tests/testthat/test_formatLongTable.R
In ISCN/SOCDRaHR2: Scripts to read in and harmonize different digital soil data archives
#To run just this file
#test_file('tests/testthat/test_formatLongTable.R')
library(testthat)
context('formatLongTable.R')
testthat::test_that("test one variable one table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC,
'river', 'S1', '5.2',
'lake', 'S2', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(sample=
as.data.table(read.csv(text = '"layer_name_id","site_name_id","header","entry","variable","type"
"S1","river","SOC","5.2","soc","value"
"S2","lake","SOC","3","soc","value"', colClasses = 'character')))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(names(expectedOutput), names(output))
#match sample table
testthat::expect_identical(expectedOutput$sample, output$sample)
})
testthat::test_that('one header assigned to two variables [[wishlist]]',{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~sampleID, ~depth,
'S1', '1',
'S1', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'sampleID', 'profile_name', 'id', '',
'T1', 'depth', 'layer_name', 'value', '',
'T1', 'depth', 'layer_bottom', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'profile_name',
'sample', 'layer_name',
'sample', 'layer_bottom')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
})
testthat::test_that("test one variable, two methods, one table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~SOC_flag, ~SOC_method,
'river', 'S1', '5.2', 'ISCN', 'gap filled',
'lake', 'S2', '3', NA, 'provided')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'SOC_flag', 'soc', 'method', '',
'T1', 'SOC_method', 'soc', 'method', ''
))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
#write.csv(output$sample, row.names=FALSE)
expectedOutput <- list(sample=data.table::as.data.table(
read.csv(text = '"layer_name_id","site_name_id","header","entry","variable","type"
"S1","river","SOC","5.2","soc","value"
"S2","lake","SOC","3","soc","value"
"S1","river","SOC_flag","ISCN","soc","method"
"S1","river","SOC_method","gap filled","soc","method"
"S2","lake","SOC_method","provided","soc","method"', stringsAsFactors=FALSE)))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(names(expectedOutput), names(output))
#match sample table
testthat::expect_identical(expectedOutput$sample, output$sample)
})
testthat::test_that('test two variables with one shared unit column',{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD, ~unit,
'river', 'S1', '5.2', '1', 'g cm-3',
'lake', 'S2', '3', '2', 'kg m-3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'BD', 'bulk_density', 'value', '',
'T1', 'unit', 'soc', 'unit', '',
'T1', 'unit', 'bulk_density', 'unit', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <-list(sample = data.table::as.data.table(
tibble::tribble(~layer_name_id, ~site_name_id, ~header, ~entry, ~variable, ~type,
"S1","river","BD","1","bulk_density","value",
"S2","lake","BD","2","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value",
"S1","river","unit","g cm-3","bulk_density","unit",
"S2","lake","unit","kg m-3","bulk_density","unit",
"S1","river","unit","g cm-3","soc","unit",
"S2","lake","unit","kg m-3","soc","unit")
))
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(names(expectedOutput), names(output))
})
testthat::test_that("test two variable one table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD,
'river', 'S1', '5.2', '1.5',
'lake', 'S2', '3', '1.1')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'BD', 'bulk_density', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(sample=data.table::as.data.table(
tibble::tribble(~layer_name_id, ~site_name_id,~header,~entry,~variable,~type,
"S1","river","BD","1.5","bulk_density","value",
"S2","lake","BD","1.1","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match tables
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that('test hard entries',{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC,
'river', 'S1', '5.2',
'lake', 'S2', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', '', 'soc', 'unit', 'g cm-3'))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id,~header,~entry,~variable,~type,
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match sample table
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that("test two target table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~MAT, ~SOC, ~BD,
'river', 'S1', '15', '5.2', '1.5',
