Revision 1230
Added by Aaron Marcuse-Kubitza almost 13 years ago
| inputs/SALVIAS/maps/VegBIEN.plots.csv | ||
|---|---|---|
| 19 | 19 |
date_finish,/obsenddate/_*/date, |
| 20 | 20 |
date_start,/obsstartdate/_*/date, |
| 21 | 21 |
Precip,/precipitation, |
| 22 |
soil_acidity,"/soilobs:[soilhorizon=unknown]/acidity/_map:[""<0.05""=0]/value/_units:[units=""%""]/value",
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| 23 |
soil_base,"/soilobs:[soilhorizon=unknown]/basesaturation/_units:[units=""%""]/value",
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| 24 |
soil_Ca,"/soilobs:[soilhorizon=unknown]/calcium/_units:[units=""%""]/value",
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| 25 |
soil_C,"/soilobs:[soilhorizon=unknown]/carbon/_units:[units=""%""]/value",
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| 26 |
soil_cation_cap,/soilobs:[soilhorizon=unknown]/cationexchangecapacity,
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| 27 |
clay_percent,"/soilobs:[soilhorizon=unknown]/clay/_units:[units=""%""]/value",
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| 28 |
soil_conductivity,/soilobs:[soilhorizon=unknown]/conductivity,
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| 29 |
soil_Mg,"/soilobs:[soilhorizon=unknown]/magnesium/_units:[units=""%""]/value",
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| 30 |
soil_N,"/soilobs:[soilhorizon=unknown]/nitrogen/_units:[units=""%""]/value",
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| 31 |
organic_percent,"/soilobs:[soilhorizon=unknown]/organic/_units:[units=""%""]/value",
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| 32 |
pH,/soilobs:[soilhorizon=unknown]/ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."
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| 33 |
soil_P,"/soilobs:[soilhorizon=unknown]/phosphorus/_map:[""<1,5""=0]/value/_units:[units=""%""]/value",
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| 34 |
soil_K,"/soilobs:[soilhorizon=unknown]/potassium/_units:[units=""%""]/value",
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| 35 |
sand_percent,"/soilobs:[soilhorizon=unknown]/sand/_units:[units=""%""]/value",
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| 36 |
silt_percent,"/soilobs:[soilhorizon=unknown]/silt/_units:[units=""%""]/value",
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| 37 |
soil_Na,"/soilobs:[soilhorizon=unknown]/sodium/_units:[units=""%""]/value",
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| 38 |
soil_texture,"/soilobs:[soilhorizon=unknown]/texture/_units:[units=""%""]/value",
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| 22 |
soil_acidity,"/soilobs/acidity/_map:[""<0.05""=0]/value/_units:[units=""%""]/value", |
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| 23 |
soil_base,"/soilobs/basesaturation/_units:[units=""%""]/value", |
|
| 24 |
soil_Ca,"/soilobs/calcium/_units:[units=""%""]/value", |
|
| 25 |
soil_C,"/soilobs/carbon/_units:[units=""%""]/value", |
|
| 26 |
soil_cation_cap,/soilobs/cationexchangecapacity, |
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| 27 |
clay_percent,"/soilobs/clay/_units:[units=""%""]/value", |
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| 28 |
soil_conductivity,/soilobs/conductivity, |
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| 29 |
soil_Mg,"/soilobs/magnesium/_units:[units=""%""]/value", |
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| 30 |
soil_N,"/soilobs/nitrogen/_units:[units=""%""]/value", |
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| 31 |
organic_percent,"/soilobs/organic/_units:[units=""%""]/value", |
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| 32 |
pH,/soilobs/ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss." |
|
| 33 |
soil_P,"/soilobs/phosphorus/_map:[""<1,5""=0]/value/_units:[units=""%""]/value", |
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| 34 |
soil_K,"/soilobs/potassium/_units:[units=""%""]/value", |
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| 35 |
sand_percent,"/soilobs/sand/_units:[units=""%""]/value", |
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| 36 |
silt_percent,"/soilobs/silt/_units:[units=""%""]/value", |
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| 37 |
soil_Na,"/soilobs/sodium/_units:[units=""%""]/value", |
|
| 38 |
soil_texture,"/soilobs/texture/_units:[units=""%""]/value", |
|
| 39 | 39 |
Temp,/temperature, |
| 40 | 40 |
SiteCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project) |
| 41 | 41 |
PlotID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata." |
| inputs/SALVIAS-CSV/maps/VegBIEN.plots.csv | ||
|---|---|---|
| 19 | 19 |
date_finish,/obsenddate/_*/date, |
| 20 | 20 |
date_start,/obsstartdate/_*/date, |
| 21 | 21 |
precip_mm,/precipitation, |
| 22 |
soil_acidity,"/soilobs:[soilhorizon=unknown]/acidity/_map:[""<0.05""=0]/value/_units:[units=""%""]/value",
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| 23 |
soil_base,"/soilobs:[soilhorizon=unknown]/basesaturation/_units:[units=""%""]/value",
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| 24 |
soil_Ca,"/soilobs:[soilhorizon=unknown]/calcium/_units:[units=""%""]/value",
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| 25 |
