Revision 11865
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/CTFS/Plot.src/new_terms.csv | ||
|---|---|---|
| 1 |
SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)" |
|
| inputs/CTFS/Genus.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
Genus.src.row_num,*Genus.src.row_num,, |
|
| 3 |
GenusID,*GenusID,, |
|
| 4 |
Genus,genus,, |
|
| 5 |
GenusReferenceID,*GenusReferenceID,, |
|
| 6 |
GenusAuthority,*GenusAuthority,, |
|
| 7 |
FamilyID,*FamilyID,, |
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| inputs/CTFS/Family.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/StemObservation.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Organism.src/new_terms.csv | ||
|---|---|---|
| 1 |
x,organismX_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>." |
|
| 2 |
y,organismY_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>." |
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| inputs/CTFS/InfraspecificEpithet.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
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| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/InfraspecificEpithet.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*InfraspecificEpithet.src.row_num |
|
| 2 |
*SubSpeciesID |
|
| 3 |
*SpeciesID |
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| 4 |
*SubSpeciesCurrentTaxonFlag |
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| 5 |
*SubSpeciesObsoleteTaxonFlag |
|
| 6 |
*SubSpeciesMnemonic |
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| 7 |
*SubSpeciesAuthority |
|
| 8 |
*InfraSpecificLevel |
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| inputs/CTFS/Plot.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Plot.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Plot.src.row_num |
|
| 2 |
*CountryID |
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| 3 |
*ReferenceX |
|
| 4 |
*ReferenceY |
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| inputs/CTFS/Genus.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Family.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Family.src.row_num |
|
| 2 |
*FamilyID |
|
| 3 |
*ReferenceID |
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| inputs/CTFS/StemObservation.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*StemObservation.src.row_num |
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| 2 |
*TreeID |
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| 3 |
*HOM |
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| 4 |
*PrimaryStem |
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| 5 |
*ExactDate |
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| inputs/CTFS/Plot/new_terms.csv | ||
|---|---|---|
| 1 |
SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)" |
|
| inputs/CTFS/import_order.txt | ||
|---|---|---|
| 1 | 1 |
Source |
| 2 |
Country.src |
|
| 3 |
Plot.src |
|
| 2 | 4 |
Plot |
| 3 | 5 |
Subplot |
| 4 | 6 |
PlotObservation |
| 5 | 7 |
SubplotObservation |
| 8 |
Family.src |
|
| 9 |
Genus.src |
|
| 10 |
SpecificEpithet.src |
|
| 11 |
InfraspecificEpithet.src |
|
| 12 |
TaxonOccurrence.src |
|
| 6 | 13 |
TaxonOccurrence |
| 14 |
Organism.src |
|
| 15 |
Stem.src |
|
| 16 |
StemObservation.src |
|
| 7 | 17 |
StemObservation |
| 8 | 18 |
AggregateObservation |
| inputs/CTFS/StemObservation/create.sql | ||
|---|---|---|
| 1 | 1 |
SELECT * |
| 2 | 2 |
FROM "StemObservation.src" |
| 3 |
LEFT JOIN "Stem.src" USING ("TreeID", "StemID")
|
|
| 4 |
LEFT JOIN "Organism.src" USING ("TreeID")
|
|
| 5 |
LEFT JOIN "InfraspecificEpithet.src" USING ("SpeciesID", "SubSpeciesID")
|
|
| 6 |
LEFT JOIN "SpecificEpithet.src" USING ("SpeciesID")
|
|
| 7 |
LEFT JOIN "Genus.src" USING ("GenusID")
|
|
| 8 |
LEFT JOIN "Family.src" USING ("FamilyID")
|
|
| 3 |
LEFT JOIN "Stem.src" USING ("*TreeID", "authorStemCode")
