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#include "socket_view.h"
void custom_socket(int sock){
int yes, no;
yes = 1;
no = 0;
setsockopt(sock, SOL_SOCKET, SO_DEBUG, &yes, sizeof(int));
setsockopt(sock, SOL_SOCKET, SO_KEEPALIVE, &yes, sizeof(int));
}
int read_full(int fds, void *buffer, size_t size){
int num, count;
count = 0;
while(1){
num = read(fds, buffer + count, size - count);
if(num < 0){
break;
} else {
count += num;
if(count == size) break;
}
}
return count;
}
#define my_write(fds, val) if(write(fds, &(val), sizeof(val)) != sizeof(val)) return -1
#define my_write_full(fds, buffer, size) if(write(fds, buffer, size) != size) return -1
int request_view_basement_info(int sock){
const unsigned char op = VIEW_OP_INFO;
my_write(sock, op);
return 1;
}
int send_view_basement_info(int sock, RefSeq *src){
int i, size;
my_write(sock, src->cache->n_ref);
for(i=0;i<src->cache->n_ref;i++){
my_write(sock, src->cache->ref_lengths[i]);
size = strlen(src->cache->index->mm->ref_name[i]);
my_write(sock, size);
my_write_full(sock, src->cache->index->mm->ref_name[i], size);
}
return 1;
}
#define my_read(fds, val) if(read_full(fds, &(val), sizeof(val)) != sizeof(val)) return NULL
#define my_read_full(fds, buffer, size) if(read_full(fds, buffer, size) != size) return NULL
#define my_read2(fds, val) if(read_full(fds, &(val), sizeof(val)) != sizeof(val)) return -1
#define my_read_full2(fds, buffer, size) if(read_full(fds, buffer, size) != size) return -1
ViewInfo* recv_view_basement_info(int sock){
ViewInfo *info;
int i, len;
info = (ViewInfo*)malloc(sizeof(ViewInfo));
my_read(sock, info->n_ref);
info->ref_names = (char**)malloc(sizeof(char*) * info->n_ref);
info->ref_lengths = (int64_t*)malloc(sizeof(int64_t) * info->n_ref);
for(i=0;i<info->n_ref;i++){
my_read(sock, info->ref_lengths[i]);
my_read(sock, len);
info->ref_names[i] = (char*)malloc(len + 1);
my_read_full(sock, info->ref_names[i], len);
info->ref_names[i][len] = 0;
}
info->last_code = 0;
info->ref_id = 0;
info->start = 0;
info->end = -1;
info->rd_size = 0;
info->rd_cap = 1024;
info->reads = (Read*)malloc(sizeof(Read) * info->rd_cap);
info->cns_size = 0;
info->cns_cap = 1024;
info->seqs = (cns_t*)malloc(sizeof(cns_t) * info->cns_cap);
return info;
}
int request_maq_data(int sock, int last_code, int ref_id, int64_t start, int64_t end){
const unsigned char op = VIEW_OP_FETCH;
my_write(sock, op);
my_write(sock, last_code);
my_write(sock, ref_id);
my_write(sock, start);
my_write(sock, end);
return 1;
}
int send_maq_data(int sock, RefSeq *refs, int code, int64_t start, int64_t end){
int s, e, size, i;
int64_t pos, m;
my_write(sock, code);
my_write(sock, refs->cache->ref_id);
i = 0;
while(i<refs->cache->size-1 && read_pos(refs->cache->reads[i].read.pos) < start){ i++; }
s = i;
while(i<refs->cache->size-2 && read_pos(refs->cache->reads[i+1].read.pos) <= end) i++;
e = i;
size = e - s + 1;
if(size > 0){
pos = read_pos(refs->cache->reads[s].read.pos);
my_write(sock, pos);
pos = read_pos(refs->cache->reads[e].read.pos);
my_write(sock, pos);
my_write(sock, size);
my_write_full(sock, refs->cache->reads + refs->cache->offset + s, sizeof(Read) * size);
m = start - refs->cns->start;
size = refs->cns->size - m;
my_write(sock, size);
my_write_full(sock, refs->cns->seqs + refs->cns->offset + m, sizeof(cns_t) * (size));
} else {
size = 0;
my_write(sock, start);
my_write(sock, start);
my_write(sock, size);
my_write(sock, size);
}
return 1;
}
int recv_maq_data(int sock, ViewInfo *info){
