Diff 21214

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biology/bowtie2/Makefile

This file was added.

/*-

* SPDX-License-Identifier: BSD-2-Clause

* Redistribution and use in source and binary forms, with or without

* modification, are permitted provided that the following conditions

* are met:

* 1. Redistributions of source code must retain the above copyright

* notice, this list of conditions and the following disclaimer.

* 2. Redistributions in binary form must reproduce the above copyright

* notice, this list of conditions and the following disclaimer in the

* documentation and/or other materials provided with the distribution.

* THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND

* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE

* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL

* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS

* OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)

* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT

* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY

* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF

* SUCH DAMAGE.

#ifndef RESCUE

#include <sys/param.h>

#include <sys/ioctl.h>

#include <sys/socket.h>

#include <sys/sysctl.h>

#include <sys/time.h>

#include <sys/nv.h>

#include <net/ethernet.h>

#include <net/if.h>

#include <net/if_dl.h>

#include <net/if_types.h>

#include <net/if_media.h>

#include <net/route.h>

#include <netinet/in.h>

#include <arpa/inet.h>

#include <assert.h>

#include <ctype.h>

#include <err.h>

#include <errno.h>

#include <fcntl.h>

#include <inttypes.h>

#include <stdio.h>

#include <stdlib.h>

#include <netdb.h>

#include <string.h>

#include <unistd.h>

#include <stdarg.h>

#include <stddef.h> /* NB: for offsetof */

#include <locale.h>

#include <langinfo.h>

#include <resolv.h>

#include "ifconfig.h"

typedef enum {

WGC_GET = 0x5,

WGC_SET = 0x6,

} wg_cmd_t;

static nvlist_t *nvl_params;

static bool do_peer;

static int allowed_ips_count;

static int allowed_ips_max;

struct allowedip {

struct sockaddr_storage a_addr;

struct sockaddr_storage a_mask;

};

struct allowedip *allowed_ips;

hrsUnsubmitted

Done

I think a_addr and a_mask should be struct sockaddr_strorage, not sockaddr. While sizeof(sockaddr) can be equal to sizeof(sockaddr_in), sizeof(sockaddr_in6) is always longer.

hrs: I think a_addr and a_mask should be struct sockaddr_strorage, not sockaddr. While sizeof…

#define ALLOWEDIPS_START 16

#define WG_KEY_LEN 32

#define WG_KEY_LEN_BASE64 ((((WG_KEY_LEN) + 2) / 3) * 4 + 1)

#define WG_KEY_LEN_HEX (WG_KEY_LEN * 2 + 1)

#define WG_MAX_STRLEN 64

static bool

key_from_base64(uint8_t key[static WG_KEY_LEN], const char *base64)

{

if (strlen(base64) != WG_KEY_LEN_BASE64 - 1) {

warnx("bad key len - need %d got %lu\n", WG_KEY_LEN_BASE64 - 1, strlen(base64));

return false;

}

if (base64[WG_KEY_LEN_BASE64 - 2] != '=') {

warnx("bad key terminator, expected '=' got '%c'", base64[WG_KEY_LEN_BASE64 - 2]);

return false;

}

return (b64_pton(base64, key, WG_KEY_LEN));

}

static void

parse_endpoint(const char *endpoint_)

{

int err;

char *base, *endpoint, *port, *colon, *tmp;

struct addrinfo hints, *res;

endpoint = base = strdup(endpoint_);

colon = rindex(endpoint, ':');

if (colon == NULL)

errx(1, "bad endpoint format %s - no port delimiter found", endpoint);

*colon = '\0';

port = colon + 1;

/* [::]:<> */

hrsUnsubmitted

Done

I think we can reuse b64_{ntop,pton}() in libc.

hrs: I think we can reuse b64_{ntop,pton}() in libc.

if (endpoint[0] == '[') {

endpoint++;

tmp = index(endpoint, ']');

if (tmp == NULL)

errx(1, "bad endpoint format %s - '[' found with no matching ']'", endpoint);

