--- /dev/null
+#include <stdio.h>
+#include <netdb.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <sys/types.h>
+#include <arpa/inet.h>
+#include <sys/socket.h>
+#include "knetfile.h"
+
+static int kftp_get_response(knetFile *ftp)
+{
+ unsigned char c;
+ int n = 0;
+ char *p;
+ while (read(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
+// fputc(c, stderr);
+ if (n >= ftp->max_response) {
+ ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
+ ftp->response = realloc(ftp->response, ftp->max_response);
+ }
+ ftp->response[n++] = c;
+ if (c == '\n') {
+ if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) && ftp->response[3] != '-') break;
+ n = 0;
+ continue;
+ }
+ }
+ if (n < 2) return -1;
+ ftp->response[n-2] = 0;
+ return strtol(ftp->response, &p, 0);
+}
+
+static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
+{
+ write(ftp->ctrl_fd, cmd, strlen(cmd));
+ return is_get? kftp_get_response(ftp) : 0;
+}
+
+static int kftp_pasv_prep(knetFile *ftp)
+{
+ char *p;
+ int v[6];
+ kftp_send_cmd(ftp, "PASV\r\n", 1);
+ for (p = ftp->response; *p && *p != '('; ++p);
+ if (*p != '(') return -1;
+ ++p;
+ sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
+ memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
+ ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
+ return 0;
+}
+
+static int kftp_pasv_connect(knetFile *ftp)
+{
+#define __err_pasv_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
+
+ struct addrinfo hints, *res;
+ struct linger lng = { 0, 0 };
+ int on;
+ char host[80], port[10];
+
+ if (ftp->pasv_port == 0) {
+ fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
+ return -1;
+ }
+ memset(&hints, 0, sizeof(struct addrinfo));
+ hints.ai_family = AF_UNSPEC;
+ hints.ai_socktype = SOCK_STREAM;
+ sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
+ sprintf(port, "%d", ftp->pasv_port);
+ if (getaddrinfo(host, port, &hints, &res) != 0) { perror("getaddrinfo"); return -1; }
+ if ((ftp->fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_pasv_connect("socket");
+ if (setsockopt(ftp->fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_pasv_connect("setsockopt");
+ if (setsockopt(ftp->fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_pasv_connect("setsockopt");
+ if (connect(ftp->fd, res->ai_addr, res->ai_addrlen) != 0) __err_pasv_connect("connect");
+ freeaddrinfo(res);
+ return 0;
+}
+
+int kftp_connect(knetFile *ftp)
+{
+#define __err_connect(func) do { perror(func); return -1; } while (0)
+
+ int on;
+ { // open socket
+ struct addrinfo hints, *res;
+ memset(&hints, 0, sizeof(struct addrinfo));
+ hints.ai_family = AF_UNSPEC;
+ hints.ai_socktype = SOCK_STREAM;
+ if (getaddrinfo(ftp->host, "21", &hints, &res) != 0) __err_connect("getaddrinfo");
+ if ((ftp->ctrl_fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
+ if (setsockopt(ftp->ctrl_fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
+ if (connect(ftp->ctrl_fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
+ freeaddrinfo(res);
+ kftp_get_response(ftp);
+ }
+ { // login
+ kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
+ kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
+ kftp_send_cmd(ftp, "TYPE I\r\n", 1);
+ }
+ return 0;
+}
+
+int kftp_reconnect(knetFile *ftp)
+{
+ if (ftp->ctrl_fd) {
+ close(ftp->ctrl_fd);
+ ftp->ctrl_fd = 0;
+ }
+ close(ftp->fd);
+ return kftp_connect(ftp);
+}
+
+// initialize ->type, ->host and ->retr
+knetFile *kftp_prep(const char *fn, const char *mode)
+{
+ knetFile *fp;
+ char *p;
+ int l;
+ if (strstr(fn, "ftp://") != fn) return 0;
+ for (p = (char*)fn + 6; *p && *p != '/'; ++p);
+ if (*p != '/') return 0;
+ l = p - fn - 6;
+ fp = calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_FTP;
+ fp->host = calloc(l + 1, 1);
+ if (strchr(mode, 'c')) fp->no_reconnect = 1;
+ strncpy(fp->host, fn + 6, l);
+ fp->retr = calloc(strlen(p) + 7, 1);
+ sprintf(fp->retr, "RETR %s\r\n", p);
+ return fp;
+}
+// place ->fd at offset off
+int kftp_connect_file(knetFile *fp, off_t off)
+{
+ if (fp->fd) {
+ close(fp->fd);
+ if (fp->no_reconnect) kftp_get_response(fp);
+ }
+ kftp_pasv_prep(fp);
+ if (off) {
+ char tmp[32];
+ sprintf(tmp, "REST %lld\r\n", (long long)off);
+ kftp_send_cmd(fp, tmp, 1);
+ }
+ kftp_send_cmd(fp, fp->retr, 0);
+ kftp_pasv_connect(fp);
+ kftp_get_response(fp);
+ fp->offset = off;
+ return 0;
+}
+
+knetFile *knet_open(const char *fn, const char *mode)
+{
+ knetFile *fp = 0;
+ if (mode[0] != 'r') {
+ fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
+ return 0;
+ }
+ if (strstr(fn, "ftp://") == fn) {
+ fp = kftp_prep(fn, mode);
+ if (fp == 0) return 0;
+ if (kftp_connect(fp) == -1) {
+ knet_close(fp);
+ return 0;
+ }
+ kftp_connect_file(fp, 0);
+ } else {
+ int fd = open(fn, O_RDONLY);
+ if (fd == -1) {
+ perror("open");
+ return 0;
+ }
+ fp = (knetFile*)calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_LOCAL;
+ fp->fd = fd;
+ }
+ return fp;
+}
+
+off_t knet_read(knetFile *fp, void *buf, off_t len)
+{
+ off_t l = read(fp->fd, buf, len);
+ fp->offset += l;
+ return l;
+}
+
+off_t knet_seek(knetFile *fp, off_t off, int whence)
+{
+ if (fp->type == KNF_TYPE_LOCAL) {
+ fp->offset = lseek(fp->fd, off, whence);
+ return fp->offset;
+ }
+ if (fp->type == KNF_TYPE_FTP) {
+ if (whence != SEEK_SET) {
+ fprintf(stderr, "[knet_seek] only SEEK_SET is supported for FTP. Offset is unchanged.\n");
+ return -1;
+ }
+ if (!fp->no_reconnect) kftp_reconnect(fp);
+ kftp_connect_file(fp, off);
+ return fp->offset;
+ }
+ return 0;
+}
+
+int knet_close(knetFile *fp)
+{
+ if (fp == 0) return 0;
+ if (fp->ctrl_fd > 0) close(fp->ctrl_fd);
+ if (fp->fd > 0) close(fp->fd);
+ free(fp->response); free(fp->retr); free(fp->host);
+ free(fp);
+ return 0;
+}
+
+#ifdef KNETFILE_MAIN
+int main(void)
+{
+ char buf[256];
+ knetFile *fp;
+// fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); knet_seek(fp, 2500000000ll, SEEK_SET);
+// fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); knet_seek(fp, 2000, SEEK_SET);
+ fp = knet_open("knetfile.c", "r"); knet_seek(fp, 2000, SEEK_SET);
+ knet_read(fp, buf, 255);
+ buf[255] = 0;
+ printf("%s\n", buf);
+ knet_close(fp);
+ return 0;
+}
+#endif
projects / samtools.git / commitdiff