rank> |
| 70 |
<taxonepithet>$Genus</taxonepithet>
|
|
| 70 |
<taxonepithet>$genus</taxonepithet>
|
|
| 71 | 71 |
<parent_id> |
| 72 | 72 |
<taxonlabel> |
| 73 | 73 |
<rank>family</rank> |
| 74 |
<taxonepithet>$Family</taxonepithet>
|
|
| 74 |
<taxonepithet>$family</taxonepithet>
|
|
| 75 | 75 |
</taxonlabel> |
| 76 | 76 |
</parent_id> |
| 77 | 77 |
</taxonlabel> |
| ... | ... | |
| 90 | 90 |
</parent_id> |
| 91 | 91 |
<taxonomicname> |
| 92 | 92 |
<_merge_prefix> |
| 93 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
|
|
| 93 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 94 | 94 |
<value> |
| 95 | 95 |
<_join_words> |
| 96 | 96 |
<1> |
| 97 | 97 |
<_join_words> |
| 98 |
<2><_filter_genus><value>$Genus</value></_filter_genus></2>
|
|
| 99 |
<3>$SpeciesName</3>
|
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| 100 |
<4>$SubSpeciesName</4>
|
|
| 98 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 99 |
<3>$specificEpithet</3>
|
|
| 100 |
<4>$subspecies</4>
|
|
| 101 | 101 |
</_join_words> |
| 102 | 102 |
</1> |
| 103 |
<2>$SpeciesAuthority</2>
|
|
| 103 |
<2>$scientificNameAuthorship</2>
|
|
| 104 | 104 |
</_join_words> |
| 105 | 105 |
</value> |
| 106 | 106 |
</_merge_prefix> |
| 107 | 107 |
</taxonomicname> |
| 108 | 108 |
</taxonlabel> |
| 109 | 109 |
</taxonlabel_id> |
| 110 |
<author>$SpeciesAuthority</author>
|
|
| 111 |
<family>$Family</family>
|
|
| 112 |
<genus>$Genus</genus>
|
|
| 113 |
<specific_epithet>$SpeciesName</specific_epithet>
|
|
| 110 |
<author>$scientificNameAuthorship</author>
|
|
| 111 |
<family>$family</family>
|
|
| 112 |
<genus>$genus</genus>
|
|
| 113 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 114 | 114 |
</taxonverbatim> |
| 115 | 115 |
</taxonverbatim_id> |
| 116 | 116 |
</taxondetermination> |
| ... | ... | |
| 118 | 118 |
</locationevent> |
| 119 | 119 |
<sourceaccessioncode> |
| 120 | 120 |
<_join> |
| 121 |
<1>$PlotID</1>
|
|
| 122 |
<2>$QuadratID</2>
|
|
| 121 |
<1>$locationID</1>
|
|
| 122 |
<2>$subplot</2>
|
|
| 123 | 123 |
</_join> |
| 124 | 124 |
</sourceaccessioncode> |
| 125 | 125 |
</location> |
| inputs/CTFS/StemObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
QuadratID,/location/authorlocationcode,Not globally unique; unique only within Site |
|
| 7 |
MeasureID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 8 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 9 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 10 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 11 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
|
| 12 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
|
| 13 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 14 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 15 |
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2, |
|
| 16 |
StemID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
|
| 17 |
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,Assuming units based on the range and precision of values. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>. |
|
| 18 |
tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
|
| 19 |
x,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>." |
|
| 20 |
y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>." |
|
| 21 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 22 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 23 |
MeasureID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
|
| 24 |
tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
|
| 25 |
MeasureID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 26 |
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2", |
|
| 27 |
SubSpeciesName,"/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", |
|
| 28 |
SpeciesName,"/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", |
|
| 29 |
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", |
|
| 30 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 31 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 32 |
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, |
|
| 33 |
SpeciesName,/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, |
|
| 34 |
SubSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 35 |
SpeciesAuthority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 36 |
SpeciesAuthority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 37 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 38 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 39 |
SpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 40 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 41 |
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 42 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 43 |
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/2",Not globally unique; unique only within Site |
|
| 44 |
Description,,** No join mapping for *Description ** |
|
| 45 |
ExactDate,,** No join mapping for *ExactDate ** |
|
| 46 |
Family.src.row_num,,** No join mapping for *Family.src.row_num ** |
|
| 47 |
FamilyID,,** No join mapping for *FamilyID ** |
|
| 48 |
FieldFamily,,** No join mapping for *FieldFamily ** |
|
| 49 |
Genus.src.row_num,,** No join mapping for *Genus.src.row_num ** |
|
| 50 |
GenusAuthority,,** No join mapping for *GenusAuthority ** |
|
| 51 |
GenusID,,** No join mapping for *GenusID ** |
|
| 52 |
GenusReferenceID,,** No join mapping for *GenusReferenceID ** |
|
| 53 |
HOM,,** No join mapping for *HOM ** |
|
| 54 |
IDLevel,,** No join mapping for *IDLevel ** |
|
| 55 |
InfraSpecificLevel,,** No join mapping for *InfraSpecificLevel ** |
|
| 56 |
InfraspecificEpithet.src.row_num,,** No join mapping for *InfraspecificEpithet.src.row_num ** |
|
| 57 |
Organism.src.row_num,,** No join mapping for *Organism.src.row_num ** |
|
| 58 |
PrimaryStem,,** No join mapping for *PrimaryStem ** |
|
| 59 |
ReferenceID,,** No join mapping for *ReferenceID ** |
|
| 60 |
SpeciesCurrentTaxonFlag,,** No join mapping for *SpeciesCurrentTaxonFlag ** |
|
| 61 |
SpeciesID,,** No join mapping for *SpeciesID ** |
|
| 62 |
SpeciesMnemonic,,** No join mapping for *SpeciesMnemonic ** |
|
| 63 |
SpeciesObsoleteTaxonFlag,,** No join mapping for *SpeciesObsoleteTaxonFlag ** |
|
| 64 |
SpeciesReferenceID,,** No join mapping for *SpeciesReferenceID ** |
|
| 65 |
SpecificEpithet.src.row_num,,** No join mapping for *SpecificEpithet.src.row_num ** |
|
| 66 |
Stem.src.row_num,,** No join mapping for *Stem.src.row_num ** |
|
| 67 |
StemDescription,,** No join mapping for *StemDescription ** |
|
| 68 |
StemObservation.src.row_num,,** No join mapping for *StemObservation.src.row_num ** |
|
| 69 |
StemTag,,** No join mapping for stem_subtag ** |
|
| 70 |
SubSpeciesAuthority,,** No join mapping for *SubSpeciesAuthority ** |
|
| 71 |
SubSpeciesCurrentTaxonFlag,,** No join mapping for *SubSpeciesCurrentTaxonFlag ** |
|
| 72 |
SubSpeciesID,,** No join mapping for *SubSpeciesID ** |
|
| 73 |
SubSpeciesMnemonic,,** No join mapping for *SubSpeciesMnemonic ** |
|
| 74 |
SubSpeciesObsoleteTaxonFlag,,** No join mapping for *SubSpeciesObsoleteTaxonFlag ** |
|
| 75 |
Tag,,** No join mapping for individual_tag ** |
|
| 76 |
TreeID,,** No join mapping for *TreeID ** |
|
| 77 |
stemTag,,** No join mapping for stemTag ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 78 | 2 | |
| inputs/CTFS/TaxonOccurrence/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/TaxonOccurrence/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<sourceaccessioncode>$PlotID</sourceaccessioncode>
|
|
| 10 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 11 | 11 |
<locationevent> |
| 12 |
<sourceaccessioncode>$CensusID</sourceaccessioncode>
|
|
| 12 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 13 | 13 |
<taxonoccurrence> |
| 14 |
<sourceaccessioncode>$SpeciesInvID</sourceaccessioncode>
|
|
| 14 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
|
|
| 15 | 15 |
<taxondetermination> |
| 16 | 16 |
<taxonverbatim_id> |
| 17 | 17 |
<taxonverbatim> |
| ... | ... | |
| 31 | 31 |
<parent_id> |
| 32 | 32 |
<taxonlabel> |
| 33 | 33 |
<rank>subspecies</rank> |
| 34 |
<taxonepithet>$SubSpeciesName</taxonepithet>
|
|
| 34 |
<taxonepithet>$subspecies</taxonepithet>
|
|
| 35 | 35 |
<parent_id> |
| 36 | 36 |
<taxonlabel> |
| 37 | 37 |
<rank>species</rank> |
| 38 |
<taxonepithet>$SpeciesName</taxonepithet>
|
|
