Fix possible buffer overflow

.gitignore

@@ -13,6 +13,9 @@
 *.la
 .dirstamp
 
+# Wasm files
+*.wasm
+
 # Executables
 hdt2rdf
 hdtInfo
@@ -54,7 +57,7 @@ stamp-h1
 .deps/
 
 *.hdt
-*.hdt.index
+*.hdt.index*
 *.nq
 *.nt
 *.rdf

libcds/include/RMQ_succinct.h

@@ -55,7 +55,7 @@ namespace cds_static
 			void  save(ostream & fp);
 			RMQ_succinct * load(istream & fp);
 
-			~RMQ_succinct();
+			virtual ~RMQ_succinct();
 
 		protected:
 			/* size of array a*/

libcds/include/TextIndexCSA.h

@@ -49,7 +49,7 @@ namespace cds_static
 			 **/
 			TextIndexCSA(uchar *text, ulong length, char *build_options);
 
-			~TextIndexCSA();
+			virtual ~TextIndexCSA();
 
 			/* Writes in numocc the number of occurrences of the substring
 			 * pattern[0..length-1] found in the text indexed by index. */

libcds/include/WaveletTreeNoptrsS.h

@@ -89,7 +89,7 @@ namespace cds_static
             uint set(uint val, uint ind) const;
 
             /** Recursive function for building the Wavelet Tree. */
-            void build_level(uint **bm, uint *symbols, uint length, uint *occs);
+            void build_level(uint **bm, uint *symbols, uint length);
     };
 };
 #endif

libcds/src/static/bitsequence/BitSequenceRRR.cpp

@@ -422,7 +422,7 @@ namespace cds_static
 			ret->create_sampling(ret->sample_rate);
 			return ret;
 		}
-		catch(exception e) {
+		catch(const exception&) {
 			delete ret;
 		}
 		return NULL;

libcds/src/static/sequence/WaveletMatrix.cpp

@@ -24,9 +24,11 @@
 namespace cds_static
 {
 
-	WaveletMatrix::WaveletMatrix(const Array &symbols2, BitSequenceBuilder * bmb, Mapper * am) : Sequence(n) {
+	WaveletMatrix::WaveletMatrix(const Array &symbols2, BitSequenceBuilder * bmb, Mapper * am) : Sequence(0) {
 		bmb->use();
 		n = symbols2.getLength();
+		this->length = n; // sets Sequence::length (Sequence(0) in initializer)
+
 		uint *symbols = new uint[n];
 		this->am = am;
 		am->use();
@@ -81,8 +83,6 @@ namespace cds_static
 		delete [] _bm;
 		// delete [] oc;
 		bmb->unuse();
-
-		this->length = n;
 	}
 
 	WaveletMatrix::WaveletMatrix(uint * symbols, size_t n, BitSequenceBuilder * bmb, Mapper * am, bool deleteSymbols) : Sequence(n) {

libcds/src/static/sequence/WaveletTreeNoptrsS.cpp

@@ -24,9 +24,10 @@
 namespace cds_static
 {
 
-    WaveletTreeNoptrsS::WaveletTreeNoptrsS(const Array &symb, BitSequenceBuilder * bmb, Mapper * am) : Sequence(n) {
+    WaveletTreeNoptrsS::WaveletTreeNoptrsS(const Array &symb, BitSequenceBuilder * bmb, Mapper * am) : Sequence(0) {
         bmb->use();
         this->n=symb.getLength();
+        this->length = this->n; // sets Sequence::length (Sequence(0) in initializer)
         this->am=am;
         bool deleteSymbols = true;
         am->use();
@@ -80,7 +81,7 @@ namespace cds_static
                 _bm[i][j]=0;
         }
 
-        build_level(_bm,new_symb,new_n,occurrences);
+        build_level(_bm,new_symb,new_n);
         bitstring = new BitSequence*[height];
         for(uint i=0;i<height;i++) {
             bitstring[i] = bmb->build(_bm[i],new_n);
@@ -148,7 +149,7 @@ namespace cds_static
                 _bm[i][j]=0;
         }
 
-        build_level(_bm,new_symb,new_n,occurrences);
+        build_level(_bm,new_symb,new_n);
         bitstring = new BitSequence*[height];
         for(uint i=0;i<height;i++) {
             bitstring[i] = bmb->build(_bm[i],new_n);
@@ -328,7 +329,7 @@ namespace cds_static
         return bytesBitstrings+occ->getSize()+ptrs;
     }
 
-    void WaveletTreeNoptrsS::build_level(uint **bm, uint *symbols, uint length, uint *occs) {
+    void WaveletTreeNoptrsS::build_level(uint **bm, uint *symbols, uint length) {
             // for (uint i = 0; i < length; i++)
             //     cout << " " << symbols[i];
             // cout << endl;

libcds/src/static/suffixtree/LCP_PT.cpp

@@ -19,7 +19,6 @@
 #include <LCP_PT.h>
 
 const int max_precomputed_cover = 8;
-const int coversizes[max_precomputed_cover+1]= {1,2,3,4,5,7,9,13,20};
 const unsigned cover0[] = {0};
 const unsigned cover1[] = {0,1};
 const unsigned cover2[] = {0,1,2};

libcds/src/static/suffixtree/factorization.cpp

@@ -23,25 +23,6 @@
 
 const unsigned int TABLEBASE[7] = {0,16,272,4368,69904,1118480,17895696};
 