*tmp = '\0';

}

bzero(&hints, sizeof(hints));

hints.ai_family = AF_UNSPEC;

err = getaddrinfo(endpoint, port, &hints, &res);

if (err)

errx(1, "%s", gai_strerror(err));

nvlist_add_binary(nvl_params, "endpoint", res->ai_addr, res->ai_addrlen);

freeaddrinfo(res);

free(base);

}

static void

in_len2mask(struct in_addr *mask, u_int len)

{

u_int i;

u_char *p;

p = (u_char *)mask;

memset(mask, 0, sizeof(*mask));

for (i = 0; i < len / NBBY; i++)

p[i] = 0xff;

if (len % NBBY)

p[i] = (0xff00 >> (len % NBBY)) & 0xff;

}

static u_int

in_mask2len(struct in_addr *mask)

{

u_int x, y;

u_char *p;

p = (u_char *)mask;

for (x = 0; x < sizeof(*mask); x++) {

if (p[x] != 0xff)

break;

}

y = 0;

if (x < sizeof(*mask)) {

for (y = 0; y < NBBY; y++) {

if ((p[x] & (0x80 >> y)) == 0)

break;

}

return x * NBBY + y;

}

static void

in6_prefixlen2mask(struct in6_addr *maskp, int len)

{

static const u_char maskarray[NBBY] = {0x80, 0xc0, 0xe0, 0xf0, 0xf8, 0xfc, 0xfe, 0xff};

int bytelen, bitlen, i;

/* sanity check */

if (len < 0 || len > 128) {

errx(1, "in6_prefixlen2mask: invalid prefix length(%d)\n",

len);

return;

}

memset(maskp, 0, sizeof(*maskp));

bytelen = len / NBBY;

bitlen = len % NBBY;

for (i = 0; i < bytelen; i++)

maskp->s6_addr[i] = 0xff;

if (bitlen)

maskp->s6_addr[bytelen] = maskarray[bitlen - 1];

}

static int

in6_mask2len(struct in6_addr *mask, u_char *lim0)

{

int x = 0, y;

u_char *lim = lim0, *p;

/* ignore the scope_id part */

if (lim0 == NULL || lim0 - (u_char *)mask > sizeof(*mask))

lim = (u_char *)mask + sizeof(*mask);

for (p = (u_char *)mask; p < lim; x++, p++) {

if (*p != 0xff)

break;

}

y = 0;

if (p < lim) {

for (y = 0; y < NBBY; y++) {

if ((*p & (0x80 >> y)) == 0)

break;

}

* when the limit pointer is given, do a stricter check on the

* remaining bits.

if (p < lim) {

if (y != 0 && (*p & (0x00ff >> y)) != 0)

return -1;

for (p = p + 1; p < lim; p++)

if (*p != 0)

return -1;

}

return x * NBBY + y;

}

static bool

parse_ip(struct allowedip *aip, const char *value)

{

hrsUnsubmitted

Done

This error message is odd because no address resolution is performed when AI_NUMERICHOST is specified. And values returned by getaddrinfo() are not compatible with ones in sysexits.h or errno, so they should not be used for errx() directly. The possible error codes are EAI_FAIL or EAI_MEMORY. "invalid address" is more descriptive for EAI_FAIL in this case, for example.

