Merge pull request #66 from JesseMckinzie/fix_compiler_warnings_v2

Fix compiler warnings

pom.xml

@@ -9,6 +9,8 @@
   <properties>
     <maven.compiler.source>1.7</maven.compiler.source>
     <maven.compiler.target>1.7</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
   </properties>
 
   <scm>

src/filepattern/cpp/external/external_filepattern.cpp

@@ -48,7 +48,7 @@ ExternalFilePattern::~ExternalFilePattern(){
 
 
 void ExternalFilePattern::printFiles(){
-    bool after = false;
+
     vector<Tuple> files;
 
     while(true){
@@ -66,7 +66,6 @@ void ExternalFilePattern::printFiles(){
             cout << endl;
         }
 
-        after = true;
         if (this->stream_.endOfValidFiles()) break;
 
     }
@@ -93,7 +92,6 @@ void ExternalFilePattern::matchFilesOneDir(){
     string file;
     smatch sm;
 
-    int count = 0;
     // iterate over files
     while(!this->stream_.isEmpty()){
         block = this->stream_.getBlock();
@@ -104,7 +102,6 @@ void ExternalFilePattern::matchFilesOneDir(){
 
             if(regex_match(file, sm, pattern_regex)){
                 this->stream_.writeValidFiles(getVariableMap(file_path, sm)); // write to txt file
-                ++count;
             }
 
         }

src/filepattern/cpp/external/external_pattern.cpp

@@ -96,6 +96,10 @@ void ExternalPattern::getMatchingInit(const vector<tuple<string, vector<Types>>>
 
     bool created = fs::create_directory(this->fp_tmpdir_);
 
+    if (!created) {
+        std::cerr << "WARNING: temporary directory " << this->fp_tmpdir_ << " could not be created.";
+    }
+
     fs::permissions(this->fp_tmpdir_, fs::perms::all);
 
     // create a path to store matching files
@@ -164,17 +168,15 @@ vector<Tuple> ExternalPattern::getMatchingBlock(){
 void ExternalPattern::groupByHelper(){
 
     std::vector<std::pair<std::vector<std::pair<std::string, Types>> , std::vector<Tuple>>> temp_group;
-    int group_idx;
+
     vector<Tuple> temp_vec;
     vector<std::pair<std::string, Types>> grouped_variables;
     string group_by;
     //for(const auto& group_by: this->group){
 
-    for(int j = 1; j < this->group_.size(); ++j){
+    for(unsigned int j = 1; j < this->group_.size(); ++j){
         group_by = this->group_[j];
 
-        group_idx = 0;
-
         for(auto& vec: this->current_group_){
 
 
@@ -189,7 +191,7 @@ void ExternalPattern::groupByHelper(){
 
             Types current_value = get<0>(vec.second[0])[group_by]; // get the value of variable
             vector<Tuple> empty_vec;
-            int i = 0;
+            unsigned int i = 0;
             int group_ptr = 0;
 
             //group files into vectors based on group_by variable
@@ -421,7 +423,7 @@ void ExternalPattern::sortFiles(){
 
 }
 
-Tuple ExternalPattern::getItem(int key){
+Tuple ExternalPattern::getItem(unsigned int key){
 
     if(key < 0) {
         if(this->stream_.getValidFilesSize() + key < 0) throw out_of_range("Index " + std::to_string(key) + " is out of range.");
@@ -459,18 +461,18 @@ vector<Tuple> ExternalPattern::getSlice(vector<Types>& key){
     string key2 = s::to_string(key[2]);
 
     if(s::is_number(key0) && key1 == "None"  && key2 == "None"){
-        int i = stoi(key0);
+        unsigned int i = stoi(key0);
 
         if(i >= this->stream_.getValidFilesSize()) throw out_of_range("Index " + std::to_string(i) + " is out of range.");
-        int j = this->stream_.getValidFilesSize();
-        int step =  1;
+        unsigned int j = this->stream_.getValidFilesSize();
+        unsigned int step =  1;
         return this->stream_.getValidFilesSlice(i, j, step);
     }
 