'lake', 'S2', '13', '3', '1.1')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'BD', 'bulk_density', 'value', '',
'T1', 'MAT', 'mat', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'site', 'site_name',
'site', 'mat',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(
site = data.table::as.data.table(
tibble::tribble(~site_name_id, ~header,~entry,~variable,~type,
"river","MAT","15","mat","value",
"lake","MAT","13","mat","value")),
sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id,~header,~entry,~variable,~type,
"S1","river","BD","1.5","bulk_density","value",
"S2","lake","BD","1.1","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
#setkey(expectedOutput$site, 'header')
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$site), c('entry'))
expectedOutput$site[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(expectedOutput, output)
testthat::expect_equivalent(expectedOutput$sample, output$sample)
testthat::expect_equivalent(expectedOutput$site, output$site)
})
testthat::test_that("test two source and two target table",{
testInput <- list(
T1 =data.table::as.data.table(
tibble::tribble(~siteID, ~MAT,
'river','15',
'lake', '13')),
T2 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD,
'river', 'S1', '5.2', '1.5',
'lake', 'S2', '3', '1.1')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T2', 'siteID', 'site_name', 'id', '',
'T1', 'siteID', 'site_name', 'id', '',
'T2', 'sampleID', 'layer_name', 'id', '',
'T2', 'SOC', 'soc', 'value', '',
'T2', 'BD', 'bulk_density', 'value', '',
'T1', 'MAT', 'mat', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'site', 'site_name',
'site', 'mat',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(
site = data.table::as.data.table(
tibble::tribble(~site_name_id,~header,~entry,~variable,~type,
"river","MAT","15","mat","value",
"lake","MAT","13","mat","value")),
sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id, ~header,~entry, ~variable, ~type,
"S1","river","BD","1.5","bulk_density","value",
"S2","lake","BD","1.1","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
cols <- setdiff(names(expectedOutput$site), c('entry'))
expectedOutput$site[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that("quasi real test",{
testInput <- list(
site = data.table::as.data.table(
tibble::tribble(~siteID, ~site_description, ~state, ~country, ~lat, ~lon, ~datum,
'lake', 'up by the lake', 'Maine', 'USA', '45.8200', '-68.8706', 'WGS84',
'river', 'down by the river', 'New Hampshire', 'USA', '46.52016', '-68.37050', 'NAD83')),
layer = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD, ~BD_notes, ~color,
'river', 'S1', '5.2', '1.5', 'dry, not seive', 'black',
'lake', 'S1', '3', '1.1', 'dry and 2mm seive', 'brown')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'site', 'siteID', 'site_name', 'id', '',
'site', 'site_description', 'description', 'string', '',
'site', 'state', 'state', 'string', '',
'site', 'country', 'country', 'string','',
'site', 'lat', 'latitude', 'value', '',
'site', 'datum', 'latitude', 'unit', '',
'site', 'lon', 'longitude', 'value', '',
'site', 'datum', 'longitude', 'unit', '',
'layer', 'siteID', 'site_name', 'id', '',
'layer', 'sampleID', 'layer_name', 'id', '',
'layer', 'SOC', 'soc', 'value', '',
'layer', '','soc', 'unit', 'g cm-3',
'layer', 'BD', 'bulk_density', 'value', '',
'layer', 'BD_notes', 'bulk_density', 'method', '',
'layer', 'color', 'color', 'string', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'site', 'site_name',
'site', 'description',
'site', 'state',
'site', 'country',
'site', 'latitude',
'site', 'longitude',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density',
'sample', 'color')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(
site = data.table::as.data.table(
tibble::tribble(~site_name_id, ~header, ~entry, ~variable, ~type,
"lake","country","USA","country","string",
"river","country","USA","country","string",
"lake","datum","WGS84","latitude","unit",
"river","datum","NAD83","latitude","unit",
"lake","datum","WGS84","longitude","unit",
"river","datum","NAD83","longitude","unit",
"lake","lat","45.8200","latitude","value",
"river","lat","46.52016","latitude","value",
"lake","lon","-68.8706","longitude","value",
"river","lon","-68.37050","longitude","value",
"lake","site_description","up by the lake","description","string",
"river","site_description","down by the river","description","string",
"lake","state","Maine","state","string",
