Merge pull request #46 from yhoogstrate/using_old_c_style_realpath_an…

…d_basename

Using old c style realpath and basename

include/utils.hpp

@@ -17,3 +17,7 @@ std::string std_string_nullbyte_safe(char *, size_t, size_t);
 std::string std_string_nullbyte_safe(char *, size_t);
 
 bool is_fasta_file(char *filename);
+
+std::string basename_cpp(std::string);
+std::string realpath_cpp(std::string);
+

src/fastafs.cpp

@@ -495,7 +495,8 @@ void fastafs::load(std::string afilename)
     if(file.is_open()) {
         // if a user can't compile this line, please replace it with C's
         // 'realpath' function and delete/free afterwards and send a PR
-        this->filename = std::filesystem::canonical(afilename);// this path must be absolute because if stuff gets send to FUSE, paths are relative to the FUSE process and probably systemd initialization
+        //this->filename = std::filesystem::canonical(afilename);// this path must be absolute because if stuff gets send to FUSE, paths are relative to the FUSE process and probably systemd initialization
+        this->filename = realpath_cpp(afilename);
 
         size = file.tellg();
 

src/fuse.cpp

@@ -478,7 +478,8 @@ fuse_instance *parse_args(int argc, char **argv, char **argv_fuse)
             std::string name; // prefix name of mounted fasta dict 2bit and fai files
             if(fname.size() == 0) { // invalid mount argument, don't bind fastafs object
                 fname = std::string(argv[mount_target_arg]);
-                name = std::filesystem::path(fname).filename();
+                //name = std::filesystem::path(fname).filename();
+                name = basename_cpp(fname);
 
                 // remove .fastafs suffix
                 size_t lastindex = name.find_last_of(".");
@@ -492,7 +493,8 @@ fuse_instance *parse_args(int argc, char **argv, char **argv_fuse)
             fi->f->load(fname);
             fi->cache = fi->f->init_ffs2f(fi->padding, true);// allow mixed case
         } else {
-            std::string basename = std::filesystem::path(std::string(argv[mount_target_arg])).filename();
+			std::string basename = basename_cpp(std::string(argv[mount_target_arg]));
+            //std::string basename = std::filesystem::path(std::string(argv[mount_target_arg])).filename();
 
             fi->u2b = new ucsc2bit(basename);// useses basename as prefix for filenames to mount: hg19.2bit -> hg19.2bit.fa
             fi->u2b->load(std::string(argv[mount_target_arg]));

src/lsfastafs.cpp

@@ -1,10 +1,12 @@
 #include <filesystem>
+#include <iostream>
 #include <string.h>
 #include <sys/xattr.h>
 
 #include <unordered_map>
 #include <vector>
 
+#include "utils.hpp"
 #include "config.hpp"
 
 
@@ -57,7 +59,11 @@ std::unordered_multimap<std::string, std::pair<std::string, std::string> > get_f
             strstr(mount_dir, arg) != NULL)) {
 
             std::string fn = std::string(mount_dir);
-            std::string basename = std::filesystem::path(fn).filename();
+
+            std::string basename = basename_cpp(fn);
+            //std::string basename = std::filesystem::path(fn).filename();
+            //std::cout << "basename: " << basename << "\n";
+
             std::string dict_fn = std::string(mount_dir)  + "/" +  basename +  ".dict";
 
             if(getxattr(mount_dir, FASTAFS_FILE_XATTR_NAME.c_str(), xattr_fastafs_file, 255) != -1

src/ucsc2bit.cpp

@@ -239,7 +239,8 @@ void ucsc2bit::load(std::string afilename)
     if(file.is_open()) {
         // if a user can't compile this line, please replace it with C's
         // 'realpath' function and delete/free afterwards and send a PR
-        this->filename = std::filesystem::canonical(afilename);// this path must be absolute because if stuff gets send to FUSE, paths are relative to the FUSE process and probably systemd initialization
+        //this->filename = std::filesystem::canonical(afilename);// this path must be absolute because if stuff gets send to FUSE, paths are relative to the FUSE process and probably systemd initialization
+        this->filename = realpath_cpp(afilename);
 
         if(file.tellg() < 16) {
             file.close();

src/utils.cpp

@@ -1,4 +1,6 @@
 
+#include <libgen.h>
+#include <string.h>
 #include <iostream>
 
 #include <openssl/sha.h>
@@ -170,3 +172,32 @@ bool is_fasta_file(char *filename)
     return false;
 }
 
+
+// https://www.systutorials.com/241216/how-to-get-the-directory-path-and-file-name-from-a-absolute-path-in-c-on-linux/
+// https://stackoverflow.com/questions/38456127/what-is-the-value-of-cplusplus-for-c17 - THEN use std::filesystem::path(filename).filename();
+std::string basename_cpp(std::string fn) {
+	char* ts = strdup(fn.c_str());
+
+	//char* dir = dirname(ts1);
+	char* filename = basename(ts);
+	//std::string filenamepp = std::string(filename);
+
+	//printf("basename: [%s]\n", filename);
+	//std::cout << "basenamepp: |" << filenamepp << "|\n";
+
+	return std::string(filename);
+}
+
+
+// https://www.linuxquestions.org/questions/programming-9/how-to-get-the-full-path-of-a-file-in-c-841046/
+// https://stackoverflow.com/questions/38456127/what-is-the-value-of-cplusplus-for-c17 - THEN use std::filesystem::canonical(filename)
+std::string realpath_cpp(std::string fn) {
+	//std::string out = "asd";
+	char *path = realpath(fn.c_str(), NULL);
+	//printf("realpath: [%s]\n", path);
+
+	//std::string realpathpp = std::string(path);
+	//std::cout << "realpath: |" << realpathpp << "|\n";
+
+	return std::string(path);
+}