more work on refactoring / rewriting parsers

src/parser/readLabFile.cpp

@@ -0,0 +1,123 @@
+/*
+ * readLabFile.cpp
+ *
+ *  Created on: 21.11.2012
+ *      Author: Gereon Kremer
+ */
+
+#include "parser.h"
+
+#include "readLabFile.h"
+
+#include "src/exceptions/wrong_file_format.h"
+#include "src/exceptions/file_IO_exception.h"
+
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+#include <clocale>
+#include <iostream>
+#include <errno.h>
+#include <time.h>
+#include <sys/stat.h>
+#include <sys/mman.h>
+#include <fcntl.h>
+#include <locale.h>
+
+#include <pantheios/pantheios.hpp>
+#include <pantheios/inserters/integer.hpp>
+
+namespace mrmc {
+
+namespace parser {
+
+
+/*!
+ * Reads a .lab file and puts the result in a labeling structure.
+ *
+ * Labelings created with this method have to be freed with the delete operator.
+ * @param node_count the number of states.
+ * @param filename   input .lab file's name.
+ * @return The pointer to the created labeling object.
+ */
+mrmc::models::AtomicPropositionsLabeling * readLabFile(int node_count, const char * filename)
+{
+	/*!
+	 *	open file and map to memory
+	 */
+	struct stat st;
+	int f = open(filename, O_RDONLY);
+	if ((f < 0) || (stat(filename, &st) != 0)) {
+		/*!
+		 * 
+		 */
+		pantheios::log_ERROR("File could not be opened.");
+		throw mrmc::exceptions::file_IO_exception();
+		return NULL;
+	}
+	
+	char* data = (char*) mmap(NULL, st.st_size, PROT_READ, MAP_PRIVATE, f, 0);
+	if (data == (char*)-1)
+	{
+		pantheios::log_ERROR("File could not be mapped. Something went wrong with mmap.");
+		close(f);
+		throw mrmc::exceptions::file_IO_exception();
+		return NULL;
+	}
+
+	char* buf = data;
+	char sep[] = " \n\t";
+	uint_fast32_t proposition_count = 0;
+	size_t cnt = 0;
+
+	do {
+		buf += cnt;
+		cnt = strcspn(buf, sep);
+		if (cnt > 0) {
+			if (strncmp(buf, "#DECLARATION", cnt) == 0) continue;
+			if (strncmp(buf, "#END", cnt) == 0) break;
+			proposition_count++;
+		}
+		else cnt = 1;
+	} while (cnt > 0);
+	
+	mrmc::models::AtomicPropositionsLabeling* result = new mrmc::models::AtomicPropositionsLabeling(node_count, proposition_count);
+	char proposition[128];
+	buf = data;
+	cnt = 0;
+	do {
+		buf += cnt;
+		cnt = strcspn(buf, sep);
+		if (cnt > 0) {
+			if (strncmp(buf, "#DECLARATION", cnt) == 0) continue;
+			if (strncmp(buf, "#END", cnt) == 0) break;
+			strncpy(proposition, buf, cnt);
+			proposition[cnt] = '\0';
+			result->addAtomicProposition(proposition);
+		}
+		else cnt = 1;
+	} while (cnt > 0);
+	buf += 4;
+	
+	uint_fast32_t node;
+	while (1) {
+		node = strtol(buf, &buf, 10);
+		while (*buf != '\0') {
+			cnt = strcspn(buf, sep);
+			if (cnt == 0) buf++;
+			else break;
+		}
+		strncpy(proposition, buf, cnt);
+		proposition[cnt] = '\0';
+		result->addAtomicPropositionToState(proposition, node);
+		buf += cnt;
+	}
+	
+	munmap(data, st.st_size);
+	close(f);	
+	return result;
+}
+
+} //namespace parser
+
+} //namespace mrmc

src/parser/readLabFile.h

@@ -0,0 +1,19 @@
+/*
+ * read_lab_file.h
+ *
+ */
+
+#pragma once
+
+#include "src/models/atomic_propositions_labeling.h"
+
+
+namespace mrmc {
+
+namespace parser {
+
+mrmc::models::AtomicPropositionsLabeling * readLabFile(int node_count, const char * filename);
+
+}
+
+}

src/parser/read_tra_file.cpp → src/parser/readTraFile.cpp

@@ -3,15 +3,13 @@
  * system of a Markov chain (DTMC) and saving it into a corresponding
  * matrix.
  *
- * Reuses code from the file "read_tra_file.c" from the old MRMC project.
- *
  * Created on: 20.11.2012
  *      Author: Gereon Kremer
  */
 
 #include "parser.h"
 