"river","state","New Hampshire","state","string")
),
sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id,~header,~entry,~variable,~type,
"S1","river","BD","1.5","bulk_density","value",
"S1","lake","BD","1.1","bulk_density","value",
"S1","river","BD_notes","dry, not seive","bulk_density","method",
"S1","lake","BD_notes","dry and 2mm seive","bulk_density","method",
"S1","river","color","black","color","string",
"S1","lake","color","brown","color","string",
"S1","river","SOC","5.2","soc","value",
"S1","lake","SOC","3","soc","value")))
cols <- setdiff(names(expectedOutput$site), c('entry'))
expectedOutput$site[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that("merge site-level inputs variables across profile-level outputs",{
testInput <- list(
T1 =data.table::as.data.table(
tibble::tribble(~siteID, ~MAT,
'river','15',
'lake', '13')),
T2 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC,
'river', 'S1', '5.2',
'river', 'S2', '4',
'lake', 'S2', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T2', 'siteID', 'site_name', 'id', '',
'T1', 'siteID', 'site_name', 'id', '',
'T2', 'sampleID', 'layer_name', 'id', '',
'T2', 'SOC', 'soc', 'value', '',
'T1', 'MAT', 'mat', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'mat',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- data.table::as.data.table(
tibble::tribble(~site_name_id, ~header, ~entry, ~variable, ~type, ~layer_name_id,
"lake","MAT","13","mat","value","S2",
"river","MAT","15","mat","value","S1",
"river","MAT","15","mat","value","S2",
"river","SOC","5.2","soc","value","S1",
"river","SOC","4","soc","value","S2",
"lake","SOC","3","soc","value","S2")
)
cols <- setdiff(names(expectedOutput), c('entry'))
expectedOutput[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
expect_equal(output$sample, expectedOutput)
})
ISCN/SOCDRaHR2 documentation built on May 26, 2023, 6:44 a.m.
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#To run just this file
#test_file('tests/testthat/test_formatLongTable.R')
library(testthat)
context('formatLongTable.R')
testthat::test_that("test one variable one table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC,
'river', 'S1', '5.2',
'lake', 'S2', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(sample=
as.data.table(read.csv(text = '"layer_name_id","site_name_id","header","entry","variable","type"
"S1","river","SOC","5.2","soc","value"
"S2","lake","SOC","3","soc","value"', colClasses = 'character')))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(names(expectedOutput), names(output))
#match sample table
testthat::expect_identical(expectedOutput$sample, output$sample)
})
testthat::test_that('one header assigned to two variables [[wishlist]]',{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~sampleID, ~depth,
'S1', '1',
'S1', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'sampleID', 'profile_name', 'id', '',
'T1', 'depth', 'layer_name', 'value', '',
'T1', 'depth', 'layer_bottom', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'profile_name',
'sample', 'layer_name',
'sample', 'layer_bottom')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
})
testthat::test_that("test one variable, two methods, one table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~SOC_flag, ~SOC_method,
'river', 'S1', '5.2', 'ISCN', 'gap filled',
'lake', 'S2', '3', NA, 'provided')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'SOC_flag', 'soc', 'method', '',
'T1', 'SOC_method', 'soc', 'method', ''
))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
#write.csv(output$sample, row.names=FALSE)
expectedOutput <- list(sample=data.table::as.data.table(
read.csv(text = '"layer_name_id","site_name_id","header","entry","variable","type"
"S1","river","SOC","5.2","soc","value"
"S2","lake","SOC","3","soc","value"
"S1","river","SOC_flag","ISCN","soc","method"
"S1","river","SOC_method","gap filled","soc","method"
"S2","lake","SOC_method","provided","soc","method"', stringsAsFactors=FALSE)))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(names(expectedOutput), names(output))
#match sample table
testthat::expect_identical(expectedOutput$sample, output$sample)
})
testthat::test_that('test two variables with one shared unit column',{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD, ~unit,
'river', 'S1', '5.2', '1', 'g cm-3',
'lake', 'S2', '3', '2', 'kg m-3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'BD', 'bulk_density', 'value', '',
