Merge pull request #45 from yhoogstrate/new_args_and_mount_with_fstab

New args and mount with fstab

CMakeLists.txt

@@ -8,7 +8,7 @@ project(fastafs)
 # Do this once in a while - find different bugs
 #set(CMAKE_CXX_COMPILER             "clang++")
 
-set(PROJECT_VERSION "1.6.1")
+set(PROJECT_VERSION "1.6.2")
 set(PACKAGE_URL "https://github.com/yhoogstrate/fastafs")
 set(PACKAGE_BUGREPORT "${PACKAGE_URL}/issues")
 
@@ -110,9 +110,23 @@ add_executable(fastafs
 					src/fuse.cpp
 					src/lsfastafs.cpp
 				)
-
 set_target_properties(fastafs PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${BUILD_DIR}")
 
+# mount-only binary, without all the other stuff 'mount.fastafs' [for fstab]
+add_executable(mount.fastafs
+					src/main_mount.cpp
+					src/fasta_to_fastafs.cpp
+					src/ucsc2bit_to_fastafs.cpp
+					src/fastafs.cpp
+					src/ucsc2bit.cpp
+					src/twobit_byte.cpp
+					src/database.cpp
+					src/utils.cpp
+					src/fuse.cpp
+					src/lsfastafs.cpp
+				)
+set_target_properties(mount.fastafs PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${BUILD_DIR}")
+
 add_library(libfastafs SHARED
 					src/fasta_to_fastafs.cpp
 					src/ucsc2bit_to_fastafs.cpp
@@ -166,6 +180,7 @@ add_test(test_utils               "${BUILD_TEST_DIR}/test_utils")
 
 # The compiled binary, usually to: /usr/local/bin/fastafs
 install(TARGETS fastafs DESTINATION "bin")
+install(TARGETS mount.fastafs DESTINATION "bin")
 install(TARGETS libfastafs LIBRARY DESTINATION "lib" PUBLIC_HEADER DESTINATION "include/libfastafs")
 
 # ----------------------------------------------------------------------

Changelog

@@ -1,3 +1,10 @@
+2019-09-06  Youri Hoogstrate
+
+    * v1.6.2
+    * Rewritten argument parsing of fuse/mounting
+    * Added binary `mount.fastafs` only for mounting, wihtout the toolkit
+    * `fastafs --version` will now also output whether the binary was compiled as debug or release.
+
 2019-08-21  Youri Hoogstrate
 
     * v1.6.1

README.md

@@ -19,7 +19,7 @@ Here we propose a solution; a mixture of 2bit compression and random on FASTA ve
 FASTAFS is compatible with 2bit files but 2bit has some limitations and does for instance not allow mounting DICT files needed for CRAM and Picard tools. The 2bit files can be convert to FASTAFS and, more importantly, a mounted FASTAFS mountpoint will not only virtualize the FASTA but also the 2bit file. Is FASTAFS this famous 15th standard (<https://xkcd.com/927/>)?
 Partially, but it is not designed to replace FASTA nor 2bit as those mountpoints should be used as flat files did before and the  virtualization of dict files is not possible when we mount 2bit files.
 
