void NaturalMappingSchemeTests::setUp() {
// We need a built index as a fixture, and we don't want to rebuild it for
// every test.
// Set up a temporary directory to put the index in.
tempDir = make_tempdir();
// Make a new index builder.
FMDIndexBuilder builder(tempDir + "/index.basename");
// Add the haplotypes file
builder.add(filename);
// Finish the index.
FMDIndex* tmpIndex = builder.build();
// Don't leak it.
delete tmpIndex;
// Save a pointer to a new index that we just load (so we don't have the
// full SA).
index = new FMDIndex(tempDir + "/index.basename");
// Make the mapping scheme, using a view of the whole index with no merging.
scheme = new NaturalMappingScheme(FMDIndexView(*index));
}
FMDIndexTests::FMDIndexTests() {
// We need a built index as a fixture, and we don't want to rebuild it for
// every test.
// Set up a temporary directory to put the index in.
tempDir = make_tempdir();
// Make a new index builder.
FMDIndexBuilder builder(tempDir + "/index.basename");
// Add the haplotypes file
builder.add(filename);
// Finish the index.
FMDIndex* tmpIndex = builder.build();
// Don't leak it.
delete tmpIndex;
// Save a pointer to a new index that we just load (so we don't have the
// full SA).
index = new FMDIndex(tempDir + "/index.basename");
}
/* Expands %i and %o in the args to the full temp files within the
temp directory. */
static int
expand_args(struct exec_info *info,const char *args_in)
{
const char *ch = args_in;
membuf_t command;
info->flags.use_temp_files=0;
info->flags.keep_temp_files=0;
if(DBG_EXTPROG)
log_debug("expanding string \"%s\"\n",args_in);
init_membuf (&command, 100);
while(*ch!='\0')
{
if(*ch=='%')
{
char *append=NULL;
ch++;
switch(*ch)
{
case 'O':
info->flags.keep_temp_files=1;
/* fall through */
case 'o': /* out */
if(!info->flags.madedir)
{
if(make_tempdir(info))
goto fail;
}
append=info->tempfile_out;
info->flags.use_temp_files=1;
break;
case 'I':
info->flags.keep_temp_files=1;
/* fall through */
case 'i': /* in */
if(!info->flags.madedir)
{
if(make_tempdir(info))
goto fail;
}
append=info->tempfile_in;
info->flags.use_temp_files=1;
break;
case '%':
append="%";
break;
}
if(append)
put_membuf_str (&command, append);
}
else
put_membuf (&command, ch, 1);
ch++;
}
put_membuf (&command, "", 1); /* Terminate string. */
info->command = get_membuf (&command, NULL);
if (!info->command)
return gpg_error_from_syserror ();
if(DBG_EXTPROG)
log_debug("args expanded to \"%s\", use %u, keep %u\n",info->command,
info->flags.use_temp_files,info->flags.keep_temp_files);
return 0;
fail:
xfree (get_membuf (&command, NULL));
return G10ERR_GENERAL;
}
/* Expands %i and %o in the args to the full temp files within the
temp directory. */
static int expand_args(struct exec_info *info,const char *args_in)
{
const char *ch=args_in;
unsigned int size,len;
info->use_temp_files=0;
info->keep_temp_files=0;
if(DBG_EXTPROG)
log_debug("expanding string \"%s\"\n",args_in);
size=100;
info->command=m_alloc(size);
len=0;
info->command[0]='\0';
while(*ch!='\0')
{
if(*ch=='%')
{
char *append=NULL;
ch++;
switch(*ch)
{
case 'O':
info->keep_temp_files=1;
/* fall through */
case 'o': /* out */
if(!info->madedir)
{
if(make_tempdir(info))
goto fail;
}
append=info->tempfile_out;
info->use_temp_files=1;
break;
case 'I':
info->keep_temp_files=1;
/* fall through */
case 'i': /* in */
if(!info->madedir)
{
if(make_tempdir(info))
goto fail;
}
append=info->tempfile_in;
info->use_temp_files=1;
break;
case '%':
append="%";
break;
}
if(append)
{
size_t applen=strlen(append);
if(applen+len>size-1)
{
if(applen<100)
applen=100;
size+=applen;
info->command=m_realloc(info->command,size);
}
strcat(info->command,append);
len+=strlen(append);
}
}
else
{
if(len==size-1) /* leave room for the \0 */
{
size+=100;
info->command=m_realloc(info->command,size);
}
info->command[len++]=*ch;
info->command[len]='\0';
}
ch++;
}
if(DBG_EXTPROG)
log_debug("args expanded to \"%s\", use %d, keep %d\n",
info->command,info->use_temp_files,info->keep_temp_files);
return 0;
fail:
m_free(info->command);
info->command=NULL;
return G10ERR_GENERAL;
}