tests/testthat/test_MicroPlate.R
In phonixor/MicroPlate: Import and handle microplate reader data.
# load the package
library(MicroPlate)
library(testthat)
library(plyr)
#
# Test MicroPlate.R
#
#
#
test_that("MicroPlate.R_$_tests",{
# file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### $ tests
# Plate
testData$test=1234567 # write
expect_equal(testData$test,1234567) # read
#TODO ADD OVERWRITE TEST...
testData$test=NULL # test remove
suppressWarnings(expect_true(is.null(testData$test))) # does give a warning
# well
testData$testw=1:96 # write
expect_true(all(testData$testw==1:96)) # read
testData$testw=20 # overwrite all same value
expect_true(all(testData$testw==20)) # read
testData$testw=NULL # test remove
suppressWarnings(expect_true(is.null(testData$testw))) # does give a warning
# measurement
testData$testm=1:24000 # write
expect_true(all(testData$testm==1:24000)) # read
testData$testm=20 # overwrite all same value
expect_true(all(testData$testm==20)) # read
testData$testm=NULL # test remove
suppressWarnings(expect_true(is.null(testData$testm))) # does give a warning
})
test_that("MicroPlate.R_basic_tests",{
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### colnames
expect_true(any(colnames(testData)=="value")) # test the colname
# expect_error((colnames(testData)="cookies")) # only 1 element while data has 8 columns # NOTE: currently it just returns an error in any case
# expect_warning((colnames(testData)=c(1,"cookies",3,4,5,6,7,8)))
# expect_true(any(colnames(testData)=="cookies")) # test if the colname was changed
# expect_equal(testData$cookies,1234567) # test if the data also changed...
### dim
#TODO level support?
expect_true(all(dim(testData)==c(24000,8)))
### instance tests
# change in one instance effectes the other
testData2=testData
testData$cookies=123 # once again at plate level
expect_equal(testData2$cookies,123) # note that we changed test and check test2
# test that you can have multiple instances that dont influence eachother
testData3=novostar.xls(file)
testData3$cookies=1234
expect_false(testData2$cookies==1234)
### copy
testData4=copy(testData)
testData4$cookies=123456
expect_false(testData$cookies==123456) # same kinda instance test
})
test_that("MicroPlate.R_[]_tests",{
# test both [] and []<-
#
#
# file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### just level
expect_equal(testData[level=1],testData[level="measurement"])
expect_equal(testData[level=2], testData[level="well"])
expect_equal(testData[level=3], testData[level="plate"])
expect_error(testData[level=4])
expect_error(testData[level="COOKIESSS!!!"]) # todo: add cookie level
### singel column
# plate
testData["newColumn"]=1
expect_equal(testData["newColumn"],1)
testData["newColumn"]=2 # overwrite
expect_equal(testData["newColumn"],2)
expect_error((testData["newColumn"]=1:24000))# try to add data at wrong level
testData["newColumn"]=NULL # remove
suppressWarnings(expect_true(is.null(testData$newColumn))) # does give a warning
# well
testData["newColumn"]=1:96 # reuse column name at different level
expect_true(all(testData["newColumn"]==1:96))
testData["newColumn"]=500 # single value overwrite
expect_true(all(testData["newColumn"]==rep(500,96)))
expect_error((testData["newColumn"]=1:24000))# try to add data at wrong level
testData["newColumn"]=NULL
suppressWarnings(expect_true(is.null(testData$newColumn))) # does give a warning
# measurement
testData["newColumn"]=1:24000 # GOES WITH BLAZING SPEED!
expect_true(all(testData["newColumn"]==1:24000))
testData["newColumn"]=500 # single value overwrite -- yup the new underlying structure makes this much faster!