-const unsigned short TABLESUM[256] = {
-	0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
-	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
-	2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
-	3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
-	4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
-	5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
-	6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
-	7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
-	8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
-	9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
-	10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
-	11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
-	12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
-	13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
-	14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
-	15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30
-};
-
 namespace cds_static
 {
 

libcds/src/static/textindex/suftest3.test.cpp

@@ -35,12 +35,8 @@
 
 #include <stdlib.h>
 #include <stdio.h>
-#if 1
-#include <sys/timeb.h>
-#else
 #include <sys/time.h>
 #include <sys/resource.h>
-#endif
 #include <comparray4.h>
 #include <limits.h>
 #include <stdbool.h>
@@ -58,20 +54,7 @@
 
 namespace cds_static
 {
-
-	#if 1
-	typedef struct timeb mytimestruct;
-	void mygettime(mytimestruct *t) {
-		ftime(t);
-	}
-	double mylaptime(mytimestruct *before,mytimestruct *after) {
-		double t;
-		t = after->time - before->time;
-		t += (double)(after->millitm - before->millitm)/1000;
-		return t;
-	}
-	#else
-	typedef mytimestruct struct rusage;
+	typedef struct rusage mytimestruct;
 	void mygettime(mytimestruct *t) {
 		getrusage(RUSAGE_SELF,t);
 	}
@@ -82,7 +65,6 @@ namespace cds_static
 			- before->ru_utime.tv_usec)/1000000;
 		return t;
 	}
-	#endif
 
 	/* Three function to variables to manage parameters */
 	static bool is_delimeter(char *delimiters, char c) {

libcds/tests/testLCP.cpp

@@ -53,8 +53,8 @@ bool testLCP(LCP *s1, LCP *s2, TextIndex *csa){
 
 
 int main(int argc, char *argv[]){
-	char *text;
-	size_t length;
+	char *text = nullptr;
+	size_t length = 0;
 	LCP *lcp_naive=NULL;
 	LCP *lcp=NULL;
 

libcds/tests/testNPR.cpp

@@ -71,8 +71,8 @@ bool testNPR(NPR *npr, LCP *lcp, TextIndex *csa,  size_t *naive_nsv, size_t *nai
 
 
 int main(int argc, char *argv[]){
-	char *text;
-	size_t length;
+	char *text = nullptr;
+	size_t length = 0;
 	LCP *lcp = NULL;
 	NPR *npr = NULL;
 

libhdt/include/HDTSpecification.hpp

@@ -72,6 +72,13 @@ class HDTSpecification
 	  */
 	const std::string& get(const std::string& key);
 
+
+	/**
+	  * Get the value of a property, or "" if the key is not found.
+	  */
+	const std::string& getOrEmpty(const std::string& key);
+
+
 	/** Set the value of a property */
 	void set(const std::string& key, const std::string& value);
 };

libhdt/src/bitsequence/BitSequence375.cpp

@@ -157,9 +157,25 @@ void BitSequence375::set(const size_t i, bool val) {
         array = &data[0];
 	}
 	if(val) {
+		#ifdef __EMSCRIPTEN__
+		/* Webassembly size_t differs from the one of
+		other architectures.
+		EDITED BY @lucafabbian, TODO: check  */
+		// fprintf(stderr, "[WARN] Unsafe cast called\n");
+		bitset((uint64_t*) &array[0], i);
+		#else
 		bitset(&array[0], i);
+		#endif
 	} else {
+		#ifdef __EMSCRIPTEN__
+		/* Webassembly size_t differs from the one of
+		other architectures.
+		EDITED BY @lucafabbian,  TODO: check */
+		// fprintf(stderr, "[WARN] Unsafe cast called\n");
+		bitclean((uint64_t*)&array[0], i);
+		#else
 		bitclean(&array[0], i);
+		#endif
 	}
 
 	numbits = i>=numbits ? i+1 : numbits;
@@ -173,7 +189,15 @@ void BitSequence375::append(bool bit) {
 
 bool BitSequence375::access(const size_t i) const
 {
+	#ifdef __EMSCRIPTEN__
+	/* Webassembly size_t differs from the one of
+	other architectures.
+	EDITED BY @lucafabbian, TODO: check */
+	//fprintf(stderr, "[WARN] Unsafe cast called\n");
+	return bitget((uint64_t*)array, i);
+	#else
 	return bitget(array, i);
+	#endif
 }
 
 void BitSequence375::save(ostream & out) const

libhdt/src/dictionary/FourSectionDictionary.cpp

@@ -56,10 +56,7 @@ FourSectionDictionary::FourSectionDictionary(HDTSpecification & spec) : blocksiz
 	objects = new csd::CSD_PFC();
 	shared = new csd::CSD_PFC();
 
