int mtnfile_console_cd(int argc, ARG args)
{
STR path;
int r = 1;
MTNSTAT *rst;
MTNSTAT *kst;
if(argc == 1){
ctx->remote_path = modstr(ctx->remote_path, "/");
return(0);
}
path = mtnfile_console_path(args[1]);
rst = mtn_stat(mtn, path);
for(kst=rst;kst;kst=kst->next){
if(S_ISDIR(kst->stat.st_mode)){
ctx->remote_path = modstr(ctx->remote_path, path);
r = 0;
break;
}
}
if(r){
mtnlogger(mtn, 0, "error: %s: not directory.\n", args[1]);
}
path = clrstr(path);
rst = clrstat(rst);
return(r);
}
STR convarg(STR a, MTNJOB *j)
{
int i;
STR p;
STR q;
if(!a){
return(NULL);
}
if(!j){
return(a);
}
i = 0;
p = newstr(a);
while(*(p + i)){
if(*(p + i) == '{'){
*(p + i) = 0;
i++;
q = newstr(p + i);
q = convarg2(q, j);
a = modstr(a, p);
a = catstr(a, q);
p = modstr(p, a);
q = clrstr(q);
continue;
}
i++;
}
clrstr(p);
return(a);
}
STR convarg3(STR a, MTNJOB *j)
{
int m;
int n;
STR s;
char *b;
if(!strcmp(a, "H")){
if(j->svr){
a = modstr(a, j->svr->host);
}else{
a = modstr(a, "local");
}
return(a);
}
b = malloc(ctx->arg_max);
a = strnum(a, b);
if(!strlen(b)){
s = joinarg(j->argl, ctx->delim);
}else{
n = atoi(b);
m = cntarg(j->argl);
s = newstr((n < m) ? j->argl[n] : "");
}
free(b);
b = NULL;
a = convarg4(a, s);
clrstr(s);
return(a);
}
STR convarg2(STR a, MTNJOB *j)
{
int i;
STR p;
STR q;
STR r;
i = 0;
p = newstr(a);
while(*(p + i)){
if(*(p + i) == '}'){
*(p + i) = 0;
i++;
q = newstr(p);
r = newstr(p + i);
q = convarg3(q, j);
a = modstr(a, q);
a = catstr(a, r);
clrstr(q);
clrstr(r);
break;
}
i++;
}
clrstr(p);
return(a);
}
STR mtnfile_console_path(STR opt)
{
int i;
STR path;
ARG dirs;
path = newstr(ctx->remote_path);
dirs = splitstr(opt, "/");
for(i=0;dirs[i];i++){
if(!strcmp(dirs[i], "..")){
path = modstr(path, dirname(path));
}else if(!strcmp(dirs[i], ".")){
}else{
if(lastchar(path) != '/'){
path = catstr(path, "/");
}
path = catstr(path, dirs[i]);
}
}
dirs = clrarg(dirs);
return(path);
}
int mtnfile_console()
{
int argc;
ARG args;
char *line;
STR prompt = newstr("mtn:/> ");
ctx->remote_path = newstr("/");
rl_attempted_completion_function = mtnfile_console_readline_callback;
while((line = readline(prompt))){
if(!strlen(line)){
free(line);
continue;
}
args = splitstr(line, " ");
argc = cntarg(args);
if(!argc){
free(line);
continue;
}else if(!strcmp(args[0], "exit")){ break;
}else if(!strcmp(args[0], "quit")){ break;
}else if(!strcmp(args[0], "help")){ mtnfile_console_help(args[1]);
}else if(!strcmp(args[0], "ls" )){ mtnfile_console_ls(argc, args);
}else if(!strcmp(args[0], "cd" )){ mtnfile_console_cd(argc, args);
}else if(!strcmp(args[0], "lcd" )){ mtnfile_console_lcd(argc, args);
}else if(!strcmp(args[0], "cat" )){ mtnfile_console_cat(argc, args);
}else if(!strcmp(args[0], "get" )){ mtnfile_console_get(argc, args);
}else if(!strcmp(args[0], "put" )){ mtnfile_console_put(argc, args);
}else if(!strcmp(args[0], "del" )){ mtnfile_console_del(argc, args);
}else{ mtnlogger(mtn, 0, "%s: no such command.\n", args[0]); }
add_history(line);
free(line);
line = NULL;
args = clrarg(args);
prompt = modstr(prompt, "mtn:");
prompt = catstr(prompt, ctx->remote_path);
prompt = catstr(prompt, "> ");
}
return(0);
}
SEXP makedf_xlink(struct iobtd *iop){
SEXP df, df_names, idvec, peakidvec, errvec, covvec, modsv;
yamldom_node_t *xlseq, *tmp, *seq, *prottmp, *peptmp;
int i, count, modstrlen;
const int ncols=5;
char *mods;
if(!(xlseq=yamldom_find_map_val(iop->root,"xlink"))){
goto err;
}
count = count_seq_elem(xlseq);
hidefromGC(idvec = allocVector(INTSXP,count));
hidefromGC(peakidvec = allocVector(INTSXP,count));
hidefromGC(errvec = allocVector(REALSXP,count));
hidefromGC(covvec = allocVector(REALSXP,count));
hidefromGC(modsv = allocVector(STRSXP,count));
i=0;
for(seq=YAMLDOM_SEQ_NODES(xlseq);seq;seq=seq->next){