|
|
| 4 |
LEFT JOIN "Organism.src" USING ("*TreeID")
|
|
| 5 |
LEFT JOIN "InfraspecificEpithet.src" USING ("*SpeciesID", "*SubSpeciesID")
|
|
| 6 |
LEFT JOIN "SpecificEpithet.src" USING ("*SpeciesID")
|
|
| 7 |
LEFT JOIN "Genus.src" USING ("*GenusID")
|
|
| 8 |
LEFT JOIN "Family.src" USING ("*FamilyID")
|
|
| inputs/CTFS/TaxonOccurrence.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
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| 0 | 3 | |
| inputs/CTFS/TaxonOccurrence.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
TaxonOccurrence.src.row_num,*TaxonOccurrence.src.row_num,, |
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| 3 |
SpeciesInvID,taxonObservationID,, |
|
| 4 |
CensusID,eventID,, |
|
| 5 |
PlotID,locationID,, |
|
| 6 |
SpeciesID,*SpeciesID,, |
|
| 7 |
SubSpeciesID,*SubSpeciesID,, |
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| inputs/CTFS/TaxonOccurrence.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*TaxonOccurrence.src.row_num |
|
| 2 |
taxonObservationID |
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| 3 |
*SpeciesID |
|
| 4 |
*SubSpeciesID |
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| inputs/CTFS/Country.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
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| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
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| 0 | 3 | |
| inputs/CTFS/Country.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
Country.src.row_num,*Country.src.row_num,, |
|
| 3 |
CountryID,*CountryID,, |
|
| 4 |
CountryName,country,, |
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| inputs/CTFS/Country.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Country.src.row_num |
|
| 2 |
*CountryID |
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| inputs/CTFS/SpecificEpithet.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
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| 0 | 3 | |
| inputs/CTFS/SpecificEpithet.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
SpecificEpithet.src.row_num,*SpecificEpithet.src.row_num,, |
|
| 3 |
SpeciesID,*SpeciesID,, |
|
| 4 |
SpeciesCurrentTaxonFlag,*SpeciesCurrentTaxonFlag,, |
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| 5 |
SpeciesObsoleteTaxonFlag,*SpeciesObsoleteTaxonFlag,, |
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| 6 |
GenusID,*GenusID,, |
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| 7 |
SpeciesReferenceID,*SpeciesReferenceID,, |
|
| 8 |
SpeciesName,specificEpithet,, |
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| 9 |
SpeciesMnemonic,*SpeciesMnemonic,, |
|
| 10 |
SpeciesAuthority,scientificNameAuthorship,, |
|
| 11 |
IDLevel,*IDLevel,, |
|
| 12 |
FieldFamily,*FieldFamily,, |
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| 13 |
Description,*Description,, |
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| inputs/CTFS/SpecificEpithet.src/new_terms.csv | ||
|---|---|---|
| 1 |
SpeciesAuthority,scientificNameAuthorship,, |
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| inputs/CTFS/SpecificEpithet.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*SpecificEpithet.src.row_num |
|
| 2 |
*SpeciesID |
|
| 3 |
*SpeciesCurrentTaxonFlag |
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| 4 |
*SpeciesObsoleteTaxonFlag |
|
| 5 |
*GenusID |
|
| 6 |
*SpeciesReferenceID |
|
| 7 |
*SpeciesMnemonic |
|
| 8 |
*IDLevel |
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| 9 |
*FieldFamily |
|
| 10 |
*Description |
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| inputs/CTFS/Stem.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Stem.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
Stem.src.row_num,*Stem.src.row_num,, |
|
| 3 |
StemID,authorStemCode,, |