expect_true(all(testData["newColumn"]==rep(500,24000)))
expect_error((testData["newColumn"]=1:96))# try to add data at wrong level
testData["newColumn"]=NULL
suppressWarnings(expect_true(is.null(testData$newColumn))) # does give a warning
### row
# plate
testData=novostar.xls(file)
testData[1,"newColumn",level="plate"]=5
expect_equal(testData[1,"newColumn"],5)
expect_error((testData[1,"newColumn"]=NULL)) # you are not allowed to delete individual values
testData[1,"newColumn",level=3]=50
expect_error(testData[10,"newColumn"]) # out of range
expect_error((testData[2,"newColumn"]=5)) # out of range assign
# well
expect_error((testData[5,"newColumn",level="well"]=5))
testData=novostar.xls(file)
testData[5,"newColumn",level="well"]=5
expect_equal(testData[5,"newColumn"],5)
testData[6,"newColumn",level=2]=50
expect_error(testData[97,"newColumn"]) # out of range
expect_error((testData[97,"newColumn"]=5)) # out of range assign
# measurement
expect_error((testData[5,"newColumn",level="measurement"]=5))
testData=novostar.xls(file)
testData[15,"newColumn",level="measurement"]=5
testData[18,"newColumn",level=1]=55
expect_equal(testData[18,"newColumn"],55)
expect_error(testData[24010,"newColumn"]) # out of range
expect_error((testData[24001,"newColumn"]=5)) # out of range assign
### just row
# TODO increase this section!!!
# boolean select
testData=novostar.xls(file)
expect_true(all(testData[1,]==c(0.2663,0,600,1,1,"Sample X1",1,"KineticData.xls"))) # first row
expect_true(all(dim(testData[testData$row==1,])==c(12,5))) # boolean selection
### multiple column
# plate
testData=novostar.xls(file)
testData$newColumn=1
testData[8:9]=matrix(1,1,2) # change
expect_true(all(testData[8:9]==c(1,1)))
testData[8:9]=1:2 # change
expect_true(all(testData[8:9]==1:2))
expect_error((testData[8:9]=1)) # you cant overwrite a block of data...
testData[c("plateName","evenNewerColumn")]=10:11 # 50% new!
expect_true(all(testData[c("plateName","evenNewerColumn")]==10:11))
# testData[c("lalala","lalalala")]=10:11# 100% new! # TODO MAKE THIS WORK!!
# expect_true(all(testData[c("lalala","lalalala")]==10:11))
testData[c("lalala","lalalala"),level=3]=10:11# 100% new
expect_true(all(testData[c("lalala","lalalala")]==10:11))
testData[c("lalala","lalalala")]=NULL # multi column delete
expect_error(testData[c("lalala","lalalala")]) # error cause rows are deleted
# well
testData=novostar.xls(file)
testData[5:6]=matrix(1,96,2)
expect_true(all(testData[5:6]==1))
expect_error((testData[5:6]=1:192)) # 2D selection requires 2D data! i will not shape the data for you! that is crazy!
testData[c("content","evenNewerColumn")]= matrix(1,96,2) # 50% new!
expect_true(all(testData[c("content","evenNewerColumn")]==1))
testData[c("lalala","lalalala"),level="well"]=matrix(2,96,2) # 100% new
expect_true(all(testData[c("lalala","lalalala")]==2))
testData[c("lalala","lalalala")]=NULL # multi column delete
expect_error(testData[c("lalala","lalalala")]) # error cause rows are deleted
# measurement
testData=novostar.xls(file)
testData[1:2]=matrix(1,24000,2)
expect_true(all(testData[1:2]==1))
testData[c("temp","evenNewerColumn")]= matrix(2,24000,2) # 50% new!
expect_true(all(testData[c("temp","evenNewerColumn")]==2))
testData[c("lalala","lalalala"),level="measurement"]=matrix("cookies!",24000,2) # 100% new
expect_true(all(testData[c("lalala","lalalala")]=="cookies!"))
testData[c("lalala","lalalala")]=NULL # multi column delete
expect_error(testData[c("lalala","lalalala")]) # error cause rows are deleted
### multiple column+row
# general
testData=novostar.xls(file)
expect_equal(class(testData[1:7,1:7]),"data.frame")
expect_error((testData[1:7,1:7]=matrix(1,7,7))) # you cant change data at multiple levels in 1 go
expect_true(all(dim(testData[1:7,1:7])==c(7,7))) # read columns different levels
expect_error((testData[1:7,1:7]=1)) #assign wrong format
expect_error((testData[1:7,1:7]=1:7))
# plate
testData=novostar.xls(file)
testData=merge(testData,testData,removeOther = F)
testData["newPlateData"]=1:2
expect_true(all(testData[1:2,8:9][,2]==1:2))
testData[1:2,8:9]=matrix(5,2,2)
expect_true(all(testData[1:2,8:9]==5))
# well
testData=novostar.xls(file)
expect_true(all(dim(testData[12:44,4:6])==c(33,3)))
testData[12:44,4:6]=matrix(123,33,3)
expect_true(all(testData[12:44,4:6]==123))
# measurement
expect_error((testData[1:7,1:2]=1)) #assign wrong format
expect_error((testData[1:7,1:2]=1:7))
testData[1:7,1:3]=matrix("cookies",7,3)
expect_true(all(testData[1:7,1:3]=="cookies")) # my favorite kinda test
### boolean selection
# plate
testData=novostar.xls(file)
expect_equal(testData[testData$plateName=="KineticData.xls","plateName"],"KineticData.xls")
expect_error((testData[testData$plateName=="KineticData.xls"]="plateOfDoom"))# should give error as i do not specify what column
testData[testData$plateName=="KineticData.xls","plateName"]="plateOfDoom"
expect_equal(testData["plateName"],"plateOfDoom")
# well
expect_error((testData[testData$row>10,"plateName"]=="KineticData.xls")) # wrong level!... and nothing selected...