| 38 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 39 | 39 |
<parent_id> |
| 40 | 40 |
<taxonlabel> |
| 41 | 41 |
<rank>genus</rank> |
| 42 |
<taxonepithet>$Genus</taxonepithet>
|
|
| 42 |
<taxonepithet>$genus</taxonepithet>
|
|
| 43 | 43 |
<parent_id> |
| 44 | 44 |
<taxonlabel> |
| 45 | 45 |
<rank>family</rank> |
| 46 |
<taxonepithet>$Family</taxonepithet>
|
|
| 46 |
<taxonepithet>$family</taxonepithet>
|
|
| 47 | 47 |
</taxonlabel> |
| 48 | 48 |
</parent_id> |
| 49 | 49 |
</taxonlabel> |
| ... | ... | |
| 62 | 62 |
</parent_id> |
| 63 | 63 |
<taxonomicname> |
| 64 | 64 |
<_merge_prefix> |
| 65 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
|
|
| 65 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 66 | 66 |
<value> |
| 67 | 67 |
<_join_words> |
| 68 | 68 |
<1> |
| 69 | 69 |
<_join_words> |
| 70 |
<2><_filter_genus><value>$Genus</value></_filter_genus></2>
|
|
| 71 |
<3>$SpeciesName</3>
|
|
| 72 |
<4>$SubSpeciesName</4>
|
|
| 70 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 71 |
<3>$specificEpithet</3>
|
|
| 72 |
<4>$subspecies</4>
|
|
| 73 | 73 |
</_join_words> |
| 74 | 74 |
</1> |
| 75 |
<2>$SpeciesAuthority</2>
|
|
| 75 |
<2>$scientificNameAuthorship</2>
|
|
| 76 | 76 |
</_join_words> |
| 77 | 77 |
</value> |
| 78 | 78 |
</_merge_prefix> |
| 79 | 79 |
</taxonomicname> |
| 80 | 80 |
</taxonlabel> |
| 81 | 81 |
</taxonlabel_id> |
| 82 |
<author>$SpeciesAuthority</author>
|
|
| 83 |
<family>$Family</family>
|
|
| 84 |
<genus>$Genus</genus>
|
|
| 85 |
<specific_epithet>$SpeciesName</specific_epithet>
|
|
| 82 |
<author>$scientificNameAuthorship</author>
|
|
| 83 |
<family>$family</family>
|
|
| 84 |
<genus>$genus</genus>
|
|
| 85 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 86 | 86 |
</taxonverbatim> |
| 87 | 87 |
</taxonverbatim_id> |
| 88 | 88 |
</taxondetermination> |
| inputs/CTFS/TaxonOccurrence/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 5 |
SpeciesInvID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 6 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 7 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 8 |
PlotID,"/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 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 10 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 11 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 12 |
SpeciesInvID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 13 |
SpeciesInvID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
|
| 14 |
SubSpeciesName,"/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", |
|
| 15 |
SpeciesName,"/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", |
|
| 16 |
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", |
|
| 17 |
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", |
|
| 18 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 19 |
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, |
|
| 20 |
SpeciesName,/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, |
|
| 21 |
SubSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 22 |
SpeciesAuthority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 23 |
SpeciesAuthority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 24 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 25 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 26 |
SpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 27 |
SpeciesInvID,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists", |
|
| 28 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 29 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 30 |
Description,,** No join mapping for *Description ** |
|
| 31 |
Family.src.row_num,,** No join mapping for *Family.src.row_num ** |
|
| 32 |
FamilyID,,** No join mapping for *FamilyID ** |
|
| 33 |
FieldFamily,,** No join mapping for *FieldFamily ** |
|
| 34 |
Genus.src.row_num,,** No join mapping for *Genus.src.row_num ** |
|
| 35 |
GenusAuthority,,** No join mapping for *GenusAuthority ** |
|
| 36 |
GenusID,,** No join mapping for *GenusID ** |
|
| 37 |
GenusReferenceID,,** No join mapping for *GenusReferenceID ** |
|
| 38 |
IDLevel,,** No join mapping for *IDLevel ** |
|
| 39 |