How about using "1" as the error code when err != 0 and gai_strerror(err) for the message?

hrs: This error message is odd because no address resolution is performed when AI_NUMERICHOST is…

struct addrinfo hints, *res;

int err;

bzero(&aip->a_addr, sizeof(aip->a_addr));

bzero(&hints, sizeof(hints));

hints.ai_family = AF_UNSPEC;

hints.ai_flags = AI_NUMERICHOST;

err = getaddrinfo(value, NULL, &hints, &res);

if (err)

errx(1, "%s", gai_strerror(err));

memcpy(&aip->a_addr, res->ai_addr, res->ai_addrlen);

freeaddrinfo(res);

return (true);

}

static void

sa_ntop(const struct sockaddr *sa, char *buf, int *port)

{

const struct sockaddr_in *sin;

const struct sockaddr_in6 *sin6;

int err;

err = getnameinfo(sa, sa->sa_len, buf, INET6_ADDRSTRLEN, NULL,

0, NI_NUMERICHOST);

if (sa->sa_family == AF_INET) {

sin = (const struct sockaddr_in *)sa;

if (port)

*port = sin->sin_port;

} else if (sa->sa_family == AF_INET6) {

sin6 = (const struct sockaddr_in6 *)sa;

if (port)

*port = sin6->sin6_port;

}

if (err)

errx(1, "%s", gai_strerror(err));

}

static void

hrsUnsubmitted

Not Done

How about reuse of in6_getprefix() in af_inet6.c?

hrs: How about reuse of in6_getprefix() in af_inet6.c?

mmacyAuthorUnsubmitted

Done

How about reuse of in6_getprefix() in af_inet6.c?

The interface is different enough that reusing it creates more work than it saves.

mmacy: > How about reuse of in6_getprefix() in af_inet6.c? The interface is different enough that…

dump_peer(const nvlist_t *nvl_peer)

{

const void *key;

const struct allowedip *aips;

const struct sockaddr *endpoint;

char outbuf[WG_MAX_STRLEN];

char addr_buf[INET6_ADDRSTRLEN];

size_t size;

int count, port;

printf("[Peer]\n");

if (nvlist_exists_binary(nvl_peer, "public-key")) {

key = nvlist_get_binary(nvl_peer, "public-key", &size);

b64_ntop((const uint8_t *)key, size, outbuf, WG_MAX_STRLEN);

printf("PublicKey = %s\n", outbuf);

}

if (nvlist_exists_binary(nvl_peer, "endpoint")) {

endpoint = nvlist_get_binary(nvl_peer, "endpoint", &size);

sa_ntop(endpoint, addr_buf, &port);

printf("Endpoint = %s:%d\n", addr_buf, ntohs(port));

}

if (!nvlist_exists_binary(nvl_peer, "allowed-ips"))

return;

aips = nvlist_get_binary(nvl_peer, "allowed-ips", &size);

if (size == 0 || size % sizeof(struct allowedip) != 0) {

errx(1, "size %zu not integer multiple of allowedip", size);

}

printf("AllowedIPs = ");

count = size / sizeof(struct allowedip);

for (int i = 0; i < count; i++) {

int mask;

sa_family_t family;

void *bitmask;

struct sockaddr *sa;

sa = __DECONST(void *, &aips[i].a_addr);

bitmask = __DECONST(void *,

((const struct sockaddr *)&aips->a_mask)->sa_data);

family = aips[i].a_addr.ss_family;

getnameinfo(sa, sa->sa_len, addr_buf, INET6_ADDRSTRLEN, NULL,

0, NI_NUMERICHOST);

sg2342_googlemail.comUnsubmitted

Not Done

struct sockaddr *sa;

- sa = __DECONST(void *, &aips->a_addr);

+ sa = __DECONST(void *, &aips[i].a_addr);

bitmask = __DECONST(void *,

sg2342_googlemail.com:

if (family == AF_INET)

mask = in_mask2len(bitmask);

else if (family == AF_INET6)

mask = in6_mask2len(bitmask, NULL);

else

errx(1, "bad family in peer %d\n", family);

printf("%s/%d", addr_buf, mask);

if (i < count -1)

printf(", ");

}

printf("\n");

}

static int

get_nvl_out_size(int sock, u_long op, size_t *size)

{

hrsUnsubmitted

Done

This should be done by getaddrinfo() with AI_NUMERICHOST, which is exactly for this purpose in an address-family independent fashion.