expect_error((testData[testData$row>2,"plateName"]=="KineticData.xls")) # wrong level!...
testData[testData$row>2,"content"]="NEW CONTENT!"
expect_true(sum(testData$content=="NEW CONTENT!")==72)
# measurement
# expect_true(sum(testData[testData$value>0.5,"value"])==7498.442)# FUCK YOU R!!! DONT HIDE STUFF FROM ME!
expect_true(sum(testData[testData$value>0.5,"value"])==7498.4418)
expect_true(max(testData[testData$value>0.5,"value"])==0.8514)
testData[testData$value>0.4,"value"]=100
expect_true(all(testData[testData$value>0.4,"value"]==100))
### diffrent level then col selection
# plate
testData=novostar.xls(file)
expect_true(length(testData["plateName",level="well"])==96)
expect_error((testData["plateName",level="well"]=1:96))
expect_error((testData[1:96,"plateName",level="well"]=1:96)) # say i want well and give well level data, but its a plate level column
expect_true(length(testData["plateName",level=1])==24000)
expect_error((testData["plateName",level="measurement"]=1:96))
# well
expect_error(testData["row",level=3])
expect_true(length(testData["row",level=1])==24000)
expect_error((testData["row",level="measurement"]=1:96)) # say i want well but give measurement level
expect_error((testData["row",level="measurement"]=1:24000))
# measurement
expect_error(testData["value",level=3]) # data level lower then requested level
expect_error(testData["value",level=2])
# restricted column names.. plate measurement etc...
# plate
expect_error((testData["plate"]=1))
expect_error((testData["measurement"]=1))
# expect_error((testData["well"]=1)) # might need to change this
})
test_that("MicroPlate.R_[]_tests_2nd_mode",{
###################
# 2nd mode test #
###################
# mp[colNamesYouWant, colname=content]
# mp[,well=96]
# mp[,well=4:12]
# file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### well=
expect_true(all(dim(testData[well=10])==c(250,8)))
expect_true(all(testData[well=10]==testData[well="A10"]))
expect_true(all(dim(testData[well=12:80])==c(17250 ,8)))
testData["content",well=10]="COOKIES!!!"
expect_equal(testData["content",well=10],"COOKIES!!!")
expect_error((testData["content",well=10]=1:250))
expect_error((testData["content",well=10,level="measurement"]=1:250))
expect_true(all(dim(testData[well=10,level=2])==c(1,5)))
# testData[well=10,level=2]=c(1,10,"lalalala") # does not work... should it?
# expect_error(testData[well=100])#out of range ... dunno if i should throw an error or return nothing...
# testData[well=10]
# testData[well=10,level=1] # works
# testData[well=10,level=2] # works
# testData[well=10,level=2]=c(1,10,"lalalala") # does not work... should it?
# testData[,well=10,level=2]# works
# testData["content",well=10,level=2] # works
# testData[well=10]
# testData[well=10]=1 # TODO: needs better error
### all kind of sexy combinations...
expect_equal(testData["row",well=4,level=2],1)
expect_equal(length(testData["content",well=10:23,level=2]),14)
expect_true(all(testData[c("row","column","content"),well=4,level=2] == c(1,4,"Sample X4")))