InfraSpecificLevel,,** No non-empty join mapping for UNUSED#InfraSpecificLevel ** |
|
| 40 |
InfraspecificEpithet.src.row_num,,** No join mapping for *InfraspecificEpithet.src.row_num ** |
|
| 41 |
ReferenceID,,** No join mapping for *ReferenceID ** |
|
| 42 |
SpeciesCurrentTaxonFlag,,** No join mapping for *SpeciesCurrentTaxonFlag ** |
|
| 43 |
SpeciesID,,** No join mapping for *SpeciesID ** |
|
| 44 |
SpeciesMnemonic,,** No join mapping for *SpeciesMnemonic ** |
|
| 45 |
SpeciesObsoleteTaxonFlag,,** No join mapping for *SpeciesObsoleteTaxonFlag ** |
|
| 46 |
SpeciesReferenceID,,** No join mapping for *SpeciesReferenceID ** |
|
| 47 |
SpecificEpithet.src.row_num,,** No join mapping for *SpecificEpithet.src.row_num ** |
|
| 48 |
SubSpeciesAuthority,,** No join mapping for *SubSpeciesAuthority ** |
|
| 49 |
SubSpeciesCurrentTaxonFlag,,** No join mapping for *SubSpeciesCurrentTaxonFlag ** |
|
| 50 |
SubSpeciesID,,** No join mapping for *SubSpeciesID ** |
|
| 51 |
SubSpeciesMnemonic,,** No join mapping for *SubSpeciesMnemonic ** |
|
| 52 |
SubSpeciesObsoleteTaxonFlag,,** No join mapping for *SubSpeciesObsoleteTaxonFlag ** |
|
| 53 |
TaxonOccurrence.src.row_num,,** No join mapping for *TaxonOccurrence.src.row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 54 | 2 | |
| inputs/CTFS/SubplotObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/SubplotObservation/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<parent_id><location><sourceaccessioncode>$PlotID</sourceaccessioncode></location></parent_id>
|
|
| 11 |
<authorlocationcode>$QuadratID</authorlocationcode>
|
|
| 10 |
<parent_id><location><sourceaccessioncode>$locationID</sourceaccessioncode></location></parent_id>
|
|
| 11 |
<authorlocationcode>$subplot</authorlocationcode>
|
|
| 12 | 12 |
<locationevent> |
| 13 | 13 |
<parent_id> |
| 14 | 14 |
<locationevent> |
| ... | ... | |
| 16 | 16 |
<location> |
| 17 | 17 |
<sourceaccessioncode> |
| 18 | 18 |
<_if name="if subplot"> |
| 19 |
<cond>$QuadratID</cond>
|
|
| 20 |
<then>$PlotID</then>
|
|
| 19 |
<cond>$subplot</cond>
|
|
| 20 |
<then>$locationID</then>
|
|
| 21 | 21 |
</_if> |
| 22 | 22 |
</sourceaccessioncode> |
| 23 | 23 |
</location> |
| 24 | 24 |
</location_id> |
| 25 |
<sourceaccessioncode>$CensusID</sourceaccessioncode>
|
|
| 25 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 26 | 26 |
</locationevent> |
| 27 | 27 |
</parent_id> |
| 28 | 28 |
</locationevent> |
| 29 | 29 |
<sourceaccessioncode> |
| 30 | 30 |
<_join> |
| 31 |
<1>$PlotID</1>
|
|
| 32 |
<2>$QuadratID</2>
|
|
| 31 |
<1>$locationID</1>
|
|
| 32 |
<2>$subplot</2>
|
|
| 33 | 33 |
</_join> |
| 34 | 34 |
</sourceaccessioncode> |
| 35 | 35 |
</location> |
| inputs/CTFS/SubplotObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
QuadratID,/location/authorlocationcode,Not globally unique; unique only within Site |
|
| 7 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 8 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 9 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 10 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
|
| 11 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
|
| 12 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 13 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 14 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 15 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 16 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 17 |
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 18 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 19 |
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/2",Not globally unique; unique only within Site |
|
| 20 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 21 | 2 | |
| inputs/CTFS/Subplot/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Subplot/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<parent_id><location><sourceaccessioncode>$PlotID</sourceaccessioncode></location></parent_id>
|
|
| 11 |
<authorlocationcode>$QuadratID</authorlocationcode>
|
|
| 10 |
<parent_id><location><sourceaccessioncode>$locationID</sourceaccessioncode></location></parent_id>
|
|
| 11 |
<authorlocationcode>$subplot</authorlocationcode>