-	string blockSizeStr = "";
-	try{
-		blockSizeStr = spec.get("dict.block.size");
-	}catch(exception& e){}
+	string blockSizeStr = spec.getOrEmpty("dict.block.size");
 
 	if(!blockSizeStr.empty() && (blockSizeStr.find_first_not_of("0123456789") == string::npos))
 	{

libhdt/src/dictionary/KyotoDictionary.cpp

@@ -50,10 +50,7 @@ KyotoDictionary::KyotoDictionary() {
 }
 
 KyotoDictionary::KyotoDictionary(HDTSpecification &specification) : spec(specification) {
-	string map = "";
-	try{
-		map = spec.get("dictionary.mapping");
-	}catch(exception& e){}
+	string map = spec.getOrEmpty("dictionary.mapping");
 	if(map=="mapping1") {
 		this->mapping = MAPPING1;
 	} else {

libhdt/src/dictionary/LiteralDictionary.cpp

@@ -57,10 +57,8 @@ LiteralDictionary::LiteralDictionary(HDTSpecification & spec) : blocksize(8) {
 	objectsLiterals = new csd::CSD_FMIndex();
 	shared = new csd::CSD_PFC();
 
-	string blockSizeStr = "";
-	try{
-		blockSizeStr = spec.get("dict.block.size");
-	}catch(exception& e){}
+	string blockSizeStr = spec.getOrEmpty("dict.block.size");
+
 	if (blockSizeStr != "") {
 		blocksize = atoi(blockSizeStr.c_str());
 	}

libhdt/src/dictionary/PlainDictionary.cpp

@@ -55,10 +55,7 @@ PlainDictionary::PlainDictionary() {
 }
 
 PlainDictionary::PlainDictionary(HDTSpecification &specification) : spec(specification) {
-	string map ="";
-	try{
-		map = spec.get("dictionary.mapping");
-	}catch(exception& e){}
+	string map =spec.getOrEmpty("dictionary.mapping");
 	if(map=="mapping1") {
 		this->mapping = MAPPING1;
 	} else {

libhdt/src/hdt/BasicHDT.cpp

@@ -96,12 +96,8 @@ void BasicHDT::createComponents() {
 
 	// DICTIONARY
 
-	std::string dictType = "";
-	try{
-		dictType = spec.get("dictionary.type");
-	}
-	catch (std::exception& e){
-	}
+	std::string dictType = spec.getOrEmpty("dictionary.type");
+
 
 	if(dictType==HDTVocabulary::DICTIONARY_TYPE_FOUR) {
 		dictionary = new FourSectionDictionary(spec);
@@ -118,11 +114,8 @@ void BasicHDT::createComponents() {
 	}
 
 	// TRIPLES
-	std::string triplesType = "";
-	try{
-		triplesType = spec.get("triples.type");
-	}catch (std::exception& e) {
-	}
+	std::string triplesType = spec.getOrEmpty("triples.type");
+
 	if(triplesType==HDTVocabulary::TRIPLES_TYPE_BITMAP) {
 		triples = new BitmapTriples(spec);
 	} else if(triplesType==HDTVocabulary::TRIPLES_TYPE_PLAIN) {
@@ -299,11 +292,8 @@ void BasicHDT::loadTriples(const char* fileName, const char* baseUri, RDFNotatio
 		triplesList->stopProcessing(&iListener);
 
 		// SORT & Duplicates
-		string ord = "";
-		try{
-			ord = spec.get("triplesOrder");
-		}catch (std::exception& e){
-		}
+		string ord = spec.getOrEmpty("triplesOrder");
+
 		TripleComponentOrder order = parseOrder(
 				ord.c_str());
 		if (order == Unknown) {
@@ -319,17 +309,10 @@ void BasicHDT::loadTriples(const char* fileName, const char* baseUri, RDFNotatio
 		cout << "Catch exception triples" << e << endl;
 		delete triplesList;
 		throw e;
-#ifndef WIN32
-	} catch (char *e) {
-		cout << "Catch exception triples" << e << endl;
-		delete triplesList;
-		throw e;
-#else
 	} catch (std::exception& e) {
 		// cerr << "Catch exception triples" << e << endl;
 		delete triplesList;
 		throw;
-#endif
 	}
 	if (triples->getType() == triplesList->getType()) {
 		delete triples;
@@ -588,12 +571,8 @@ void BasicHDT::loadTriplesFromHDTs(const char** fileNames, size_t numFiles, cons
 		triplesList->stopProcessing(&iListener);
 
 		// SORT & Duplicates
-		string ord = "";
-		try{
-			ord = spec.get("triplesOrder");
-		}
-		catch (std::exception& e){
-		}
+		string ord = spec.getOrEmpty("triplesOrder");
+
 		TripleComponentOrder order = parseOrder(ord.c_str());
 		if (order == Unknown) {
 			order = SPO;