Refactoring of to-PRISM language translations: addition of PrismLanguageTranslator abstract class (preliminary version of) and connection with SBML/reactions/PEPA translators. Also, add support for SBML import to Prism class (but not used elsewhere yet).

git-svn-id: https://www.prismmodelchecker.org/svn/prism/prism/trunk@10687 bbc10eb1-c90d-0410-af57-cb519fbb1720

prism/src/prism/PEPA2Prism.java

@@ -0,0 +1,91 @@
+package prism;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintStream;
+
+public class PEPA2Prism extends PrismLanguageTranslator
+{
+	private File modelFile;
+
+	@Override
+	public String getName()
+	{
+		return "pepa";
+	}
+
+	@Override
+	public void load(File file) throws PrismException
+	{
+		modelFile = file;
+	}
+
+	@Override
+	public void load(String s) throws PrismException
+	{
+		try {
+			// Create temporary file containing pepa model
+			modelFile = File.createTempFile("tempPepa" + System.currentTimeMillis(), ".pepa");
+			FileWriter write = new FileWriter(modelFile);
+			write.write(s);
+			write.close();
+		} catch (IOException e) {
+			if (modelFile != null) {
+				modelFile.delete();
+				modelFile = null;
+			}
+			throw new PrismException("Couldn't create temporary file for PEPA conversion");
+		}
+	}
+
+	@Override
+	public void load(InputStream in) throws PrismException
+	{
+		try {
+			// Create temporary file containing pepa model
+			modelFile = File.createTempFile("tempPepa" + System.currentTimeMillis(), ".pepa");
+			FileWriter write = new FileWriter(modelFile);
+			int byteIn = in.read();
+			while (byteIn != -1) {
+				write.write(byteIn);
+				byteIn = in.read();
+			}
+			write.close();
+		} catch (IOException e) {
+			if (modelFile != null) {
+				modelFile.delete();
+				modelFile = null;
+			}
+			throw new PrismException("Couldn't create temporary file for PEPA conversion");
+		}
+	}
+
+	@Override
+	public String translateToString() throws PrismException
+	{
+		// Translate PEPA model to PRISM model string
+		String prismModelString = null;
+		try {
+			prismModelString = pepa.compiler.Main.compile("" + modelFile);
+		} catch (pepa.compiler.InternalError e) {
+			if (modelFile != null) {
+				modelFile.delete();
+				modelFile = null;
+			}
+			throw new PrismException("Could not import PEPA model:\n" + e.getMessage());
+		}
+		if (modelFile != null) {
+			modelFile.delete();
+			modelFile = null;
+		}
+		return prismModelString;
+	}
+
+	@Override
+	public void translate(PrintStream out) throws PrismException
+	{
+		out.print(translateToString());
+	}
+}

prism/src/prism/Prism.java

@@ -34,6 +34,8 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -1405,17 +1407,7 @@ public class Prism extends PrismComponent implements PrismSettingsListener
 	 */
 	public ModulesFile importPepaFile(File file) throws PrismException, PrismLangException
 	{
-		String modelString;
-
-		// compile pepa file to string
-		try {
-			modelString = pepa.compiler.Main.compile("" + file);
-		} catch (pepa.compiler.InternalError e) {
-			throw new PrismException("Could not import PEPA file:\n" + e.getMessage());
-		}
-
-		// parse string as prism model and return
-		return parseModelString(modelString);
+		return importModelFile("pepa", file);
 	}
 
 	/**
@@ -1424,34 +1416,68 @@ public class Prism extends PrismComponent implements PrismSettingsListener
 	 */
 	public ModulesFile importPepaString(String s) throws PrismException, PrismLangException
 	{
-		File pepaFile = null;
-		String modelString;
+		return importModelString("pepa", s);
+	}
 
-		// create temporary file containing pepa model
-		try {
-			pepaFile = File.createTempFile("tempPepa" + System.currentTimeMillis(), ".pepa");
-			FileWriter write = new FileWriter(pepaFile);
-			write.write(s);
-			write.close();
-		} catch (IOException e) {
-			if (pepaFile != null)
-				pepaFile.delete();
-			throw new PrismException("Couldn't create temporary file for PEPA conversion");
-		}
+	/**
+	 * Import a PRISM model from an SBML model in a file
+	 * @param file File to read in
+	 */
+	public ModulesFile importSBMLFile(File file) throws PrismException, PrismLangException
+	{
+		return importModelFile("sbml", file);
+	}
 
