Version 7.3.0

Version 7.3.0

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "lib/DCI"]
 	path = lib/DCI
 	url = https://github.com/Open-Systems-Pharmacology/DCI.git
+[submodule "lib/Schema"]
+	path = lib/Schema
+	url = https://github.com/Open-Systems-Pharmacology/OSPSuite.SimModel.Schema.git

README.md

@@ -24,11 +24,11 @@ nuget restore packages.config -PackagesDirectory packages
 ```
 * create the package and setup
 ```
-rake create_setup[7.1.0]
+rake create_setup[7.2.0]
 ```
 
 ## Code Status
-[![Build status](https://ci.appveyor.com/api/projects/status/6wssc33akfebg3yk/branch/master?svg=true&passingText=master%20-%20passing)](https://ci.appveyor.com/project/open-systems-pharmacology-ci/r-toolbox/branch/master)
+[![Build status](https://ci.appveyor.com/api/projects/status/6wssc33akfebg3yk/branch/develop?svg=true&passingText=develop%20-%20passing)](https://ci.appveyor.com/project/open-systems-pharmacology-ci/r-toolbox/branch/develop)
 
 ## Code of conduct
 Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc...) is expected to follow the Open Systems Pharmacology [code of conduct](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODE_OF_CONDUCT.md).

appveyor.yml

@@ -1,5 +1,5 @@
 environment:
-  app_version: '7.2.0'
+  app_version: '7.3.0'
   R_INSTALL_DIR: 'C:\ProgramData\R\'
   R_TOOLS_INSTALL_DIR: 'C:\ProgramData\RTools\'
 

packages.config

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  	<package id="OSPSuite.FuncParser" version="2.0.0.1" />
-  	<package id="OSPSuite.SimModelSolver_CVODES282" version="2.0.0.1" />
-	<package id="OSPSuite.SimModel" version="2.2.0.6"/>
-	<package id="OSPSuite.SimModelComp" version="2.2.0.6"/>
+  	<package id="OSPSuite.FuncParser" version="3.0.0.6"/>
+  	<package id="OSPSuite.SimModelSolver_CVODES282" version="3.0.0.7" />
+	<package id="OSPSuite.SimModel" version="3.0.0.16"/>
+	<package id="OSPSuite.SimModelComp" version="3.0.0.16"/>
 </packages>

rakefile

@@ -95,6 +95,10 @@ def add_component_files_to_archive
     copy_files 'OSPSuite.SimModelComp', 'xml'
   end
 
+  copy_depdencies lib_dir, decompressed_lib_dir do
+    copy_schema_xsd
+  end
+
   command_line = %W[a #{zip_archive} #{decompressed_dir}]
   zip command_line
 end
@@ -124,8 +128,8 @@ def copy_setup_files
   end
 
   copy_depdencies lib_dir, toolbox_src_dir do
-    copy_dci_dll
-    copy_dcir_dll
+    copy_files File.join('DCI','x86'), 'dll'
+    copy_files File.join('DCIR','x86'), 'dll'
   end
 
   copy_depdencies src_dir, toolbox_R_dir do

setup/NAMESPACE

@@ -1,3 +1,3 @@
 exportPattern("^[^\\.]")