#
# testData[well=4,level=2]
# testData[well=8]
# testData[,well=8]
# testData[,,well=8]
#
#
# testData["value",well=8]
#
# testData["content",well="B6",level=1]#should give error!
# testData["content",well="B6",level=2]
# testData["content",well="B6",level=3]#should crash
# testData["content",row=2,column=6,level=2]
# testData["content",column=2,level=2]
})
test_that("MicroPlate.R_ stress/compare tests",{
# its probably a bad idea to keep this in the stress test
# ... stress unit test sounds like a silly idea in general..
# # file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
# file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
# testData=novostar.xls(file)
#
### OLD
# file="../testdata/"
# workspace = getwd()
# testdir=file.path(workspace, "tests/testdata/enzymeAssays")
# file=file.path(testdir, "GJS_layout3263.tab")
# layoutData=readLayoutFile(file=file)
# file2=file.path(testdir, "3263.dbf")
# newData=novostar.dbf(path=file2)
# testData=new("MicroPlate")
#
# system.time(replicate(50, addPlate(testData,newData=newData,layoutData=layoutData)))
# tdf=testData[] # 2MB ish
#
# system.time(replicate(1000,testData$value)) # 3 sec
# system.time(replicate(1000,tdf$value)) # .4 sec
# # about Data = 10x slower then data.frame
#
# system.time(replicate(1000,testData["value"])) # 24 sec
# system.time(replicate(1000,tdf["value"])) # .3 sec
# # many many times slower
#
# system.time(replicate(1000,testData["content"])) # .5 sec
# system.time(replicate(1000,tdf["content"])) # 1.2 sec #... that is ... weird...
# # that is ... weird... is this factor vs string?
# # oooh crap... this is 600 vs 30000 rows....
# system.time(replicate(1000,testData["content",level="measurement"])) # 55 sec
# # that is ... many many times slower
#
# system.time(replicate(1000,testData["row",level="measurement"])) # 27 sec
# system.time(replicate(1000,tdf["row"])) # .4 sec
# # eeeugh....
#
#
# testData=new("Data")
# system.time(replicate(100, addPlate(testData,newData=newData,layoutData=layoutData))) # 5sec
# testData
#
#
# tdf=testData[] # 2MB ish
# system.time(replicate(10,testData$value))
# system.time(replicate(10,tdf$value))
#
# system.time(replicate(10000,testData["value"]))
# system.time(replicate(10000,tdf["value"]))
#
#
# testData[]
# testData
})
phonixor/MicroPlate documentation built on May 25, 2019, 6:01 a.m.
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# load the package
library(MicroPlate)
library(testthat)
library(plyr)
#
# Test MicroPlate.R
#
#
#
test_that("MicroPlate.R_$_tests",{
# file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### $ tests
# Plate
testData$test=1234567 # write
expect_equal(testData$test,1234567) # read
#TODO ADD OVERWRITE TEST...
testData$test=NULL # test remove
suppressWarnings(expect_true(is.null(testData$test))) # does give a warning
# well
testData$testw=1:96 # write
expect_true(all(testData$testw==1:96)) # read
testData$testw=20 # overwrite all same value
expect_true(all(testData$testw==20)) # read
testData$testw=NULL # test remove
suppressWarnings(expect_true(is.null(testData$testw))) # does give a warning
# measurement
testData$testm=1:24000 # write
expect_true(all(testData$testm==1:24000)) # read
testData$testm=20 # overwrite all same value
expect_true(all(testData$testm==20)) # read
testData$testm=NULL # test remove
suppressWarnings(expect_true(is.null(testData$testm))) # does give a warning
})
test_that("MicroPlate.R_basic_tests",{
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### colnames
expect_true(any(colnames(testData)=="value")) # test the colname
# expect_error((colnames(testData)="cookies")) # only 1 element while data has 8 columns # NOTE: currently it just returns an error in any case
# expect_warning((colnames(testData)=c(1,"cookies",3,4,5,6,7,8)))
# expect_true(any(colnames(testData)=="cookies")) # test if the colname was changed
# expect_equal(testData$cookies,1234567) # test if the data also changed...
### dim
#TODO level support?
