[Stacomir-commits] r209 - in pkg/stacomir: . R inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 15 22:09:28 CEST 2016
Author: briand
Date: 2016-09-15 22:09:28 +0200 (Thu, 15 Sep 2016)
New Revision: 209
Added:
pkg/stacomir/inst/tests/testthat/test-00zRefclasses.R
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationMult.r
pkg/stacomir/R/Bilan_stades_pigm.r
pkg/stacomir/R/RefHorodate.r
pkg/stacomir/R/funstatJournalier.r
pkg/stacomir/R/interface_BilanConditionEnv.r
pkg/stacomir/R/interface_BilanFonctionnementDC.r
pkg/stacomir/R/interface_BilanFonctionnementDF.r
pkg/stacomir/R/interface_BilanMigration.r
pkg/stacomir/R/interface_BilanMigrationConditionEnv.r
pkg/stacomir/R/interface_BilanMigrationInterannuelle.r
pkg/stacomir/R/interface_BilanMigrationMult.r
pkg/stacomir/R/interface_BilanMigrationPar.r
pkg/stacomir/R/interface_Bilan_carlot.r
pkg/stacomir/R/interface_Bilan_taille.r
pkg/stacomir/R/interface_bilan_poids_moyen.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R
pkg/stacomir/man/choice_c-RefHorodate-method.Rd
Log:
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/DESCRIPTION 2016-09-15 20:09:28 UTC (rev 209)
@@ -2,7 +2,7 @@
Version: 0.5.0
Date: 2016-09-01
Title: Fish Migration Monitoring (stacomiR)
-Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand at eptb-vilaine.fr"),
+Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00 at gmail.com"),
person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"))
Description: Graphical outputs and treatment for a database of fishway
monitoring. It is a part of the STACOMI project developed in France by the ONEMA
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/NAMESPACE 2016-09-15 20:09:28 UTC (rev 209)
@@ -60,7 +60,7 @@
import(sqldf)
import(stacomirtools)
import(stringr)
-importFrom(grDevices,X11)
+importFrom(grDevices,dev.new)
importFrom(grDevices,gray)
importFrom(grDevices,rainbow)
importFrom(graphics,axis)
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/BilanEspeces.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -292,6 +292,6 @@
#gWidgets::addSpring(group)
#graphes=ggraphics(width=600,height=400)
add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
- grDevices::X11()
+ dev.new()
assign("graphes",graphes,envir=.GlobalEnv)
}
\ No newline at end of file
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -120,22 +120,20 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("choice_c",signature=signature("BilanFonctionnementDF"),definition=function(object,df,horodatedebut,horodatefin,...){
- # fonctionnementDF<-BfDF
+ # fonctionnementDF<-BfDF;df=2;horodatedebut="2013-01-01";horodatefin="2013-12-31"
fonctionnementDF<-object
assign("fonctionnementDF",fonctionnementDF,envir=envir_stacomi)
funout(get("msg",envir=envir_stacomi)$interface_BilanFonctionnementDC.1)
fonctionnementDF at df<-charge(fonctionnementDF at df)
fonctionnementDF at df<-choice_c(fonctionnementDF at df,df)
- # assigns the parameter (horodatedebut) of the method to the object using choice_c method for RefDF
- fonctionnementDF at horodatedebut<-choice_c(fonctionnementDF at horodatedebut,
+ # assigns the parameter (horodatedebut) of the method to the object using choice_c method for RefDC
+ fonctionnementDF at horodatedebut<-choice_c(object=fonctionnementDF at horodatedebut,
nomassign="fonctionnementDF_date_debut",
funoutlabel=get("msg",envir=envir_stacomi)$interface_Bilan_lot.5,
- decal=-2,
horodate=horodatedebut)
- fonctionnementDF at horodatefin<-choice_c(fonctionnementDF at horodate,
+ fonctionnementDF at horodatefin<-choice_c(fonctionnementDF at horodatefin,
nomassign="fonctionnementDF_date_fin",