soil_C,"/soilobs:[soilhorizon=unknown]/carbon/_units:[units=""%""]/value",
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| 26 |
soil_cation_cap,/soilobs:[soilhorizon=unknown]/cationexchangecapacity,
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| 27 |
clay_percent,"/soilobs:[soilhorizon=unknown]/clay/_units:[units=""%""]/value",
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| 28 |
soil_conductivity,/soilobs:[soilhorizon=unknown]/conductivity,
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| 29 |
soil_Mg,"/soilobs:[soilhorizon=unknown]/magnesium/_units:[units=""%""]/value",
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| 30 |
soil_N,"/soilobs:[soilhorizon=unknown]/nitrogen/_units:[units=""%""]/value",
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| 31 |
organic_percent,"/soilobs:[soilhorizon=unknown]/organic/_units:[units=""%""]/value",
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| 32 |
pH,/soilobs:[soilhorizon=unknown]/ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."
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| 33 |
soil_P,"/soilobs:[soilhorizon=unknown]/phosphorus/_map:[""<1,5""=0]/value/_units:[units=""%""]/value",
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| 34 |
soil_K,"/soilobs:[soilhorizon=unknown]/potassium/_units:[units=""%""]/value",
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| 35 |
sand_percent,"/soilobs:[soilhorizon=unknown]/sand/_units:[units=""%""]/value",
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| 36 |
silt_percent,"/soilobs:[soilhorizon=unknown]/silt/_units:[units=""%""]/value",
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| 37 |
soil_Na,"/soilobs:[soilhorizon=unknown]/sodium/_units:[units=""%""]/value",
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| 38 |
soil_texture,/soilobs:[soilhorizon=unknown]/texture,
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| 22 |
soil_acidity,"/soilobs/acidity/_map:[""<0.05""=0]/value/_units:[units=""%""]/value", |
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| 23 |
soil_base,"/soilobs/basesaturation/_units:[units=""%""]/value", |
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| 24 |
soil_Ca,"/soilobs/calcium/_units:[units=""%""]/value", |
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| 25 |
soil_C,"/soilobs/carbon/_units:[units=""%""]/value", |
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| 26 |
soil_cation_cap,/soilobs/cationexchangecapacity, |
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| 27 |
clay_percent,"/soilobs/clay/_units:[units=""%""]/value", |
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| 28 |
soil_conductivity,/soilobs/conductivity, |
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| 29 |
soil_Mg,"/soilobs/magnesium/_units:[units=""%""]/value", |
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| 30 |
soil_N,"/soilobs/nitrogen/_units:[units=""%""]/value", |
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| 31 |
organic_percent,"/soilobs/organic/_units:[units=""%""]/value", |
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| 32 |
pH,/soilobs/ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss." |
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| 33 |
soil_P,"/soilobs/phosphorus/_map:[""<1,5""=0]/value/_units:[units=""%""]/value", |
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| 34 |
soil_K,"/soilobs/potassium/_units:[units=""%""]/value", |
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| 35 |
sand_percent,"/soilobs/sand/_units:[units=""%""]/value", |
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| 36 |
silt_percent,"/soilobs/silt/_units:[units=""%""]/value", |
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| 37 |
soil_Na,"/soilobs/sodium/_units:[units=""%""]/value", |
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| 38 |
soil_texture,/soilobs/texture, |
|
| 39 | 39 |
temp_c,/temperature, |
| 40 | 40 |
plot_code,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project) |
| 41 | 41 |
PLOT_ID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata." |
| schemas/vegbien.sql | ||
|---|---|---|
| 2186 | 2186 |
CREATE TABLE soilobs ( |
| 2187 | 2187 |
soilobs_id integer NOT NULL, |
| 2188 | 2188 |
locationevent_id integer NOT NULL, |
| 2189 |
horizon text NOT NULL, |
|
| 2189 |
horizon text DEFAULT 'unknown'::text NOT NULL,
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|
| 2190 | 2190 |
description text, |
| 2191 | 2191 |
depthtop double precision, |
| 2192 | 2192 |
depthbottom double precision, |
| mappings/VegX-VegBIEN.plots.csv | ||
|---|---|---|
| 25 | 25 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 26 | 26 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceaccessioncode]/value,/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
| 27 | 27 |
/simpleUserdefined[name=precipMm]/value,/precipitation, |
| 28 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value,/soilobs:[soilhorizon=unknown]/acidity,
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| 29 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value,/soilobs:[soilhorizon=unknown]/basesaturation,
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| 30 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value,/soilobs:[soilhorizon=unknown]/calcium,
