[Stacomir-commits] r391 - in pkg/stacomir: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 9 15:44:20 CEST 2017
Author: briand
Date: 2017-06-09 15:44:19 +0200 (Fri, 09 Jun 2017)
New Revision: 391
Added:
pkg/stacomir/man/getdbname.Rd
Modified:
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/Bilan_carlot.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/data.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/man/bfDF.Rd
pkg/stacomir/man/write_database-BilanAgedemer-method.Rd
pkg/stacomir/man/write_database-BilanMigration-method.Rd
pkg/stacomir/man/write_database-Bilan_poids_moyen-method.Rd
Log:
Correction connection problem when database name is not standard in graphical interface
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -349,17 +349,19 @@
#' into the tj_caracteristiquelot_car table in the user's scheme
#'
#' The sea age caracteristic is calculated from the mesured or calculated size of salmon and with a size/age rule
-#' defined by the user
+#' defined by the user . the name of the database is retreived from the odbc link
+#' defined in calcmig.csv
#' @param object an object of class \link{BilanAgedemer-class}
#' @param silent : Default FALSE, if TRUE the program should no display messages.
-#' @param dbname : the name of the database, defaults to "bd_contmig_nat"
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-setMethod("write_database",signature=signature("BilanAgedemer"),definition=function(object,silent=TRUE,dbname="bd_contmig_nat"){
+setMethod("write_database",signature=signature("BilanAgedemer"),definition=function(object,silent=TRUE){
# dbname="bd_contmig_nat"
bilan_adm<-object
host=get("sqldf.options",envir=envir_stacomi)["sqldf.host"]
port=get("sqldf.options",envir=envir_stacomi)["sqldf.port"]
+ # getting the database name
+ dbname<-getdbname()
calcdata<-bilan_adm at calcdata[["data"]]
data_in_base<-bilan_adm at data
if (nrow(calcdata)==0) {
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/BilanMigration.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -578,12 +578,12 @@
#' by this function.
#' @param object an object of class \code{\linkS4class{BilanMigration}}
#' @param silent : TRUE to avoid messages
-#' @param dbname : the name of the database, defaults to "bd_contmig_nat"
#' @param check_for_bjo : do you want to check if data are already present in the bjo table, and delete them,
#' this param was added otherwise connect method when called from BilanMigrationInterAnnuelle runs in loops
#' @note the user is asked whether or not he wants to overwrite data, if no
#' data are present in the database, the import is done anyway. The name of the database
-#' is not passed in odbc link, here defaults to "bd_contmig_nat"
+#' is retrieved from the odbc link
+#'
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
@@ -593,13 +593,15 @@
#' write_database(bilanMigration=bM_Arzal,silent=FALSE)
#' }
#' @export
-setMethod("write_database",signature=signature("BilanMigration"),definition=function(object,silent=TRUE,dbname="bd_contmig_nat",check_for_bjo=TRUE){
+setMethod("write_database",signature=signature("BilanMigration"),definition=function(object,silent=TRUE,check_for_bjo=TRUE){
# dbname="bd_contmig_nat";host="localhost";silent=FALSE;port=5432
# object=bM
#host : the host for sqldf, defaults to "localhost"
#port : the port, defaults to 5432
host=get("sqldf.options",envir=envir_stacomi)["sqldf.host"]
port=get("sqldf.options",envir=envir_stacomi)["sqldf.port"]
+ # getting the database name
+ dbname<-getdbname()
bilanMigration<-object
if (class(bilanMigration)!="BilanMigration") stop("the bilanMigration should be of class BilanMigration")
if (class(silent)!="logical") stop("the silent argument should be a logical")
@@ -655,6 +657,7 @@
# check = FALSE tells the method not to check for missing data (we don't want that check when the
# write database is called from the bilanMigration class
if (check_for_bjo) bil=connect(bil,silent=silent,check=FALSE)
+
hconfirm=function(h,...){
# suppression des donnees actuellement presentes dans la base
@@ -707,6 +710,7 @@
sql<-stringr::str_c("INSERT INTO ",get("sch",envir=envir_stacomi),"t_bilanmigrationjournalier_bjo (",
"bjo_dis_identifiant,bjo_tax_code,bjo_std_code,bjo_annee,bjo_jour,bjo_valeur,bjo_labelquantite,bjo_horodateexport,bjo_org_code)",
" SELECT * FROM aat_bilanmigrationjournalier_bjo;")
+
invisible(utils::capture.output(
sqldf::sqldf(x=sql,
drv="PostgreSQL",
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -171,7 +171,8 @@
} # end for loop to write new bilans
# reloading everything
object at data<-fn_connect()
- compared_numbers<-fn_check()
+ compared_numbers<-fn_check()
+
} # end if any...