|
|
| 12 | 12 |
<sourceaccessioncode> |
| 13 | 13 |
<_join> |
| 14 |
<1>$PlotID</1>
|
|
| 15 |
<2>$QuadratID</2>
|
|
| 14 |
<1>$locationID</1>
|
|
| 15 |
<2>$subplot</2>
|
|
| 16 | 16 |
</_join> |
| 17 | 17 |
</sourceaccessioncode> |
| 18 |
<sublocationxposition_m>$StartX</sublocationxposition_m>
|
|
| 19 |
<sublocationyposition_m>$StartY</sublocationyposition_m>
|
|
| 18 |
<sublocationxposition_m>$subplotX</sublocationxposition_m>
|
|
| 19 |
<sublocationyposition_m>$subplotY</sublocationyposition_m>
|
|
| 20 | 20 |
</location> |
| 21 | 21 |
</path> |
| 22 | 22 |
</_simplifyPath> |
| inputs/CTFS/Subplot/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 3 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
QuadratID,/location/authorlocationcode,Not globally unique; unique only within Site |
|
| 7 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 8 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
|
| 9 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",Not globally unique; unique only within Site |
|
| 10 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 11 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 12 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 13 |
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
|
| 14 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 15 |
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/2",Not globally unique; unique only within Site |
|
| 16 |
StartX,/location/sublocationxposition_m, |
|
| 17 |
StartY,/location/sublocationyposition_m, |
|
| 18 |
DimX,,** No join mapping for *DimX ** |
|
| 19 |
DimY,,** No join mapping for *DimY ** |
|
| 20 |
QuadratName,,** No non-empty join mapping for OMIT#QuadratName ** QuadratID is used for the same purpose |
|
| 21 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 22 | 2 | |
| inputs/CTFS/PlotObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/PlotObservation/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<sourceaccessioncode>$PlotID</sourceaccessioncode>
|
|
| 10 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 11 | 11 |
<locationevent> |
| 12 |
<authoreventcode>$PlotCensusNumber</authoreventcode>
|
|
| 13 |
<sourceaccessioncode>$CensusID</sourceaccessioncode>
|
|
| 14 |
<obsenddate>$EndDate</obsenddate>
|
|
| 15 |
<obsstartdate>$StartDate</obsstartdate>
|
|
| 12 |
<authoreventcode>$authorEventCode</authoreventcode>
|
|
| 13 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 14 |
<obsenddate>$endDate</obsenddate>
|
|
| 15 |
<obsstartdate>$startDate</obsstartdate>
|
|
| 16 | 16 |
</locationevent> |
| 17 | 17 |
</location> |
| 18 | 18 |
</path> |
| inputs/CTFS/PlotObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 3 |
PlotCensusNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 4 |
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
PlotCensusNumber,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 7 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 8 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 9 |
EndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 10 |
PlotCensusNumber,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 11 |
StartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 12 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 13 |
PlotCensusNumber,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 14 |
EndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/1", |
|
| 15 |
StartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
|
| 16 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 17 |
EndDate,/location/locationevent/obsenddate/_alt/1, |
|
| 18 |
StartDate,/location/locationevent/obsstartdate/_alt/1, |
|
| 19 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 20 |
PlotCensusNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 21 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 22 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 23 |
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 24 |
Description,,** No join mapping for *Description ** |
|
| 25 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 26 | 2 | |
| inputs/CTFS/AggregateObservation/postprocess.sql | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