funoutlabel=get("msg",envir=envir_stacomi)$interface_Bilan_lot.6,
- decal=-1,
horodate=horodatefin)
return(fonctionnementDF)
})
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/BilanMigration.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -363,7 +363,7 @@
#----------------------------------
# bilan migration avec poids (civelles
#-----------------------------------------
- #grDevices::X11()
+
fungraph_civelle(bilanMigration=bilanMigration,
table=data_without_hole,
time.sequence=bilanMigration at time.sequence,
@@ -377,7 +377,6 @@
#----------------------------------
# bilan migration standard
#-----------------------------------------
- #grDevices::X11()
#silent=TRUE
fungraph(bilanMigration=bilanMigration,
tableau=data_without_hole,
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/BilanMigrationMult.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -373,7 +373,7 @@
#----------------------------------
# bilan migration avec poids (civelles
#-----------------------------------------
- grDevices::X11()
+ dev.new()
fungraph_civelle(bilanMigration=bilanMigrationMult,
table=data_without_hole,
time.sequence=bilanMigrationMult at time.sequence,
@@ -387,7 +387,7 @@
#----------------------------------
# bilan migration standard
#-----------------------------------------
- grDevices::X11()
+ dev.new()
#silent=TRUE
fungraph(bilanMigration=bilanMigrationMult,
tableau=data_without_hole,
Modified: pkg/stacomir/R/Bilan_stades_pigm.r
===================================================================
--- pkg/stacomir/R/Bilan_stades_pigm.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/Bilan_stades_pigm.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -456,10 +456,10 @@
VIA3= fnstade(par1=Vparm$pigment_stage[[4]],VB=FALSE,phicum=phicum,neg=FALSE,lmax=lmax)
VIA3c=cumsum(VIA3$y)/sum(VIA3$y) # surface
if(graph){
- grDevices::X11()
+ dev.new()
matplot(VB$x,cbind(VB$y,VIA0$y,VIA1$y,VIA2$y,VIA3$y))
- grDevices::X11()
+ dev.new()
matplot(VB$x,cbind(VBc,VIA0c,VIA1c,VIA2c,VIA3c))
}
#traitement a part de VB
@@ -905,7 +905,7 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=.GlobalEnv)
- grDevices::X11()
+ dev.new()
# A cet endroit sinon ouvre plusieurs fenetres pour plusieurs choses
}
Modified: pkg/stacomir/R/RefHorodate.r
===================================================================
--- pkg/stacomir/R/RefHorodate.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/RefHorodate.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -104,17 +104,18 @@
#' @param label Label for the gframe
#' @param nomassing The name assigned in environment envir_stacomi
#' @param funoutlabel, text displayed by the interface
-#' @param decale Default 0, number of years to shift forward or backward, the date will be set to the first day of the year
#' @param affichecal Default TRUE, should the calendar be displayed
-#' @param horodate The horodate to set, formats "%d/%m/%Y %H:%M:%s", "%d/%m/%y %H:%M:%s", "%Y-%m-%d %H:%M:%s"
+#' @param horodate The horodate to set, formats "\%d/\%m/\%Y \%H:\%M:\%s", "\%d/\%m/\%y \%H:\%M:\%s", "\%Y-\%m-\%d \%H:\%M:\%s" formats
+#' can also be passed with the date set to the minute \%d/\%m/\%Y \%H:\%M or the day \%d/\%m/\%Y
#' \dots are accepted
#' @return An object of class \link{RefHorodate-class} with slot \emph{horodate} set
setMethod("choice_c",signature=signature("RefHorodate"),definition=function(object,
nomassign="horodate",
funoutlabel="nous avons le choix dans la date\n",
- decal=0,
+ #decal=0,
horodate
) {
+ # horodate="2013-01-01"
# parse the horohorodate
if (length(horodate)>1) stop("horodate should be a vector of length 1")