-#include "src/parser/read_tra_file.h"
+#include "src/parser/readTraFile.h"
 #include "src/exceptions/file_IO_exception.h"
 #include "src/exceptions/wrong_file_format.h"
 #include "boost/integer/integer_mask.hpp"
@@ -44,9 +42,6 @@ char* skipWS(char* buf)
 	}
 }
 
-// Disable C4996 - This function or variable may be unsafe.
-#pragma warning(disable:4996)
-
 /*!
  * This method does the first pass through the .tra file and computes
  * the number of non-zero elements that are not diagonal elements,
@@ -57,12 +52,12 @@ char* skipWS(char* buf)
  * @return The number of non-zero elements that are not on the diagonal
  * @param buf Data to scan. Is expected to be some char array.
  */
-static uint_fast32_t make_first_pass(char* buf)
+static uint_fast32_t makeFirstPass(char* buf)
 {
 	uint_fast32_t non_zero = 0;
 	
-	/*
-		check file header and extract number of transitions
+	/*!
+	 *	check file header and extract number of transitions
 	 */
 	if (strncmp(buf, "STATES ", 7) != 0) return 0;
 	buf += 7; // skip "STATES "
@@ -72,8 +67,8 @@ static uint_fast32_t make_first_pass(char* buf)
 	buf += 12; // skip "TRANSITIONS "
 	if ((non_zero = strtol(buf, &buf, 10)) == 0) return 0;
 	
-	/*
-		check all transitions for non-zero diagonal entrys
+	/*!
+	 *	check all transitions for non-zero diagonal entrys
 	 */
 	unsigned int row, col;
 	double val;
@@ -98,17 +93,21 @@ static uint_fast32_t make_first_pass(char* buf)
  * @return a pointer to the created sparse matrix.
  */
 
-sparse::StaticSparseMatrix<double> * read_tra_file(const char * filename) {
-	if (setlocale( LC_NUMERIC, "de_DE" ) == 0)
-	{
-		fprintf(stderr, "could not set locale\n");
-	}
-	/*
-		open file and map to memory
+sparse::StaticSparseMatrix<double> * readTraFile(const char * filename) {
+	/*!
+	*	enforce locale where decimal point is '.'
+	*/
+	setlocale( LC_NUMERIC, "C" );
+	
+	/*!
+	 *	open file and map to memory
 	 */
 	struct stat st;
 	int f = open(filename, O_RDONLY);
 	if((f < 0) || (stat(filename, &st) != 0)) {
+		/*!
+		 *	stat() or open() failed
+		 */
 		pantheios::log_ERROR("File ", filename, " was not readable (Does it exist?)");
 		throw exceptions::file_IO_exception("mrmc::read_tra_file: Error opening file! (Does it exist?)");
 		return NULL;
@@ -116,35 +115,41 @@ sparse::StaticSparseMatrix<double> * read_tra_file(const char * filename) {
 	char *data = (char*)mmap(NULL, st.st_size, PROT_READ, MAP_PRIVATE|MAP_DENYWRITE, f, 0);
 	if (data == (char*)-1)
 	{
+		/*!
+		 *	mmap() failed
+		 */
 		pantheios::log_ERROR("Could not map the file to memory. Something went wrong with mmap.");
 		throw exceptions::file_IO_exception("mrmc::read_tra_file: Error mapping file to memory");
 		close(f);
 		return NULL;
 	}
 	
-	/*
-		perform first pass
+	/*!
+	 *	perform first pass, i.e. count entries that are not zero and not on the diagonal
 	 */
-	uint_fast32_t non_zero = make_first_pass(data);
+	uint_fast32_t non_zero = makeFirstPass(data);
 	if (non_zero == 0)
 	{
+		/*!
+		 *	first pass returned zero, this means the file format was wrong
+		 */
 		close(f);
 		munmap(data, st.st_size);
 		throw mrmc::exceptions::wrong_file_format();
 		return NULL;
 	}
 	
-	/*
-		perform second pass
-		
-		from here on, we already know that the file header is correct
+	/*!
+	 *	perform second pass
+	 *	
+	 *	from here on, we already know that the file header is correct
 	 */
 	char* buf = data;
 	uint_fast32_t rows;
 	sparse::StaticSparseMatrix<double> *sp = NULL;
 
-	/*
-		read file header, extract number of states
+	/*!
+	 *	read file header, extract number of states
 	 */
 	buf += 7; // skip "STATES "
 	rows = strtol(buf, &buf, 10);
@@ -156,13 +161,17 @@ sparse::StaticSparseMatrix<double> * read_tra_file(const char * filename) {
                         pantheios::integer(rows), " rows and ",
                         pantheios::integer(non_zero), " Non-Zero-Elements");
                         