-- runtime: 0.3 s ("Time: 256.926 ms") @starscream
|
| 4 | 4 |
SELECT set_col_types(:table_str, ARRAY[ |
| 5 |
('minDBHcm', 'double precision')
|
|
| 6 |
, ('maxDBHcm', 'double precision')
|
|
| 5 |
('diameterBreastHeight_min_cm', 'double precision')
|
|
| 6 |
, ('diameterBreastHeight_max_cm', 'double precision')
|
|
| 7 | 7 |
]::col_cast[]); |
| 8 | 8 |
|
| 9 | 9 |
|
| 10 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_cm'), $$_avg("minDBHcm", "maxDBHcm")$$); -- runtime: 0.4 s ("Time: 431.405 ms") @starscream
|
|
| 10 |
SELECT mk_derived_col((:table_str, 'diameterBreastHeight_cm'), $$_avg("diameterBreastHeight_min_cm", "diameterBreastHeight_max_cm")$$); -- runtime: 0.4 s ("Time: 431.405 ms") @starscream
|
|
| inputs/CTFS/AggregateObservation/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/AggregateObservation/map.csv | ||
|---|---|---|
| 20 | 20 |
minDBHcm,diameterBreastHeight_min_cm,, |
| 21 | 21 |
PlotSize,plotArea_ha,,Assuming units based on the range and precision of values compared to the PlotShape values |
| 22 | 22 |
PlotShape,footprintWKT,, |
| 23 |
diameterBreastHeight_cm,diameterBreastHeight_cm,, |
|
| inputs/CTFS/AggregateObservation/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$Plot</authorlocationcode>
|
|
| 11 |
<area_m2><_ha_to_m2><value>$PlotSize</value></_ha_to_m2></area_m2>
|
|
| 12 |
<elevation_m>$Elevation </elevation_m>
|
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 11 |
<area_m2><_ha_to_m2><value>$plotArea_ha</value></_ha_to_m2></area_m2>
|
|
| 12 |
<elevation_m>$elevationInMeters</elevation_m>
|
|
| 13 | 13 |
<locationevent> |
| 14 |
<authoreventcode>$CensusName</authoreventcode>
|
|
| 15 |
<obsenddate>$EndDate</obsenddate>
|
|
| 16 |
<obsstartdate>$StartDate</obsstartdate>
|
|
| 14 |
<authoreventcode>$authorEventCode</authoreventcode>
|
|
| 15 |
<obsenddate>$endDate</obsenddate>
|
|
| 16 |
<obsstartdate>$startDate</obsstartdate>
|
|
| 17 | 17 |
<taxonoccurrence> |
| 18 | 18 |
<aggregateoccurrence> |
| 19 |
<count>$Abund</count>
|
|
| 19 |
<count>$individualCount</count>
|
|
| 20 | 20 |
<plantobservation> |
| 21 |
<specimenreplicate><sourceaccessioncode>$DWstagingID</sourceaccessioncode></specimenreplicate>
|
|
| 21 |
<specimenreplicate><sourceaccessioncode>$occurrenceID</sourceaccessioncode></specimenreplicate>
|
|
| 22 | 22 |
<stemobservation><diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m></stemobservation> |
| 23 | 23 |
</plantobservation> |
| 24 | 24 |
</aggregateoccurrence> |
| 25 |
<growthform>$VegCategory</growthform>
|
|
| 26 |
<sourceaccessioncode>$DWstagingID</sourceaccessioncode>
|
|
| 25 |
<growthform>$growthForm</growthform>
|
|
| 26 |
<sourceaccessioncode>$occurrenceID</sourceaccessioncode>
|
|
| 27 | 27 |
<taxondetermination> |
| 28 | 28 |
<taxonverbatim_id> |
| 29 | 29 |
<taxonverbatim> |
| ... | ... | |
| 47 | 47 |
<parent_id> |
| 48 | 48 |
<taxonlabel> |
| 49 | 49 |
<rank>species</rank> |
| 50 |
<taxonepithet>$speciesname</taxonepithet>
|
|
| 50 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 51 | 51 |
<parent_id> |
| 52 | 52 |
<taxonlabel> |
| 53 | 53 |
<rank>genus</rank> |
| 54 |
<taxonepithet>$Genus </taxonepithet>
|
|
| 54 |
<taxonepithet>$genus</taxonepithet>
|
|
| 55 | 55 |
</taxonlabel> |
| 56 | 56 |
</parent_id> |
| 57 | 57 |
</taxonlabel> |
| ... | ... | |
| 68 | 68 |
</parent_id> |
| 69 | 69 |
<taxonomicname> |
| 70 | 70 |
<_join_words> |
| 71 |
<2><_filter_genus><value>$Genus </value></_filter_genus></2>
|
|
| 72 |
<3>$speciesname</3>
|
|
| 71 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 72 |
<3>$specificEpithet</3>
|
|
| 73 | 73 |
<4>$subspecies</4> |
| 74 | 74 |
</_join_words> |
| 75 | 75 |
</taxonomicname> |
| 76 | 76 |
</taxonlabel> |
| 77 | 77 |
</taxonlabel_id> |
| 78 |
<genus>$Genus </genus>
|
|
| 79 |
<specific_epithet>$speciesname</specific_epithet>
|
|
| 78 |
<genus>$genus</genus>
|
|
| 79 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 80 | 80 |
</taxonverbatim> |
| 81 | 81 |
</taxonverbatim_id> |
| 82 | 82 |
</taxondetermination> |
| ... | ... | |
| 87 | 87 |
<place> |
| 88 | 88 |
<coordinates_id> |
| 89 | 89 |
<coordinates> |
| 90 |
