int main_searchvariants(int argc, char* argv[],char *server_url)
{
int cmd;
int i;
search_variant_request *request=(search_variant_request*)malloc(1*sizeof(search_variant_request));
int size_variants = 0;
int size_calls = 0;
request->name = "null";
request->pageToken ="null";
char debug = 0;
static struct option long_options[]={
{"variantSetIds",required_argument,0,'v'},
{"referenceName",required_argument,0,'r'},
{"start",required_argument,0,'s'},
{"end",required_argument,0,'e'},
{"callSetIds",required_argument,0,'c'},
{"variantName",required_argument,0,'n'},
{"debug",no_argument,0,'d'},
{0,0,0,0}
};
//if(argc < 2)
while((cmd=getopt_long(argc,argv,"v:r:s:e:c:n:d",long_options,NULL))!=-1)
{
switch(cmd)
{
case 'v':
if(optarg==NULL||(strcmp(optarg,"")==0))
{
error("--variantSetIds string can't be empty.\n");
}
else
{
size_variants = count_ids(optarg);
request->variantSetIds = (char**)malloc(size_variants*sizeof(char*));
set_ids(optarg,request->variantSetIds,size_variants);
}
break;
case 'r':
if(optarg==NULL||(strcmp(optarg,"")==0))
{
error("--referenceName string can't be empty.\n");
}
else
{
request->referenceName = optarg;
}
break;
case 's': request->start = atol(optarg);
if(request->start < 0)
{
error("--start integer must be no negative.");
}
break;
case 'e': request->end = atol(optarg);
if(request->end < 0)
{
perror("--end integer must be no negative.");
}
break;
case 'c': if(optarg==NULL||(strcmp(optarg,"")==0))
{
size_calls = 0;
}
else
{
size_calls = count_ids(optarg);
request->callSetIds = (char**)malloc(size_calls*sizeof(char*));
set_ids(optarg,request->callSetIds,size_calls);
}
break;
case 'n': request->name = optarg; break;
case 'd': debug = 1; break;
case '?': usage();
default: error("Unknown argument %s\n",optarg);
}
}
if(size_variants==0)
{
usage();
}
start_user(server_url);
char* vcf_file_name;
//process each variantSet
for(i=0; i<size_variants; i++)
{
vcf_file_name = get_variantSetId_vcf_name(request,i);
create_vcf_file(vcf_file_name);
while(strcmp(request->pageToken,"NULL")!=0)
{
user->post_fields = create_request_string(request,i,size_calls);
//printf("post field string: %s \n",user->post_fields);
client_search_request(user,"variants");
//printf("%s\n",user->response);
write_vcf_file(user->response,vcf_file_name);
request->pageToken = get_pageToken();
//printf("%s \n",request->pageToken);
if(debug)
{
printf("%s\n",user->response);
}
}
}
end_user();
return 0;
}
static void run_loaded_program(size_t argc, char** argv, uintptr_t kstack_top)
{
// copy phdrs to user stack
size_t stack_top = current.stack_top - current.phdr_size;
memcpy((void*)stack_top, (void*)current.phdr, current.phdr_size);
current.phdr = stack_top;
// copy argv to user stack
for (size_t i = 0; i < argc; i++) {
size_t len = strlen((char*)(uintptr_t)argv[i])+1;
stack_top -= len;
memcpy((void*)stack_top, (void*)(uintptr_t)argv[i], len);
argv[i] = (void*)stack_top;
}
// copy envp to user stack
const char* envp[] = {
// environment goes here
};
size_t envc = sizeof(envp) / sizeof(envp[0]);
for (size_t i = 0; i < envc; i++) {
size_t len = strlen(envp[i]) + 1;
stack_top -= len;
memcpy((void*)stack_top, envp[i], len);
envp[i] = (void*)stack_top;
}
// align stack
stack_top &= -sizeof(void*);
struct {
long key;
long value;
} aux[] = {
{AT_ENTRY, current.entry},
{AT_PHNUM, current.phnum},
{AT_PHENT, current.phent},
{AT_PHDR, current.phdr},
{AT_PAGESZ, RISCV_PGSIZE},
{AT_SECURE, 0},
{AT_RANDOM, stack_top},
{AT_NULL, 0}
};
// place argc, argv, envp, auxp on stack
#define PUSH_ARG(type, value) do { \
*((type*)sp) = (type)value; \
sp += sizeof(type); \
} while (0)
#define STACK_INIT(type) do { \
unsigned naux = sizeof(aux)/sizeof(aux[0]); \
stack_top -= (1 + argc + 1 + envc + 1 + 2*naux) * sizeof(type); \
stack_top &= -16; \
long sp = stack_top; \
PUSH_ARG(type, argc); \
for (unsigned i = 0; i < argc; i++) \
PUSH_ARG(type, argv[i]); \
PUSH_ARG(type, 0); /* argv[argc] = NULL */ \
for (unsigned i = 0; i < envc; i++) \
PUSH_ARG(type, envp[i]); \
PUSH_ARG(type, 0); /* envp[envc] = NULL */ \
for (unsigned i = 0; i < naux; i++) { \
PUSH_ARG(type, aux[i].key); \
PUSH_ARG(type, aux[i].value); \
} \
} while (0)
STACK_INIT(uintptr_t);
if (current.cycle0) { // start timer if so requested
current.time0 = rdtime();
current.cycle0 = rdcycle();
current.instret0 = rdinstret();
}
trapframe_t tf;
init_tf(&tf, current.entry, stack_top);
__clear_cache(0, 0);
write_csr(sscratch, kstack_top);
start_user(&tf);
}