-	/* Creating matrix
+	/*!	
+	 *	Creating matrix
 	 *	Memory for diagonal elements is automatically allocated, hence only the number of non-diagonal
 	 *	non-zero elements has to be specified (which is non_zero, computed by make_first_pass)
 	 */
 	sp = new sparse::StaticSparseMatrix<double>(rows);
 	if (sp == NULL)
 	{
+		/*!
+		 *	creating the matrix failed
+		 */
 		close(f);
 		munmap(data, st.st_size);
 		throw std::bad_alloc();
@@ -172,8 +181,8 @@ sparse::StaticSparseMatrix<double> * read_tra_file(const char * filename) {
 
 	uint_fast64_t row, col;
 	double val;
-	/*
-		read all transitions from file
+	/*!
+	 *	read all transitions from file
 	 */
 	while (1)
 	{
@@ -189,7 +198,9 @@ sparse::StaticSparseMatrix<double> * read_tra_file(const char * filename) {
 		sp->addNextValue(row,col,val);	
 	}
 	
-	// clean up
+	/*!
+	 * clean up
+	 */	
 	close(f);
 	munmap(data, st.st_size);
 

src/parser/readTraFile.h

@@ -0,0 +1,19 @@
+/*
+ * read_tra_file.h
+ *
+ *  Created on: 15.08.2012
+ *      Author: Thomas Heinemann
+ */
+
+#pragma once
+
+#include "src/sparse/static_sparse_matrix.h"
+
+namespace mrmc {
+	namespace parser {
+	
+		mrmc::sparse::StaticSparseMatrix<double> * readTraFile(const char * filename);
+		
+	}
+}
+