expect_true(all(dim(testData)==c(24000,8)))
### instance tests
# change in one instance effectes the other
testData2=testData
testData$cookies=123 # once again at plate level
expect_equal(testData2$cookies,123) # note that we changed test and check test2
# test that you can have multiple instances that dont influence eachother
testData3=novostar.xls(file)
testData3$cookies=1234
expect_false(testData2$cookies==1234)
### copy
testData4=copy(testData)
testData4$cookies=123456
expect_false(testData$cookies==123456) # same kinda instance test
})
test_that("MicroPlate.R_[]_tests",{
# test both [] and []<-
#
#
# file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### just level
expect_equal(testData[level=1],testData[level="measurement"])
expect_equal(testData[level=2], testData[level="well"])
expect_equal(testData[level=3], testData[level="plate"])
expect_error(testData[level=4])
expect_error(testData[level="COOKIESSS!!!"]) # todo: add cookie level
### singel column
# plate
testData["newColumn"]=1
expect_equal(testData["newColumn"],1)
testData["newColumn"]=2 # overwrite
expect_equal(testData["newColumn"],2)
expect_error((testData["newColumn"]=1:24000))# try to add data at wrong level
testData["newColumn"]=NULL # remove
suppressWarnings(expect_true(is.null(testData$newColumn))) # does give a warning
# well
testData["newColumn"]=1:96 # reuse column name at different level
expect_true(all(testData["newColumn"]==1:96))
testData["newColumn"]=500 # single value overwrite
expect_true(all(testData["newColumn"]==rep(500,96)))
expect_error((testData["newColumn"]=1:24000))# try to add data at wrong level
testData["newColumn"]=NULL
suppressWarnings(expect_true(is.null(testData$newColumn))) # does give a warning
# measurement
testData["newColumn"]=1:24000 # GOES WITH BLAZING SPEED!
expect_true(all(testData["newColumn"]==1:24000))
testData["newColumn"]=500 # single value overwrite -- yup the new underlying structure makes this much faster!
expect_true(all(testData["newColumn"]==rep(500,24000)))
expect_error((testData["newColumn"]=1:96))# try to add data at wrong level
testData["newColumn"]=NULL
suppressWarnings(expect_true(is.null(testData$newColumn))) # does give a warning
### row
# plate
testData=novostar.xls(file)
testData[1,"newColumn",level="plate"]=5
expect_equal(testData[1,"newColumn"],5)
expect_error((testData[1,"newColumn"]=NULL)) # you are not allowed to delete individual values
testData[1,"newColumn",level=3]=50
expect_error(testData[10,"newColumn"]) # out of range
expect_error((testData[2,"newColumn"]=5)) # out of range assign
# well
expect_error((testData[5,"newColumn",level="well"]=5))
testData=novostar.xls(file)
testData[5,"newColumn",level="well"]=5
expect_equal(testData[5,"newColumn"],5)
testData[6,"newColumn",level=2]=50
expect_error(testData[97,"newColumn"]) # out of range
expect_error((testData[97,"newColumn"]=5)) # out of range assign
# measurement
expect_error((testData[5,"newColumn",level="measurement"]=5))
testData=novostar.xls(file)
testData[15,"newColumn",level="measurement"]=5
testData[18,"newColumn",level=1]=55
expect_equal(testData[18,"newColumn"],55)
expect_error(testData[24010,"newColumn"]) # out of range
expect_error((testData[24001,"newColumn"]=5)) # out of range assign
### just row
# TODO increase this section!!!
# boolean select
testData=novostar.xls(file)
expect_true(all(testData[1,]==c(0.2663,0,600,1,1,"Sample X1",1,"KineticData.xls"))) # first row
expect_true(all(dim(testData[testData$row==1,])==c(12,5))) # boolean selection
### multiple column
# plate
testData=novostar.xls(file)
testData$newColumn=1
testData[8:9]=matrix(1,1,2) # change
expect_true(all(testData[8:9]==c(1,1)))
testData[8:9]=1:2 # change
expect_true(all(testData[8:9]==1:2))
expect_error((testData[8:9]=1)) # you cant overwrite a block of data...
testData[c("plateName","evenNewerColumn")]=10:11 # 50% new!
expect_true(all(testData[c("plateName","evenNewerColumn")]==10:11))
# testData[c("lalala","lalalala")]=10:11# 100% new! # TODO MAKE THIS WORK!!
# expect_true(all(testData[c("lalala","lalalala")]==10:11))
testData[c("lalala","lalalala"),level=3]=10:11# 100% new
expect_true(all(testData[c("lalala","lalalala")]==10:11))
testData[c("lalala","lalalala")]=NULL # multi column delete
expect_error(testData[c("lalala","lalalala")]) # error cause rows are deleted
# well
testData=novostar.xls(file)
testData[5:6]=matrix(1,96,2)
expect_true(all(testData[5:6]==1))
expect_error((testData[5:6]=1:192)) # 2D selection requires 2D data! i will not shape the data for you! that is crazy!