|
| 4 |
TreeID,*TreeID,, |
|
| 5 |
StemTag,stem_subtag,, |
|
| 6 |
StemDescription,*StemDescription,, |
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| inputs/CTFS/Stem.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Stem.src.row_num |
|
| 2 |
*TreeID |
|
| 3 |
stem_subtag |
|
| 4 |
*StemDescription |
|
| inputs/CTFS/TaxonOccurrence/create.sql | ||
|---|---|---|
| 1 | 1 |
SELECT * |
| 2 | 2 |
FROM "TaxonOccurrence.src" |
| 3 |
LEFT JOIN "InfraspecificEpithet.src" USING ("SpeciesID", "SubSpeciesID")
|
|
| 4 |
LEFT JOIN "SpecificEpithet.src" USING ("SpeciesID")
|
|
| 5 |
LEFT JOIN "Genus.src" USING ("GenusID")
|
|
| 6 |
LEFT JOIN "Family.src" USING ("FamilyID")
|
|
| 3 |
LEFT JOIN "InfraspecificEpithet.src" USING ("*SpeciesID", "*SubSpeciesID")
|
|
| 4 |
LEFT JOIN "SpecificEpithet.src" USING ("*SpeciesID")
|
|
| 5 |
LEFT JOIN "Genus.src" USING ("*GenusID")
|
|
| 6 |
LEFT JOIN "Family.src" USING ("*FamilyID")
|
|
| inputs/CTFS/TaxonOccurrence/map.csv | ||
|---|---|---|
| 4 | 4 |
SpeciesID,*SpeciesID,, |
| 5 | 5 |
SubSpeciesID,*SubSpeciesID,, |
| 6 | 6 |
TaxonOccurrence.src.row_num,*TaxonOccurrence.src.row_num,, |
| 7 |
SpeciesInvID,taxonOccurrenceID,,
|
|
| 7 |
SpeciesInvID,taxonObservationID,,
|
|
| 8 | 8 |
CensusID,eventID,, |
| 9 | 9 |
PlotID,locationID,, |
| 10 | 10 |
InfraspecificEpithet.src.row_num,*InfraspecificEpithet.src.row_num,, |
| inputs/CTFS/TaxonOccurrence/unmapped_terms.csv | ||
|---|---|---|
| 3 | 3 |
*SpeciesID |
| 4 | 4 |
*SubSpeciesID |
| 5 | 5 |
*TaxonOccurrence.src.row_num |
| 6 |
taxonObservationID |
|
| 6 | 7 |
*InfraspecificEpithet.src.row_num |
| 7 | 8 |
*SubSpeciesCurrentTaxonFlag |
| 8 | 9 |
*SubSpeciesObsoleteTaxonFlag |
| inputs/CTFS/Organism.src/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/CTFS/Organism.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
Organism.src.row_num,*Organism.src.row_num,, |
|
| 3 |
TreeID,*TreeID,, |
|
| 4 |
QuadratID,subplot,,Not globally unique; unique only within Site |
|
| 5 |
PlotID,locationID,, |
|
| 6 |
Tag,individual_tag,, |
|
| 7 |
x,organismX_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>." |
|
| 8 |
y,organismY_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>." |
|
| 9 |
SpeciesID,*SpeciesID,, |
|
| 10 |
SubSpeciesID,*SubSpeciesID,, |
|
| inputs/CTFS/Organism.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Organism.src.row_num |
|
| 2 |
*TreeID |
|
| 3 |
individual_tag |
|
| 4 |
*SpeciesID |
|
| 5 |
*SubSpeciesID |
|
| inputs/CTFS/InfraspecificEpithet.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
InfraspecificEpithet.src.row_num,*InfraspecificEpithet.src.row_num,, |
|
| 3 |
SubSpeciesID,*SubSpeciesID,, |
|
| 4 |
SpeciesID,*SpeciesID,, |
|
| 5 |
SubSpeciesCurrentTaxonFlag,*SubSpeciesCurrentTaxonFlag,, |
|
| 6 |
SubSpeciesObsoleteTaxonFlag,*SubSpeciesObsoleteTaxonFlag,, |
|
| 7 |
SubSpeciesName,subspecies,, |
|
| 8 |
SubSpeciesMnemonic,*SubSpeciesMnemonic,, |
|
| 9 |
SubSpeciesAuthority,*SubSpeciesAuthority,, |
|
| 10 |
InfraSpecificLevel,*InfraSpecificLevel,, |
|
| inputs/CTFS/Plot.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
Plot.src.row_num,*Plot.src.row_num,, |
|
| 3 |
PlotID,locationID,, |
|
| 4 |
PlotName,locationName,, |
|
| 5 |
LocationName,locality,, |
|
| 6 |
CountryID,*CountryID,, |
|
| 7 |
Latitude,decimalLatitude,, |
|
| 8 |
Longitude,decimalLongitude,, |
|
| 9 |
Elevation,elevationInMeters,,"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>. |
|
| 10 |
|
|
| 11 |
[1] Using the following query: |
|
| 12 |
----- |
|
| 13 |
SELECT ""Elevation""::real, ""LocationName"" |
|
| 14 |
FROM ""CTFS"".""Plot"" |
|
| 15 |
GROUP BY ""Elevation""::real , ""LocationName"" |
|
| 16 |
ORDER BY ""Elevation""::real DESC |
|
| 17 |
-----" |
|
| 18 |
ReferenceX,*ReferenceX,,Rarely used |
|
| 19 |
ReferenceY,*ReferenceY,,Rarely used |