-## installation and compilation
+## Installation and compilation
 
 Currently the package uses cmake for compilation
 Required dependencies are:
@@ -165,6 +165,30 @@ aaaa
 c
 ```
 
+### Find all running `fastafs mount` / `mount.fastafs` instances
+
+The output format of `fastafs ps` is: `<pid>\t<source>\t<destination>\n`
+
+```
+$ fastafs ps
+16383	/home/youri/.local/share/fastafs/test.fastafs	/mnt/tmp
+```
+
+### Mounting via fstab (for instance on linux boot)
+
+You can add the following line(s) to /etc/fstab to make fastafs mount during boot:
+
+```
+mount.fastafs#/home/youri/.local/share/fastafs/hg19.fastafs /mnt/fastafs/hg19 fuse auto,allow_other 0 0
+```
+
+Here `mount.fastafs` refers to the binary that only does mounting, without the rest of the toolkit.
+This is followed by a hash-tag and the path of the desired fastafs file. The next value is the mount point followed by the argument indicating it runs fuse.
+The `auto,allow_other` refers to the `-o` argument.
+Here `auto` ensures it is mounted automatically after boot.
+Given that a system mounts as root user, the default permission of the mount point will be only for root. 
+By setting `allow_other`, file system users get permissions to the mountpoint.
+
 ## Contributing
 Feel free to start a discussion or to contribute to the GPL licensed code.
 

src/fuse.cpp

@@ -230,8 +230,9 @@ static int do_getxattr(const char* path, const char* name, char* value, size_t s
             sprintf(mypid, "%d", getpid());
             size_t pid_size = (size_t) strlen(mypid);
 
+
             if(size > pid_size) {
-                strncpy(value,  mypid, pid_size);
+                strcpy(value,  mypid);// if statement makes strncpy unneeded
                 value[pid_size] = '\0';
 
                 return (int) pid_size + 1;
@@ -328,9 +329,11 @@ fuse_operations operations  = {
 
 
 
+
 void print_fuse_help()
 {
-    std::cout << "usage: fasfafs <mount: fastafs UID> <mountpoint> [options]\n";
+    std::cout << "usage: fasfafs mount <mount: fastafs UID> <mountpoint> [options]\n";
+    std::cout << "usage: mount.fastafs <mount: fastafs UID> <mountpoint> [options]\n";
     std::cout << "\n";
     std::cout << "general options:\n";
     std::cout << "    -2   --2bit            virtualise a 2bit file rather than FASTAFS UID\n";
@@ -410,59 +413,96 @@ fuse_instance *parse_args(int argc, char **argv, char **argv_fuse)
 
     fuse_instance *fi = new fuse_instance({nullptr, nullptr, true, nullptr, 60, 0});
 
-    //printf("argc=%i",argc);
+    //fuse option variable to send to fuse
     argv_fuse[fi->argc_fuse++] = (char *) "fastafs"; // becomes fuse.fastafs
 
-    //fi->argv_fuse[0] = argv[0];
-    //fi->argv_fuse[1] = argv[1];
-    int i = 2;
-    while(i < argc) {
-        printf("processing argv[%i] = '%s';\n", i, argv[i]);
-        if(i < argc - 3) { // all arguments that take 2 arguments "--p", "50"
-            if(strcmp(argv[i], "-p") == 0 or strcmp(argv[i], "--padding") == 0) {
-                try {
-                    sscanf(argv[++i], "%u", &fi->padding);
-                } catch(std::exception const & e) {
-                    std::cerr << "ERROR: invalid padding value, must be integer value ranging from 0 to max-int size\n";
-                    exit(1);
+    std::vector<char*> fuse_options = {}; // those that need to be appended later
+
+    char current_argument = '\0';// could be o for '-o', etc.
+
+    std::vector<int> full_args = {};
+    for(unsigned int i = 0; i < argc; ++i) {
+        printf("processing argv[%i] = '%s'     [current argument=%i]\n", i, argv[i], (int) current_argument);
+
+        if(current_argument != '\0') { // parse the arguments' value
+            switch(current_argument) {
+            case 'p': // scanning padding value
+                if(!sscanf(argv[i], "%u", &fi->padding)) {
+                    throw std::invalid_argument("Invalid argument (padding value): " + std::string(argv[i]));
                 }
-            } else { // arguments that need to be send to fuse
-                //argv_test[fi->argc_fuse] = argv[i];
-                argv_fuse[fi->argc_fuse++] = argv[i];
+                break;
+            default:
+                //throw std::invalid_argument("Invalid argument: " + std::string(argv[i]));
+                fuse_options.push_back(argv[i]); // could be values that correspond to fuse arguments, such as: -o, -f, etc.
+                break;
+            }
+
+            current_argument = '\0';// reset
+        } else if(argv[i][0] == '-') {
+            if(strlen(argv[i]) == 1) {
