10 #include <sys/socket.h>
13 static int socket_wait(int fd, int is_read)
15 fd_set fds, *fdr = 0, *fdw = 0;
18 tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
21 if (is_read) fdr = &fds;
23 ret = select(fd+1, fdr, fdw, 0, &tv);
24 if (ret == -1) perror("select");
28 static int socket_connect(const char *host, const char *port)
30 #define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
33 struct linger lng = { 0, 0 };
34 struct addrinfo hints, *res;
35 memset(&hints, 0, sizeof(struct addrinfo));
36 hints.ai_family = AF_UNSPEC;
37 hints.ai_socktype = SOCK_STREAM;
38 if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
39 if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
40 if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
41 if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
42 if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
47 static off_t my_read(int fd, void *buf, off_t len)
49 off_t rest = len, curr, l = 0;
51 if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
52 curr = read(fd, buf + l, rest);
54 l += curr; rest -= curr;
59 /*************************
60 * FTP specific routines *
61 *************************/
63 static int kftp_get_response(knetFile *ftp)
68 if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
69 while (read(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
71 if (n >= ftp->max_response) {
72 ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
73 ftp->response = realloc(ftp->response, ftp->max_response);
75 ftp->response[n++] = c;
77 if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
78 && ftp->response[3] != '-') break;
84 ftp->response[n-2] = 0;
85 return strtol(ftp->response, &p, 0);
88 static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
90 if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
91 write(ftp->ctrl_fd, cmd, strlen(cmd));
92 return is_get? kftp_get_response(ftp) : 0;
95 static int kftp_pasv_prep(knetFile *ftp)
99 kftp_send_cmd(ftp, "PASV\r\n", 1);
100 for (p = ftp->response; *p && *p != '('; ++p);
101 if (*p != '(') return -1;
103 sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
104 memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
105 ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
110 static int kftp_pasv_connect(knetFile *ftp)
112 char host[80], port[10];
113 if (ftp->pasv_port == 0) {
114 fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
117 sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
118 sprintf(port, "%d", ftp->pasv_port);
119 ftp->fd = socket_connect(host, port);
120 if (ftp->fd == -1) return -1;
124 int kftp_connect(knetFile *ftp)
126 ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
127 if (ftp->ctrl_fd == -1) return -1;
128 kftp_get_response(ftp);
129 kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
130 kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
131 kftp_send_cmd(ftp, "TYPE I\r\n", 1);
135 int kftp_reconnect(knetFile *ftp)
137 if (ftp->ctrl_fd >= 0) {
142 return kftp_connect(ftp);
145 // initialize ->type, ->host and ->retr
146 knetFile *kftp_parse_url(const char *fn, const char *mode)
151 if (strstr(fn, "ftp://") != fn) return 0;
152 for (p = (char*)fn + 6; *p && *p != '/'; ++p);
153 if (*p != '/') return 0;
155 fp = calloc(1, sizeof(knetFile));
156 fp->type = KNF_TYPE_FTP;
158 fp->port = strdup("ftp");
159 fp->host = calloc(l + 1, 1);
160 if (strchr(mode, 'c')) fp->no_reconnect = 1;
161 strncpy(fp->host, fn + 6, l);
162 fp->retr = calloc(strlen(p) + 8, 1);
163 sprintf(fp->retr, "RETR %s\r\n", p);
164 fp->seek_offset = -1;
167 // place ->fd at offset off
168 int kftp_connect_file(knetFile *fp)
173 if (fp->no_reconnect) kftp_get_response(fp);
178 sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
179 kftp_send_cmd(fp, tmp, 1);
181 kftp_send_cmd(fp, fp->retr, 0);
182 kftp_pasv_connect(fp);
183 ret = kftp_get_response(fp);
185 fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
194 /**************************
195 * HTTP specific routines *
196 **************************/
198 knetFile *khttp_parse_url(const char *fn, const char *mode)
203 if (strstr(fn, "http://") != fn) return 0;
205 for (p = (char*)fn + 7; *p && *p != '/'; ++p);
207 fp = calloc(1, sizeof(knetFile));
208 fp->http_host = calloc(l + 1, 1);
209 strncpy(fp->http_host, fn + 7, l);
210 fp->http_host[l] = 0;
