rc_t TarNode_MakeXML(const KXMLNode* xml_node, FSNode** self, char* errmsg, const char* rel_path)
{
rc_t rc = 0;
if( xml_node == NULL || self == NULL ) {
rc = RC(rcExe, rcNode, rcConstructing, rcParam, rcNull);
} else {
char name[4096];
size_t sz;
rc = KXMLNodeReadAttrCString(xml_node, "name", name, sizeof(name), &sz);
if( rc != 0 || sz == 0 || name[0] == '\0' ) {
strcpy(errmsg, "attribute 'name'");
rc = rc ? rc : RC(rcExe, rcDoc, rcValidating, rcAttr, rcInvalid);
} else if( (rc = FSNode_Make(self, name, &TarNode_vtbl)) == 0 ) {
((TarNode*)*self)->rel_path = rel_path;
strcpy(errmsg, "processing Item(s)");
if( (rc = TarNode_MakeFileList(xml_node, &((TarNode*)*self)->files, errmsg, rel_path, (*self)->name)) != 0 ) {
FSNode_Release(*self);
*self = NULL;
}
}
}
return rc;
}
static
rc_t SRAConfigParse(const KXMLNode* xml_node, SRAConfigFlags* flags, char* errmsg)
{
rc_t rc = 0;
uint32_t i;
char at[4096];
size_t sz;
char* attr_name[] = { "run-directory", "SRA-archive", "SRA-archive-lite", "fastq", "SFF" };
SRAConfigFlags attr_val[] = { eSRAFuseRunDir, eSRAFuseFileArc, eSRAFuseFileArcLite, eSRAFuseFileFastq, eSRAFuseFileSFF };
if( *flags & eSRAFuseInitial ) {
*flags = 0;
}
for(i = 0; rc == 0 && i < sizeof(attr_name)/sizeof(attr_name[0]); i++) {
if( (rc = KXMLNodeReadAttrCString(xml_node, attr_name[i], at, sizeof(at), &sz)) == 0 ) {
if( strcasecmp(at, "true") == 0 ) {
*flags = *flags | attr_val[i];
} else if( strcasecmp(at, "false") == 0 ) {
*flags = *flags & ~(attr_val[i]);
} else {
strcpy(errmsg, "SRAConfig attribute ");
strcat(errmsg, attr_name[i]);
strcat(errmsg, " value '");
strcat(errmsg, at);
strcat(errmsg, "'");
rc = RC(rcExe, rcDoc, rcReading, rcData, rcInvalid);
}
} else if( GetRCState(rc) == rcNotFound ) {
rc = 0;
}
}
return rc;
}
rc_t XML_ParseBool(const KXMLNode* xml_node, const char* attr, bool* val, bool optional)
{
rc_t rc;
char b[16];
size_t sz;
if( (rc = KXMLNodeReadAttrCString(xml_node, attr, b, sizeof(b), &sz)) == 0 ) {
if( strcasecmp(b, "true") == 0 || strcasecmp(b, "on") == 0 || strcasecmp(b, "yes") == 0 ) {
*val = true;
} else if( strcasecmp(b, "false") == 0 || strcasecmp(b, "off") == 0 || strcasecmp(b, "no") == 0 ) {
*val = false;
} else {
rc = RC(rcExe, rcDoc, rcReading, rcAttr, rcInvalid);
}
} else if( optional && GetRCObject(rc) == rcAttr && GetRCState(rc) == rcNotFound ) {
rc = 0;
}
return rc;
}
rc_t XML_ParseTimestamp(const KXMLNode* xml_node, const char* attr, KTime_t* timestamp, bool optional)
{
rc_t rc;
char ts[128];
size_t sz;
if( (rc = KXMLNodeReadAttrCString(xml_node, attr, ts, sizeof(ts), &sz)) == 0 ) {
struct tm tm;
memset(&tm, 0, sizeof(tm));
if( strptime(ts, "%Y-%m-%dT%H:%M:%S", &tm) != NULL ) {
*timestamp = mktime(&tm);
} else {
rc = RC(rcExe, rcDoc, rcReading, rcAttr, rcInvalid);
}
} else if( optional && GetRCObject(rc) == rcAttr && GetRCState(rc) == rcNotFound ) {
rc = 0;
}
return rc;
}
static rc_t XmlMetaInitMembers(BSTree* tr, const KXMLNode* node) {
rc_t rc = 0;
const char path[] = "Member";
uint32_t count = 0;
uint32_t idx = 0;
const KXMLNodeset *members = NULL;
if (rc == 0) {
rc = KXMLNodeOpenNodesetRead(node, &members, path);
DISP_RC(rc, path);
}
if (rc == 0) {
rc = KXMLNodesetCount(members, &count);
DISP_RC(rc, path);
}
for (idx = 0; idx < count && rc == 0; ++idx) {
const KXMLNode *node = NULL;
char member_name[256] = "";
if (rc == 0) {
rc = KXMLNodesetGetNodeRead(members, &node, idx);
DISP_RC(rc, path);
}
if (rc == 0) {
size_t size = 0;