-useDynLib(DCIR6_0, .registration = TRUE)
-useDynLib(DCIR6_0, RDCI_Configure, RDCI_DestroyAllComponents, RDCI_DestroyComponent, RDCI_GetInputTable, RDCI_GetInputTables, RDCI_GetLastError, RDCI_GetOutputTable, RDCI_GetOutputTables, RDCI_GetParameterTable, RDCI_GetParameterTables, RDCI_Help, RDCI_Invoke, RDCI_LoadComponent, RDCI_LoadInputTable, RDCI_LoadParameterTable, RDCI_LongInf, RDCI_LongNaN, RDCI_LongNegInf, RDCI_ProcessData, RDCI_ProcessMetaData, RDCI_SaveInputTable, RDCI_SaveOutputTable, RDCI_SaveParameterTable, RDCI_SetInputTable, RDCI_SetInputTables, RDCI_SetOutputTable, RDCI_SetOutputTables, RDCI_SetParameterTable, RDCI_SetParameterTables)
+useDynLib(DCIR6_1, .registration = TRUE)
+useDynLib(DCIR6_1, RDCI_Configure, RDCI_DestroyAllComponents, RDCI_DestroyComponent, RDCI_GetInputTable, RDCI_GetInputTables, RDCI_GetLastError, RDCI_GetOutputTable, RDCI_GetOutputTables, RDCI_GetParameterTable, RDCI_GetParameterTables, RDCI_Help, RDCI_Invoke, RDCI_LoadComponent, RDCI_LoadInputTable, RDCI_LoadParameterTable, RDCI_LongInf, RDCI_LongNaN, RDCI_LongNegInf, RDCI_ProcessData, RDCI_ProcessMetaData, RDCI_SaveInputTable, RDCI_SaveOutputTable, RDCI_SaveParameterTable, RDCI_SetInputTable, RDCI_SetInputTables, RDCI_SetOutputTable, RDCI_SetOutputTables, RDCI_SetParameterTable, RDCI_SetParameterTables)

src/code/MobiSettings.R

@@ -10,7 +10,7 @@ MobiSettings <- function(libraryName = "MoBiToolboxForR")
       Sys.setenv(path = paste(libpath, Sys.getenv("path"), sep =";"))
       MobiSettings <- list("SimModelSchema" = paste(libpath,"\\OSPSuite.SimModel.xsd", sep=""),
                            "SimModelComp" = paste(libpath, "\\OSPSuite_SimModelComp.xml", sep=""),
-                           "RInterface" = paste(libpath,"\\DCIR6_0.dll", sep=""));
+                           "RInterface" = paste(libpath,"\\DCIR6_1.dll", sep=""));
     }
   }
 

src/code/findTableIndex.R

@@ -34,18 +34,33 @@ findTableIndex <- function(path_id = numeric(0), tableID = numeric(0), isReferen
   		indx <- 1:counts
   		if (path_id != '*')
   		{
+  		  # As escaping of certain symbols in path names had to be done manually in previous releases but is performed
+  		  # automatically now, a warning message is displayed when manual escaping is detected. This warning message
+  		  # should be removed in future.
+  		  for (symbol in c("\\(", "\\)", "\\[", "\\]")){
+  		    if (grepl(symbol, path_id, fixed = TRUE)){
+  		      warning(paste(path_id, ": Escaping of the characters '(', ')', '[', and '[' in path names should not be done manually!"), immediate. = TRUE )
+  		      break
+  		    }
+  		  }
         searchValue <- path_id
         searchValue <- gsub('|', '\\|', searchValue, fixed = TRUE)
         searchValue <- gsub('&', '\\&', searchValue, fixed = TRUE)
+        searchValue <- gsub('(', '\\(', searchValue, fixed = TRUE)
+        searchValue <- gsub(')', '\\)', searchValue, fixed = TRUE)
+        searchValue <- gsub('[', '\\[', searchValue, fixed = TRUE)
+        searchValue <- gsub(']', '\\]', searchValue, fixed = TRUE)
         searchValue <- gsub('*', '.*', searchValue, fixed = TRUE)
         searchValue <- paste("^", searchValue, "$", sep="")
         searchPathes <- Table$Path
 
         indx <- grep(searchValue, searchPathes, perl = TRUE)                     
   		}
-    } else
-    {
-      indx <- 0
+    }
+    # If no parameter found, return a zero-lenght integer vector to match the behavior of which().