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| 31 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value,/soilobs:[soilhorizon=unknown]/carbon,
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| 32 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=cationCap]/value,/soilobs:[soilhorizon=unknown]/cationexchangecapacity,
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| 33 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=clayPercent]/value,/soilobs:[soilhorizon=unknown]/clay,
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| 34 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value,/soilobs:[soilhorizon=unknown]/conductivity,
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| 35 |
->/*s/abioticObservation[*ID]/magnesium,/soilobs:[soilhorizon=unknown]/magnesium,
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| 36 |
->/*s/abioticObservation[*ID]/nitrogen,/soilobs:[soilhorizon=unknown]/nitrogen,
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| 37 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=organicPercent]/value,/soilobs:[soilhorizon=unknown]/organic,
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| 38 |
->/*s/abioticObservation[*ID]/ph,/soilobs:[soilhorizon=unknown]/ph,
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| 39 |
->/*s/abioticObservation[*ID]/phosphorus,/soilobs:[soilhorizon=unknown]/phosphorus,
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| 40 |
->/*s/abioticObservation[*ID]/pottasium,/soilobs:[soilhorizon=unknown]/potassium,
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| 41 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=sandPercent]/value,/soilobs:[soilhorizon=unknown]/sand,
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| 42 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=siltPercent]/value,/soilobs:[soilhorizon=unknown]/silt,
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| 43 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value,/soilobs:[soilhorizon=unknown]/sodium,
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| 44 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/soilobs:[soilhorizon=unknown]/texture,
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| 28 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value,/soilobs/acidity, |
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| 29 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value,/soilobs/basesaturation, |
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| 30 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value,/soilobs/calcium, |
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| 31 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value,/soilobs/carbon, |
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| 32 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=cationCap]/value,/soilobs/cationexchangecapacity, |
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| 33 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=clayPercent]/value,/soilobs/clay, |
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| 34 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value,/soilobs/conductivity, |
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| 35 |
->/*s/abioticObservation[*ID]/magnesium,/soilobs/magnesium, |
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| 36 |
->/*s/abioticObservation[*ID]/nitrogen,/soilobs/nitrogen, |
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| 37 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=organicPercent]/value,/soilobs/organic, |
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| 38 |
->/*s/abioticObservation[*ID]/ph,/soilobs/ph, |
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| 39 |
->/*s/abioticObservation[*ID]/phosphorus,/soilobs/phosphorus, |
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| 40 |
->/*s/abioticObservation[*ID]/pottasium,/soilobs/potassium, |
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| 41 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=sandPercent]/value,/soilobs/sand, |
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| 42 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=siltPercent]/value,/soilobs/silt, |
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| 43 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value,/soilobs/sodium, |
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| 44 |
->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/soilobs/texture, |
|
| 45 | 45 |
/temperature,/temperature, |
| 46 | 46 |
/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/waterdepth/max, |
| 47 | 47 |
/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/waterdepth/min, |
| mappings/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 25 | 25 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 26 | 26 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceaccessioncode]/value,/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
| 27 | 27 |
/*ID->/*s/plotObservation/simpleUserdefined[name=precipMm]/value,/*_id/locationevent/precipitation, |
| 28 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/acidity,
