+++ /dev/null
-/* The MIT License
-
- Copyright (c) 2008 Genome Research Ltd (GRL).
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Contact: Heng Li <lh3@sanger.ac.uk> */
-
-/* Probably I will not do socket programming in the next few years and
- therefore I decide to heavily annotate this file, for Linux and
- Windows as well. -lh3 */
-
-#include <time.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
-#include <errno.h>
-#include <unistd.h>
-#include <sys/types.h>
-
-#ifndef _WIN32
-#include <netdb.h>
-#include <arpa/inet.h>
-#include <sys/socket.h>
-#endif
-
-#include "knetfile.h"
-
-/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
- * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
- * integer -1. In knetfile.c, I use "int" for socket type
- * throughout. This should be improved to avoid confusion.
- *
- * In Linux/Mac, recv() and read() do almost the same thing. You can see
- * in the header file that netread() is simply an alias of read(). In
- * Windows, however, they are different and using recv() is mandatory.
- */
-
-/* This function tests if the file handler is ready for reading (or
- * writing if is_read==0). */
-static int socket_wait(int fd, int is_read)
-{
- fd_set fds, *fdr = 0, *fdw = 0;
- struct timeval tv;
- int ret;
- tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
- FD_ZERO(&fds);
- FD_SET(fd, &fds);
- if (is_read) fdr = &fds;
- else fdw = &fds;
- ret = select(fd+1, fdr, fdw, 0, &tv);
-#ifndef _WIN32
- if (ret == -1) perror("select");
-#else
- if (ret == 0)
- fprintf(stderr, "select time-out\n");
- else if (ret == SOCKET_ERROR)
- fprintf(stderr, "select: %d\n", WSAGetLastError());
-#endif
- return ret;
-}
-
-#ifndef _WIN32
-/* This function does not work with Windows due to the lack of
- * getaddrinfo() in winsock. It is addapted from an example in "Beej's
- * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
-static int socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
-
- int on = 1, fd;
- struct linger lng = { 0, 0 };
- struct addrinfo hints, *res;
- memset(&hints, 0, sizeof(struct addrinfo));
- hints.ai_family = AF_UNSPEC;
- hints.ai_socktype = SOCK_STREAM;
- /* In Unix/Mac, getaddrinfo() is the most convenient way to get
- * server information. */
- if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
- if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
- /* The following two setsockopt() are used by ftplib
- * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
- * necessary. */
- if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
- if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
- if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
- freeaddrinfo(res);
- return fd;
-}
-#else
-/* MinGW's printf has problem with "%lld" */
-char *int64tostr(char *buf, int64_t x)
-{
- int cnt;
- int i = 0;
- do {
- buf[i++] = '0' + x % 10;
- x /= 10;
- } while (x);
- buf[i] = 0;
- for (cnt = i, i = 0; i < cnt/2; ++i) {
- int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
- }
- return buf;
-}
-
-int64_t strtoint64(const char *buf)
-{
- int64_t x;
- for (x = 0; *buf != '\0'; ++buf)
- x = x * 10 + ((int64_t) *buf - 48);
- return x;
-}
-/* In windows, the first thing is to establish the TCP connection. */
-int knet_win32_init()
-{
- WSADATA wsaData;
- return WSAStartup(MAKEWORD(2, 2), &wsaData);
-}
-void knet_win32_destroy()
-{
- WSACleanup();
-}
-/* A slightly modfied version of the following function also works on
- * Mac (and presummably Linux). However, this function is not stable on
- * my Mac. It sometimes works fine but sometimes does not. Therefore for
- * non-Windows OS, I do not use this one. */
-static SOCKET socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func) \
- do { \
- fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \
- return -1; \
- } while (0)
-
- int on = 1;
- SOCKET fd;
- struct linger lng = { 0, 0 };
- struct sockaddr_in server;
- struct hostent *hp = 0;
- // open socket
- if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
- if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
- if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
- // get host info
- if (isalpha(host[0])) hp = gethostbyname(host);
- else {
- struct in_addr addr;
- addr.s_addr = inet_addr(host);
- hp = gethostbyaddr((char*)&addr, 4, AF_INET);
- }
- if (hp == 0) __err_connect("gethost");
- // connect
- server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
- server.sin_family= AF_INET;
- server.sin_port = htons(atoi(port));
- if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
- // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
- return fd;
-}
-#endif
-
-static off_t my_netread(int fd, void *buf, off_t len)
-{
- off_t rest = len, curr, l = 0;
- /* recv() and read() may not read the required length of data with
