######################################################################
#
# $Id: websFunc.R 261 2007-04-20 16:36:47Z jari $
#
# Copyright (C) Authors contributing to this file.
# 
# This file is part of BASE - BioArray Software Environment.
# Available at http://base.thep.lu.se/
# 
# BASE is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# 
# BASE is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330,
# Boston, MA  02111-1307, USA.
######################################################################

######################################################################
#
# These R function are just simple wrappers of the
# methods defined in the BaseWebService perl module.
#
# One can use the below functions pretty much in the
# same ways as the perl module object methods.
#
# See the webs-test.R for an example of how to use
# these R functions.
######################################################################

# Function to login
login <- function(url, login, passwd)
{
  # obj <- .PerlNew("BaseWebService", "baseUrl", "http://localhost:8080/base2")
  # obj <- .PerlNew("BaseWebService", "baseUrl", "http://base2.thep.lu.se:8080/demo")
  obj <- .PerlNew("BaseWebService", "baseUrl", url);
  obj$login(login, passwd);
  ret <- obj;
  ret;
}

# Logout
logout <- function(obj)
{
  obj$logout();
}


getProjects <- function(obj)
{
  # Get the projects
  projs <- obj$getProjects();

  # Store in better list
  ret = list();
  for (i in 1:length(projs)) {
    name <- as.character(projs[[i]]["name"]);
    desc <- as.character(projs[[i]]["description"]);
    id   <- as.integer(projs[[i]]["id"]);
    ret[[i]] <- list(name=name, description=desc, id=id);
  }
  
  ret;
  # Note that the 'ret' is a list of lists.
}


setActiveProject <- function(obj, id)
{
  obj$setActiveProject(as.integer(id));
}


getExperiments <- function(obj)
{
  exps <- obj$getExperiments();
  
  # Store in better list
  ret = list();
  for (i in 1:length(exps)) {
    name <- as.character(exps[[i]]["name"]);
    desc <- as.character(exps[[i]]["description"]);
    id   <- as.integer(exps[[i]]["id"]);
    ret[[i]] <- list(name=name, description=desc, id=id);
  }

  ret;
  # Note that the 'ret' is a list of lists.
}


getRawBioAssays_by_expID <- function(obj, id)
{
  files <- obj$getRawBioAssays_by_expID(as.integer(id));
  
  # Store in better list
  ret = list();
  for (i in 1:length(files)) {
    cel <- as.character(files[[i]]["celFile"]);
    cdf <- as.character(files[[i]]["cdfFile"]);
    ret[[i]] <- list(celFile=cel, cdfFile=cdf);
  }

  ret;
  # Note that the 'ret' is a list of lists.
}


downloadRawBioAssays_by_expID <- function(obj, id, path)
{
  obj$downloadRawBioAssays_by_expID(as.integer(id), path);
  
}