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| 29 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/basesaturation,
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| 30 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/calcium,
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| 31 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/carbon,
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| 32 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=cationCap]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/cationexchangecapacity,
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| 33 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=clayPercent]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/clay,
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| 34 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/conductivity,
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| 35 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/magnesium,/*_id/locationevent/soilobs:[soilhorizon=unknown]/magnesium,
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| 36 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/nitrogen,/*_id/locationevent/soilobs:[soilhorizon=unknown]/nitrogen,
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| 37 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=organicPercent]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/organic,
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| 38 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/ph,/*_id/locationevent/soilobs:[soilhorizon=unknown]/ph,
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| 39 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/phosphorus,/*_id/locationevent/soilobs:[soilhorizon=unknown]/phosphorus,
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| 40 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/pottasium,/*_id/locationevent/soilobs:[soilhorizon=unknown]/potassium,
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| 41 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=sandPercent]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/sand,
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| 42 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=siltPercent]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/silt,
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| 43 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/sodium,
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| 44 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/*_id/locationevent/soilobs:[soilhorizon=unknown]/texture,
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| 28 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value,/*_id/locationevent/soilobs/acidity, |
|
| 29 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value,/*_id/locationevent/soilobs/basesaturation, |
|
| 30 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value,/*_id/locationevent/soilobs/calcium, |
|
| 31 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value,/*_id/locationevent/soilobs/carbon, |
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| 32 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=cationCap]/value,/*_id/locationevent/soilobs/cationexchangecapacity, |
|
| 33 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=clayPercent]/value,/*_id/locationevent/soilobs/clay, |
|
| 34 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value,/*_id/locationevent/soilobs/conductivity, |
|
| 35 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/magnesium,/*_id/locationevent/soilobs/magnesium, |
|
| 36 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/nitrogen,/*_id/locationevent/soilobs/nitrogen, |
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| 37 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=organicPercent]/value,/*_id/locationevent/soilobs/organic, |
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| 38 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/ph,/*_id/locationevent/soilobs/ph, |
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| 39 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/phosphorus,/*_id/locationevent/soilobs/phosphorus, |
|
| 40 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/pottasium,/*_id/locationevent/soilobs/potassium, |
|
| 41 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=sandPercent]/value,/*_id/locationevent/soilobs/sand, |
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| 42 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=siltPercent]/value,/*_id/locationevent/soilobs/silt, |
|
| 43 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value,/*_id/locationevent/soilobs/sodium, |
|
| 44 |
/*ID->/*s/plotObservation->/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value,/*_id/locationevent/soilobs/texture, |
|
| 45 | 45 |
/*ID->/*s/plotObservation/temperature,/*_id/locationevent/temperature, |
| 46 | 46 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/*_id/locationevent/waterdepth/max, |
| 47 | 47 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/*_id/locationevent/waterdepth/min, |
Also available in: Unified diff
VegBIEN: soilobs: Added default value for horizon. Adjusted mappings to remove now-unecessary horizon value.