if (is.null(horodate)) stop("horodate should not be null")
@@ -130,6 +131,12 @@
if (is.na(.horodate)){
.horodate=strptime(horodate, format="%d/%m/%Y %H:%M")
}
+ if (is.na(.horodate)){
+ .horodate=strptime(horodate, format="%d/%m/%y")
+ }
+ if (is.na(.horodate)){
+ .horodate=strptime(horodate, format="%d/%m/%Y")
+ }
} else if (grepl("-",horodate)){
.horodate=strptime(horodate, format="%Y-%m-%d %H:%M:%s")
if (is.na(.horodate)){
@@ -141,6 +148,12 @@
if (is.na(.horodate)){
.horodate=strptime(horodate, format="%d-%m-%Y %H:%M")
}
+ if (is.na(.horodate)){
+ .horodate=strptime(horodate, format="%Y-%m-%d")
+ }
+ if (is.na(.horodate)){
+ .horodate=strptime(horodate, format="%d-%m-%Y")
+ }
}
} else if (class(horodate)=="Date"){
@@ -148,20 +161,12 @@
} else if (class(horodate)[2]=="POSIXt"){
.horodate=horodate
}
+ if (is.na(.horodate)) stop("Formatting problem, the character vector you are trying to pass as horodate could not
+be parsed. Check example or documentation")
object at horodate=.horodate
- if (decal!=0){
- # Returns the first horodate of a year shifted by decal
- # @param horodate The horodate to shift (class POSIXt)
- # @param decal number of year to shift
- # @return A POSIXt
- shiftyear<-function(horodate,decal){
- anneeprec=as.numeric(strftime(horodate,"%Y"))+decal
- return(strptime(paste(anneeprec,"-01-01",sep=""),format="%Y-%m-%d"))
- }
- object at horodate<-shiftyear(object at horodate,decal)
- }
validObject(object)
assign(nomassign,object,envir_stacomi)
funout(funoutlabel)
+ return(object)
})
Modified: pkg/stacomir/R/funstatJournalier.r
===================================================================
--- pkg/stacomir/R/funstatJournalier.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/funstatJournalier.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -11,7 +11,7 @@
annee=unique(strftime(as.POSIXlt(time.sequence),"%Y"))
somme=tapply(tableau$Effectif_total, mois, sum, na.rm=TRUE) # sums
moyennes_journalieres=tapply(tableau$Effectif_total, mois, mean, na.rm=TRUE) # means
- ecarts_types=tapply(tableau$Effectif_total, mois, sd, na.rm=TRUE) # std. deviations
+ ecarts_types=tapply(tableau$Effectif_total, mois, stats::sd, na.rm=TRUE) # std. deviations
nombre=as.integer(tapply(tableau$Effectif_total, mois, function(x) sum(!is.na(x)))) # counts
resum=rbind(nombre,somme,moyennes_journalieres,ecarts_types)
@@ -27,7 +27,7 @@
resum=data.frame(resum)
resum["somme","bilan"]=round(sum(tableau$Effectif_total, na.rm=TRUE),2)
resum["moyennes_journalieres","bilan"]=round(mean(tableau$Effectif_total, na.rm=TRUE),2)
- resum["ecarts_types","bilan"]=round(sd(tableau$Effectif_total, na.rm=TRUE),2)
+ resum["ecarts_types","bilan"]=round(stats::sd(tableau$Effectif_total, na.rm=TRUE),2)
if (taxon=="Anguilla anguilla"& stade=="civelle")
{
resum["poids_depuis_effectif","bilan"]=round(sum(tableau$poids_depuis_effectif, na.rm=TRUE),2)
Modified: pkg/stacomir/R/interface_BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/interface_BilanConditionEnv.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanConditionEnv.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -42,5 +42,5 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/interface_BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/interface_BilanFonctionnementDC.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanFonctionnementDC.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -49,5 +49,5 @@
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