-		// compile pepa file to string
-		try {
-			modelString = pepa.compiler.Main.compile("" + pepaFile);
-		} catch (pepa.compiler.InternalError e) {
-			if (pepaFile != null)
-				pepaFile.delete();
-			throw new PrismException("Could not import PEPA file:\n" + e.getMessage());
-		}
+	/**
+	 * Import a PRISM model from an SBML model in a string
+	 * @param file File to read in
+	 */
+	public ModulesFile importSBMLString(String s) throws PrismException, PrismLangException
+	{
+		return importModelString("sbml", s);
+	}
 
-		// parse string as prism model and return
-		return parseModelString(modelString);
+	/**
+	 * Import a PRISM model by translating from another language
+	 */
+	public ModulesFile importModelFile(String lang, File file) throws PrismException, PrismLangException
+	{
+		PrismLanguageTranslator importer = createPrismLanguageTranslator(lang);
+		importer.load(file);
+		String prismModelString = importer.translateToString();
+		return parseModelString(prismModelString);
+	}
+
+	/**
+	 * Import a PRISM model by translating from another language
+	 */
+	public ModulesFile importModelString(String lang, String s) throws PrismException, PrismLangException
+	{
+		PrismLanguageTranslator importer = createPrismLanguageTranslator(lang);
+		importer.load(s);
+		String prismModelString = importer.translateToString();
+		return parseModelString(prismModelString);
 	}
 
+	/**
+	 * Create a translator to the PRISM language.
+	 */
+	private PrismLanguageTranslator createPrismLanguageTranslator(String lang) throws PrismException
+	{
+		PrismLanguageTranslator importer = null;
+		switch (lang) {
+		case "pepa":
+			importer = new PEPA2Prism();
+			break;
+		case "sbml":
+			importer = new SBML2Prism();
+			break;
+		default:
+			throw new PrismException("Unknown import language \"" + lang + "\"");
+		}
+		return importer;
+	}
+	
 	/**
 	 * Import a PRISM model from a PRISM preprocessor file
 	 * @param file File to read in

prism/src/prism/PrismLanguageTranslator.java

@@ -0,0 +1,94 @@
+//==============================================================================
+//	
+//	Copyright (c) 2015-
+//	Authors:
+//	* Dave Parker <d.a.parker@cs.bham.ac.uk> (University of Birmingham)
+//	
+//------------------------------------------------------------------------------
+//	
+//	This file is part of PRISM.
+//	
+//	PRISM 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.
+//	
+//	PRISM 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 PRISM; if not, write to the Free Software Foundation,
+//	Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+//	
+//==============================================================================
+
+package prism;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+import java.io.PrintStream;
+import java.io.UnsupportedEncodingException;
+
+/**
+ * Base class for classes that convert to PRISM language models from other languages.
+ */
+public abstract class PrismLanguageTranslator
+{
+	/**
+	 * Get a name associated with the language to be translated from.
+	 */
+	public abstract String getName();
+	
+	/**
+	 * Load a model to be translated from an input stream.
+	 */
+	public abstract void load(InputStream in) throws PrismException;
+	
+	/**
+	 * Load a model to be translated from a string.
+	 */
+	public void load(String modelString) throws PrismException
+	{
+		load(new ByteArrayInputStream(modelString.getBytes()));
+	}
+	
+	/**
+	 * Load a model to be translated from a file.
+	 */
+	public void load(File file) throws PrismException
+	{
+		FileInputStream in;
+		try {
+			in = new FileInputStream(file);
+		} catch (FileNotFoundException e) {
+			throw new PrismException("File \"" + file.getPath() + "\" not found");
+		}
+		load(in);
+	}
+	
+	/**
+	 * Translate the loaded model to a PRISM language model and write it to an output stream.
+	 */
+	public abstract void translate(PrintStream out) throws PrismException;
+	
+	/**
+	 * Translate the loaded model to a PRISM language model and return it as a string.
+	 */
+	public String translateToString() throws PrismException
+	{
+		ByteArrayOutputStream os = new ByteArrayOutputStream();
+		PrintStream out = new PrintStream(os);
+		translate(out);
+		try {
+			return os.toString("UTF-8");
+		} catch (UnsupportedEncodingException e) {
+			throw new PrismException("Error translating output stream to string: " + e.getMessage());
+		}
+	}
+}