<footprintgeometry_dwc>$PlotShape</footprintgeometry_dwc>
|
|
| 90 |
<footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
|
|
| 91 | 91 |
<latitude_deg> |
| 92 | 92 |
<_nullIf> |
| 93 | 93 |
<null>0</null> |
| 94 | 94 |
<type>float</type> |
| 95 |
<value>$Latitude </value>
|
|
| 95 |
<value>$decimalLatitude</value>
|
|
| 96 | 96 |
</_nullIf> |
| 97 | 97 |
</latitude_deg> |
| 98 | 98 |
<longitude_deg> |
| 99 | 99 |
<_nullIf> |
| 100 | 100 |
<null>0</null> |
| 101 | 101 |
<type>float</type> |
| 102 |
<value>$Longitude </value>
|
|
| 102 |
<value>$decimalLongitude</value>
|
|
| 103 | 103 |
</_nullIf> |
| 104 | 104 |
</longitude_deg> |
| 105 | 105 |
</coordinates> |
| 106 | 106 |
</coordinates_id> |
| 107 |
<country>$Country</country>
|
|
| 107 |
<country>$country</country>
|
|
| 108 | 108 |
<matched_place_id> |
| 109 | 109 |
<place> |
| 110 | 110 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| ... | ... | |
| 115 | 115 |
<_nullIf> |
| 116 | 116 |
<null>0</null> |
| 117 | 117 |
<type>float</type> |
| 118 |
<value>$Latitude </value>
|
|
| 118 |
<value>$decimalLatitude</value>
|
|
| 119 | 119 |
</_nullIf> |
| 120 | 120 |
</latitude_deg> |
| 121 | 121 |
<longitude_deg> |
| 122 | 122 |
<_nullIf> |
| 123 | 123 |
<null>0</null> |
| 124 | 124 |
<type>float</type> |
| 125 |
<value>$Longitude </value>
|
|
| 125 |
<value>$decimalLongitude</value>
|
|
| 126 | 126 |
</_nullIf> |
| 127 | 127 |
</longitude_deg> |
| 128 | 128 |
</coordinates> |
| 129 | 129 |
</coordinates_id> |
| 130 |
<country>$Country</country>
|
|
| 131 |
<stateprovince>$Province</stateprovince> |
|
| 130 |
<country>$country</country>
|
|
| 131 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 132 | 132 |
</place> |
| 133 | 133 |
</matched_place_id> |
| 134 |
<stateprovince>$Province</stateprovince> |
|
| 134 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 135 | 135 |
</place> |
| 136 | 136 |
</place_id> |
| 137 | 137 |
</locationplace> |
| inputs/CTFS/AggregateObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
DWstagingID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
Plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 4 |
CensusName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 5 |
DWstagingID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
|
| 6 |
DWstagingID,"/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", |
|
| 7 |
Plot,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 8 |
PlotSize,/location/area_m2/_ha_to_m2/value,Assuming units based on the range and precision of values compared to the PlotShape values |
|
| 9 |
Elevation ,/location/elevation_m/_alt/1,Assuming units based on the range and precision of values |
|
| 10 |
DWstagingID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 11 |
CensusName,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 12 |
CensusName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 13 |
EndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 14 |
StartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 15 |
Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 16 |
CensusName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 17 |
EndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/1", |
|
| 18 |
StartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
|
| 19 |
EndDate,/location/locationevent/obsenddate/_alt/1, |
|
| 20 |
StartDate,/location/locationevent/obsstartdate/_alt/1, |
|
| 21 |
Abund,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
|
| 22 |
DWstagingID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
DWstagingID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 24 |
diameterBreastHeight_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value, |
|
| 25 |
CensusName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 26 |
Plot,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 27 |
VegCategory,/location/locationevent/taxonoccurrence/growthform, |
|
| 28 |
DWstagingID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 29 |
DWstagingID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 30 |
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", |
|
| 31 |
speciesname,"/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 |