testData[c("content","evenNewerColumn")]= matrix(1,96,2) # 50% new!
expect_true(all(testData[c("content","evenNewerColumn")]==1))
testData[c("lalala","lalalala"),level="well"]=matrix(2,96,2) # 100% new
expect_true(all(testData[c("lalala","lalalala")]==2))
testData[c("lalala","lalalala")]=NULL # multi column delete
expect_error(testData[c("lalala","lalalala")]) # error cause rows are deleted
# measurement
testData=novostar.xls(file)
testData[1:2]=matrix(1,24000,2)
expect_true(all(testData[1:2]==1))
testData[c("temp","evenNewerColumn")]= matrix(2,24000,2) # 50% new!
expect_true(all(testData[c("temp","evenNewerColumn")]==2))
testData[c("lalala","lalalala"),level="measurement"]=matrix("cookies!",24000,2) # 100% new
expect_true(all(testData[c("lalala","lalalala")]=="cookies!"))
testData[c("lalala","lalalala")]=NULL # multi column delete
expect_error(testData[c("lalala","lalalala")]) # error cause rows are deleted
### multiple column+row
# general
testData=novostar.xls(file)
expect_equal(class(testData[1:7,1:7]),"data.frame")
expect_error((testData[1:7,1:7]=matrix(1,7,7))) # you cant change data at multiple levels in 1 go
expect_true(all(dim(testData[1:7,1:7])==c(7,7))) # read columns different levels
expect_error((testData[1:7,1:7]=1)) #assign wrong format
expect_error((testData[1:7,1:7]=1:7))
# plate
testData=novostar.xls(file)
testData=merge(testData,testData,removeOther = F)
testData["newPlateData"]=1:2
expect_true(all(testData[1:2,8:9][,2]==1:2))
testData[1:2,8:9]=matrix(5,2,2)
expect_true(all(testData[1:2,8:9]==5))
# well
testData=novostar.xls(file)
expect_true(all(dim(testData[12:44,4:6])==c(33,3)))
testData[12:44,4:6]=matrix(123,33,3)
expect_true(all(testData[12:44,4:6]==123))
# measurement
expect_error((testData[1:7,1:2]=1)) #assign wrong format
expect_error((testData[1:7,1:2]=1:7))
testData[1:7,1:3]=matrix("cookies",7,3)
expect_true(all(testData[1:7,1:3]=="cookies")) # my favorite kinda test
### boolean selection
# plate
testData=novostar.xls(file)
expect_equal(testData[testData$plateName=="KineticData.xls","plateName"],"KineticData.xls")
expect_error((testData[testData$plateName=="KineticData.xls"]="plateOfDoom"))# should give error as i do not specify what column
testData[testData$plateName=="KineticData.xls","plateName"]="plateOfDoom"
expect_equal(testData["plateName"],"plateOfDoom")
# well
expect_error((testData[testData$row>10,"plateName"]=="KineticData.xls")) # wrong level!... and nothing selected...
expect_error((testData[testData$row>2,"plateName"]=="KineticData.xls")) # wrong level!...
testData[testData$row>2,"content"]="NEW CONTENT!"
expect_true(sum(testData$content=="NEW CONTENT!")==72)
# measurement
# expect_true(sum(testData[testData$value>0.5,"value"])==7498.442)# FUCK YOU R!!! DONT HIDE STUFF FROM ME!
expect_true(sum(testData[testData$value>0.5,"value"])==7498.4418)
expect_true(max(testData[testData$value>0.5,"value"])==0.8514)
testData[testData$value>0.4,"value"]=100
expect_true(all(testData[testData$value>0.4,"value"]==100))
### diffrent level then col selection
# plate
testData=novostar.xls(file)
expect_true(length(testData["plateName",level="well"])==96)
expect_error((testData["plateName",level="well"]=1:96))
expect_error((testData[1:96,"plateName",level="well"]=1:96)) # say i want well and give well level data, but its a plate level column
expect_true(length(testData["plateName",level=1])==24000)
expect_error((testData["plateName",level="measurement"]=1:96))
# well
expect_error(testData["row",level=3])
expect_true(length(testData["row",level=1])==24000)
expect_error((testData["row",level="measurement"]=1:96)) # say i want well but give measurement level
expect_error((testData["row",level="measurement"]=1:24000))
# measurement
expect_error(testData["value",level=3]) # data level lower then requested level
expect_error(testData["value",level=2])