'T1', 'unit', 'soc', 'unit', '',
'T1', 'unit', 'bulk_density', 'unit', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <-list(sample = data.table::as.data.table(
tibble::tribble(~layer_name_id, ~site_name_id, ~header, ~entry, ~variable, ~type,
"S1","river","BD","1","bulk_density","value",
"S2","lake","BD","2","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value",
"S1","river","unit","g cm-3","bulk_density","unit",
"S2","lake","unit","kg m-3","bulk_density","unit",
"S1","river","unit","g cm-3","soc","unit",
"S2","lake","unit","kg m-3","soc","unit")
))
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(names(expectedOutput), names(output))
})
testthat::test_that("test two variable one table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD,
'river', 'S1', '5.2', '1.5',
'lake', 'S2', '3', '1.1')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'BD', 'bulk_density', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(sample=data.table::as.data.table(
tibble::tribble(~layer_name_id, ~site_name_id,~header,~entry,~variable,~type,
"S1","river","BD","1.5","bulk_density","value",
"S2","lake","BD","1.1","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match tables
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that('test hard entries',{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC,
'river', 'S1', '5.2',
'lake', 'S2', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', '', 'soc', 'unit', 'g cm-3'))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id,~header,~entry,~variable,~type,
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match sample table
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that("test two target table",{
testInput <- list(T1 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~MAT, ~SOC, ~BD,
'river', 'S1', '15', '5.2', '1.5',
'lake', 'S2', '13', '3', '1.1')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T1', 'siteID', 'site_name', 'id', '',
'T1', 'sampleID', 'layer_name', 'id', '',
'T1', 'SOC', 'soc', 'value', '',
'T1', 'BD', 'bulk_density', 'value', '',
'T1', 'MAT', 'mat', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'site', 'site_name',
'site', 'mat',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(
site = data.table::as.data.table(
tibble::tribble(~site_name_id, ~header,~entry,~variable,~type,
"river","MAT","15","mat","value",
"lake","MAT","13","mat","value")),
sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id,~header,~entry,~variable,~type,
"S1","river","BD","1.5","bulk_density","value",
"S2","lake","BD","1.1","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
#setkey(expectedOutput$site, 'header')
#setkey(expectedOutput$sample, 'header')
cols <- setdiff(names(expectedOutput$site), c('entry'))
expectedOutput$site[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(expectedOutput, output)
testthat::expect_equivalent(expectedOutput$sample, output$sample)
testthat::expect_equivalent(expectedOutput$site, output$site)
})
testthat::test_that("test two source and two target table",{
testInput <- list(
T1 =data.table::as.data.table(
tibble::tribble(~siteID, ~MAT,
'river','15',
'lake', '13')),
T2 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD,
'river', 'S1', '5.2', '1.5',
'lake', 'S2', '3', '1.1')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T2', 'siteID', 'site_name', 'id', '',
'T1', 'siteID', 'site_name', 'id', '',
'T2', 'sampleID', 'layer_name', 'id', '',
'T2', 'SOC', 'soc', 'value', '',
'T2', 'BD', 'bulk_density', 'value', '',
'T1', 'MAT', 'mat', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'site', 'site_name',
'site', 'mat',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(
site = data.table::as.data.table(
tibble::tribble(~site_name_id,~header,~entry,~variable,~type,
"river","MAT","15","mat","value",
"lake","MAT","13","mat","value")),
sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id, ~header,~entry, ~variable, ~type,
"S1","river","BD","1.5","bulk_density","value",
"S2","lake","BD","1.1","bulk_density","value",
"S1","river","SOC","5.2","soc","value",
"S2","lake","SOC","3","soc","value")))
cols <- setdiff(names(expectedOutput$site), c('entry'))
expectedOutput$site[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that("quasi real test",{
testInput <- list(
site = data.table::as.data.table(
tibble::tribble(~siteID, ~site_description, ~state, ~country, ~lat, ~lon, ~datum,