#-------------------------------------------------------------------------------------
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/Bilan_carlot.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -226,6 +226,7 @@
} else {
if (!silent) funout(gettext("You need to launch computation first, clic on calc\n",domain="R-stacomiR"),arret=TRUE)
}
+ name_param<-bilan_carlot
if (plot.type==1){
g<-ggplot(bilan_carlot at data,aes(x=car_valeur_quantitatif))
g<-g+stat_density(aes(ymax = ..density.., ymin = -..density..),
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -542,10 +542,9 @@
#' Function to write data to the stacomi database for \link{Bilan_poids_moyen-class}
#'
#' Data will be written in tj_coefficientconversion_coe table, if the class retrieves some data
-#' from the database, those will be deleted first.
+#' from the database, those will be deleted first.
#' @param object An object of class \link{Bilan_poids_moyen-class}
#' @param silent Boolean, if TRUE, information messages are not displayed
-#' @param dbname default "bd_contmig_nat"
#' @return An object of class \link{Bilan_poids_moyen-class}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
@@ -553,6 +552,8 @@
#silent=FALSE;dbname="bd_contmig_nat";host="localhost";port=5432
host=get("sqldf.options",envir=envir_stacomi)["sqldf.host"]
port=get("sqldf.options",envir=envir_stacomi)["sqldf.port"]
+ # getting the database name
+ dbname<-getdbname()
bilPM<-object
if (!"import_coe"%in% names(bilPM at calcdata)) funout(gettext("Attention, you must fit a model before trying to write the predictions in the database",domain="R-stacomiR"),arret=TRUE)
# first delete existing data from the database
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/data.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -106,13 +106,13 @@
#' Overview of the fishway operation at Arzal in (Vilaine France).
#'
-#' This data corresponds to the data collected at the vertical slot fishway
+#' This dataset corresponds to the data collected at the vertical slot fishway
#' in 2015, the fishway is working daily with a cycle depending on tide. This dataset
-#' is used to show an example of acdetailed output for an object of class \link{BilanFonctionnementDF-class} with data loaded
+#' is used to show an example of detailed output for an object of class \link{BilanFonctionnementDF-class} with data loaded
#'
#' @format An object of class BilanFonctionnementDF with 4 slots:
#' \describe{
-#' #' \item{data}{ A dataframe with 4261 obs. of 7 variables
+#' \item{data}{ A dataframe with 4261 obs. of 7 variables
#' \describe{
#' \item{per_dis_identifiant}{The number of the DF}
#' \item{per_date_debut}{Starting time a POSIXct}
@@ -130,7 +130,7 @@
#' }
#' \item{df}{the \code{RefDF} object with 3 slots filled with data corresponding to the iav postgres schema}
#' \item{horodatedebut}{the \code{RefHorodate} with horodate set for starting date}
-#' \item{horodatefin}{the \code{RefHorodate} with horodate set for ending date} #'
+#' \item{horodatefin}{the \code{RefHorodate} with horodate set for ending date}'
#' }
#' @keywords data
"bfDF"
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/R/utilitaires.r 2017-06-09 13:44:19 UTC (rev 391)
@@ -406,4 +406,18 @@
bonordre<-match(cs$color,levels(cs$color))
cs$color = factor(cs$color,levels(cs$color)[bonordre])
return(cs)
+}
+
+
+#' Retreives the dbnames from a connection using "baseOBC"
+#' @return A string with the name of the database
+getdbname<-function(){
+ req<-new("RequeteODBC")
+ req at baseODBC<-get("baseODBC",envir=envir_stacomi)
+ req at sql<-str_c("select * from ",get("sch",envir=envir_stacomi),"t_bilanmigrationjournalier_bjo limit 1")
+ res<-connect(req)
+ odbc<-res at connection
+ aa<-strsplit(attributes(odbc)$connection.string,";")
+ dbname=gsub("DATABASE=","",aa[[1]][2])
+ return(dbname)
}
\ No newline at end of file
Modified: pkg/stacomir/man/bfDF.Rd
===================================================================
--- pkg/stacomir/man/bfDF.Rd 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/man/bfDF.Rd 2017-06-09 13:44:19 UTC (rev 391)
@@ -6,7 +6,7 @@
\title{Overview of the fishway operation at Arzal in (Vilaine France).}
\format{An object of class BilanFonctionnementDF with 4 slots:
\describe{
-#' \item{data}{ A dataframe with 4261 obs. of 7 variables
+ \item{data}{ A dataframe with 4261 obs. of 7 variables
\describe{
\item{per_dis_identifiant}{The number of the DF}
\item{per_date_debut}{Starting time a POSIXct}
