[Stacomir-commits] r387 - in pkg/stacomir: data inst/config inst/tests/testthat
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 8 13:31:11 CEST 2017
Author: briand
Date: 2017-06-08 13:31:10 +0200 (Thu, 08 Jun 2017)
New Revision: 387
Modified:
pkg/stacomir/data/bilPM.rda
pkg/stacomir/data/bilan_adm.rda
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
Log:
final changes for Rcheck & tests
Modified: pkg/stacomir/data/bilPM.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/data/bilan_adm.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/inst/config/generate_data.R
===================================================================
--- pkg/stacomir/inst/config/generate_data.R 2017-06-08 09:22:43 UTC (rev 386)
+++ pkg/stacomir/inst/config/generate_data.R 2017-06-08 11:31:10 UTC (rev 387)
@@ -3,7 +3,7 @@
# In data :
#For sets of data, set up a package to use lazy-loading of data.
#
-#For objects which are system data, for example lookup tables used in calculations
+#For objects which are system data, for example lookup tables used in bilcalculations
#within the function, use a file ‘R/sysdata.rda’ in the package sources or create the
#objects by R code at package installation time.
#
@@ -389,6 +389,7 @@
# generates dataset for BilanPoidsMoyen : iav
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
+Sys.setenv(LANG = "EN")
require(stacomiR)
stacomi(gr_interface=FALSE,
login_window=FALSE,
@@ -451,6 +452,8 @@
bilan_adm at taxons@data[,"tax_nom_commun"]<-iconv(bilan_adm at taxons@data[,"tax_nom_commun"],from="latin1",to="UTF8")
bilan_adm at par@data[,"par_nom"]<-iconv(bilan_adm at par@data[,"par_nom"],from="latin1",to="UTF8")
bilan_adm at stades@data[,"std_libelle"]<-iconv(bilan_adm at stades@data[,"std_libelle"],from="latin1",to="UTF8")
+bilan_adm at data$car_valeur_quantitatif[bilan_adm at data$car_par_code=="C001"]<-
+ bilan_adm at data$car_valeur_quantitatif[bilan_adm at data$car_par_code=="C001"]/10
bilan_adm<-calcule(bilan_adm)
devtools::use_data(bilan_adm,internal=FALSE,overwrite=TRUE)
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2017-06-08 09:22:43 UTC (rev 386)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2017-06-08 11:31:10 UTC (rev 387)
@@ -41,6 +41,26 @@
rm("envir_stacomi",envir =.GlobalEnv)
})
+
+#test_that("testconnection to logrami serveur",{
+# require(stacomiR)
+# stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=TRUE)
+# baseODBC<-get("baseODBC",envir=envir_stacomi)
+# baseODBC[1]<- "BD_CONTMIG_SERVEUR"
+# baseODBC[c(2,3)]<-rep('logrami',2)
+# assign("baseODBC",baseODBC,envir_stacomi)
+# sch<-get("sch",envir=envir_stacomi)
+# assign("sch",paste('logrami',".", sep=""),envir_stacomi)
+# con=new("ConnectionODBC")
+# con at baseODBC=baseODBC
+# con<-connect(con)
+# expect_is(connect(con),'ConnectionODBC')
+# expect_equal(con at etat,"Connection in progress")
+# odbcCloseAll()
+# rm("envir_stacomi",envir =.GlobalEnv)
+# })
+
+
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
require(stacomiR)
envir_stacomi <<- new.env(parent = emptyenv())
Modified: pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2017-06-08 09:22:43 UTC (rev 386)
+++ pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2017-06-08 11:31:10 UTC (rev 387)
@@ -93,7 +93,7 @@
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi) # "iav."