hrs: This should be done by getaddrinfo() with AI_NUMERICHOST, which is exactly for this purpose in…

struct ifdrv ifd;

int err;

memset(&ifd, 0, sizeof(ifd));

strlcpy(ifd.ifd_name, name, sizeof(ifd.ifd_name));

ifd.ifd_cmd = op;

ifd.ifd_len = 0;

ifd.ifd_data = NULL;

err = ioctl(sock, SIOCGDRVSPEC, &ifd);

if (err)

return (err);

*size = ifd.ifd_len;

return (0);

}

static int

do_cmd(int sock, u_long op, void *arg, size_t argsize, int set)

{

struct ifdrv ifd;

memset(&ifd, 0, sizeof(ifd));

hrsUnsubmitted

Not Done

This should be done by using getnameinfo(). inet_ntop() is not compatible with IPv6 scoped address, so care must be taken in sin6_scope_id. There is no need to consider such complexity when getnameinfo() is used.

hrs: This should be done by using getnameinfo(). inet_ntop() is not compatible with IPv6 scoped…

strlcpy(ifd.ifd_name, name, sizeof(ifd.ifd_name));

ifd.ifd_cmd = op;

ifd.ifd_len = argsize;

ifd.ifd_data = arg;

return (ioctl(sock, set ? SIOCSDRVSPEC : SIOCGDRVSPEC, &ifd));

}

static

DECL_CMD_FUNC(peerlist, val, d)

{

size_t size, peercount;

void *packed;

const nvlist_t *nvl, *nvl_peer;

const nvlist_t *const *nvl_peerlist;

if (get_nvl_out_size(s, WGC_GET, &size))

errx(1, "can't get peer list size");

if ((packed = malloc(size)) == NULL)

errx(1, "malloc failed for peer list");

if (do_cmd(s, WGC_GET, packed, size, 0))

errx(1, "failed to obtain peer list");

nvl = nvlist_unpack(packed, size, 0);

if (!nvlist_exists_nvlist_array(nvl, "peer-list"))

return;

nvl_peerlist = nvlist_get_nvlist_array(nvl, "peer-list", &peercount);

for (int i = 0; i < peercount; i++, nvl_peerlist++) {

nvl_peer = *nvl_peerlist;

dump_peer(nvl_peer);

}

static void

peerfinish(int s, void *arg)

{

nvlist_t *nvl, **nvl_array;

void *packed;

size_t size;

if ((nvl = nvlist_create(0)) == NULL)

errx(1, "failed to allocate nvlist");

if ((nvl_array = calloc(sizeof(void *), 1)) == NULL)

errx(1, "failed to allocate nvl_array");

if (!nvlist_exists_binary(nvl_params, "public-key"))

errx(1, "must specify a public-key for adding peer");

if (!nvlist_exists_binary(nvl_params, "endpoint"))

errx(1, "must specify an endpoint for adding peer");

if (allowed_ips_count == 0)

errx(1, "must specify at least one range of allowed-ips to add a peer");

nvl_array[0] = nvl_params;

nvlist_add_nvlist_array(nvl, "peer-list", (const nvlist_t * const *)nvl_array, 1);

packed = nvlist_pack(nvl, &size);

if (do_cmd(s, WGC_SET, packed, size, true))

errx(1, "failed to install peer");

}

static

DECL_CMD_FUNC(peerstart, val, d)

{

do_peer = true;

callback_register(peerfinish, NULL);

allowed_ips = malloc(ALLOWEDIPS_START * sizeof(struct allowedip));

allowed_ips_max = ALLOWEDIPS_START;

if (allowed_ips == NULL)

errx(1, "failed to allocate array for allowedips");

}

static

DECL_CMD_FUNC(setwglistenport, val, d)