|
| 20 |
SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)" |
|
| 21 |
ShapeOfSite,footprintWKT,, |
|
| 22 |
DescriptionOfSite,locationRemarks,, |
|
| inputs/CTFS/Genus.src/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Genus.src.row_num |
|
| 2 |
*GenusID |
|
| 3 |
*GenusReferenceID |
|
| 4 |
*GenusAuthority |
|
| 5 |
*FamilyID |
|
| inputs/CTFS/Family.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
Family.src.row_num,*Family.src.row_num,, |
|
| 3 |
FamilyID,*FamilyID,, |
|
| 4 |
Family,family,, |
|
| 5 |
ReferenceID,*ReferenceID,, |
|
| inputs/CTFS/StemObservation.src/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
StemObservation.src.row_num,*StemObservation.src.row_num,, |
|
| 3 |
MeasureID,individualID,, |
|
| 4 |
CensusID,eventID,, |
|
| 5 |
StemID,authorStemCode,, |
|
| 6 |
TreeID,*TreeID,, |
|
| 7 |
DBH,diameterBreastHeight_cm,,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>. |
|
| 8 |
HOM,*HOM,, |
|
| 9 |
PrimaryStem,*PrimaryStem,, |
|
| 10 |
ExactDate,*ExactDate,, |
|
| inputs/CTFS/StemObservation.src/new_terms.csv | ||
|---|---|---|
| 1 |
MeasureID,individualID,, |
|
| inputs/CTFS/Plot/map.csv | ||
|---|---|---|
| 1 | 1 |
CTFS,VegCore,Filter,Comments |
| 2 |
CountryID,*CountryID,, |
|
| 3 |
Plot.src.row_num,*Plot.src.row_num,, |
|
| 4 |
PlotID,locationID,, |
|
| 5 |
PlotName,locationName,, |
|
| 6 |
LocationName,locality,, |
|
| 7 |
Latitude,decimalLatitude,, |
|
| 8 |
Longitude,decimalLongitude,, |
|
| 9 |
Elevation,elevationInMeters,,"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>. |
|
| 10 |
|
|
| 11 |
[1] Using the following query: |
|
| 12 |
----- |
|
| 13 |
SELECT ""Elevation""::real, ""LocationName"" |
|
| 14 |
FROM ""CTFS"".""Plot"" |
|
| 15 |
GROUP BY ""Elevation""::real , ""LocationName"" |
|
| 16 |
ORDER BY ""Elevation""::real DESC |
|
| 17 |
-----" |
|
| 18 |
ReferenceX,*ReferenceX,,Rarely used |
|
| 19 |
ReferenceY,*ReferenceY,,Rarely used |
|
| 20 |
SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)" |
|
| 21 |
ShapeOfSite,footprintWKT,, |
|
| 22 |
DescriptionOfSite,locationRemarks,, |
|
| 23 |
Country.src.row_num,*Country.src.row_num,, |
|
| 24 |
CountryName,country,, |
|
| 2 |
*CountryID,*CountryID,, |
|
| 3 |
*Plot.src.row_num,*Plot.src.row_num,, |
|
| 4 |
locationID,locationID,, |
|
| 5 |
locationName,locationName,, |
|
| 6 |
locality,locality,, |
|
| 7 |
decimalLatitude,decimalLatitude,, |
|
| 8 |
decimalLongitude,decimalLongitude,, |
|
| 9 |
elevationInMeters,elevationInMeters,, |
|
| 10 |
*ReferenceX,*ReferenceX,, |
|
| 11 |
*ReferenceY,*ReferenceY,, |
|
| 12 |
plotArea_ha,plotArea_ha,, |
|
| 13 |
footprintWKT,footprintWKT,, |
|
| 14 |
locationRemarks,locationRemarks,, |
|
| 15 |
*Country.src.row_num,*Country.src.row_num,, |
|
| 16 |
country,country,, |
|
| inputs/CTFS/Plot/header.csv | ||
|---|---|---|
| 1 |
CountryID,Plot.src.row_num,PlotID,PlotName,LocationName,Latitude,Longitude,Elevation,ReferenceX,ReferenceY,SizeOfSite,ShapeOfSite,DescriptionOfSite,Country.src.row_num,CountryName |
|
| 1 |
*CountryID,*Plot.src.row_num,locationID,locationName,locality,decimalLatitude,decimalLongitude,elevationInMeters,*ReferenceX,*ReferenceY,plotArea_ha,footprintWKT,locationRemarks,*Country.src.row_num,country |
|
| inputs/CTFS/Plot/create.sql | ||
|---|---|---|
| 1 | 1 |
SELECT * |
| 2 | 2 |
FROM "Plot.src" |
| 3 |
LEFT JOIN "Country.src" USING ("CountryID")
|
|
| 3 |
LEFT JOIN "Country.src" USING ("*CountryID")
|
|
Also available in: Unified diff
bugfix: inputs/CTFS/import_order.txt: added *.src so that these would be installed under new-style import as well. this means that their columns will now be automapped, requiring the names to be renamed to VegCore names in */create.sql. note that VegCore taxonOccurrenceID has been renamed to taxonObservationID since this was last run.