my_read2(sock, info->last_code);
my_read2(sock, info->ref_id);
my_read2(sock, info->start);
my_read2(sock, info->end);
my_read2(sock, info->rd_size);
if(info->rd_size >= info->rd_cap){
info->rd_cap = info->rd_size;
info->reads = (Read*)realloc(info->reads, sizeof(Read) * info->rd_cap);
}
if(info->rd_size) my_read_full2(sock, info->reads, sizeof(Read) * info->rd_size);
my_read2(sock, info->cns_size);
if(info->cns_size >= info->cns_cap){
info->cns_cap = info->cns_size;
info->seqs = (cns_t*)realloc(info->seqs, sizeof(cns_t) * info->cns_cap);
}
if(info->cns_size) my_read_full2(sock, info->seqs, sizeof(cns_t) * info->cns_size);
return 1;
}
ViewServer* createViewServer(const char *map_file, const char *cns_file, int listen_port, int max_conns){
ViewServer *server;
MapIndex *index;
RefSeq *refs;
int i, j;
struct sockaddr_in name;
if(max_conns < 1) return NULL;
server = (ViewServer*)malloc(sizeof(ViewServer));
server->v_max = max_conns;
server->srcs = (RefSeq**)malloc(sizeof(RefSeq*) * server->v_max);
for(i=0;i<server->v_max;i++){
index = load_map_index(map_file, 0);
if(index == NULL){ return NULL; }
refs = (RefSeq*)malloc(sizeof(RefSeq));
refs->cache = read_cache_init(index);
refs->show_id = 0;
refs->show_start = 0;
refs->tooltips = NULL;
refs->cns = NULL;
if(cns_file) refs->cns = open_cns_cache(cns_file);
if(refs->cns == NULL) refs->cns = cns_cache_init();
else {
justify_cns_cache(refs->cns, refs->cache->index->mm->ref_name, refs->cache->index->mm->n_ref);
for(j=0;j<refs->cache->index->mm->n_ref;j++){
refs->cache->ref_lengths[j] = refs->cns->ref_lengths[j];
if(refs->cache->index->trees[j]->right < refs->cns->ref_lengths[j]){
refs->cache->index->trees[j]->right = refs->cns->ref_lengths[j];
}
}
}
server->srcs[i] = refs;
}
server->socket = -1;
server->socket = socket(PF_INET, SOCK_STREAM, 0);
if(server->socket < 0){
perror("socket");
freeViewServer(server);
return NULL;
}
name.sin_family = AF_INET;
name.sin_port = htons(listen_port);
name.sin_addr.s_addr = htonl(INADDR_ANY);
if(bind(server->socket, (struct sockaddr *)&name, sizeof(name)) < 0){
perror("bind");
freeViewServer(server);
return NULL;
}
server->stop = 1;
server->debug = 0;
return server;
}
int service_core(ViewServer *server, int sock){
unsigned char op;
int i, ref_id, idx, last_idx, ret;
int64_t start, end;
RefSeq *refs;
switch(read(sock, &op, 1)){
case 1: break;
case 0:
default:
return -1;
}
switch(op){
case VIEW_OP_CLOSE:
if(server->debug){
fprintf(stderr, " -- Server recv VIEW_OP_CLOSE in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__);
}
return -1;
case VIEW_OP_INFO:
if(server->debug){
fprintf(stderr, " -- Server recv VIEW_OP_INFO in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__);
}
return send_view_basement_info(sock, server->srcs[0]);
case VIEW_OP_FETCH:
if(server->debug){
fprintf(stderr, " -- Server recv VIEW_OP_FETCH in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__);
}
my_read2(sock, last_idx);
my_read2(sock, ref_id);
my_read2(sock, start);
my_read2(sock, end);
if(last_idx < 0 || last_idx >= server->v_max) return -1;
refs = server->srcs[last_idx];
idx = last_idx;
for(i=0;i<server->v_max;i++){
if(i == last_idx) continue;
if(server->srcs[i]->show_id == ref_id){
if(refs->show_id != ref_id){
refs = server->srcs[i];
idx = i;
} else {
if(server->srcs[i]->show_start >= start && server->srcs[i]->show_start <= start + 32 * 1024){
if(refs->show_start >= start && refs->show_start <= start + 32 * 1024){