{

struct addrinfo hints, *res;

const struct sockaddr_in *sin;

const struct sockaddr_in6 *sin6;

u_long ul;

int err;

bzero(&hints, sizeof(hints));

hints.ai_family = AF_UNSPEC;

hints.ai_flags = AI_NUMERICHOST;

err = getaddrinfo(NULL, val, &hints, &res);

if (err)

errx(1, "%s", gai_strerror(err));

if (res->ai_family == AF_INET) {

sin = (struct sockaddr_in *)res->ai_addr;

ul = sin->sin_port;

} else if (res->ai_family == AF_INET6) {

sin6 = (struct sockaddr_in6 *)res->ai_addr;

ul = sin6->sin6_port;

} else {

errx(1, "unknown family");

}

ul = ntohs((u_short)ul);

nvlist_add_number(nvl_params, "listen-port", ul);

}

static

DECL_CMD_FUNC(setwgprivkey, val, d)

{

uint8_t key[WG_KEY_LEN];

if (!key_from_base64(key, val))

errx(1, "invalid key %s", val);

nvlist_add_binary(nvl_params, "private-key", key, WG_KEY_LEN);

}

static

DECL_CMD_FUNC(setwgpubkey, val, d)

{

uint8_t key[WG_KEY_LEN];

if (!do_peer)

errx(1, "setting public key only valid when adding peer");

if (!key_from_base64(key, val))

errx(1, "invalid key %s", val);

nvlist_add_binary(nvl_params, "public-key", key, WG_KEY_LEN);

}

static

DECL_CMD_FUNC(setallowedips, val, d)

{

char *base, *allowedip, *mask;

u_long ul;

char *endp;

struct allowedip *aip;

if (!do_peer)

errx(1, "setting allowed ip only valid when adding peer");

if (allowed_ips_count == allowed_ips_max) {

/* XXX grow array */

}

aip = &allowed_ips[allowed_ips_count];

base = allowedip = strdup(val);

mask = index(allowedip, '/');

if (mask == NULL)

errx(1, "mask separator not found in allowedip %s", val);

*mask = '\0';

mask++;

parse_ip(aip, allowedip);

ul = strtoul(mask, &endp, 0);

if (*endp != '\0')

errx(1, "invalid value for allowedip mask");

bzero(&aip->a_mask, sizeof(aip->a_mask));

if (aip->a_addr.ss_family == AF_INET)

in_len2mask((struct in_addr *)&((struct sockaddr *)&aip->a_mask)->sa_data, ul);

else if (aip->a_addr.ss_family == AF_INET6)

in6_prefixlen2mask((struct in6_addr *)&((struct sockaddr *)&aip->a_mask)->sa_data, ul);

else

errx(1, "invalid address family %d\n", aip->a_addr.ss_family);

allowed_ips_count++;

if (allowed_ips_count > 1)

nvlist_free_binary(nvl_params, "allowed-ips");

nvlist_add_binary(nvl_params, "allowed-ips", allowed_ips,

allowed_ips_count*sizeof(*aip));

dump_peer(nvl_params);

free(base);

}

static

DECL_CMD_FUNC(setendpoint, val, d)

{

if (!do_peer)

errx(1, "setting endpoint only valid when adding peer");

parse_endpoint(val);

}

static void

wireguard_status(int s)

{

size_t size;

void *packed;

nvlist_t *nvl;

hrsUnsubmitted

Done

Resolving a port number when it is specified as a symbol should be supported for consistency with the other ifconfig(8) arguments. getaddrinfo() with no hostname works as a replacement of strtoul().

hrs: Resolving a port number when it is specified as a symbol should be supported for consistency…

char buf[WG_KEY_LEN_BASE64];

const void *key;

uint16_t listen_port;

if (get_nvl_out_size(s, WGC_GET, &size))

return;

if ((packed = malloc(size)) == NULL)

return;

if (do_cmd(s, WGC_GET, packed, size, 0))

return;

nvl = nvlist_unpack(packed, size, 0);

if (nvlist_exists_number(nvl, "listen-port")) {

listen_port = nvlist_get_number(nvl, "listen-port");

printf("\tlisten-port: %d\n", listen_port);