@@ -24,15 +24,15 @@
}
\item{df}{the \code{RefDF} object with 3 slots filled with data corresponding to the iav postgres schema}
\item{horodatedebut}{the \code{RefHorodate} with horodate set for starting date}
- \item{horodatefin}{the \code{RefHorodate} with horodate set for ending date} #'
+ \item{horodatefin}{the \code{RefHorodate} with horodate set for ending date}'
}}
\usage{
bfDF
}
\description{
-This data corresponds to the data collected at the vertical slot fishway
+This dataset corresponds to the data collected at the vertical slot fishway
in 2015, the fishway is working daily with a cycle depending on tide. This dataset
-is used to show an example of acdetailed output for an object of class \link{BilanFonctionnementDF-class} with data loaded
+is used to show an example of detailed output for an object of class \link{BilanFonctionnementDF-class} with data loaded
}
\keyword{data}
Added: pkg/stacomir/man/getdbname.Rd
===================================================================
--- pkg/stacomir/man/getdbname.Rd (rev 0)
+++ pkg/stacomir/man/getdbname.Rd 2017-06-09 13:44:19 UTC (rev 391)
@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utilitaires.r
+\name{getdbname}
+\alias{getdbname}
+\title{Retreives the dbnames from a connection using "baseOBC"}
+\usage{
+getdbname()
+}
+\value{
+A string with the name of the database
+}
+\description{
+Retreives the dbnames from a connection using "baseOBC"
+}
+
Modified: pkg/stacomir/man/write_database-BilanAgedemer-method.Rd
===================================================================
--- pkg/stacomir/man/write_database-BilanAgedemer-method.Rd 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/man/write_database-BilanAgedemer-method.Rd 2017-06-09 13:44:19 UTC (rev 391)
@@ -6,19 +6,17 @@
\title{Command line method to write the caracteristic "sea age" (car_par_code='A124')
into the tj_caracteristiquelot_car table in the user's scheme}
\usage{
-\S4method{write_database}{BilanAgedemer}(object, silent = TRUE,
- dbname = "bd_contmig_nat")
+\S4method{write_database}{BilanAgedemer}(object, silent = TRUE)
}
\arguments{
\item{object}{an object of class \link{BilanAgedemer-class}}
\item{silent}{: Default FALSE, if TRUE the program should no display messages.}
-
-\item{dbname}{: the name of the database, defaults to "bd_contmig_nat"}
}
\description{
The sea age caracteristic is calculated from the mesured or calculated size of salmon and with a size/age rule
-defined by the user
+defined by the user . the name of the database is retreived from the odbc link
+defined in calcmig.csv
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/man/write_database-BilanMigration-method.Rd
===================================================================
--- pkg/stacomir/man/write_database-BilanMigration-method.Rd 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/man/write_database-BilanMigration-method.Rd 2017-06-09 13:44:19 UTC (rev 391)
@@ -7,15 +7,13 @@
t_bilanmigrationjournalier_bjo table}
\usage{
\S4method{write_database}{BilanMigration}(object, silent = TRUE,
- dbname = "bd_contmig_nat", check_for_bjo = TRUE)
+ check_for_bjo = TRUE)
}
\arguments{
\item{object}{an object of class \code{\linkS4class{BilanMigration}}}
\item{silent}{: TRUE to avoid messages}
-\item{dbname}{: the name of the database, defaults to "bd_contmig_nat"}
-
\item{check_for_bjo}{: do you want to check if data are already present in the bjo table, and delete them,
this param was added otherwise connect method when called from BilanMigrationInterAnnuelle runs in loops}
}
@@ -26,7 +24,7 @@
\note{
the user is asked whether or not he wants to overwrite data, if no
data are present in the database, the import is done anyway. The name of the database
-is not passed in odbc link, here defaults to "bd_contmig_nat"
+is retrieved from the odbc link
}
\examples{
\dontrun{
Modified: pkg/stacomir/man/write_database-Bilan_poids_moyen-method.Rd
===================================================================
--- pkg/stacomir/man/write_database-Bilan_poids_moyen-method.Rd 2017-06-09 11:48:50 UTC (rev 390)
+++ pkg/stacomir/man/write_database-Bilan_poids_moyen-method.Rd 2017-06-09 13:44:19 UTC (rev 391)
@@ -12,8 +12,6 @@
\item{object}{An object of class \link{Bilan_poids_moyen-class}}
\item{silent}{Boolean, if TRUE, information messages are not displayed}
-
-\item{dbname}{default "bd_contmig_nat"}
}
\value{
An object of class \link{Bilan_poids_moyen-class}
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