rc = KXMLNodeReadAttrCString(node, "member_name",
member_name, sizeof member_name, &size);
if (rc) {
if (GetRCState(rc) == rcInsufficient) {
member_name[sizeof member_name - 1] = '\0';
rc = 0;
}
}
}
if (rc == 0) {
rc = XmlMetaInitMemser(tr, node, path, member_name);
}
RELEASE(KXMLNode, node);
}
RELEASE(KXMLNodeset, members);
return rc;
}
static
rc_t TarNode_MakeFileList(const KXMLNode* xml_node, const TarFileList** files, char* errmsg, const char* rel_path, const char* name)
{
rc_t rc = 0;
time_t now = time(NULL);
uint32_t count = 0;
*files = NULL;
if( (rc = KXMLNodeCountChildNodes(xml_node, &count)) == 0 ) {
if( count == 0 ) {
rc = RC(rcExe, rcDoc, rcValidating, rcData, rcEmpty);
} else if( (rc = TarFileList_Make(files, count, name)) == 0 ) {
uint32_t i = 0;
while(rc == 0 && i < count) {
const KXMLNode* n = NULL;
const char* n_name;
if( (rc = KXMLNodeGetNodeRead(xml_node, &n, i++)) == 0 && (rc = KXMLNodeElementName(n, &n_name)) == 0 ) {
if( strcmp(n_name, "Item") != 0 ) {
rc = RC(rcExe, rcDoc, rcValidating, rcNode, rcUnexpected);
strcpy(errmsg, n_name);
} else {
size_t sz_read;
char path[4096], name[4096];
KTime_t ts = now;
uint64_t fsz = 0;
bool exec = false;
if( (rc = KXMLNodeReadAttrCString(n, "path", name, sizeof(name), &sz_read)) == 0 ) {
if( name[0] == '\0' ) {
rc = RC(rcExe, rcDoc, rcValidating, rcAttr, rcEmpty);
} else if( name[0] == '/' ) {
memmove(path, name, sz_read + 1);
} else {
KDirectory* dir = NULL;
if( (rc = KDirectoryNativeDir(&dir)) == 0 &&
(rc = KDirectoryResolvePath(dir, true, path, sizeof(path), "%s/%s", rel_path, name)) == 0 ) {
DEBUG_LINE(8, "%s/%s resolved to %s", rel_path, name, path);
}
KDirectoryRelease(dir);
}
if( rc != 0 ) {
strcpy(errmsg, "TAR/Item/@path");
}
}
if( rc == 0 && (rc = XML_ParseTimestamp(n, "timestamp", &ts, true)) != 0 ) {
strcpy(errmsg, "TAR/Item/@timestamp");
}
if( rc == 0 && (rc = XML_ParseBool(n, "executable", &exec, true)) != 0 ) {
strcpy(errmsg, "TAR/Item/@executable");
}
if( rc == 0 && (rc = KXMLNodeReadAttrAsU64(n, "size", &fsz)) != 0 ) {
strcpy(errmsg, "TAR/Item/@size");
}
if( rc == 0 ) {
name[0] = '\0';
rc = KXMLNodeReadAttrCString(n, "name", name, sizeof(name), &sz_read);
if( (GetRCObject(rc) == (enum RCObject)rcAttr && GetRCState(rc) == rcNotFound) || name[0] == '\0' ) {
char* x = strrchr(path, '/');
strcpy(name, x ? x + 1 : path);
rc = 0;
} else if( rc == 0 && name[0] == '/' ) {
strcat(errmsg, "Item/@name cannot be absolute");
rc = RC(rcExe, rcDoc, rcValidating, rcName, rcInvalid);
} else if( rc != 0 ) {
strcpy(errmsg, "Item/@name");
}
}
if( rc == 0 ) {
const KNamelist* attr = NULL;
if( (rc = KXMLNodeListAttr(n, &attr)) == 0 ) {
uint32_t j = 0, count = 0;
if( (rc = KNamelistCount(attr, &count)) == 0 && count > 0 ) {
while( rc == 0 && j < count ) {
const char *attr_nm = NULL;
if( (rc = KNamelistGet(attr, j++, &attr_nm)) != 0 ) {
break;
}
if( strcmp("path", attr_nm) == 0 || strcmp("name", attr_nm) == 0 ||
strcmp("timestamp", attr_nm) == 0 || strcmp("size", attr_nm) == 0 ||
strcmp("executable", attr_nm) == 0 ) {
continue;
}
rc = RC(rcExe, rcDoc, rcValidating, rcDirEntry, rcInvalid);
strcpy(errmsg, "unknown attribute TAR/Item/@");
strcat(errmsg, attr_nm);
}
}
ReleaseComplain(KNamelistRelease, attr);
}
}
if( rc == 0 && (rc = TarFileList_Add(*files, path, name, fsz, ts, exec)) != 0 ) {
strcpy(errmsg, "adding to TAR");
}
}
ReleaseComplain(KXMLNodeRelease, n);
}
}
if( rc != 0 ) {
TarFileList_Release(*files);
*files = NULL;
}
}
}
return rc;
}