}

if (nvlist_exists_binary(nvl, "private-key")) {

sg2342_googlemail.comUnsubmitted

Not Done

Why? it breaks "ifconfig wgX name" and the other *_status implementations in ifconfig seem to be content with just failing the ioctl.

sg2342_googlemail.com: Why? it breaks "ifconfig wgX name" and the other *_status implementations in ifconfig seem to…

key = nvlist_get_binary(nvl, "private-key", &size);

b64_ntop((const uint8_t *)key, size, buf, WG_MAX_STRLEN);

printf("\tprivate-key: %s\n", buf);

}

if (nvlist_exists_binary(nvl, "public-key")) {

key = nvlist_get_binary(nvl, "public-key", &size);

b64_ntop((const uint8_t *)key, size, buf, WG_MAX_STRLEN);

printf("\tpublic-key: %s\n", buf);

}

static struct cmd wireguard_cmds[] = {

DEF_CLONE_CMD_ARG("listen-port", setwglistenport),

DEF_CLONE_CMD_ARG("private-key", setwgprivkey),

DEF_CMD("peer-list", 0, peerlist),

DEF_CMD("peer", 0, peerstart),

DEF_CMD_ARG("public-key", setwgpubkey),

DEF_CMD_ARG("allowed-ips", setallowedips),

DEF_CMD_ARG("endpoint", setendpoint),

};

static struct afswtch af_wireguard = {

.af_name = "af_wireguard",

.af_af = AF_UNSPEC,

.af_other_status = wireguard_status,

};

static void

wg_create(int s, struct ifreq *ifr)

{

struct iovec iov;

void *packed;

size_t size;

setproctitle("ifconfig %s create ...\n", name);

if (!nvlist_exists_number(nvl_params, "listen-port"))

goto legacy;

if (!nvlist_exists_binary(nvl_params, "private-key"))

goto legacy;

hrsUnsubmitted

Not Done

Please add ifdef INET and/or ifdef INET6 to address family specific routines.

hrs: Please add ifdef INET and/or ifdef INET6 to address family specific routines.

mmacyAuthorUnsubmitted

Done

Please add ifdef INET and/or ifdef INET6 to address family specific routines.

mmacy: > Please add ifdef INET and/or ifdef INET6 to address family specific routines.

mmacyAuthorUnsubmitted

Done

Please add ifdef INET and/or ifdef INET6 to address family specific routines.

As far as I can tell, the desire is to eliminate dependencies on external routines when one is building world without one or the other. Adding ifdefs for code that is private to this file just makes it harder to maintain with zero net benefit.

mmacy: > Please add ifdef INET and/or ifdef INET6 to address family specific routines. As far as I…

packed = nvlist_pack(nvl_params, &size);

if (packed == NULL)

errx(1, "failed to setup create request");

iov.iov_len = size;

iov.iov_base = packed;

ifr->ifr_data = (caddr_t)&iov;

if (ioctl(s, SIOCIFCREATE2, ifr) < 0)

err(1, "SIOCIFCREATE2");

return;

legacy:

ifr->ifr_data == NULL;

if (ioctl(s, SIOCIFCREATE, ifr) < 0)

err(1, "SIOCIFCREATE");

}

static __constructor void

wireguard_ctor(void)

{

int i;

nvl_params = nvlist_create(0);

for (i = 0; i < nitems(wireguard_cmds); i++)

cmd_register(&wireguard_cmds[i]);

af_register(&af_wireguard);

clone_setdefcallback_prefix("wg", wg_create);

}

olivierUnsubmitted

Not Done

Since r366917, clone_setdefcallback() was renamed clone_setdefcallback_prefix()

olivier: Since r366917, clone_setdefcallback() was renamed clone_setdefcallback_prefix()

#endif

View Options

biology/bowtie2/distinfo

This file was added.