# restricted column names.. plate measurement etc...
# plate
expect_error((testData["plate"]=1))
expect_error((testData["measurement"]=1))
# expect_error((testData["well"]=1)) # might need to change this
})
test_that("MicroPlate.R_[]_tests_2nd_mode",{
###################
# 2nd mode test #
###################
# mp[colNamesYouWant, colname=content]
# mp[,well=96]
# mp[,well=4:12]
# file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
testData=novostar.xls(file)
### well=
expect_true(all(dim(testData[well=10])==c(250,8)))
expect_true(all(testData[well=10]==testData[well="A10"]))
expect_true(all(dim(testData[well=12:80])==c(17250 ,8)))
testData["content",well=10]="COOKIES!!!"
expect_equal(testData["content",well=10],"COOKIES!!!")
expect_error((testData["content",well=10]=1:250))
expect_error((testData["content",well=10,level="measurement"]=1:250))
expect_true(all(dim(testData[well=10,level=2])==c(1,5)))
# testData[well=10,level=2]=c(1,10,"lalalala") # does not work... should it?
# expect_error(testData[well=100])#out of range ... dunno if i should throw an error or return nothing...
# testData[well=10]
# testData[well=10,level=1] # works
# testData[well=10,level=2] # works
# testData[well=10,level=2]=c(1,10,"lalalala") # does not work... should it?
# testData[,well=10,level=2]# works
# testData["content",well=10,level=2] # works
# testData[well=10]
# testData[well=10]=1 # TODO: needs better error
### all kind of sexy combinations...
expect_equal(testData["row",well=4,level=2],1)
expect_equal(length(testData["content",well=10:23,level=2]),14)
expect_true(all(testData[c("row","column","content"),well=4,level=2] == c(1,4,"Sample X4")))
#
# testData[well=4,level=2]
# testData[well=8]
# testData[,well=8]
# testData[,,well=8]
#
#
# testData["value",well=8]
#
# testData["content",well="B6",level=1]#should give error!
# testData["content",well="B6",level=2]
# testData["content",well="B6",level=3]#should crash
# testData["content",row=2,column=6,level=2]
# testData["content",column=2,level=2]
})
test_that("MicroPlate.R_ stress/compare tests",{
# its probably a bad idea to keep this in the stress test
# ... stress unit test sounds like a silly idea in general..
# # file=paste(getwd(),"/tests/testdata/parsers/novostar.xls/KineticData.xls",sep="")
# file=paste(getwd(),"/../testdata/parsers/novostar.xls/KineticData.xls",sep="")
# testData=novostar.xls(file)
#
### OLD
# file="../testdata/"
# workspace = getwd()
# testdir=file.path(workspace, "tests/testdata/enzymeAssays")
# file=file.path(testdir, "GJS_layout3263.tab")
# layoutData=readLayoutFile(file=file)
# file2=file.path(testdir, "3263.dbf")
# newData=novostar.dbf(path=file2)
# testData=new("MicroPlate")
#
# system.time(replicate(50, addPlate(testData,newData=newData,layoutData=layoutData)))
# tdf=testData[] # 2MB ish
#
# system.time(replicate(1000,testData$value)) # 3 sec
# system.time(replicate(1000,tdf$value)) # .4 sec
# # about Data = 10x slower then data.frame
#
# system.time(replicate(1000,testData["value"])) # 24 sec
# system.time(replicate(1000,tdf["value"])) # .3 sec
# # many many times slower
#
# system.time(replicate(1000,testData["content"])) # .5 sec
# system.time(replicate(1000,tdf["content"])) # 1.2 sec #... that is ... weird...
# # that is ... weird... is this factor vs string?
# # oooh crap... this is 600 vs 30000 rows....
# system.time(replicate(1000,testData["content",level="measurement"])) # 55 sec
# # that is ... many many times slower
#
# system.time(replicate(1000,testData["row",level="measurement"])) # 27 sec
# system.time(replicate(1000,tdf["row"])) # .4 sec
# # eeeugh....
#
#
# testData=new("Data")
# system.time(replicate(100, addPlate(testData,newData=newData,layoutData=layoutData))) # 5sec
# testData
#
#
# tdf=testData[] # 2MB ish
# system.time(replicate(10,testData$value))
# system.time(replicate(10,tdf$value))
#
# system.time(replicate(10000,testData["value"]))
# system.time(replicate(10000,tdf["value"]))
#
#
# testData[]
# testData
})
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