+    # This way, a not found parameter should be recognized by checking for (length(indx) == 0)
+    else{
+      indx <- integer(0);
     }
 	}
 	return(indx)	

src/code/getObserverFormula.R

@@ -49,7 +49,8 @@ getObserverFormula <- function(path_id = "*", options = {}, DCI_Info = {})
 
 	if (length(indx) == 0)
 	{
-		stop(paste("Observer with path_id", path_id, "does not exist for specified type", options$Type))
+	warning(paste("Observer with path_id", path_id, "does not exist for specified type", options$Type))
+	  return(list(Value = NULL, Index = NULL));
 	}
 
 	if (toupper(options$Type) != "REFERENCE")

src/code/getParameter.R

@@ -67,7 +67,8 @@ getParameter <- function(path_id = "*", options = {}, DCI_Info = {})
 
 	if (length(indx) == 0)
 	{
-		stop(paste("Parameter with path_id", path_id, "does not exist for specified parameter type", options$Type))
+	  warning(paste("Parameter with path_id", path_id, "does not exist for specified parameter type", options$Type))
+	  return(list(Value = NULL, Index = NULL));
 	}
 
 	if (toupper(options$Type) != "REFERENCE")
@@ -116,6 +117,21 @@ getParameter <- function(path_id = "*", options = {}, DCI_Info = {})
         id <- Table$ID[i]
         x <- ParameterTable$Time[which(ParameterTable$ID == id)]
         y <- ParameterTable$Value[which(ParameterTable$ID == id)]
+
+        # for parameter type current search also readonly options if not found in variable options
+        if ((length(x) == 0) & (toupper(options$Type) == "CURRENT"))
+        {
+          iParameterTable = which(names(DCI_Info$InputTab) == "AllTableParameters");
+          if (toupper(options$Type) != "REFERENCE")
+          {
+            ParameterTable <- DCI_Info$InputTab[[iParameterTable]]
+          } else {
+            ParameterTable <- DCI_Info$ReferenceTab[[iParameterTable]]	
+          }
+          x <- ParameterTable$Time[which(ParameterTable$ID == id)]
+          y <- ParameterTable$Value[which(ParameterTable$ID == id)]
+        }
+
         newy <- approx(x=x, y=y, xout=options$TimeProfile, method="linear", rule=2)$y
         if (length(options$TimeProfile) > 1) 
         {

src/code/getSpeciesInitialValue.R

@@ -58,7 +58,8 @@ getSpeciesInitialValue <- function(path_id = "*", options = {}, DCI_Info = {})
 	}
 	if (length(indx) == 0)
 	{
-		stop(paste("Initial value with path_id", path_id, "does not exist for specified type", options$Type))
+	  warning(paste("Table parameter with path_id", path_id, "does not exist for specified parameter type", options$Type))
+	  return(list(Value = NULL, Index = NULL));
 	}
 
 	if (toupper(options$Type) != "REFERENCE")

src/code/getTableParameter.R

@@ -57,7 +57,8 @@ getTableParameter <- function(path_id = "*", options = {}, DCI_Info = {})
 
   if (length(indx) == 0)
   {
-    stop(paste("Parameter with path_id", path_id, "does not exist for specified parameter type", options$Type))
+    warning(paste("Table parameter with path_id", path_id, "does not exist for specified parameter type", options$Type))
+    return(list(ID = NULL, Time = NULL, Value = NULL, RestartSolver = NULL));
   }
 
   if (toupper(options$Type) != "REFERENCE")

src/code/initSimulation.R

@@ -67,7 +67,7 @@ CheckXML <- function(XML)
 	return(0)
 }
 
-initSimulation <- function(XML = "", ParamList = numeric(0), whichInitParam = "", further_options = "", Version = "6_0", SimulationNumber = 1)
+initSimulation <- function(XML = "", ParamList = numeric(0), whichInitParam = "", further_options = "", Version = "6_1", SimulationNumber = 1)
 {
 	DCI_Info <- list()
 	if (XML == "")
@@ -84,9 +84,9 @@ initSimulation <- function(XML = "", ParamList = numeric(0), whichInitParam = ""
 		stop ("No parameters can be initialized. Please provide either 'ParamList' or 'whichInitParam' with one the following valid keywords: all, none, allNonFormula.")
 	}
 
-	# load DCIR6_0-DLL
+	# load DCIR6_1-DLL
 
-	if (length(grep("DCIR6_0", names(getLoadedDLLs()), fixed =TRUE)) ==0)
+	if (length(grep("DCIR6_1", names(getLoadedDLLs()), fixed =TRUE)) ==0)
 	{
 		dyn.load(DCI_Info$MOBI_SETTINGS$RInterface)
 	}