prism/src/prism/Reactions2Prism.java

@@ -31,7 +31,6 @@ import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintStream;
 import java.util.ArrayList;
@@ -44,7 +43,7 @@ import parser.PrismParser;
 /**
  * Base class for classes that build/store a set of biological reactions and then convert to PRISM.
  */
-public class Reactions2Prism
+public abstract class Reactions2Prism extends PrismLanguageTranslator
 {
 	// Log for output of warnings, messages
 	protected PrismLog mainLog = null;
@@ -104,7 +103,7 @@ public class Reactions2Prism
 	/**
 	 * Process the currently loaded reaction set model, convert to PRISM code, export to an OutputStream. 
 	 */
-	protected void convertToPRISMCode(OutputStream out) throws PrismException
+	protected void convertToPRISMCode(PrintStream out) throws PrismException
 	{
 		StringBuilder sb = convertToPRISMCode();
 		try {

prism/src/prism/ReactionsText2Prism.java

@@ -28,8 +28,10 @@ package prism;
 
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileReader;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PrintStream;
 import java.util.ArrayList;
 
 /**
@@ -37,32 +39,9 @@ import java.util.ArrayList;
  */
 public class ReactionsText2Prism extends Reactions2Prism
 {
-	/**
-	 * Calling point for command-line script:
-	 * e.g. java -cp classes prism.ReactionsText2Prism myfile.txt 100
-	 * (100 denotes (integer) maximum for species population sizes, default is 100)
-	 */
-	public static void main(String args[])
-	{
-		PrismLog errLog = new PrismPrintStreamLog(System.err);
-		try {
-			if (args.length < 1) {
-				System.err.println("Usage: java -cp classes prism.ReactionsText2Prism <file> [max_amount]");
-				System.exit(1);
-			}
-			ReactionsText2Prism rt2prism = new ReactionsText2Prism(errLog);
-			try {
-				if (args.length > 1)
-					rt2prism.setMaxAmount(Integer.parseInt(args[1]));
-			} catch (NumberFormatException e) {
-				throw new PrismException("Invalid max amount \"" + args[1] + "\"");
-			}
-			rt2prism.translate(new File(args[0]));
-		} catch (PrismException e) {
-			errLog.println("Error: " + e.getMessage() + ".");
-		}
-	}
-
+	/** Name of the original file */
+	protected String parsedFileName;
+	
 	// Enums
 
 	private enum SectionType {
@@ -81,25 +60,24 @@ public class ReactionsText2Prism extends Reactions2Prism
 		super(mainLog);
 	}
 
-	/**
-	 * Main method: load reactions file, process and send resulting PRISM file to stdout
-	 */
-	public void translate(File file) throws PrismException
+	@Override
+	public String getName()
 	{
-		// Read in file
-		extractModelFromFile(file);
-		// Generate PRISM code
-		prismCodeHeader = "// File generated by reactions-to-PRISM conversion\n";
-		prismCodeHeader += "// Original file: " + file.getPath() + "\n\n";
-		convertToPRISMCode(System.out);
+		return "reactions";
 	}
 
-	/**
-	 * Build the reaction set model from a parsed SBML file.
-	 */
-	private void extractModelFromFile(File file) throws PrismException
+	@Override
+	public void load(File file) throws PrismException
+	{
+		// Store filename for later use before parsing
+		parsedFileName = file.getPath();
+		super.load(file);
+	}
+
+	@Override
+	public void load(InputStream in) throws PrismException
 	{
-		BufferedReader in;
+		BufferedReader buf;
 		SectionType secType = null;
 		String s, s2, ss[], ss2[];
 		int i, lineNum = 0;
@@ -115,9 +93,9 @@ public class ReactionsText2Prism extends Reactions2Prism
 
 		try {
 			// Open file for reading
-			in = new BufferedReader(new FileReader(file));
+			buf = new BufferedReader(new InputStreamReader(in));
 			// Read remaining lines
-			s = in.readLine();
+			s = buf.readLine();
 			lineNum++;
 			while (s != null) {
 				// Strip comments
@@ -213,7 +191,7 @@ public class ReactionsText2Prism extends Reactions2Prism
 								reaction.addProduct(product, 1);
 							}
 							// Next line
-							s = in.readLine();
+							s = buf.readLine();
 							lineNum++;
 							if (s == null)
 								throw new PrismException("missing line in reaction definition");
@@ -244,18 +222,58 @@ public class ReactionsText2Prism extends Reactions2Prism
 					}
 				}
 				// read next line
-				s = in.readLine();
+				s = buf.readLine();
 				lineNum++;
 			}
 
