sess <- NeticaSession()
startSession(sess)
curd <- getwd()
## Insures we are building nets from scratch
setwd(tempdir())


netman1 <- read.csv(paste(library(help="Peanut")$path, "auxdata",
                          "Mini-PP-Nets.csv", sep=.Platform$file.sep),
                    row.names=1,stringsAsFactors=FALSE)

nodeman1 <- read.csv(paste(library(help="Peanut")$path, "auxdata",
                           "Mini-PP-Nodes.csv", sep=.Platform$file.sep),
                     row.names=1,stringsAsFactors=FALSE)

omegamat <- read.csv(paste(library(help="Peanut")$path, "auxdata",
                           "miniPP-omega.csv", sep=.Platform$file.sep),
                     row.names=1,stringsAsFactors=FALSE)
class(omegamat) <- c("OmegMat",class(omegamat))

Q1 <- read.csv(paste(library(help="Peanut")$path, "auxdata",
                           "miniPP-Q.csv", sep=.Platform$file.sep),
               stringsAsFactors=FALSE)
class(Q1) <- c("Qmat",class(Q1))

Nethouse <- BNWarehouse(manifest=netman1,session=sess,key="Name")

Nodehouse <- NNWarehouse(manifest=nodeman1,
                         key=c("Model","NodeName"),
                         session=sess)


## Test building with the Omega matrix.  Start by making a blank net.
CM <- WarehouseSupply(Nethouse,"miniPP_CM")
CM1 <- Omega2Pnet(omegamat,CM,Nodehouse,override=TRUE,debug=TRUE)

Om2 <- Pnet2Omega(CM1,NetworkAllNodes(CM1))
omegamat$PriorWeight <- rep("",nrow(omegamat)) #Coverted to logical on read.
stopifnot(all.equal(Om2,omegamat))

Qmat2Pnet(Q1, Nethouse,Nodehouse,debug=TRUE)

## Hard code the model list so always in the same order.
obs <-sapply(list(sess$nets$PPcompEM,sess$nets$PPconjEM,sess$nets$PPtwostepEM),
             NetworkAllNodes)

Q2 <- Pnet2Qmat(obs,NetworkAllNodes(CM),debug=TRUE)

## Fix columns marked as logical because they were blank.
Q1$LinkScale <- as.numeric(Q1$LinkScale)
Q1$PriorWeight <- rep("",nrow(Q1)) #Coverted to logical on read.

all.equal(Q1[,-1],Q2)


if (false) {
  setwd("~/Projects/PNetica/inst/testnets/")
  Nets <- GetNamedNetworks(ls(sess$nets),sess)
  sapply(Nets,function(n) PnetPriorWeight(n) <- 10)
  sapply(Nets,BuildAllTables)
  WriteNetworks(Nets,paste(ls(sess$nets),"dne",sep="."))
}

stopSession(sess)
setwd(curd)