# A cet endroit sinon ouvre plusieurs fenetres pour plusieurs choses
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/interface_BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/interface_BilanFonctionnementDF.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanFonctionnementDF.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -13,16 +13,17 @@
gWidgets::add(ggroupboutons,group)
choice(fonctionnementDF at df)
+ # here decale =-1 or -2 will make the bilan for the year preceeding the current date
choice(fonctionnementDF at horodatedebut,
label=get("msg",envir=envir_stacomi)$interface_Bilan_lot.3,
nomassign="fonctionnementDF_date_debut",
funoutlabel=get("msg",envir=envir_stacomi)$interface_Bilan_lot.5,
- decal=-2)
+ decal=-1)
choice(fonctionnementDF at horodatefin,
label=get("msg",envir=envir_stacomi)$interface_Bilan_lot.4,
nomassign="fonctionnementDF_date_fin",
funoutlabel=get("msg",envir=envir_stacomi)$interface_Bilan_lot.6,
- decal=-1)
+ decal=-2)
aBarchart=gWidgets::gaction(label="barchart",icon="barplot",handler=funbarchartDF,tooltip=get("msg",envir=envir_stacomi)$interface_BilanFonctionnementDC.2)
aBox=gWidgets::gaction(label="boites",icon="graph2",handler=funboxDF,tooltip=get("msg",envir=envir_stacomi)$interface_BilanFonctionnementDC.3)
@@ -38,5 +39,5 @@
add(group, gmenu(toolbarlist))
add(group,gbutton(text = "graph", handler = function(h,...){X11()}))
gWidgets::addSpring(group)
- grDevices::X11()
+ dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/interface_BilanMigration.r
===================================================================
--- pkg/stacomir/R/interface_BilanMigration.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanMigration.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -34,5 +34,5 @@
#graphes=ggraphics(width=600,height=600)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/interface_BilanMigrationConditionEnv.r
===================================================================
--- pkg/stacomir/R/interface_BilanMigrationConditionEnv.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanMigrationConditionEnv.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -36,5 +36,5 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/interface_BilanMigrationInterannuelle.r
===================================================================
--- pkg/stacomir/R/interface_BilanMigrationInterannuelle.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanMigrationInterannuelle.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -89,7 +89,7 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
# A cet endroit sinon ouvre plusieurs fenetres pour plusieurs choses
Modified: pkg/stacomir/R/interface_BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/interface_BilanMigrationMult.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanMigrationMult.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -46,6 +46,6 @@
#graphes=ggraphics(width=650,height=650)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
}
Modified: pkg/stacomir/R/interface_BilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/interface_BilanMigrationPar.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_BilanMigrationPar.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -45,6 +45,6 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/interface_Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/interface_Bilan_carlot.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_Bilan_carlot.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -78,6 +78,6 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
# A cet endroit sinon ouvre plusieurs fenetres pour plusieurs choses
}
Modified: pkg/stacomir/R/interface_Bilan_taille.r
===================================================================
