/*
* Try to locate in RefSeq Archives:
* check for pattern '(\w{4}\d{2})[\.\d]+'; the archive is $1
* use the scheme "x-ncbi-legrefseq" for vfs to recognize special case
*/
static
rc_t SRAPathFullREFSEQArchive(NCBISRAPath const *self,
char const rep[],
char const vol[],
char const accession[],
char path[],
size_t path_max
)
{
size_t const rep_sz = strlen(rep);
size_t const vol_sz = strlen(vol);
char const *const rep_sep = (rep_sz > 0 && rep[rep_sz - 1] != '/') ? "/" : "";
char const *const vol_sep = (vol_sz > 0 && vol[vol_sz - 1] != '/') ? "/" : "";
size_t sz;
unsigned i;
VFSManager *vfs;
rc_t rc = VFSManagerMake(&vfs);
VPath *vpath;
KDirectory const *dir;
KPathType type;
if (rc)
return rc;
for (i = 0; i < 4; ++i) {
int const ch = accession[i];
if (ch == 0 || !isalpha(ch))
return RC(rcSRA, rcMgr, rcAccessing, rcPath, rcIncorrect);
}
for ( ; ; ++i) {
int const ch = accession[i];
if (ch == 0)
break;
if (ch != '.' && !isdigit(ch))
return RC(rcSRA, rcMgr, rcAccessing, rcPath, rcIncorrect);
}
if (i < 8)
return RC(rcSRA, rcMgr, rcAccessing, rcPath, rcIncorrect);
rc = string_printf(path, path_max, &sz, "x-ncbi-legrefseq:%s%s%s%s%.6s", rep, rep_sep, vol, vol_sep, accession);
if (rc) return rc;
i = sz;
rc = VPathMake(&vpath, path + 17);
if (rc) return rc;
rc = VFSManagerOpenDirectoryRead(vfs, &dir, vpath);
VPathRelease(vpath);
VFSManagerRelease(vfs);
if (rc) return rc;
type = KDirectoryPathType(dir, "tbl/%s", accession);
KDirectoryRelease(dir);
if (type != kptDir)
return RC(rcSRA, rcMgr, rcAccessing, rcPath, rcIncorrect);
rc = string_printf(path + i, path_max - i, &sz, "#tbl/%s", accession);
return rc;
}
/* ----------------------------------------------------------------------
* SCHEME:PATH/FILE?QUERY
*
* form_one is just a file
* form_two is just a path and a file (can ignore scheme until more schemes supported)
* form_three is all parts except path present which for here acts like form_one
* form_four is all four parts
*
* path is the directory path leading to root
* root will be the directory containing the archive
* base will be the archive as a directory
*/
static
rc_t open_root_then_run ()
{
static const char dot[] = ".";
char rootstr [8192];
char basestr [8192];
const char * colon;
rc_t rc;
colon = strchr (options.arcstr, ':');
if (colon == NULL) /* no scheme so it has to be a plain path */
{
char * last_slash;
strcpy (basestr, options.arcstr);
last_slash = strrchr (basestr, '/');
if (last_slash == NULL) /* in this directory */
{
options.rootstr = dot;
options.basestr = options.arcstr;
/* done */
}
else
{
*last_slash = '\0';
options.rootstr = basestr;
options.basestr = last_slash + 1;
/* done */
}
}
else
{
char * end_of_root;
char * last_slash;
strcpy (rootstr, colon+1);
end_of_root = strchr (rootstr, '?');
if (end_of_root == NULL)
end_of_root = strchr (rootstr, '#');
if (end_of_root)
*end_of_root = '\0';
options.rootstr = rootstr;
last_slash = strchr (rootstr, '/');
if (last_slash == NULL)
{
/* no path */
options.rootstr = dot;
options.basestr = options.arcstr;
/* done */
}
else
{
size_t x,z;
*last_slash = '\0';
options.rootstr = rootstr;
/* scheme */
z = string_size (rootstr);
x = string_copy (basestr, sizeof (basestr), options.arcstr, (colon + 1) - options.arcstr);
strcpy (basestr + x, options.arcstr + x + z + 1);
options.basestr = basestr;
/* done */
}
}
{
KDirectory * cwd;
rc = VFSManagerGetCWD (options.vfsmgr, &cwd);
if (rc)
;
else
{
rc = KDirectoryOpenXTocDirRead (cwd, &options.root, true,
options.xml, "%s", options.rootstr);
if (rc)
PLOGERR (klogErr, (klogErr, rc,
"failed to open XFS from '$(P)' using '$(P)'",
"P=%s", options.basestr, options.xmlstr));
else
{
rc = VFSManagerMakePath (options.vfsmgr, &options.basepath, "%s", options.basestr);
if (rc)
PLOGERR (klogErr, (klogErr, rc,
"failed to make vpath from '$(P)'",
"P=%s", options.basestr));
else
{
rc = VFSManagerOpenDirectoryRead (options.vfsmgr,
&options.base,
options.basepath);
if (rc == 0)
{
rc = build_vpath_then_run ();
KDirectoryRelease (options.base);
}
KDirectoryRelease (options.root);
}
VPathRelease (options.basepath);
}
KDirectoryRelease (cwd);
}
}
return rc;
}