assign("sch","iav.",envir_stacomi)
- # this chunk is not launched from examples but loads the bM_Arzal dataset if connection works
+ # this chunk is not launched from examples but loads the bM_Arzal dataset if connection works
bM_Arzal=new("BilanMigration")
bM_Arzal=choice_c(bM_Arzal,
dc=5,
@@ -106,7 +106,7 @@
expect_length(bM_Arzal at data,11)
rm("envir_stacomi",envir =.GlobalEnv)
-})
+ })
test_that("Test example 02_BilanMigration",
{
@@ -171,8 +171,8 @@
data("bM_Arzal")
bM_Arzal<-calcule(bM_Arzal,silent=TRUE)
expect_equal(
- sum(bM_Arzal at calcdata$dc_5$data$Effectif_total),
- sum(bM_Arzal at data[bM_Arzal at data$ope_dic_identifiant==5,"value"]))
+ sum(bM_Arzal at calcdata$dc_5$data$Effectif_total),
+ sum(bM_Arzal at data[bM_Arzal at data$ope_dic_identifiant==5,"value"]))
write_database(object=bM_Arzal,silent=TRUE)
# using setAs to transform the bilanMigration into BilanMigrationInterAnnuelle
bili=as(bM_Arzal,"BilanMigrationInterAnnuelle")
@@ -184,15 +184,15 @@
sum(bM_Arzal at calcdata$dc_5$data$Effectif_total),
bila at data$effectif,
label="The sum of number in the BilanMigration are different to the
-number in the BilanAnnuel class"
- )
-
+ number in the BilanAnnuel class"
+ )
+
bili<-connect(bili,check=TRUE,silent=TRUE)
expect_equal(
- sum(bM_Arzal at calcdata$dc_5$data$Effectif_total),
- sum(bili at data$bjo_valeur[bili at data$bjo_labelquantite=="Effectif_total"]),
- label="The sum of number in the BilanMigration are different to the
- number in the BilanMigrationInterAnnuelle")
+ sum(bM_Arzal at calcdata$dc_5$data$Effectif_total),
+ sum(bili at data$bjo_valeur[bili at data$bjo_labelquantite=="Effectif_total"]),
+ label="The sum of number in the BilanMigration are different to the
+ number in the BilanMigrationInterAnnuelle")
rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -271,4 +271,56 @@
plot(bM_Arzal_civ,silent=TRUE,bty="n")
summary(bM_Arzal_civ,silent=TRUE)
rm("envir_stacomi",envir =.GlobalEnv)
+ })
+# here require setting a connection to logrami server under the name BD_CONTMIG_NAT_SERVEUR
+test_that("test connexion to logrami server",
+ {
+ require(stacomiR)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=TRUE)
+ baseODBC<-get("baseODBC",envir=envir_stacomi)
+ baseODBC[1]<- "BD_CONTMIG_SERVEUR"
+ baseODBC[c(2,3)]<-rep('logrami',2)
+ assign("baseODBC",baseODBC,envir_stacomi)
+ sch<-get("sch",envir=envir_stacomi)
+ assign("sch",paste('logrami',".", sep=""),envir_stacomi)
+ sqldf.options<-get("sqldf.options",envir=envir_stacomi)
+ getpassword<-function(){
+ require(tcltk);
+ wnd<-tktoplevel();tclVar("")->passVar;
+ #Label
+ tkgrid(tklabel(wnd,text="Enter password:"));
+ #Password box
+ tkgrid(tkentry(wnd,textvariable=passVar,show="*")->passBox);
+ #Hitting return will also submit password
+ tkbind(passBox,"<Return>",function() tkdestroy(wnd));
+ #OK button
+ tkgrid(tkbutton(wnd,text="OK",command=function() tkdestroy(wnd)));
+ #Wait for user to click OK
+ tkwait.window(wnd);
+ password<-tclvalue(passVar);
+ return(password);
+ }
+ sqldf.options["sqldf.host"]<-getpassword()
+ sqldf.options["sqldf.port"]<-5432
+ assign("sqldf.options",sqldf.options,envir_stacomi)
+ bilanMigration=new('BilanMigration')
+ bilanMigration=choice_c(bilanMigration,
+ dc=23,
+ taxons=c("Petromyzon marinus"),
+ stades=c(5),
+ datedebut="2015-01-01",
+ datefin="2015-12-31")
+ bilanMigration<-charge(bilanMigration, silent=TRUE)
+ bilanMigration=connect(bilanMigration, silent=TRUE)
+ bilanMigration=calcule(bilanMigration, silent=TRUE)
+
+ bmi<-new("BilanMigrationInterAnnuelle")
+ bmi<-choice_c(bmi,
+ dc=c(101,107),
+ taxons=c("Silurus glanis"),
+ stades=c(5),
+ anneedebut="2014",
+ anneefin="2016",
+ silent=TRUE)
+ bmi<-connect(bmi, silent=FALSE)
})
\ No newline at end of file
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