--- pkg/stacomir/R/interface_Bilan_taille.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_Bilan_taille.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -54,7 +54,7 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
assign("toolbarlist",toolbarlist,envir=.GlobalEnv)
assign("ggroupboutonsbas",ggroupboutonsbas,envir =.GlobalEnv)
}
Modified: pkg/stacomir/R/interface_bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/interface_bilan_poids_moyen.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/interface_bilan_poids_moyen.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -28,7 +28,7 @@
#graphes=ggraphics(width=600,height=400)
#add(ggrouptotal1,graphes ) # on ajoute au groupe horizontal
#assign("graphes",graphes,envir=envir_stacomi)
- grDevices::X11()
+ dev.new()
# A cet endroit sinon ouvre plusieurs fenetres pour plusieurs choses
choice(bilan_poids_moyen at liste)
choice(bilan_poids_moyen at dc,objectBilan=NULL,is.enabled=TRUE)
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/stacomi.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -223,7 +223,7 @@
eval(interface_chooselang(),envir = .GlobalEnv)
}
hX11=function(h,...){
- grDevices::X11()
+ dev.new()
}
@@ -283,13 +283,15 @@
#' @importFrom utils select.list write.table data
#' @importFrom stats ftable
#' @importFrom stats xtabs
+#' @importFrom grDevices dev.new
+#' @importFrom stats sd
#' @importFrom reshape2 dcast
#' @importFrom reshape2 melt
#' @importFrom lattice barchart trellis.par.get trellis.par.set simpleKey
#' @importFrom grid gpar
#' @importFrom graphics layout matplot mtext points polygon segments par axis text legend rect axis.Date
#' @importFrom stats as.formula coef na.fail nls pbeta predict sd
-#' @importFrom grDevices X11 X11 gray rainbow
+#' @importFrom grDevices gray rainbow
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#'
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/R/utilitaires.r 2016-09-15 20:09:28 UTC (rev 209)
@@ -138,11 +138,11 @@
# the access to csv file failed despite database_expected=true
# if the file does not open, we switch to the file located within the package
cat("C:/program files/calcmig.csv does not exist, switching to defaut package file")
- data("calcmig")
+ data("calcmig",envir=environment())
}
} else {
# no access to the database is expected, we are using the file in the data directory of the package
- data("calcmig")
+ data("calcmig",envir=environment())
test<-FALSE
}
tableau_config = t(calcmig) # renvoit une liste
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-09-15 20:09:28 UTC (rev 209)
@@ -1,9 +1,9 @@
context("stacomi base connection")
test_that("Test existence of csv file",{
- filecsv<-"C:/Program Files/stacomi/calcmig.csv";
- expect_equivalent(file.access(filecsv,0),0)
- }
+ filecsv<-"C:/Program Files/stacomi/calcmig.csv";
+ expect_equivalent(file.access(filecsv,0),0)
+ }
)
@@ -11,7 +11,7 @@
data("calcmig",package = "stacomiR")
calcmig<-calcmig
expect_equal(length(calcmig),11)
-
+
}
)
@@ -28,19 +28,19 @@
context("Database connection")
test_that("Test that stacomirtools connects",{
- require(stacomiR)
- envir_stacomi <<- new.env(parent = emptyenv())
- msg<-messages()
- mylinks=chargecsv(database_expected=TRUE)
- baseODBC=mylinks[["baseODBC"]]
- con=new("ConnectionODBC")
- con at baseODBC=baseODBC
- con<-connect(con)
- expect_is(connect(con),'ConnectionODBC')
- expect_equal(con at etat,NULL)
- odbcCloseAll()
- rm("envir_stacomi",envir =.GlobalEnv)
-})
+ require(stacomiR)
+ envir_stacomi <<- new.env(parent = emptyenv())
+ msg<-messages()
+ mylinks=chargecsv(database_expected=TRUE)
+ baseODBC=mylinks[["baseODBC"]]