 			// close file
-			in.close();
+			buf.close();
 		} catch (IOException e) {
-			throw new PrismException("File I/O error reading from \"" + file + "\"");
+			throw new PrismException("I/O error reading reactions: " + e.getMessage());
 		} catch (NumberFormatException e) {
-			throw new PrismException("Error detected at line " + lineNum + " of file \"" + file + "\"");
+			throw new PrismException("Error detected at line " + lineNum + " of reactions file");
+		} catch (PrismException e) {
+			throw new PrismException("Error detected (" + e.getMessage() + ") at line " + lineNum + " of reactions file");
+		}
+	}
+
+	@Override
+	public void translate(PrintStream out) throws PrismException
+	{
+		// Generate PRISM code
+		prismCodeHeader = "// File generated by reactions-to-PRISM conversion\n";
+		if (parsedFileName != null) {
+			prismCodeHeader += "// Original file: " + parsedFileName + "\n\n";
+		}
+		convertToPRISMCode(out);
+		// Reset filename storage
+		parsedFileName = null;
+	}
+	
+	/**
+	 * Calling point for command-line script:
+	 * e.g. java -cp classes prism.ReactionsText2Prism myfile.txt 100
+	 * (100 denotes (integer) maximum for species population sizes, default is 100)
+	 */
+	public static void main(String args[])
+	{
+		PrismLog errLog = new PrismPrintStreamLog(System.err);
+		try {
+			if (args.length < 1) {
+				System.err.println("Usage: java -cp classes prism.ReactionsText2Prism <file> [max_amount]");
+				System.exit(1);
+			}
+			ReactionsText2Prism rt2prism = new ReactionsText2Prism(errLog);
+			try {
+				if (args.length > 1)
+					rt2prism.setMaxAmount(Integer.parseInt(args[1]));
+			} catch (NumberFormatException e) {
+				throw new PrismException("Invalid max amount \"" + args[1] + "\"");
+			}
+			rt2prism.load(new File(args[0]));
+			rt2prism.translate(System.out);
 		} catch (PrismException e) {
-			throw new PrismException("Error detected (" + e.getMessage() + ") at line " + lineNum + " of file \"" + file + "\"");
+			errLog.println("Error: " + e.getMessage() + ".");
 		}
 	}
 }

prism/src/prism/SBML2Prism.java

@@ -29,6 +29,7 @@ package prism;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.PrintStream;
 import java.util.ArrayList;
 
 import javax.xml.parsers.DocumentBuilder;
@@ -47,33 +48,10 @@ import org.xml.sax.SAXParseException;
 
 public class SBML2Prism extends Reactions2Prism implements EntityResolver
 {
-	/**
-	 * Calling point for command-line script:
-	 * This is probably the sbml2prism (found in etc/scripts)
-	 * But it can also be called as, e.g.: java -cp classes prism.SBML2Prism myfile.sbml 100
-	 * (100 denotes (integer) maximum for species population sizes, default is 100)
-	 * (also used to compute amounts from (real-valued) concentrations)
-	 */
-	public static void main(String args[])
-	{
-		PrismLog errLog = new PrismPrintStreamLog(System.err);
-		try {
-			if (args.length < 1) {
-				System.err.println("Usage: sbml2prism <sbml_file> [max_amount]");
-				System.exit(1);
-			}
-			SBML2Prism sbml2prism = new SBML2Prism(errLog);
-			try {
-				if (args.length > 1)
-					sbml2prism.setMaxAmount(Integer.parseInt(args[1]));
-			} catch (NumberFormatException e) {
-				throw new PrismException("Invalid max amount \"" + args[1] + "\"");
-			}
-			sbml2prism.translate(new File(args[0]));
-		} catch (PrismException e) {
-			errLog.println("Error: " + e.getMessage() + ".");
-		}
-	}
+	/** Name of the original SBML file */
+	protected String parsedFileName;
+	/** Temporary storage of the parsed XML */
+	protected Document parsedSBML;
 
 	// Constructors
 
@@ -87,29 +65,26 @@ public class SBML2Prism extends Reactions2Prism implements EntityResolver
 		super(mainLog);
 	}
 
-	/**
-	 * Main method: load SBML file, process and send resulting PRISM file to stdout
-	 */
-	public void translate(File file) throws PrismException
+	@Override
+	public String getName()
 	{
-		// Read in SBML
-		Document doc = parseSBML(file);
-		checkSBMLVersion(doc);
-		extractModelFromSBML(doc);
-		// Generate PRISM code
-		prismCodeHeader = "// File generated by automatic SBML-to-PRISM conversion\n";
-		prismCodeHeader += "// Original SBML file: " + file.getPath() + "\n\n";
-		convertToPRISMCode(System.out);
+		return "sbml";
 	}
 
