+/* 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 "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;
}
#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)
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");
return fd;
}
#else
+/* In windows, the first thing is to establish the TCP connection. */
int knet_win32_init()
{
WSADATA wsaData;
{
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 { perror(func); return -1; } while (0)
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;
}
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;
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);
{
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) {
perror("lseek");
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);
}
projects / samtools.git / commitdiff