+ con=new("ConnectionODBC")
+ con at baseODBC=baseODBC
+ con<-connect(con)
+ expect_is(connect(con),'ConnectionODBC')
+ expect_equal(con at etat,NULL)
+ odbcCloseAll()
+ rm("envir_stacomi",envir =.GlobalEnv)
+ })
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
require(stacomiR)
@@ -90,7 +90,7 @@
expect_true(exists("logw"))
dispose(logw)
rm("envir_stacomi",envir =.GlobalEnv)
-})
+ })
test_that("Test that gWidget gr_interface is loaded, without database_expected, nor login window",{
require(stacomiR)
@@ -137,5 +137,142 @@
# objects should have the same length but different languages
expect_identical(length(msg),length(msgbase))
rm("envir_stacomi",envir =.GlobalEnv)
- rm(list=ls(all=TRUE))
})
+
+
+context("Database integrity")
+
+
+test_that("Test that tickets have been launched",
+ {
+ require(stacomiR)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+ req<-new("RequeteODBC")
+ req at baseODBC<-get("baseODBC", envir=envir_stacomi)
+ sch=get("sch",envir=envir_stacomi)
+ req at sql=paste("select * from ",sch," ts_maintenance_main")
+ req<-stacomirtools::connect(req)
+ result<-req at query
+ # using dput(ticket)
+ tickets<-structure(list(
+ main_ticket = c(59L,
+ 40L,
+ 42L,
+ 67L,
+ 72L,
+ 121L,
+ 122L,
+ 81L,
+ 61L,
+ 152L,
+ 147L), main_description = c("creation de la table de maintenance",
+ "ajout des clé étrangères manquantes",
+ "modification des propriétaires sur les tables à séquence et grant select sur ref.tr_typedf_tdf oublié",
+ "org code rajouté dans les tables t_operationmarquage_omq, tj_coefficientconversion_coe,tj_prelevementlot_prl",
+ "creation d'une tableref.ts_messager_msr pour l'internationalisation",
+ "ajout de la notion de cohorte pour les saumons passant très précocément",
+ "Mise à jour des localisations anatomiques",
+ "Mise à jour vers la version 0.4 alpha, mise à jour des référentiels du SANDRE, script ticjet81_mise_en_conformite_sandre, révision 98",
+ "Mise à jour vers la version 0.4 alpha, mise à jour ds constraintes stationmesure modification limites coordonnées géographiques",
+ "Mise à jour vers la version 0.4 alpha, problèmes de clé étrangères, script total",
+ "Mise à jour vers la version 0.4 alpha, creation des masques"
+ )),
+ .Names = c("main_ticket", "main_description"),
+ class = "data.frame",
+ row.names = c(NA,
+ 11L))
+ check_exist_tickets=tickets$main_ticket%in%result$main_ticket
+ for (i in 1:nrow(tickets)){
+ expect_true(check_exist_tickets[i],label=paste('Missing ticket :',tickets$main_ticket[i]))
+ }
+ })
+
+test_that("All foreign keys are present",
+ {
+ require(stacomiR)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+ req<-new("RequeteODBC")
+ baseODBC<-get("baseODBC", envir=envir_stacomi)
+ baseODBC$uid=readline(prompt="Enter superuser name: ")
+ baseODBC$pwd=readline(prompt="Enter superuser password: ")
+ req at baseODBC<-baseODBC
+ req at sql=paste("SELECT
+ distinct on (tc.constraint_name) tc.constraint_name, tc.table_name
+ FROM
+ information_schema.table_constraints AS tc
+ JOIN information_schema.key_column_usage AS kcu
+ ON tc.constraint_name = kcu.constraint_name
+ JOIN information_schema.constraint_column_usage AS ccu
+ ON ccu.constraint_name = tc.constraint_name
+ WHERE constraint_type = 'FOREIGN KEY';")
+ req<-stacomirtools::connect(req)
+ result<-req at query
+ fk<-structure(list(constraint_name = c("c_fk_act_lot_identifiant",
+ "c_fk_act_mqe_reference", "c_fk_act_org_code", "c_fk_bjo_org_code",
+ "c_fk_bjo_std_code", "c_fk_bjo_tax_code", "c_fk_bme_std_code",
+ "c_fk_bme_tax_code", "c_fk_car_lot_identifiant", "c_fk_car_org_code",
+ "c_fk_car_par_code", "c_fk_car_val_identifiant", "c_fk_coe_org_code",