-	/**
-	 * Parse SBML file {@code file} and return as an XML Document object.
-	 */
-	private Document parseSBML(File file) throws PrismException
+	@Override
+	public void load(File file) throws PrismException
+	{
+		// Store filename for later use before parsing
+		parsedFileName = file.getPath();
+		super.load(file);
+	}
+
+	@Override
+	public void load(InputStream in) throws PrismException
 	{
 		DocumentBuilderFactory factory;
 		DocumentBuilder builder;
-		Document doc = null;
+		parsedSBML = null;
 
 		// Create XML parser
 		factory = DocumentBuilderFactory.newInstance();
@@ -138,23 +113,22 @@ public class SBML2Prism extends Reactions2Prism implements EntityResolver
 			throw new PrismException("Couldn't create XML parser");
 		}
 
-		// Parse
+		// Parse XML
 		try {
-			doc = builder.parse(file);
+			parsedSBML = builder.parse(in);
 		} catch (IOException e) {
-			throw new PrismException("Couldn't load file \"" + file.getPath() + "\": " + e.getMessage());
+			throw new PrismException("Error reading SBML: " + e.getMessage());
 		} catch (SAXException e) {
 			throw new PrismException("Invalid XML file:\n" + e.getMessage());
 		}
-
-		return doc;
 	}
 
-	// Function used by parseSBML() above to find the SBML DTD
-	// (this currently unused since we do not validate the SBML file when reading)
-	// (and since the DTD specified in the SBML files is not local)
-	// (if validation is enabled, put the DTD file "sbml.dtd" in PRISM's "dtds" directory)
-
+	/**
+	 * Function used by parseSBML() above to find the SBML DTD
+	 * (this currently unused since we do not validate the SBML file when reading)
+	 * (and since the DTD specified in the SBML files is not local)
+	 * (if validation is enabled, put the DTD file "sbml.dtd" in PRISM's "dtds" directory)
+	 */
 	public InputSource resolveEntity(String publicId, String systemId) throws SAXException, IOException
 	{
 		InputSource inputSource = null;
@@ -170,6 +144,21 @@ public class SBML2Prism extends Reactions2Prism implements EntityResolver
 		return inputSource;
 	}
 
+	@Override
+	public void translate(PrintStream out) throws PrismException
+	{
+		checkSBMLVersion(parsedSBML);
+		extractModelFromSBML(parsedSBML);
+		// Generate PRISM code
+		prismCodeHeader = "// File generated by automatic SBML-to-PRISM conversion\n";
+		if (parsedFileName != null) {
+			prismCodeHeader += "// Original SBML file: " + parsedFileName + "\n\n";
+		}
+		convertToPRISMCode(out);
+		// Reset filename storage
+		parsedFileName = null;
+	}
+
 	/**
 	 * Check that we can handle whatever level/version this file is.
 	 */
@@ -348,4 +337,33 @@ public class SBML2Prism extends Reactions2Prism implements EntityResolver
 			reactionList.add(reaction);
 		}
 	}
+
+	/**
+	 * Calling point for command-line script:
+	 * This is probably the sbml2prism (found in etc/scripts)
+	 * But it can also be called as, e.g.: java -cp classes prism.SBML2Prism myfile.sbml 100
+	 * (100 denotes (integer) maximum for species population sizes, default is 100)
+	 * (also used to compute amounts from (real-valued) concentrations)
+	 */
+	public static void main(String args[])
+	{
+		PrismLog errLog = new PrismPrintStreamLog(System.err);
+		try {
+			if (args.length < 1) {
+				System.err.println("Usage: sbml2prism <sbml_file> [max_amount]");
+				System.exit(1);
+			}
+			SBML2Prism sbml2prism = new SBML2Prism(errLog);
+			try {
+				if (args.length > 1)
+					sbml2prism.setMaxAmount(Integer.parseInt(args[1]));
+			} catch (NumberFormatException e) {
+				throw new PrismException("Invalid max amount \"" + args[1] + "\"");
+			}
+			sbml2prism.load(new File(args[0]));
+			sbml2prism.translate(System.out);
+		} catch (PrismException e) {
+			errLog.println("Error: " + e.getMessage() + ".");
+		}
+	}
 }