     // A start and stop index is provided with no step size, i.e. valid_files[i:j]
     if(s::is_number(key0) && s::is_number(key1)  && key2 == "None"){
-        int i =  stoi(key0);
-        int j = stoi(key1);
+        unsigned int i =  stoi(key0);
+        unsigned int j = stoi(key1);
 
         if(i > this->stream_.getValidFilesSize()) throw out_of_range("Index " + std::to_string(i) + " is out of range.");
         if(j > this->stream_.getValidFilesSize()) throw out_of_range("Index " + std::to_string(j) + " is out of range.");
@@ -483,8 +485,8 @@ vector<Tuple> ExternalPattern::getSlice(vector<Types>& key){
 
     // A start, stop, and step is provided
     if(s::is_number(key0) && s::is_number(key1)  && s::is_number(key2)){
-        int i = stoi(key0);
-        int j = stoi(key1);
+        unsigned int i = stoi(key0);
+        unsigned int j = stoi(key1);
 
         if(i > this->stream_.getValidFilesSize()) throw out_of_range("Index " + std::to_string(i) + " is out of range.");
         if(j > this->stream_.getValidFilesSize()) throw out_of_range("Index " + std::to_string(j) + " is out of range.");
@@ -494,10 +496,10 @@ vector<Tuple> ExternalPattern::getSlice(vector<Types>& key){
     }
 
     if(s::is_number(key0) && key1 == "None" && s::is_number(key2)){
-        int i = stoi(key0);
+        unsigned int i = stoi(key0);
         if(i > this->stream_.getValidFilesSize()) throw out_of_range("Index " + std::to_string(i) + " is out of range.");
 
-        int j = this->stream_.getValidFilesSize();
+        unsigned int j = this->stream_.getValidFilesSize();
         int step =  stoi(key2);
         return this->stream_.getValidFilesSlice(i, j, step);
     }

src/filepattern/cpp/external/external_pattern.hpp

@@ -230,7 +230,7 @@ class ExternalPattern : public Pattern {
 
         void sortFiles();
 
-        Tuple getItem(int key);
+        Tuple getItem(unsigned int key);
 
         std::vector<Tuple> getItemList(std::vector<int>& key);
 

src/filepattern/cpp/external/external_stringpattern.cpp

@@ -47,7 +47,6 @@ void ExternalStringPattern::matchFiles(){
     string file;
     smatch sm;
 
-    int count = 0;
     // iterate over files
     while(!this->stream_.isEmpty()){
 
@@ -57,7 +56,6 @@ void ExternalStringPattern::matchFiles(){
 
             if(regex_match(file, sm, pattern_regex)){
                 this->stream_.writeValidFiles(getVariableMap(file, sm)); // write to txt file
-                ++count;
             }
         }
     }

src/filepattern/cpp/external/external_stringpattern.hpp

@@ -59,7 +59,6 @@ class ExternalStringPattern : public ExternalPattern {
         fs::directory_iterator iterator_; // File iterator for given path
         fs::recursive_directory_iterator recursive_iterator_; // Recursive iterator
         bool end_of_file_; // True if end of temp file is reached
-        bool recursive_; // True if recursive iterator through subdirectories
         int total_files_; // Total number of matched files (will be deleted)
 
 

src/filepattern/cpp/internal/filepattern.cpp

@@ -56,18 +56,11 @@ FilePatternObject::FilePatternObject(const string& path, const string& file_patt
     this->sortFiles();
 }
 
-void FilePatternObject::printFiles(){
-    for(const auto& file: this->iterator_){
-        //cout << file << endl;
-    }
-}
-
 void FilePatternObject::matchFilesOneDir(){
 
     Map mapping;
     vector<string> parsed_regex;
 