+                throw std::invalid_argument("Invalid argument: " + std::string(argv[i]));
             }
-        } else if(i < argc - 2) { // all arguments that one argument "--lowercase" switches etc
-            if(strcmp(argv[i], "-2") == 0 or strcmp(argv[i], "--2bit") == 0) {
+
+            switch(argv[i][1]) {
+            case '2': // a fastafs specific flag
                 fi->from_fastafs = false;
-            } else { // arguments that need to be send to fuse
-                //argv_test[fi->argc_fuse] = argv[i];
-                argv_fuse[fi->argc_fuse++] = argv[i];
+                break;
+
+            case 'f': // fuse specific flags
+            case 's':
+            case 'd':
+                fuse_options.push_back(argv[i]);
+                break;
+
+            case 'o': // argument, fuse specific
+                current_argument = argv[i][1];
+                fuse_options.push_back(argv[i]); // fuse specific
+                break;
+
+            default: // argument, fastafs spcific (such as '-p' followed by '50')
+                current_argument = argv[i][1];
+                break;
             }
-        } else if(i == argc - 2) { // this refers to the fastafs object
-            if(fi->from_fastafs) {
-                database d = database();
-                std::string fname = d.get(argv[i]);
-
-                if(fname.size() == 0) { // invalid mount argument, don't bind fastafs object
-                    print_fuse_help();
-                    exit(1);
-                } else { // valid fastafs and bind fastafs object
-                    fi->f = new fastafs(std::string(argv[i]));
-                    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[i])).filename();
+        } else {
+            full_args.push_back(i); // args such as 'sudo', 'fastafs' 'fastafs-uid' and '/mount/point' of which only the last 2 are needed
+        }
+    }
 
-                fi->u2b = new ucsc2bit(basename);// useses basename as prefix for filenames to mount: hg19.2bit -> hg19.2bit.fa
-                fi->u2b->load(std::string(argv[i]));
+    if(full_args.size() >= 2) {
+        int mount_target_arg = full_args[full_args.size() - 2 ]; // last two arguments are <fastafs file> and <mount point>, location to last 2 args not starting with --/- are in this vector
+
+        if(fi->from_fastafs) {
+            database d = database();
+            std::string fname = d.get(argv[mount_target_arg]);
+
+            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();
+
+                // remove .fastafs suffix
+                size_t lastindex = name.find_last_of(".");
+                name = name.substr(0, lastindex);
+
+            } else {
+                name = std::string(argv[mount_target_arg]);
             }
-        } else { // mountpoint
-            //argv_test[fi->argc_fuse] = argv[i];
-            argv_fuse[fi->argc_fuse++] = argv[i];
+
+            fi->f = new fastafs(name);
+            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();
+
+            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]));
         }
 
-        i++;
+        //argv_fuse[fi->argc_fuse++] = argv[mount_target_arg];
+        argv_fuse[fi->argc_fuse++] = argv[mount_target_arg + 1];
+        for(size_t j = 0; j < fuse_options.size(); j++) {
+            argv_fuse[fi->argc_fuse++] = fuse_options[j];
+        }
     }
 
     return fi;
@@ -504,6 +544,3 @@ void fuse(int argc, char *argv[])
     //http://www.maastaar.net/fuse/linux/filesystem/c/2016/05/21/writing-a-simple-filesystem-using-fuse/
 }
 
-
-
-

src/main.cpp

@@ -77,7 +77,12 @@ int main(int argc, char *argv[])
         if(strcmp(argv[1], "--help") == 0 or strcmp(argv[1], "-h") == 0) {
             usage();
         } else if(strcmp(argv[1], "--version") == 0) {
-            std::cout << PACKAGE << " v" << PACKAGE_VERSION << GIT_SHA1_STRING << "\n\n";
+#if DEBUG
+            std::cout << PACKAGE << " v" << PACKAGE_VERSION << GIT_SHA1_STRING << "-debug\n\n";
+#else
+            std::cout << PACKAGE << " v" << PACKAGE_VERSION << GIT_SHA1_STRING << "-release\n\n";
+#endif //DEBUG
+
             std::cout << "Copyright (C) 2017 Youri Hoogstrate." << "\n";
             std::cout << "License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/gpl.html>.\n";
             std::cout << "This is free software: you are free to change and redistribute it.\n";

src/main_mount.cpp

@@ -0,0 +1,13 @@
+
+#include <iostream>
+
+#include "config.hpp"
+#include "fuse.hpp"
+
+int main(int argc, char *argv[])
+{
+    fuse(argc, argv);
+
+    return 0;
+}
+