211 for (q = fp->http_host; *q && *q != ':'; ++q);
212 if (*q == ':') *q++ = 0;
214 proxy = getenv("http_proxy");
215 // set ->host, ->port and ->path
217 fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
218 fp->port = strdup(*q? q : "http");
219 fp->path = strdup(*p? p : "/");
221 fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
222 for (q = fp->host; *q && *q != ':'; ++q);
223 if (*q == ':') *q++ = 0;
224 fp->port = strdup(*q? q : "http");
225 fp->path = strdup(fn);
227 fp->type = KNF_TYPE_HTTP;
228 fp->ctrl_fd = fp->fd = -1;
229 fp->seek_offset = -1;
233 int khttp_connect_file(knetFile *fp)
237 if (fp->fd >= 0) close(fp->fd);
238 fp->fd = socket_connect(fp->host, fp->port);
239 buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
240 l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
242 l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
243 l += sprintf(buf + l, "\r\n");
244 write(fp->fd, buf, l);
246 while (read(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
247 if (buf[l] == '\n' && l >= 3)
248 if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
252 if (l < 14) { // prematured header
257 ret = strtol(buf + 8, &p, 0); // HTTP return code
258 if (ret == 200 && fp->offset) { // 200 (complete result); then skip beginning of the file
259 off_t rest = fp->offset;
261 off_t l = rest < 0x10000? rest : 0x10000;
262 rest -= my_read(fp->fd, buf, l);
264 } else if (ret != 206 && ret != 200) {
266 fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
276 /********************
278 ********************/
280 knetFile *knet_open(const char *fn, const char *mode)
283 if (mode[0] != 'r') {
284 fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
287 if (strstr(fn, "ftp://") == fn) {
288 fp = kftp_parse_url(fn, mode);
289 if (fp == 0) return 0;
290 if (kftp_connect(fp) == -1) {
294 kftp_connect_file(fp);
295 } else if (strstr(fn, "http://") == fn) {
296 fp = khttp_parse_url(fn, mode);
297 if (fp == 0) return 0;
298 khttp_connect_file(fp);
299 } else { // local file
300 int fd = open(fn, O_RDONLY);
305 fp = (knetFile*)calloc(1, sizeof(knetFile));
306 fp->type = KNF_TYPE_LOCAL;
310 if (fp && fp->fd < 0) {
317 knetFile *knet_dopen(int fd, const char *mode)
319 knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
320 fp->type = KNF_TYPE_LOCAL;
325 off_t knet_read(knetFile *fp, void *buf, off_t len)
328 if (fp->fd < 0) return 0;
329 if (fp->type == KNF_TYPE_FTP) {
330 if (fp->is_ready == 0) {
331 if (!fp->no_reconnect) kftp_reconnect(fp);
332 kftp_connect_file(fp);
334 } else if (fp->type == KNF_TYPE_HTTP) {
335 if (fp->is_ready == 0)
336 khttp_connect_file(fp);
338 l = my_read(fp->fd, buf, len);
343 int knet_seek(knetFile *fp, off_t off, int whence)
345 if (whence == SEEK_SET && off == fp->offset) return 0;
346 if (fp->type == KNF_TYPE_LOCAL) {
347 off_t offset = lseek(fp->fd, off, whence);
354 } else if (fp->type == KNF_TYPE_FTP || fp->type == KNF_TYPE_HTTP) {
355 if (whence != SEEK_SET) { // FIXME: we can surely allow SEEK_CUR and SEEK_END in future
356 fprintf(stderr, "[knet_seek] only SEEK_SET is supported for FTP/HTTP. Offset is unchanged.\n");
366 int knet_close(knetFile *fp)
368 if (fp == 0) return 0;
369 if (fp->ctrl_fd >= 0) close(fp->ctrl_fd); // FTP specific
370 if (fp->fd >= 0) close(fp->fd);
371 free(fp->host); free(fp->port);
372 free(fp->response); free(fp->retr); // FTP specific
373 free(fp->path); free(fp->http_host); // HTTP specific
384 buf = calloc(0x100000, 1);
386 fp = knet_open("knetfile.c", "r");
387 knet_seek(fp, 1000, SEEK_SET);
388 } else if (type == 1) { // NCBI FTP, large file
389 fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
390 knet_seek(fp, 2500000000ll, SEEK_SET);
391 l = knet_read(fp, buf, 255);
392 } else if (type == 2) {
393 fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
394 knet_seek(fp, 1000, SEEK_SET);
395 } else if (type == 3) {
396 fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
397 knet_seek(fp, 1000, SEEK_SET);
398 } else if (type == 4) {
399 fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
400 knet_read(fp, buf, 10000);
401 knet_seek(fp, 20000, SEEK_SET);
402 knet_seek(fp, 10000, SEEK_SET);
403 l = knet_read(fp, buf+10000, 10000000) + 10000;
405 if (type != 4 && type != 1) {
406 knet_read(fp, buf, 255);
409 } else write(fileno(stdout), buf, l);