+ "c_fk_coe_qte_code", "c_fk_coe_std_code", "c_fk_coe_tax_code",
+ "c_fk_dft_df_identifiant", "c_fk_dft_org_code", "c_fk_dft_tdf_code",
+ "c_fk_dic_dif_identifiant", "c_fk_dic_dis_identifiant", "c_fk_dic_org_code",
+ "c_fk_dic_tdc_code", "c_fk_dif_dis_identifiant", "c_fk_dif_org_code",
+ "c_fk_dif_ouv_identifiant", "c_fk_dtx_dif_identifiant", "c_fk_dtx_org_code",
+ "c_fk_dtx_tax_code", "c_fk_env_org_code", "c_fk_env_stm_identifiant",
+ "c_fk_env_val_identifiant", "c_fk_lot_dev_code", "c_fk_lot_lot_identifiant",
+ "c_fk_lot_ope_identifiant", "c_fk_lot_org_code", "c_fk_lot_qte_code",
+ "c_fk_lot_std_code", "c_fk_lot_tax_code", "c_fk_maa_mal_id",
+ "c_fk_mac_valeurqualitatifdefaut", "c_fk_mae_mao_id", "c_fk_mae_stm_identifiant",
+ "c_fk_mal_mas_id", "c_fk_mao_mas_id", "c_fk_mqe_loc_code", "c_fk_mqe_nmq_code",
+ "c_fk_mqe_omq_reference", "c_fk_mqe_org_code", "c_fk_mrl_msr_id",
+ "c_fk_omq_org_code", "c_fk_ope_dic_identifiant", "c_fk_ope_org_code",
+ "c_fk_ouv_nov_code", "c_fk_ouv_org_code", "c_fk_ouv_sta_code",
+ "c_fk_pco_imp_code", "c_fk_pco_loc_code", "c_fk_pco_lot_identifiant",
+ "c_fk_pco_org_code", "c_fk_pco_pat_code", "c_fk_per_dis_identifiant",
+ "c_fk_per_org_code", "c_fk_per_tar_code", "c_fk_prl_loc_code",
+ "c_fk_prl_lot_identifiant", "c_fk_prl_org_code", "c_fk_prl_pre_nom",
+ "c_fk_prl_typeprelevement", "c_fk_qal_par_code", "c_fk_qan_par_code",
+ "c_fk_sta_org_code", "c_fk_std_code", "c_fk_stm_org_code", "c_fk_stm_par_code",
+ "c_fk_stm_sta_code", "c_fk_tav_dic_identifiant", "c_fk_tav_org_code",
+ "c_fk_tax_ntx_code", "c_fk_tax_tax_tax_code", "c_fk_txe_ech_code",
+ "c_fk_txe_org_code", "c_fk_txe_ouv_identifiant", "c_fk_txe_sta_code",
+ "c_fk_txe_std_code", "c_fk_txe_tax_code", "c_fk_txv_org_code",
+ "c_fk_txv_std_code", "c_fk_txv_tax_code", "c_fk_val_qal_code"
+ ), table_name = c("tj_actionmarquage_act", "tj_actionmarquage_act",
+ "tj_actionmarquage_act", "t_bilanmigrationjournalier_bjo", "t_bilanmigrationjournalier_bjo",
+ "t_bilanmigrationjournalier_bjo", "t_bilanmigrationmensuel_bme",
+ "t_bilanmigrationmensuel_bme", "tj_caracteristiquelot_car", "tj_caracteristiquelot_car",
+ "tj_caracteristiquelot_car", "tj_caracteristiquelot_car", "tj_coefficientconversion_coe",
+ "tj_coefficientconversion_coe", "tj_coefficientconversion_coe",
+ "tj_coefficientconversion_coe", "tj_dfesttype_dft", "tj_dfesttype_dft",
+ "tj_dfesttype_dft", "t_dispositifcomptage_dic", "t_dispositifcomptage_dic",
+ "t_dispositifcomptage_dic", "t_dispositifcomptage_dic", "t_dispositiffranchissement_dif",
+ "t_dispositiffranchissement_dif", "t_dispositiffranchissement_dif",
+ "tj_dfestdestinea_dtx", "tj_dfestdestinea_dtx", "tj_dfestdestinea_dtx",
+ "tj_conditionenvironnementale_env", "tj_conditionenvironnementale_env",
+ "tj_conditionenvironnementale_env", "t_lot_lot", "t_lot_lot",
+ "t_lot_lot", "t_lot_lot", "t_lot_lot", "t_lot_lot", "t_lot_lot",
+ "ts_masqueordreaffichage_maa", "ts_masquecaracteristiquelot_mac",
+ "ts_masqueconditionsenvironnementales_mae", "ts_masqueconditionsenvironnementales_mae",
+ "ts_masquelot_mal", "ts_masqueope_mao", "t_marque_mqe", "t_marque_mqe",
+ "t_marque_mqe", "t_marque_mqe", "ts_messagerlang_mrl", "t_operationmarquage_omq",
+ "t_operation_ope", "t_operation_ope", "t_ouvrage_ouv", "t_ouvrage_ouv",
+ "t_ouvrage_ouv", "tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco",
+ "tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco", "tj_pathologieconstatee_pco",
+ "t_periodefonctdispositif_per", "t_periodefonctdispositif_per",
+ "t_periodefonctdispositif_per", "tj_prelevementlot_prl", "tj_prelevementlot_prl",
+ "tj_prelevementlot_prl", "tj_prelevementlot_prl", "tj_prelevementlot_prl",
+ "tr_parametrequalitatif_qal", "tr_parametrequantitatif_qan",
+ "t_station_sta", "ts_taxonvideo_txv", "tj_stationmesure_stm",
+ "tj_stationmesure_stm", "tj_stationmesure_stm", "ts_taillevideo_tav",
+ "ts_taillevideo_tav", "tr_taxon_tax", "tr_taxon_tax", "tj_tauxechappement_txe",
+ "tj_tauxechappement_txe", "tj_tauxechappement_txe", "tj_tauxechappement_txe",
+ "tj_tauxechappement_txe", "tj_tauxechappement_txe", "ts_taxonvideo_txv",
+ "ts_taxonvideo_txv", "ts_taxonvideo_txv", "tr_valeurparametrequalitatif_val"
+ )), .Names = c("constraint_name", "table_name"), row.names = c(NA,
+ 90L), class = "data.frame")
+ check_exist_fk=fk$constraint_name%in%result$constraint_name
+ for (i in 1:nrow(fk)){
+ expect_true(check_exist_fk[i],label=paste("Missing foreign key :",fk$constraint_name,"table :",fk$table_name))
+ }
+ rm(list=ls(all=TRUE))
+ })
\ No newline at end of file
Added: pkg/stacomir/inst/tests/testthat/test-00zRefclasses.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00zRefclasses.R (rev 0)
+++ pkg/stacomir/inst/tests/testthat/test-00zRefclasses.R 2016-09-15 20:09:28 UTC (rev 209)
@@ -0,0 +1,48 @@
+context("RefHorodate")
+test_that("Test that the parsing of many kind of dates works",
+ {
+ require(stacomiR)
+ refHorodate<-new("RefHorodate")
+ # regular expression to test string "1] nous avons le choix dans la date\n"
+ # default string returned by the method
+ expect_that(refHorodate<-choice_c(refHorodate,
+ horodate="01/01/2013 00:00:00"),prints_text("^\\[1\\].+date.+"))
+ expect_that(refHorodate<-choice_c(refHorodate,
+ horodate="01/01/2013 00:00"),prints_text("^\\[1\\].+date.+"))
+ expect_that(refHorodate<-choice_c(refHorodate,
+ horodate="01-01-2013 00:00"),prints_text("^\\[1\\].+date.+"))
+ expect_that(refHorodate<-choice_c(refHorodate,
+ horodate="2013-01-01 00:00"),prints_text("^\\[1\\].+date.+"))
+ expect_that(refHorodate<-choice_c(refHorodate,
+ horodate="01-01-2013"),prints_text("^\\[1\\].+date.+"))
+ refHorodate<-choice_c(refHorodate,
+ horodate="2013/01/01 00:00:00")
+ rm("envir_stacomi",envir =.GlobalEnv)
+ })
+
+
+
+test_that("Test that the parsing of wrong character formats gets an error",
+ {
+ require(stacomiR)
+ refHorodate<-new("RefHorodate")
+ expect_error(refHorodate<-choice_c(refHorodate,
+ horodate="2013 01 01"))
+ rm("envir_stacomi",envir =.GlobalEnv)
+ })
+
+context("RefDF")
+
+test_that("Test that RefDF choice_c method loads character, numeric, but not rubbish",
+ {
+ require(stacomiR)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+ refDF<-new("RefDF")
+ refDF<-charge(refDF)
+ expect_silent(refDF<-choice_c(refDF, 2))
+ expect_silent(refDF<-choice_c(refDF, "2"))
+ options(warn = 0)
+ expect_error(refDF<-choice_c(refDF, "semoule"))
+ options(warn = 2)
+ rm("envir_stacomi",envir =.GlobalEnv)
+ })
Modified: pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R 2016-09-11 19:23:57 UTC (rev 208)
+++ pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R 2016-09-15 20:09:28 UTC (rev 209)
@@ -11,18 +11,20 @@
assign("sch","iav.",envir_stacomi)
BfDF<-new("BilanFonctionnementDF")
- options(warn = 2)
BfDF<-choice_c(BfDF,
2,
horodatedebut="2013-01-01",
horodatefin="2013-12-31")
- options(warn = 0)
- # there should be data in
expect_gt(nrow(BfDF at df@data),0,
label="There should be data loaded by the choice_c method in the data slot of
the RefDF slot,nrow(BfDF at df@data)")
expect_s4_class(BfDF,
"BilanMigration")
- rm("envir_stacomi",envir =.GlobalEnv)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 209
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