-    int i, j;
     string s;
     string file, file_path;
     Tuple member;

src/filepattern/cpp/internal/filepattern.hpp

@@ -35,12 +35,6 @@ class FilePatternObject : public InternalPattern {
          */
         void matchFiles();
 
-        /**
-         * @brief Print the valid files to the console.
-         *
-         */
-        void printFiles();
-
     private:
         //std::string path; // path to directory
         fs::directory_iterator iterator_; // File iterator for given path

src/filepattern/cpp/internal/internal_pattern.cpp

@@ -9,14 +9,13 @@ void InternalPattern::nextGroup() {}
 void InternalPattern::groupByHelper(const vector<string>& groups){
 
     std::vector<std::pair<std::vector<std::pair<std::string, Types>> , std::vector<Tuple>>> temp;
-    int group_idx;
     vector<Tuple> temp_vec;
     vector<std::pair<std::string, Types>> grouped_variables;
-    for(const auto& group_by: groups){
 
-        group_idx = 0;
+    for(const auto& group_by: groups){
 
         for(auto& vec: this->valid_grouped_files_){
+
             grouped_variables.clear();
             for(auto& g: vec.first) grouped_variables.push_back(g);
             // Sort the matched files by the group_by parameter
@@ -26,7 +25,7 @@ void InternalPattern::groupByHelper(const vector<string>& groups){
 
             Types current_value = get<0>(vec.second[0])[group_by]; // get the value of variable
             vector<Tuple> empty_vec;
-            int i = 0;
+            unsigned int i = 0;
             int group_ptr = 0;
 
             //group files into vectors based on group_by variable
@@ -90,7 +89,7 @@ void InternalPattern::groupBy(vector<string>& groups) {
     Types current_value = get<0>(this->valid_files_[0])[group_by]; // get the value of variable
 
     vector<Tuple> empty_vec;
-    int i = 0;
+    unsigned int i = 0;
     int group_ptr = 0;
 
     //group files into vectors based on group_by variable
@@ -222,7 +221,7 @@ void InternalPattern::sortFiles(){
     });
 }
 
-Tuple InternalPattern::getItem(int key){
+Tuple InternalPattern::getItem(unsigned int key){
     if(key < 0) {
         if(this->valid_files_.size() + key < 0) throw out_of_range("Index " + std::to_string(key) + " is out of range.");
         return this->valid_files_[this->valid_files_.size()+key];

src/filepattern/cpp/internal/internal_pattern.hpp

@@ -83,7 +83,7 @@ class InternalPattern : public Pattern {
          */
         std::string outputName(std::vector<Tuple>& vec);
 
-        Tuple getItem(int key);
+        Tuple getItem(unsigned int key);
 
         std::vector<Tuple> getItemList(std::vector<int>& key);
 

src/filepattern/cpp/pattern.cpp

@@ -95,7 +95,6 @@ tuple<string, vector<string>, vector<string>> Pattern::getRegex(string& pattern,
     std::smatch sm, m; // regex matches
 
     string temp;
-    wchar_t last;
     // extract bracket expressions from pattern and store regex
     while (regex_search(patternCopy, m, e)){
         temp = m[0];
@@ -158,16 +157,16 @@ Tuple Pattern::getVariableMapMultDir(const string& filePath, const smatch& sm){
     string basename;
     string file = s::getBaseName(filePath);
     // iterate over matched files, checking if filename already exists
-    for(int i = 0; i < this->valid_files_.size(); i++){
+    for (auto& valid_file: this->valid_files_) {
         #ifdef JAVA_BINDING
-        basename = s::getBaseName(s::to_string(get<1>(this->valid_files_[i])[0])); // store the basename
+        basename = s::getBaseName(s::to_string(get<1>(valid_file)[0])); // store the basename
         #else
-        basename = s::getBaseName(get<1>(this->valid_files_[i])[0].string()); // store the basename
+        basename = s::getBaseName(get<1>(valid_file)[0].string()); // store the basename
         #endif
         // if the filename is found, add the filepath to the vector in the second member of the tuple
         if(basename == file){
             matched = true;
-            get<1>(this->valid_files_[i]).push_back(filePath); // Add path to existing mapping
+            get<1>(valid_file).push_back(filePath); // Add path to existing mapping
             break;
         }
     }
@@ -188,7 +187,7 @@ Tuple Pattern::getVariableMap(const string& filePath, const smatch& sm){
 
