static stKVDatabaseConf *constructFromString(const char *xmlString) {
stHash *hash = hackParseXmlString(xmlString);
stKVDatabaseConf *databaseConf = NULL;
const char *type = getXmlValueRequired(hash, "conf_type");
const char *dbTag = getXmlValueRequired(hash, "db_tag");
if (!stString_eq(type, dbTag)) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "Database XML tag \"%s\" did not match st_kv_database_conf type attribute", dbTag, type);
}
if (stString_eq(type, "tokyo_cabinet")) {
databaseConf = stKVDatabaseConf_constructTokyoCabinet(getXmlValueRequired(hash, "database_dir"));
} else if (stString_eq(type, "kyoto_tycoon")) {
databaseConf = stKVDatabaseConf_constructKyotoTycoon(getXmlValueRequired(hash, "host"),
getXmlPort(hash),
getXmlTimeout(hash),
getXMLMaxKTRecordSize(hash),
getXMLMaxKTBulkSetSize(hash),
getXMLMaxKTBulkSetNumRecords(hash),
getXmlValueRequired(hash, "database_dir"),
stHash_search(hash, "database_name"));
} else if (stString_eq(type, "mysql")) {
databaseConf = stKVDatabaseConf_constructMySql(getXmlValueRequired(hash, "host"), getXmlPort(hash),
getXmlValueRequired(hash, "user"), getXmlValueRequired(hash, "password"),
getXmlValueRequired(hash, "database_name"), getXmlValueRequired(hash, "table_name"));
} else {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "invalid database type \"%s\"", type);
}
stHash_destruct(hash);
return databaseConf;
}
/* Parse XML string into a hash. This parses all attributes of all tags
* into values. st_kv_database_conf type is stored as conf_type,
* database tag is stores as db_tag. This does minimal error checking
* and is really lame.
*/
static stHash *hackParseXmlString(const char *xmlString) {
stHash *hash = stHash_construct3(stHash_stringKey, stHash_stringEqualKey, free, free);
char *toReplace[5] = { "</", "<", "/>", ">", "=" };
char *cA = stString_replace(xmlString, toReplace[0], " "), *cA2;
for (int64_t i = 1; i < 5; i++) {
cA2 = stString_replace(cA, toReplace[i], " ");
free(cA);
cA = cA2;
}
getExpectedToken(&cA2, "st_kv_database_conf");
stHash_insert(hash, stString_copy("conf_type"), getKeyValue(&cA2, "type"));
stHash_insert(hash, stString_copy("db_tag"), getNextToken(&cA2));
char *key;
while (((key = getNextToken(&cA2)) != NULL) && !stString_eq(key, "st_kv_database_conf")) {
char *value = getNextToken(&cA2);
if (value == NULL) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "failed to to get value for key \"%s\"", key);
}
if (stHash_search(hash, key) != NULL) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "got a duplicate entry in the database conf string \"%s\"", key);
}
stHash_insert(hash, key, value);
}
if(!stString_eq(key, "st_kv_database_conf")) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "got an unexpected final entry \"%s\"", key);
}
free(key);
free(cA);
return hash;
}
/* assert sanity of nodeCompLink */
void mafTreeNodeCompLink_assert(struct mafTreeNodeCompLink *ncLink) {
#ifndef NDEBUG
if (ncLink != NULL) {
assert(stString_eq(stTree_getLabel(ncLink->node), ncLink->comp->seq->orgSeqName));
}
#endif
}
static void getExpectedToken(char **tokenStream, const char *expected) {
char *cA = getNextToken(tokenStream);
if (!stString_eq(cA, expected)) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID,
"BUG: expected the token: %s in database XML string, but I got: %s from the stream %s",
expected, cA, *tokenStream);
}
free(cA);
}
bool stTree_equals(stTree *tree1, stTree *tree2) {
if (stTree_getBranchLength(tree1) != stTree_getBranchLength(tree2)) {
return false;
}
if (!stString_eq(stTree_getLabel(tree1), stTree_getLabel(tree2))) {
return false;
}
int numChildren = stTree_getChildNumber(tree1);
if (stTree_getChildNumber(tree2) != numChildren) {
return false;
}
for (int i = 0; i < numChildren; i++) {
if (!stTree_equals(stTree_getChild(tree1, i), stTree_getChild(tree2, i))) {
return false;
}
}
return true;
}