src/parser/read_lab_file.cpp

@@ -1,181 +0,0 @@
-/*
- * read_lab_file.cpp
- *
- *  Created on: 10.09.2012
- *      Author: Thomas Heinemann
- */
-
-#include "parser.h"
-
-#include "read_lab_file.h"
-
-#include "src/exceptions/wrong_file_format.h"
-#include "src/exceptions/file_IO_exception.h"
-
-#include <cstring>
-#include <cstdlib>
-#include <cstdio>
-
-#include <pantheios/pantheios.hpp>
-#include <pantheios/inserters/integer.hpp>
-
-#ifdef WIN32
-#	define STRTOK_FUNC strtok_s
-#else
-#	define STRTOK_FUNC strtok_r
-#endif
-
-// Disable C4996 - This function or variable may be unsafe.
-#pragma warning(disable:4996)
-
-
-namespace mrmc {
-
-namespace parser {
-
-
-/*!
- * Reads a .lab file and puts the result in a labeling structure.
- *
- * Labelings created with this method have to be freed with the delete operator.
- * @param node_count the number of states.
- * @param filename   input .lab file's name.
- * @return The pointer to the created labeling object.
- */
-mrmc::models::AtomicPropositionsLabeling * read_lab_file(int node_count, const char * filename)
-{
-   /* Note that this function uses strtok_r on char-array s.
-    * This function will modify this string.
-    * However, as only the result of its tokenization is used, this is not a problem.
-    *
-    * Thread-safety is ensured by using strtok_r instead of strtok.
-    */
-   FILE *P;
-
-   //TODO (Thomas Heinemann): handle files with lines that are longer than BUFFER_SIZE
-   //TODO (Thomas Heinemann): Throw errors if fgets return NULL in the declaration. (fixed by Philipp. Or?)
-
-   char s[BUFFER_SIZE];              //String buffer
-   char *saveptr = NULL;             //Buffer for strtok_r
-   char sep[] = " \n\t";             //Separators for the tokens
-
-   P = fopen(filename, "r");
-
-   if (P == NULL) {
-      pantheios::log_ERROR("File could not be opened.");
-      throw mrmc::exceptions::file_IO_exception();
-	  return NULL;
-   }
-
-   if (!fgets(s, BUFFER_SIZE, P) || strcmp(s, "#DECLARATION\n")) {
-		fclose(P);
-		pantheios::log_ERROR("Wrong declaration section (\"#DECLARATION\" missing).");
-		throw mrmc::exceptions::wrong_file_format();
-		return NULL;
-   }
-
-
-
-   uint_fast32_t buffer_size_count = 1;
-   uint_fast32_t buffer_start = 0;
-   char* decl_buffer = new char[buffer_size_count*BUFFER_SIZE];
-   bool need_next_iteration = true;
-
-   do {
-      decl_buffer[buffer_size_count*BUFFER_SIZE - 1] = '\xff';
-      if (fgets(decl_buffer + buffer_start, buffer_size_count*BUFFER_SIZE - buffer_start, P)) {
-         if ((decl_buffer[buffer_size_count*BUFFER_SIZE - 1] != '\xff') &&
-             (decl_buffer[buffer_size_count*BUFFER_SIZE - 2] != '\n')) {
-            //fgets changed the last bit -> read string has maximum length
-            //AND line is longer than size of decl_buffer
-            char* temp_buffer = decl_buffer;
-            decl_buffer = NULL;
-
-            buffer_size_count++;
-            decl_buffer = new char[buffer_size_count*BUFFER_SIZE];
-
-            buffer_start = (buffer_size_count - 1) * BUFFER_SIZE;
-
-            memcpy(decl_buffer, temp_buffer, buffer_start - 1);
-            delete[] temp_buffer;
-         } else {
-            need_next_iteration = false;
-         }
-      } else {
-         pantheios::log_ERROR("EOF in the declaration section");
-         throw mrmc::exceptions::wrong_file_format();
-		 delete[] decl_buffer;
-		 return NULL;
-      }
-   } while (need_next_iteration);
-
-   uint_fast32_t proposition_count = 0;
-   char * proposition;
-   int pos = 0;
-
-   if (decl_buffer[pos] != ' ' && decl_buffer[pos] != '\t' && decl_buffer[pos] != '\0') {
-      proposition_count++;
-   }
-
-   while (decl_buffer[pos] != '\0') {
-      if ((decl_buffer[pos] == ' ' || decl_buffer[pos] == '\t') &&
-          (decl_buffer[pos + 1] != ' ' && decl_buffer[pos + 1] != '\t' && decl_buffer[pos + 1] != '\0')) {
-         proposition_count++;
-      }
-      pos++;
-   }
-
-   mrmc::models::AtomicPropositionsLabeling* result = new mrmc::models::AtomicPropositionsLabeling(node_count, proposition_count);
-
-   //Here, all propositions are to be declared...
-   for (proposition = STRTOK_FUNC(decl_buffer, sep, &saveptr);
-        proposition != NULL;
-        proposition = STRTOK_FUNC(NULL, sep, &saveptr)) {
-      result -> addAtomicProposition(proposition);
-   }
-
-   // Free decl_buffer
-   delete[] decl_buffer;
-
-
-   saveptr = NULL;                        //resetting save pointer for strtok_r
-
-   if (!fgets(s, BUFFER_SIZE, P) || strcmp(s, "#END\n")) {
-		fclose(P);
-		delete result;
-		pantheios::log_ERROR("Wrong declaration section (\"#END\" missing).");
-		throw mrmc::exceptions::wrong_file_format();
-		return NULL;
-   }
-
-   while (fgets(s, BUFFER_SIZE, P)) {
-      char * token = NULL;
-      uint_fast32_t node = 0;
-      /* First token has to be a number identifying the node,
-       * hence it is treated differently from the other tokens.
-       */
-      token = STRTOK_FUNC(s, sep, &saveptr);
-      if (sscanf(token, "%u", &node) == 0) {
-         fclose(P);
-         delete result;
-         pantheios::log_ERROR("Line assigning propositions does not start with a node number.");
-         throw mrmc::exceptions::wrong_file_format();
-		 return NULL;
-      }
-      do {
-         token = STRTOK_FUNC(NULL, sep, &saveptr);
-         if (token == NULL) {
-            break;
-         }
-         result->addAtomicPropositionToState(token, node);
-      } while (token != NULL);
-
-   }
-
-   fclose(P);
-   return result;
-}
-
-} //namespace parser
-
-} //namespace mrmc

src/parser/read_lab_file.h

@@ -1,24 +0,0 @@
-/*
- * read_lab_file.h
- *
- *  Created on: 10.09.2012
- *      Author: thomas
- */
-
-#ifndef READ_LAB_FILE_H_
-#define READ_LAB_FILE_H_
-
-#include "src/models/atomic_propositions_labeling.h"
-
-
-namespace mrmc {
-
-namespace parser {
-
-mrmc::models::AtomicPropositionsLabeling * read_lab_file(int node_count, const char * filename);
-
-}
-
-}
-
-#endif /* READ_LAB_FILE_H_ */

src/parser/read_tra_file.h

@@ -1,20 +0,0 @@
-/*
- * read_tra_file.h
- *
- *  Created on: 15.08.2012
- *      Author: Thomas Heinemann
- */
-
-#ifndef READ_TRA_FILE_H_
-#define READ_TRA_FILE_H_
-#include "src/sparse/static_sparse_matrix.h"
-namespace mrmc{
-namespace parser {
-
-mrmc::sparse::StaticSparseMatrix<double> * read_tra_file(const char * filename);
-
-}
-}
-
-
-#endif /* READ_TRA_FILE_H_ */