     string str;
     // Extract capture groups from filename and store in mapping
-    for(int i = 1; i < sm.size(); ++i){
+    for(unsigned int i = 1; i < sm.size(); ++i){
 
         str = sm[i];
 

src/filepattern/cpp/pattern_object.hpp

@@ -82,13 +82,13 @@ class PatternObject {
 
         virtual std::vector<Tuple> getMatchingBlock() = 0;
 
-        virtual Tuple getItem(int key) = 0;
+        virtual Tuple getItem(unsigned int key) = 0;
 
         virtual std::vector<Tuple> getItemList(std::vector<int>& key) = 0;
 
         size_t length() const {return valid_files_.size();};
 
-        const std::pair<std::vector<std::pair<std::string, Types>> , std::vector<Tuple>>& get_grouped_file_by_idx(int idx) {
+        const std::pair<std::vector<std::pair<std::string, Types>> , std::vector<Tuple>>& get_grouped_file_by_idx(unsigned int idx) {
 
             if (idx < 0 || idx >= this->valid_grouped_files_.size()) {
 

src/filepattern/cpp/util/fs_stream.cpp

@@ -344,7 +344,7 @@ Tuple FilesystemStream::getFileByIndex(int i) {
     return temp;
 }
 
-int FilesystemStream::getValidFilesSize(){
+unsigned int FilesystemStream::getValidFilesSize(){
     return this->valid_files_size_;
 }
 

src/filepattern/cpp/util/fs_stream.hpp

@@ -32,7 +32,7 @@ class FilesystemStream {
 
     public:
         int counter_; // for debugging (to be removed)
-        int map_size_; // size of maps in stream
+        unsigned int map_size_; // size of maps in stream
 
         /**
          * @brief Construct a new Filesystem Stream object.
@@ -145,7 +145,7 @@ class FilesystemStream {
 
         Tuple getFileByIndex(int i);
 
-        int getValidFilesSize();
+        unsigned int getValidFilesSize();
 
         std::vector<Tuple> getValidFilesSlice(int i, int j, int step);
 
@@ -170,7 +170,7 @@ class FilesystemStream {
         bool empty_; // no more files remaining
         bool valid_files_empty_; // no more matched files
         long double block_size_; // max amount of memory to use
-        int valid_files_size_;
+        unsigned int valid_files_size_;
 
         /**
          * @brief Updates the amount of memory being used

src/filepattern/cpp/util/util.hpp

@@ -370,7 +370,7 @@ namespace m {
      * @return true The end of the file has not been reached and the map is modified
      * @return false The end of the file has been reached and the mao is not modified
      */
-    inline bool getMap(std::ifstream& infile, Tuple& member, int map_size) {
+    inline bool getMap(std::ifstream& infile, Tuple& member, long unsigned int map_size) {
 
         std::string str;
         Map map;
@@ -523,7 +523,7 @@ namespace d {
         if (s::endsWith(path_to_dir, ".txt")) path_to_dir = path_to_dir.substr(0, path_to_dir.find_last_of('/'));
         fs::path path = path_to_dir;
         try {
-            uintmax_t n = fs::remove_all(path);
+            fs::remove_all(path);
         }
         catch (fs::filesystem_error& e) {}
     }
@@ -562,7 +562,7 @@ namespace f {
 
         file.seekg(std::ios::beg);
 
-        for(int i=0; i < num - 1; ++i){
+        for(unsigned int i=0; i < num - 1; ++i){
             file.ignore(std::numeric_limits<std::streamsize>::max(),'\n');
         }