- * one call. They have to be called repeatedly. */
- while (rest) {
- if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
- curr = netread(fd, buf + l, rest);
- /* According to the glibc manual, section 13.2, a zero returned
- * value indicates end-of-file (EOF), which should mean that
- * read() will not return zero if EOF has not been met but data
- * are not immediately available. */
- if (curr == 0) break;
- l += curr; rest -= curr;
- }
- return l;
-}
-
-/*************************
- * FTP specific routines *
- *************************/
-
-static int kftp_get_response(knetFile *ftp)
-{
-#ifndef _WIN32
- unsigned char c;
-#else
- char c;
-#endif
- int n = 0;
- char *p;
- if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
- while (netread(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)
-{
- if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
- netwrite(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)
-{
- 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;
- }
- 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);
- ftp->fd = socket_connect(host, port);
- if (ftp->fd == -1) return -1;
- return 0;
-}
-
-int kftp_connect(knetFile *ftp)
-{
- ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
- if (ftp->ctrl_fd == -1) return -1;
- kftp_get_response(ftp);
- 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 != -1) {
- netclose(ftp->ctrl_fd);
- ftp->ctrl_fd = -1;
- }
- netclose(ftp->fd);
- ftp->fd = -1;
- return kftp_connect(ftp);
-}
-
-// initialize ->type, ->host, ->retr and ->size
-knetFile *kftp_parse_url(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->fd = -1;
- /* the Linux/Mac version of socket_connect() also recognizes a port
- * like "ftp", but the Windows version does not. */
- fp->port = strdup("21");
- 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) + 8, 1);
- sprintf(fp->retr, "RETR %s\r\n", p);
- fp->size_cmd = calloc(strlen(p) + 8, 1);
- sprintf(fp->size_cmd, "SIZE %s\r\n", p);
- fp->seek_offset = 0;
- return fp;
-}
-// place ->fd at offset off
-int kftp_connect_file(knetFile *fp)
-{
- int ret;
- long long file_size;
- if (fp->fd != -1) {
- netclose(fp->fd);
- if (fp->no_reconnect) kftp_get_response(fp);
- }
- kftp_pasv_prep(fp);
- kftp_send_cmd(fp, fp->size_cmd, 1);
-#ifndef _WIN32
- if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
- {
- fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
- return -1;
- }
-#else
- const char *p = fp->response;
- while (*p != ' ') ++p;
- while (*p < '0' || *p > '9') ++p;
- file_size = strtoint64(p);
-#endif
- fp->file_size = file_size;
- if (fp->offset>=0) {
- char tmp[32];
-#ifndef _WIN32
- sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
-#else
- strcpy(tmp, "REST ");
- int64tostr(tmp + 5, fp->offset);
- strcat(tmp, "\r\n");
-#endif
- kftp_send_cmd(fp, tmp, 1);
- }
- kftp_send_cmd(fp, fp->retr, 0);
- kftp_pasv_connect(fp);
- ret = kftp_get_response(fp);
- if (ret != 150) {
- fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
- netclose(fp->fd);
- fp->fd = -1;
- return -1;
- }
- fp->is_ready = 1;
- return 0;
-}
-
-
-/**************************
- * HTTP specific routines *
- **************************/
-
-knetFile *khttp_parse_url(const char *fn, const char *mode)
-{
- knetFile *fp;
- char *p, *proxy, *q;
- int l;
- if (strstr(fn, "http://") != fn) return 0;
- // set ->http_host
- for (p = (char*)fn + 7; *p && *p != '/'; ++p);
- l = p - fn - 7;
- fp = calloc(1, sizeof(knetFile));
- fp->http_host = calloc(l + 1, 1);
- strncpy(fp->http_host, fn + 7, l);
- fp->http_host[l] = 0;
- for (q = fp->http_host; *q && *q != ':'; ++q);
- if (*q == ':') *q++ = 0;
- // get http_proxy
- proxy = getenv("http_proxy");
- // set ->host, ->port and ->path
- if (proxy == 0) {
- fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
- fp->port = strdup(*q? q : "80");
- fp->path = strdup(*p? p : "/");
- } else {
- fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
- for (q = fp->host; *q && *q != ':'; ++q);
- if (*q == ':') *q++ = 0;
- fp->port = strdup(*q? q : "80");
- fp->path = strdup(fn);
- }
- fp->type = KNF_TYPE_HTTP;
- fp->ctrl_fd = fp->fd = -1;
- fp->seek_offset = 0;
- return fp;
-}
-
-int khttp_connect_file(knetFile *fp)
-{
- int ret, l = 0;
- char *buf, *p;
- if (fp->fd != -1) netclose(fp->fd);
- fp->fd = socket_connect(fp->host, fp->port);
- buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
- l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
- l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
- l += sprintf(buf + l, "\r\n");
- netwrite(fp->fd, buf, l);
- l = 0;
- while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
- if (buf[l] == '\n' && l >= 3)
- if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
- ++l;
- }
- buf[l] = 0;
- if (l < 14) { // prematured header
- netclose(fp->fd);
- fp->fd = -1;