if(!(peptmp=yamldom_find_map_val(seq,"peps")))
goto err;
peptmp = YAMLDOM_SEQ_NODES(peptmp);
push_elem(INTEGER(idvec),i,seq,"id",strtoint);
push_elem(REAL(errvec),i,seq,"error",strtodouble);
push_elem(REAL(covvec),i,seq,"fragcov",strtodouble);
/* peaklist id (via prot -> param) */
if(!(prottmp=yamldom_find_map_val(peptmp,"prot")))
goto err;
tmp = YAMLDOM_DEREF(prottmp);
if(!(tmp=yamldom_find_map_val(tmp,"peaks")))
goto err;
tmp = YAMLDOM_DEREF(tmp);
push_elem(INTEGER(peakidvec),i,tmp,"id",strtoint);
if(!(tmp=yamldom_find_map_val(tmp,"param")))
goto err;
tmp = YAMLDOM_DEREF(tmp);
modstrlen = getmodstrlen(yamldom_find_map_val(tmp,"vmod"));
if(!(mods=malloc(modstrlen)))
goto err;
modstr(yamldom_find_map_val(seq,"mods"),mods);
if(mods && *mods)
SET_STRING_ELT(modsv, i, mkChar(mods));
else
SET_STRING_ELT(modsv, i, mkChar(""));
free(mods);
i++;
}
make_list_names(df_names, ncols, "xlid", "peakid", "error", "frag.cov", "mods");
make_dataframe(df, RNULL, df_names, ncols, idvec, peakidvec, errvec, covvec, modsv);
unhideGC();
return df;
err:
unhideGC();
return RNULL;
}
ARG parse(int argc, char *argv[])
{
int r;
char *p;
STR buff;
ARG args;
if(argc < 2){
usage();
exit(0);
}
optind = 0;
while((r = getopt_long(argc, argv, "+hVvnBbig:j:e:I:RALT:P:N:m:p:d:f:D:", get_optlist(), NULL)) != -1){
switch(r){
case 'h':
usage();
exit(0);
case 'V':
version();
exit(0);
case 'F':
ctx->info = 1;
break;
case 'f':
ctx->arg_num = ctx->arg_num ? ctx->arg_num : 1;
if(!strcmp("-", optarg)){
ctx->afd = 0;
}else{
ctx->afd = open(optarg, O_RDONLY);
if(ctx->afd == -1){
mtnlogger(mtn, 0, "[error] %s: %s %s\n", __func__, optarg, strerror(errno));
exit(1);
}
}
break;
case 't':
test();
exit(0);
case 'v':
ctx->verbose = 1;
break;
case 'n':
ctx->dryrun = 1;
break;
case 'i':
ctx->conv = 1;
break;
case 'g':
mtn->groupstr = newstr(optarg);
mtn->grouparg = splitstr(optarg, ",");
break;
case 'j':
ctx->cpu_lim = atoi(optarg) * 10;
break;
case 'e':
ctx->echo = newstr(optarg);
setbuf(stdout, NULL);
break;
case 'I':
ctx->stdin = newstr(optarg);
break;
case 'O':
ctx->stdout = newstr(optarg);
break;
case 'E':
ctx->stderr = newstr(optarg);
break;
case 'S':
ctx->putarg = splitstr(optarg, ",");
break;
case 'G':
ctx->getarg = splitstr(optarg, ",");
break;
case 'B':
ctx->text = 0;
break;
case 'b':
ctx->nobuf = 0;
break;
case 'R':
ctx->opt_R = 1;
break;
case 'A':
ctx->opt_A = 1;
break;
case 'L':
ctx->opt_L = 1;
break;
case 'P':
ctx->job_max = atoi(optarg);
break;
case 'N':
ctx->arg_num = atoi(optarg);
break;
case 'm':
strcpy(mtn->mcast_addr, optarg);
break;
case 'p':
mtn->mcast_port = atoi(optarg);
break;
case 'd':
ctx->delim = modstr(ctx->delim, optarg);
break;
case 'D':
mtn->loglevel = atoi(optarg);
break;
case 'T':
buff = newstr(optarg);
p = strtok(buff, ",");
while(p){
ctx->targets = addarg(ctx->targets, p);
p = strtok(NULL, ",");
}
break;
case '?':
usage();
exit(1);
}
}
if(ctx->opt_R && ctx->opt_A){
usage();
exit(1);
}
if(ctx->opt_R && ctx->targets[0]){
usage();
exit(1);
}
if(ctx->opt_A && ctx->targets[0]){
usage();
exit(1);
}
if(ctx->opt_R){
ctx->mode = ctx->opt_L ? MTNEXECMODE_HYBRID : MTNEXECMODE_REMOTE;
}else if(ctx->opt_A){
ctx->mode = ctx->opt_L ? MTNEXECMODE_ALL1 : MTNEXECMODE_ALL0;
}else{
ctx->mode = ctx->targets[0] ? MTNEXECMODE_TARGET : MTNEXECMODE_LOCAL;
}
if(ctx->info){
info();
exit(0);
}
ctx->verbose = ctx->dryrun ? 0 : ctx->verbose;
args = newarg(0);
while(optind < argc){
if(strcmp(argv[optind], ":::") == 0){
optind++;
ctx->linearg = newarg(0);
break;
}
args = addarg(args, argv[optind++]);
}
if(ctx->linearg){
while(optind < argc){
ctx->linearg = addarg(ctx->linearg, argv[optind++]);
}
ctx->arg_num = ctx->arg_num ? ctx->arg_num : 1;
}
if((args[0] == NULL) && (ctx->arg_num == 0)){
ctx->arg_num = 1;
}
return(args);
}