'lake', 'up by the lake', 'Maine', 'USA', '45.8200', '-68.8706', 'WGS84',
'river', 'down by the river', 'New Hampshire', 'USA', '46.52016', '-68.37050', 'NAD83')),
layer = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC, ~BD, ~BD_notes, ~color,
'river', 'S1', '5.2', '1.5', 'dry, not seive', 'black',
'lake', 'S1', '3', '1.1', 'dry and 2mm seive', 'brown')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'site', 'siteID', 'site_name', 'id', '',
'site', 'site_description', 'description', 'string', '',
'site', 'state', 'state', 'string', '',
'site', 'country', 'country', 'string','',
'site', 'lat', 'latitude', 'value', '',
'site', 'datum', 'latitude', 'unit', '',
'site', 'lon', 'longitude', 'value', '',
'site', 'datum', 'longitude', 'unit', '',
'layer', 'siteID', 'site_name', 'id', '',
'layer', 'sampleID', 'layer_name', 'id', '',
'layer', 'SOC', 'soc', 'value', '',
'layer', '','soc', 'unit', 'g cm-3',
'layer', 'BD', 'bulk_density', 'value', '',
'layer', 'BD_notes', 'bulk_density', 'method', '',
'layer', 'color', 'color', 'string', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'site', 'site_name',
'site', 'description',
'site', 'state',
'site', 'country',
'site', 'latitude',
'site', 'longitude',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc',
'sample', 'bulk_density',
'sample', 'color')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- list(
site = data.table::as.data.table(
tibble::tribble(~site_name_id, ~header, ~entry, ~variable, ~type,
"lake","country","USA","country","string",
"river","country","USA","country","string",
"lake","datum","WGS84","latitude","unit",
"river","datum","NAD83","latitude","unit",
"lake","datum","WGS84","longitude","unit",
"river","datum","NAD83","longitude","unit",
"lake","lat","45.8200","latitude","value",
"river","lat","46.52016","latitude","value",
"lake","lon","-68.8706","longitude","value",
"river","lon","-68.37050","longitude","value",
"lake","site_description","up by the lake","description","string",
"river","site_description","down by the river","description","string",
"lake","state","Maine","state","string",
"river","state","New Hampshire","state","string")
),
sample=data.table::as.data.table(
tibble::tribble(~layer_name_id,~site_name_id,~header,~entry,~variable,~type,
"S1","river","BD","1.5","bulk_density","value",
"S1","lake","BD","1.1","bulk_density","value",
"S1","river","BD_notes","dry, not seive","bulk_density","method",
"S1","lake","BD_notes","dry and 2mm seive","bulk_density","method",
"S1","river","color","black","color","string",
"S1","lake","color","brown","color","string",
"S1","river","SOC","5.2","soc","value",
"S1","lake","SOC","3","soc","value")))
cols <- setdiff(names(expectedOutput$site), c('entry'))
expectedOutput$site[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
cols <- setdiff(names(expectedOutput$sample), c('entry'))
expectedOutput$sample[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
#match number of tables
testthat::expect_equal(expectedOutput, output)
})
testthat::test_that("merge site-level inputs variables across profile-level outputs",{
testInput <- list(
T1 =data.table::as.data.table(
tibble::tribble(~siteID, ~MAT,
'river','15',
'lake', '13')),
T2 = data.table::as.data.table(
tibble::tribble(~siteID, ~sampleID, ~SOC,
'river', 'S1', '5.2',
'river', 'S2', '4',
'lake', 'S2', '3')))
inputKey <- data.table::as.data.table(
tibble::tribble(~table, ~header, ~variable, ~type, ~entry,
'T2', 'siteID', 'site_name', 'id', '',
'T1', 'siteID', 'site_name', 'id', '',
'T2', 'sampleID', 'layer_name', 'id', '',
'T2', 'SOC', 'soc', 'value', '',
'T1', 'MAT', 'mat', 'value', ''))
outputKey <- data.table::as.data.table(
(tibble::tribble(~table, ~variable,
'sample', 'mat',
'sample', 'site_name',
'sample', 'layer_name',
'sample', 'soc')))
output <- formatLongTable(data.ls = testInput, sourceKey = inputKey, targetKey = outputKey)
expectedOutput <- data.table::as.data.table(
tibble::tribble(~site_name_id, ~header, ~entry, ~variable, ~type, ~layer_name_id,
"lake","MAT","13","mat","value","S2",
"river","MAT","15","mat","value","S1",
"river","MAT","15","mat","value","S2",
"river","SOC","5.2","soc","value","S1",
"river","SOC","4","soc","value","S2",
"lake","SOC","3","soc","value","S2")
)
cols <- setdiff(names(expectedOutput), c('entry'))
expectedOutput[,(cols) := lapply(.SD, as.factor), .SDcols=cols]
expect_equal(output$sample, expectedOutput)
})
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