- return -1;
- }
- ret = strtol(buf + 8, &p, 0); // HTTP return code
- if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
- off_t rest = fp->offset;
- while (rest) {
- off_t l = rest < 0x10000? rest : 0x10000;
- rest -= my_netread(fp->fd, buf, l);
- }
- } else if (ret != 206 && ret != 200) {
- free(buf);
- fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
- netclose(fp->fd);
- fp->fd = -1;
- return -1;
- }
- free(buf);
- fp->is_ready = 1;
- return 0;
-}
-
-/********************
- * Generic routines *
- ********************/
-
-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_parse_url(fn, mode);
- if (fp == 0) return 0;
- if (kftp_connect(fp) == -1) {
- knet_close(fp);
- return 0;
- }
- kftp_connect_file(fp);
- } else if (strstr(fn, "http://") == fn) {
- fp = khttp_parse_url(fn, mode);
- if (fp == 0) return 0;
- khttp_connect_file(fp);
- } else { // local file
-#ifdef _WIN32
- /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
- * be undefined on some systems, although it is defined on my
- * Mac and the Linux I have tested on. */
- int fd = open(fn, O_RDONLY | O_BINARY);
-#else
- int fd = open(fn, O_RDONLY);
-#endif
- if (fd == -1) {
- perror("open");
- return 0;
- }
- fp = (knetFile*)calloc(1, sizeof(knetFile));
- fp->type = KNF_TYPE_LOCAL;
- fp->fd = fd;
- fp->ctrl_fd = -1;
- }
- if (fp && fp->fd == -1) {
- knet_close(fp);
- return 0;
- }
- return fp;
-}
-
-knetFile *knet_dopen(int fd, const char *mode)
-{
- knetFile *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 = 0;
- if (fp->fd == -1) return 0;
- if (fp->type == KNF_TYPE_FTP) {
- if (fp->is_ready == 0) {
- if (!fp->no_reconnect) kftp_reconnect(fp);
- kftp_connect_file(fp);
- }
- } else if (fp->type == KNF_TYPE_HTTP) {
- if (fp->is_ready == 0)
- khttp_connect_file(fp);
- }
- if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
- off_t rest = len, curr;
- while (rest) {
- curr = read(fp->fd, buf + l, rest);
- if (curr == 0) break;
- l += curr; rest -= curr;
- }
- } else l = my_netread(fp->fd, buf, len);
- fp->offset += l;
- return l;
-}
-
-off_t knet_seek(knetFile *fp, int64_t off, int whence)
-{
- if (whence == SEEK_SET && off == fp->offset) return 0;
- if (fp->type == KNF_TYPE_LOCAL) {
- /* Be aware that lseek() returns the offset after seeking,
- * while fseek() returns zero on success. */
- off_t offset = lseek(fp->fd, off, whence);
- if (offset == -1) {
- // Be silent, it is OK for knet_seek to fail when the file is streamed
- // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
- return -1;
- }
- fp->offset = offset;
- return 0;
- }
- else if (fp->type == KNF_TYPE_FTP)
- {
- if (whence==SEEK_CUR)
- fp->offset += off;
- else if (whence==SEEK_SET)
- fp->offset = off;
- else if ( whence==SEEK_END)
- fp->offset = fp->file_size+off;
- fp->is_ready = 0;
- return 0;
- }
- else if (fp->type == KNF_TYPE_HTTP)
- {
- if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
- fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
- errno = ESPIPE;
- return -1;
- }
- if (whence==SEEK_CUR)
- fp->offset += off;
- else if (whence==SEEK_SET)
- fp->offset = off;
- fp->is_ready = 0;
- return 0;
- }
- errno = EINVAL;
- fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
- return -1;
-}
-
-int knet_close(knetFile *fp)
-{
- if (fp == 0) return 0;
- if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
- if (fp->fd != -1) {
- /* On Linux/Mac, netclose() is an alias of close(), but on
- * Windows, it is an alias of closesocket(). */
- if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
- else netclose(fp->fd);
- }
- free(fp->host); free(fp->port);
- free(fp->response); free(fp->retr); // FTP specific
- free(fp->path); free(fp->http_host); // HTTP specific
- free(fp);
- return 0;
-}
-
-#ifdef KNETFILE_MAIN
-int main(void)
-{
- char *buf;
- knetFile *fp;
- int type = 4, l;
-#ifdef _WIN32
- knet_win32_init();
-#endif
- buf = calloc(0x100000, 1);
- if (type == 0) {
- fp = knet_open("knetfile.c", "r");
- knet_seek(fp, 1000, SEEK_SET);
- } else if (type == 1) { // NCBI FTP, large file
- 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);
- l = knet_read(fp, buf, 255);
- } else if (type == 2) {
- fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
- knet_seek(fp, 1000, SEEK_SET);
- } else if (type == 3) {
- fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
- knet_seek(fp, 1000, SEEK_SET);
- } else if (type == 4) {
- fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
- knet_read(fp, buf, 10000);
- knet_seek(fp, 20000, SEEK_SET);
- knet_seek(fp, 10000, SEEK_SET);
- l = knet_read(fp, buf+10000, 10000000) + 10000;
- }
- if (type != 4 && type != 1) {
- knet_read(fp, buf, 255);
- buf[255] = 0;
- printf("%s\n", buf);
- } else write(fileno(stdout), buf, l);
- knet_close(fp);
- free(buf);
- return 0;
-}
-#endif
projects / pysam.git / blobdiff