if(server->srcs[i]->show_start < refs->show_start){
refs = server->srcs[i];
idx = i;
}
} else {
refs = server->srcs[i];
idx = i;
}
}
}
}
}
ret = read_cache_put(refs->cache, ref_id, start, end);
if(ret < 0) return -1;
refs->show_id = ref_id;
refs->show_start = start;
if(refs->cns->stream && ref_id >= 0 && ref_id < refs->cns->n_mm_ref && refs->cns->mm_map[ref_id] >= 0){
cns_cache_put(refs->cns, refs->cns->mm_map[ref_id], start, end);
} else {
cns_cache_guess(refs->cns, refs->cache);
}
if(server->debug){
fprintf(stderr, " -- Server fetch %d %ld %ld in %s -- %s:%d --\n", ref_id, start, end, __FUNCTION__, __FILE__, __LINE__);
}
return send_maq_data(sock, refs, idx, start, end);
default:
return 0;
}
}
int runViewServer(ViewServer *server){
int i, sock, state;
size_t size;
fd_set active_fd_set, read_fd_set;
struct timeval timeout;
struct sockaddr_in clientname;
if(listen(server->socket, server->v_max) < 0){
perror("listen");
return -1;
}
FD_ZERO(&active_fd_set);
FD_SET(server->socket, &active_fd_set);
server->stop = 0;
while(!server->stop){
read_fd_set = active_fd_set;
timeout.tv_sec = 5;
timeout.tv_usec = 0;
state = select(FD_SETSIZE, &read_fd_set, NULL, NULL, &timeout);
if(state != 1) continue;
for(i=0;i<FD_SETSIZE;i++){
if(FD_ISSET(i, &read_fd_set)){
if(i == server->socket){
size = sizeof(clientname);
sock = accept(server->socket, (struct sockaddr *)&clientname, &size);
if(sock < 0){
perror("accept");
continue;
}
if(server->debug){
fprintf(stdout, "Server: connect from host %s, port %hd client_id(%d).\n",
inet_ntoa(clientname.sin_addr),
ntohs(clientname.sin_port), sock);
}
custom_socket(sock);
FD_SET(sock, &active_fd_set);
} else {
switch(service_core(server, i)){
case VIEW_RES_ERROR:
close(i);
if(server->debug){
fprintf(stderr, " -- Close client(%d) in %s -- %s:%d --\n", i, __FUNCTION__, __FILE__, __LINE__);
}
FD_CLR(i, &active_fd_set);
break;
}
}
}
}
}
for(i=0;i<FD_SETSIZE;i++){
if(i == server->socket) continue;
if(!FD_ISSET(i, &active_fd_set)) continue;
close(i);
}
return 0;
}
void stopViewServer(ViewServer *server){
server->stop = 1;
}
void freeViewServer(ViewServer *server){
int i;
if(server->socket >= 0) close(server->socket);
for(i=0;i<server->v_max;i++){
read_cache_free(server->srcs[i]->cache);
close_cns_cache(server->srcs[i]->cns);
free(server->srcs[i]);
}
free(server->srcs);
free(server);
}
void freeViewInfo(ViewInfo *info){
int i;
free(info->ref_lengths);
free(info->reads);
free(info->seqs);
for(i=0;i<info->n_ref;i++){
free(info->ref_names[i]);
}
free(info->ref_names);
free(info);
}
void freeViewClient(ViewClient *client){
if(client->info) freeViewInfo(client->info);
free(client);
}
ViewClient* connectViewClient(char *host, int port){
ViewClient *client;
int sock;
struct sockaddr_in name;
struct hostent *hostinfo;
sock = socket(PF_INET, SOCK_STREAM, 0);
if(sock < 0){
perror("socket");
return NULL;
}
custom_socket(sock);
name.sin_family = AF_INET;
name.sin_port = htons (port);
hostinfo = gethostbyname (host);
if (hostinfo == NULL){
fprintf (stderr, "Unknown host %s:%d.\n", host, port);
return NULL;
}
name.sin_addr = *(struct in_addr *) hostinfo->h_addr;
if(connect(sock, (struct sockaddr *) &name, sizeof(name)) < 0){
perror("connect");
return NULL;
}
client = (ViewClient*)malloc(sizeof(ViewClient));
client->socket = sock;
if(request_view_basement_info(client->socket) == -1){
free(client);
perror("write");
return NULL;
}
client->info = recv_view_basement_info(client->socket);
if(client->info == NULL){
free(client);
return NULL;
}
return client;
}
int fetch_maq_data(ViewClient *client, int ref_id, int64_t start, int64_t end){
if(request_maq_data(client->socket, client->info->last_code, ref_id, start, end) == VIEW_RES_ERROR) return VIEW_RES_ERROR;
if(recv_maq_data(client->socket, client->info) == VIEW_RES_ERROR) return VIEW_RES_ERROR;
return 1;
}
void closeViewClient(ViewClient *client){
const unsigned char op = VIEW_OP_CLOSE;
if(client->socket >= 0){
write(client->socket, &op, sizeof(op));
close(client->socket);
}
freeViewClient(client);
}
void socketview_usage(char *prog){
printf(
"Setup Server: %s -s <port> <map file> [<cns file> [<width> [<height>]]]\n"
"Run Client : %s -c <host> <port> [<ref_id> <start> <end>]\n", prog, prog);
exit(0);
}
int print_map(char* ref_name, maplet *m1){
int j;
FILE *fpout;
fpout = stdout;
fprintf(fpout, "%s\t%s\t%d\t%c\t%d\t%u\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t",
m1->name, ref_name, (m1->pos>>1) + 1,
(m1->pos&1)? '-' : '+', m1->dist, m1->flag, m1->map_qual, (signed char)m1->seq[MAX_READLEN-1],
m1->alt_qual, m1->info1&0xf, m1->info2, m1->c[0], m1->c[1], m1->size);
for (j = 0; j != m1->size; ++j) {
if (m1->seq[j] == 0) fputc('n', fpout);
else if ((m1->seq[j]&0x3f) < 27) fputc("acgt"[m1->seq[j]>>6&3], fpout);
else fputc("ACGT"[m1->seq[j]>>6&3], fpout);
}
fputc('\t', fpout);
for (j = 0; j != m1->size; ++j)
fputc((m1->seq[j]&0x3f) + 33, fpout);
fputc('\n', fpout);
return 1;
}
int main(int argc, char **argv){
ViewServer *server;
ViewClient *client;
int i, c;
int ref_id;
int64_t start, end;
char *host, *map_file, *cns_file;
int port;
c = 0;
c = getopt(argc, argv, "sc");
if(c == -1) socketview_usage(argv[0]);
host = map_file = cns_file = NULL;
if(c == 's'){
if(argc > optind) port = atoi(argv[optind++]);
else socketview_usage(argv[0]);
if(argc > optind) map_file = argv[optind++];
else socketview_usage(argv[0]);
if(argc > optind) cns_file = argv[optind++];
else cns_file = NULL;
server = createViewServer(map_file, cns_file, port, 6);
server->debug = 1;
if(server == NULL){
printf("Cannot create View\n");
return 1;
}
runViewServer(server);
exit(0);
} else if(c == 'c'){
if(argc > optind) host = argv[optind++];
else socketview_usage(argv[0]);
if(argc > optind) port = atoi(argv[optind++]);
else socketview_usage(argv[0]);
if(argc > optind) ref_id = atoi(argv[optind++]);
else ref_id = -1;
if(argc > optind) start = atol(argv[optind++]) - 1;
else start = 0;
if(argc > optind) end = atol(argv[optind++]) - 1;
else end = 0;
client = connectViewClient(host, port);
if(client == NULL){
fprintf(stderr, "Cannot connect to %s:%d\n", host, port);
return 1;
}
if(ref_id == -1){
printf("Number of references: %d\n", client->info->n_ref);
for(i=0;i<client->info->n_ref;i++){
printf("%d\t%s\t%ld\n", i, client->info->ref_names[i], client->info->ref_lengths[i]);
}
} else {
if(fetch_maq_data(client, ref_id, start, end) == -1){
fprintf(stderr, "Error in fetching maq data\n");
} else {
for(i=0;i<client->info->cns_size;i++){
printf("%c", cns_get_ref(client->info->seqs[i]));
}
printf("\n");
for(i=0;i<client->info->cns_size;i++){
printf("%c", cns_get_cns(client->info->seqs[i]));
}
printf("\n");
for(i=0;i<client->info->rd_size;i++){
print_map(client->info->ref_names[client->info->ref_id], &(client->info->reads[i].read));
}
}
}
closeViewClient(client);
} else {
printf("Unknown option %c\n", c);
socketview_usage(argv[0]);
}
return 0;
}
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