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", |
|
| 33 |
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, |
|
| 34 |
speciesname,/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, |
|
| 35 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 36 |
Genus ,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 37 |
speciesname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 38 |
PlotShape,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc, |
|
| 39 |
Latitude ,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 40 |
Longitude ,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 41 |
Country,/location/locationplace/*_id/place/country, |
|
| 42 |
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" |
|
| 43 |
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" |
|
| 44 |
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 45 |
Province,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 46 |
Province,/location/locationplace/*_id/place/stateprovince, |
|
| 47 |
MeanDate,,** No join mapping for *MeanDate ** |
|
| 48 |
maxDBHcm,,** No join mapping for diameterBreastHeight_max_cm ** |
|
| 49 |
minDBHcm,,** No join mapping for diameterBreastHeight_min_cm ** |
|
| 50 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 51 | 2 | |
| inputs/CTFS/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/CTFS/Plot/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Plot/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$PlotName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$PlotID</sourceaccessioncode>
|
|
| 12 |
<area_m2><_ha_to_m2><value>$SizeOfSite</value></_ha_to_m2></area_m2>
|
|
| 13 |
<elevation_m>$Elevation</elevation_m>
|
|
| 14 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$LocationName</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 12 |
<area_m2><_ha_to_m2><value>$plotArea_ha</value></_ha_to_m2></area_m2>
|
|
| 13 |
<elevation_m>$elevationInMeters</elevation_m>
|
|
| 14 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 15 | 15 |
<locationnarrative> |
| 16 | 16 |
<_merge> |
| 17 |
<1>$LocationName</1>
|
|
| 18 |
<4>$DescriptionOfSite</4>
|
|
| 17 |
<1>$locality</1>
|
|
| 18 |
<4>$locationRemarks</4>
|
|
| 19 | 19 |
</_merge> |
| 20 | 20 |
</locationnarrative> |
| 21 | 21 |
<locationplace> |
| ... | ... | |
| 23 | 23 |
<place> |
| 24 | 24 |
<coordinates_id> |
| 25 | 25 |
<coordinates> |
| 26 |
<footprintgeometry_dwc>$ShapeOfSite</footprintgeometry_dwc>
|
|
| 26 |
<footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
|
|
| 27 | 27 |
<latitude_deg> |
| 28 | 28 |
<_nullIf> |
| 29 | 29 |
<null>0</null> |
| 30 | 30 |
<type>float</type> |
| 31 |
<value>$Latitude</value> |
|
| 31 |
<value>$decimalLatitude</value>
|
|
| 32 | 32 |
</_nullIf> |
| 33 | 33 |
</latitude_deg> |
| 34 | 34 |
<longitude_deg> |
| 35 | 35 |
<_nullIf> |
| 36 | 36 |
<null>0</null> |
| 37 | 37 |
<type>float</type> |
| 38 |
<value>$Longitude</value> |
|
| 38 |
<value>$decimalLongitude</value>
|
|
| 39 | 39 |
</_nullIf> |
| 40 | 40 |
</longitude_deg> |
| 41 | 41 |
</coordinates> |
| 42 | 42 |
</coordinates_id> |
| 43 |
<country>$CountryName</country>
|
|
| 43 |
<country>$country</country>
|
|
| 44 | 44 |
<matched_place_id> |
| 45 | 45 |
<place> |
| 46 | 46 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| ... | ... | |
| 51 | 51 |
<_nullIf> |
| 52 | 52 |
<null>0</null> |
| 53 | 53 |
<type>float</type> |
| 54 |
<value>$Latitude</value> |
|
| 54 |
<value>$decimalLatitude</value>
|
|
| 55 | 55 |
</_nullIf> |
| 56 | 56 |
</latitude_deg> |
| 57 | 57 |
<longitude_deg> |
| 58 | 58 |
<_nullIf> |
| 59 | 59 |
<null>0</null> |
| 60 | 60 |
<type>float</type> |
| 61 |
<value>$Longitude</value> |
|
| 61 |
<value>$decimalLongitude</value>
|
|
| 62 | 62 |
</_nullIf> |
| 63 | 63 |
</longitude_deg> |
| 64 | 64 |
</coordinates> |
| 65 | 65 |
</coordinates_id> |
| 66 |
<country>$CountryName</country>
|
|
| 66 |
<country>$country</country>
|
|
| 67 | 67 |
</place> |
| 68 | 68 |
</matched_place_id> |
| 69 | 69 |
</place> |
Also available in: Unified diff
inputs/CTFS/: switched to new-style import, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource