[Stacomir-commits] r175 - in pkg/stacomir: . R inst inst/config inst/tests inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 23 11:58:47 CEST 2016
Author: briand
Date: 2016-08-23 11:58:46 +0200 (Tue, 23 Aug 2016)
New Revision: 175
Added:
pkg/stacomir/inst/tests/
pkg/stacomir/inst/tests/testthat/
Removed:
pkg/stacomir/inst/test/
pkg/stacomir/inst/tests/test-00stacomirbaseconnection.R
pkg/stacomir/inst/tests/test-BilanMigrationMult.R
Modified:
pkg/stacomir/NAMESPACE
pkg/stacomir/R/RefMsg.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/inst/config/testthat.R
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/man/chargecsv.Rd
pkg/stacomir/man/createmessage-RefMsg-method.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/funout.Rd
pkg/stacomir/man/husr.Rd
Log:
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/NAMESPACE 2016-08-23 09:58:46 UTC (rev 175)
@@ -3,6 +3,7 @@
export(chargecsv)
export(fun_bilanMigrationMult)
export(fun_bilanMigrationMult_Overlaps)
+export(fun_char_spe)
export(fun_weight_conversion)
export(funbarchartDC)
export(funbarchartDF)
@@ -26,6 +27,7 @@
export(interface_BilanEspeces)
export(messages)
export(stacomi)
+export(vector_to_listsql)
exportClasses(BilanConditionEnv)
exportClasses(BilanEspeces)
exportClasses(BilanFonctionnementDC)
@@ -43,6 +45,7 @@
exportMethods(charge_avec_filtre)
exportMethods(choice_c)
exportMethods(connect)
+exportMethods(createmessage)
exportMethods(cumplot)
exportMethods(plot1)
exportMethods(print)
Modified: pkg/stacomir/R/RefMsg.r
===================================================================
--- pkg/stacomir/R/RefMsg.r 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/R/RefMsg.r 2016-08-23 09:58:46 UTC (rev 175)
@@ -56,6 +56,8 @@
#' @note When coming from the database, doublequotes are now escaped with an antislash (/"), those at the beginning and end are left as doublequotes,
#' the others are single quote when they are to be pasted within the text as code example. The remainder "c("a","b","c") are rebuilt into vectors by the function
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
+#' @keywords internal
setMethod("createmessage",signature=signature("RefMsg"),definition=function(object,pre_launch_test) {
if (pre_launch_test){
#object=new("RefMsg")
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/R/stacomi.r 2016-08-23 09:58:46 UTC (rev 175)
@@ -89,32 +89,31 @@
#' Internal function, tests the connection and if it works loads the stacomi interface
#' @note \code{gr_interface} is copied by stacomi into envir_stacomi. Same for \code{pre_launch_test}
#'
-#' @param h a handler
-#' @param ...
+#' @param h A handler
+#' @param ... Other arguments
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-
husr=function(h,...){
baseODBC<-get("baseODBC",envir=envir_stacomi)
# assigned when passing through stacomi
gr_interface<-get("gr_interface",envir_stacomi) # logical true or false
pre_launch_test<-get("pre_launch_test",envir_stacomi) # logical true or false
+ login_window<-get("login_window",envir_stacomi) # logical true or false
# test de la connection
- if (login_window){
- con=new("ConnectionODBC")
- if (gr_interface){
+ if (login_window & gr_interface&pre_launch_test){
baseODBC[2]<-svalue(usrname)
baseODBC[3]<-svalue(usrpwd)
+ assign("sch",paste(baseODBC[2],".",sep=""),envir=envir_stacomi)
+ assign("baseODBC",baseODBC,envir=envir_stacomi)
} else {
- # we take default values from calmig
- # nothing is happening there
+ # nothing sch and baseODBC have been assigned from default value in stacomi()
}
- assign("sch",paste(baseODBC[2],".",sep=""),envir=envir_stacomi)
- assign("baseODBC",baseODBC,envir=envir_stacomi)
- con at baseODBC=get("baseODBC",envir=envir_stacomi)
+
# we dispose loginwindow
- if (exists("logw")) dispose(logw)
- }
+
+
if (pre_launch_test){
+ con=new("ConnectionODBC")
+ con at baseODBC=get("baseODBC",envir=envir_stacomi)
e=expression(con<-connect(con))
con=tryCatch(eval(e),error=get("msg",envir=envir_stacomi)$interface_graphique_log.7) #finally=odbcClose(con at connection)clause inutile car si �a plante la connection n'est pas ouverte
test<-con at etat==get("msg",envir=envir_stacomi)$ConnectionODBC.6
@@ -282,20 +281,26 @@
#' @export
stacomi=function(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE){
# first loading of connection and odbc info using chargexml()
+ envir_stacomi <<- new.env(parent = emptyenv())
assign("gr_interface",gr_interface,envir=envir_stacomi)
assign("pre_launch_test",pre_launch_test,envir=envir_stacomi)
- # the first messages are necessary for the first access to the database, they are in French
- envir_stacomi <- new.env(parent = emptyenv())
+ assign("login_window",login_window,envir=envir_stacomi)
+ # the first messages are necessary for the first access to the database, they are in French
msg<-messages()
mylinks=chargecsv()
baseODBC=mylinks[["baseODBC"]]
datawd=mylinks[["datawd"]]
lang=mylinks[["lang"]]
sqldf.options=mylinks[["sqldf.options"]]
+ # values assigned in the envir_stacomi
assign("lang",lang,envir=envir_stacomi)
- assign("baseODBC",baseODBC,envir=envir_stacomi)
assign("datawd",datawd,envir=envir_stacomi)
assign("sqldf.options",sqldf.options,envir=envir_stacomi)
+
+ # the following values may be overridden later in husr()
+ assign("baseODBC",baseODBC,envir=envir_stacomi)
+ assign("sch",paste(baseODBC[2],".",sep=""),envir=envir_stacomi)
+
refMsg=new("RefMsg")
createmessage(refMsg,pre_launch_test)
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/R/utilitaires.r 2016-08-23 09:58:46 UTC (rev 175)
@@ -237,6 +237,7 @@
#' @param text a text string which might contain no utf8 characters
#' @return text
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
fun_char_spe<-function(text){
text=gsub("\u00e9","e",text) #é
text=gsub("\u00e8","e",text) #è
@@ -258,6 +259,7 @@
#' @param wash Should the console be cleared after displaying the message
#' @return nblignes Assigned in .Global
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funout<-function(text,arret=FALSE,wash=FALSE){
if (exists("gSortie")) {
if (wash) dispose(gSortie)
@@ -281,18 +283,21 @@
#' files/stacomi/calcmig.csv file
#'
#' be sure to configure your odbc link to the
-#' database, the name is the name of the first column of the calcmig.csv file
-#' uid, pwd are identifier and password to connect to the database, they should
-#' correspond to your own schema in the database pgwd, is the path to the R
-#' source if you plan not to use the compiler but develop from source
-#' https://r-forge.r-project.org/scm/?group_id=1019 datawd, is the the
+#' database, the name is the name of the first column of the calcmig.csv file.
+#' \code{uid}, \code{pwd} are identifier and password to connect to the database, they should
+#' correspond to your own schema in the database. \code{pgwd} is the path to the R
+#' source if you plan not to use the compiler but run manually using inst/config/stacomi_manual_launch.R for development.\cr
+#' \code{datawd}, is the the
#' directory where you want to place the outputs, mostly tables, from the
#' program, default to ~//CalcmigData lang, is either one of French, English or
#' Spanish
+#' other fields correspond to sqldf options.
+#' @note A version of the calcmig.csv is packaged in the config directory of the stacomiR library.
#'
#' @return a list with the datawd place and the baseODBC vector
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
+#' @keywords internal
chargecsv=function(){
#library(XML) # chargement du package XML
options(guiToolkit = "RGtk2")
@@ -341,6 +346,7 @@
#' @param vect a character vector
#' @return listsql a list of value
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
vector_to_listsql<-function(vect)
{
Modified: pkg/stacomir/inst/config/testthat.R
===================================================================
--- pkg/stacomir/inst/config/testthat.R 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/inst/config/testthat.R 2016-08-23 09:58:46 UTC (rev 175)
@@ -1,4 +1,4 @@
require(testthat)
-test_dir("F:/workspace/stacomir/pkg/stacomir/inst/test/testthat")
+test_dir("F:/workspace/stacomir/pkg/stacomir/inst/tests/testthat")
Deleted: pkg/stacomir/inst/tests/test-00stacomirbaseconnection.R
===================================================================
--- pkg/stacomir/inst/test/test-00stacomirbaseconnection.R 2016-08-19 19:56:13 UTC (rev 164)
+++ pkg/stacomir/inst/tests/test-00stacomirbaseconnection.R 2016-08-23 09:58:46 UTC (rev 175)
@@ -1,32 +0,0 @@
-# Author: cedric.briand
-###############################################################################
-
-
-context("stacomi base connection")
-
-test_that("existence du fichier csv",{
- filecsv<-"C:/Program Files/stacomi/calcmig.csv";
- expect_equivalent(file.access(filecsv,0),0)
- }
-
-)
-
-test_that("Teste que le lien ODBC existe et a la bonne longueur",{
- result<-chargecsv();
- expect_equal(length(result),3)
- expect_equal(length(result$baseODBC),3)
- expect_equal(length(result$sqldf),3)
- })
-
-test_that("Teste que l'environnement de travail est bien cr��",{
- expect_true(exists("envir_stacomi"))
- })
-
-
-
-test_that("Teste la m�thode charge les messages de r�f�rence",
- {
- object=new("RefMsg")
- object<-charge(object)
- expect_true(nrow(object at messager)>0)
- })
\ No newline at end of file
Deleted: pkg/stacomir/inst/tests/test-BilanMigrationMult.R
===================================================================
--- pkg/stacomir/inst/test/test-BilanMigrationMult.R 2016-08-19 19:56:13 UTC (rev 164)
+++ pkg/stacomir/inst/tests/test-BilanMigrationMult.R 2016-08-23 09:58:46 UTC (rev 175)
@@ -1,37 +0,0 @@
-# Author: cedric.briand
-###############################################################################
-
-context("BilanMigrationMult")
-test_that("Teste une instance de bilanMigrationMult",{
- bilanMigrationMult<-new("BilanMigrationMult")
- bilanMigrationMult<-load(bilanMigrationMult,
- dc=c(6,7),
- taxons=c("Anguilla anguilla","Salmo salar"),
- stades=c("AGG","AGJ","CIV"),
- datedebut="2012-01-01",
- datefin="2012-12-31")
- expect_s4_class(bilanMigrationMult,
- "BilanMigrationMult")})
-test_that("Teste une autre instance de bilanMigrationMult",{
- bilanMigrationMult<-new("BilanMigrationMult")
- bilanMigrationMult<-load(bilanMigrationMult,
- dc=c(6,7),
- taxons=c(2038,2220),
- stades=c("AGG","AGJ","CIV"),
- datedebut="2012-01-01",
- datefin="31/12/2012")
- expect_s4_class(bilanMigrationMult,
- "BilanMigrationMult")})
-test_that("Teste une une instance avec erreur (dc n'existe pas)",
- {
- bilanMigrationMult<-new("BilanMigrationMult")
- expect_error(load(bilanMigrationMult,
- dc=c(6,70),
- taxons=c("Anguilla anguilla","Salmo salar"),
- stades=c("AGG","AGJ","CIV"),
- datedebut="2012-01-01",
- datefin="31/12/2012"))
- })
-
-
-
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/test/testthat/test-00stacomir.R 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-08-23 09:58:46 UTC (rev 175)
@@ -27,6 +27,7 @@
test_that("Test that stacomirtools connects",{
require(stacomiR)
+ envir_stacomi <<- new.env(parent = emptyenv())
msg<-messages()
mylinks=chargecsv()
baseODBC=mylinks[["baseODBC"]]
@@ -34,18 +35,18 @@
con at baseODBC=baseODBC
con<-connect(con)
expect_is(connect(con),'ConnectionODBC')
- expect_equal(con at etat,"connected")
+ expect_equal(con at etat,NULL)
odbcCloseAll()
})
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
require(stacomiR)
-
+ envir_stacomi <<- new.env(parent = emptyenv())
msg<-messages()
mylinks=chargecsv()
baseODBC=mylinks[["baseODBC"]]
requete=new("RequeteODBC")
- requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
+ requete at baseODBC<-baseODBC
requete at sql="select count(*) from ref.tr_taxon_tax"
requete<-stacomirtools::connect(requete)
expect_true(as.numeric(requete at query)>0)
@@ -54,12 +55,13 @@
test_that("Tests positive count for sch.t_operation_ope",{
require(stacomiR)
+ envir_stacomi <<- new.env(parent = emptyenv())
msg<-messages()
mylinks=chargecsv()
baseODBC=mylinks[["baseODBC"]]
sch<-paste(baseODBC[2],".",sep="")
requete=new("RequeteODBC")
- requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
+ requete at baseODBC<-baseODBC
requete at sql=paste("select count(*) from ",sch,"t_operation_ope",sep="")
requete<-stacomirtools::connect(requete)
expect_true(as.numeric(requete at query)>0)
@@ -71,6 +73,7 @@
test_that("Test that working environment is created",{
require(stacomiR)
+ stacomi(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE)
expect_true(exists("envir_stacomi"))
})
@@ -110,7 +113,7 @@
object<-createmessage(object,TRUE)
msgbase<-get("msg",envir=envir_stacomi)
require(stacomiR)
- stacomi(gr_interface=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
msg<-get("msg",envir=envir_stacomi)
# objects should have the same length but different languages
expect_identical(length(msg),length(msgbase))
Modified: pkg/stacomir/man/chargecsv.Rd
===================================================================
--- pkg/stacomir/man/chargecsv.Rd 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/man/chargecsv.Rd 2016-08-23 09:58:46 UTC (rev 175)
@@ -12,16 +12,21 @@
}
\description{
be sure to configure your odbc link to the
-database, the name is the name of the first column of the calcmig.csv file
-uid, pwd are identifier and password to connect to the database, they should
-correspond to your own schema in the database pgwd, is the path to the R
-source if you plan not to use the compiler but develop from source
-https://r-forge.r-project.org/scm/?group_id=1019 datawd, is the the
+database, the name is the name of the first column of the calcmig.csv file.
+ \code{uid}, \code{pwd} are identifier and password to connect to the database, they should
+correspond to your own schema in the database. \code{pgwd} is the path to the R
+source if you plan not to use the compiler but run manually using inst/config/stacomi_manual_launch.R for development.\cr
+ \code{datawd}, is the the
directory where you want to place the outputs, mostly tables, from the
program, default to ~//CalcmigData lang, is either one of French, English or
Spanish
+ other fields correspond to sqldf options.
}
+\note{
+A version of the calcmig.csv is packaged in the config directory of the stacomiR library.
+}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
+\keyword{internal}
Modified: pkg/stacomir/man/createmessage-RefMsg-method.Rd
===================================================================
--- pkg/stacomir/man/createmessage-RefMsg-method.Rd 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/man/createmessage-RefMsg-method.Rd 2016-08-23 09:58:46 UTC (rev 175)
@@ -23,4 +23,5 @@
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
+\keyword{internal}
Modified: pkg/stacomir/man/envir_stacomi.Rd
===================================================================
--- pkg/stacomir/man/envir_stacomi.Rd 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/man/envir_stacomi.Rd 2016-08-23 09:58:46 UTC (rev 175)
@@ -5,7 +5,7 @@
\alias{envir_stacomi}
\title{Environment where most objects from the package are stored and then loaded
by the charge method}
-\format{An object of class \code{environment} of length 0.}
+\format{An object of class \code{environment} of length 10.}
\usage{
envir_stacomi
}
Modified: pkg/stacomir/man/funout.Rd
===================================================================
--- pkg/stacomir/man/funout.Rd 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/man/funout.Rd 2016-08-23 09:58:46 UTC (rev 175)
@@ -23,4 +23,5 @@
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
+\keyword{internal}
Modified: pkg/stacomir/man/husr.Rd
===================================================================
--- pkg/stacomir/man/husr.Rd 2016-08-23 08:20:45 UTC (rev 174)
+++ pkg/stacomir/man/husr.Rd 2016-08-23 09:58:46 UTC (rev 175)
@@ -7,9 +7,9 @@
husr(h, ...)
}
\arguments{
-\item{h}{a handler}
+\item{h}{A handler}
-\item{...}{}
+\item{...}{Other arguments}
}
\description{
Internal function, tests the connection and if it works loads the stacomi interface
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