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gStore/test/kvstore_test.cpp

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/*=============================================================================
# Filename: kvstore_test.cpp
# Author: Bookug Lobert
# Mail: zengli-bookug@pku.edu.cn
# Last Modified: 2017-03-06 15:46
# Description: test the efficience of insert, delete, search
=============================================================================*/
#include "../Util/Util.h"
#include "../Util/Triple.h"
#include "../KVstore/KVstore.h"
#include "../Parser/DBparser.h"
#include "../Parser/RDFParser.h"
using namespace std;
string db_name = "kvstore_test.db";
string rdf_path = "/home/data/DBpedia/database/dbpedia170M.nt";
int triples_num;
int entity_num;
int sub_num;
int pre_num;
int literal_num;
KVstore* kvstore;
string six_tuples_file;
//triple num per group for insert/delete
//can not be too high, otherwise the heap will over
static const int GROUP_SIZE = 1000;
//manage the ID allocate and garbage
static const int START_ID_NUM = 0;
//static const int START_ID_NUM = 1000;
/////////////////////////////////////////////////////////////////////////////////
//NOTICE:error if >= LITERAL_FIRST_ID
string free_id_file_entity; //the first is limitID, then free id list
int limitID_entity; //the current maxium ID num(maybe not used so much)
BlockInfo* freelist_entity; //free id list, reuse BlockInfo for Storage class
int allocEntityID();
void freeEntityID(int _id);
/////////////////////////////////////////////////////////////////////////////////
//NOTICE:error if >= 2*LITERAL_FIRST_ID
string free_id_file_literal;
int limitID_literal;
BlockInfo* freelist_literal;
int allocLiteralID();
void freeLiteralID(int _id);
/////////////////////////////////////////////////////////////////////////////////
//NOTICE:error if >= 2*LITERAL_FIRST_ID
string free_id_file_predicate;
int limitID_predicate;
BlockInfo* freelist_predicate;
int allocPredicateID();
void freePredicateID(int _id);
/////////////////////////////////////////////////////////////////////////////////
void initIDinfo(); //initialize the members
void resetIDinfo(); //reset the id info for build
void readIDinfo(); //read and build the free list
void writeIDinfo(); //write and empty the free list
//==================================================================================================================================================
//NOTICE:
//there are 3 ways to manage a dynamic-garbage ID list
//1. push all unused IDs into list, get top each time to alloc, push freed one to tail, push more large one if NULL
//(can use bit array if stored in disk)
//2. when free, change the mapping for non-free one whose ID is the largest currently
//(sometimes maybe the copy cost is very high)
//3. NULL first and push one if freed, get one if not empty(limit+1 if NULL)
//(when stored in disk, maybe consume larger space)
//However, this method can keep the used largest easily(no!! 1->2->3, delete 2 and delete 3, then the max 1 is not kept by limit!)
void initIDinfo()
{
//NOTICE:keep that limit-1 the maxium using ID
this->free_id_file_entity = this->getStorePath() + "/freeEntityID.dat";
this->limitID_entity = 0;
this->freelist_entity = NULL;
this->free_id_file_literal = this->getStorePath() + "/freeLiteralID.dat";
this->limitID_literal = 0;
this->freelist_literal = NULL;
this->free_id_file_predicate = this->getStorePath() + "/freePredicateID.dat";
this->limitID_predicate = 0;
this->freelist_predicate = NULL;
}
void
Database::resetIDinfo()
{
this->initIDinfo();
//this->limitID_entity = Database::START_ID_NUM;
//NOTICE:add base LITERAL_FIRST_ID for literals
//this->limitID_literal = Database::START_ID_NUM;
//this->limitID_predicate = Database::START_ID_NUM;
//BlockInfo* tmp = NULL;
//for (int i = Database::START_ID_NUM - 1; i >= 0; --i)
//{
//tmp = new BlockInfo(i, this->freelist_entity);
//this->freelist_entity = tmp;
//tmp = new BlockInfo(i, this->freelist_literal);
//this->freelist_literal = tmp;
//tmp = new BlockInfo(i, this->freelist_predicate);
//this->freelist_predicate = tmp;
//}
}
void
Database::readIDinfo()
{
this->initIDinfo();
FILE* fp = NULL;
int t = -1;
BlockInfo* bp = NULL;
fp = fopen(this->free_id_file_entity.c_str(), "r");
if (fp == NULL)
{
cout << "read entity id info error" << endl;
return;
}
//QUERY:this will reverse the original order, if change?
//Notice that if we cannot ensure that IDs are uporder and continuous, we can
//not keep an array for IDs like _entity_bitset
BlockInfo *tmp = NULL, *cur = NULL;
fread(&(this->limitID_entity), sizeof(int), 1, fp);
fread(&t, sizeof(int), 1, fp);
while (!feof(fp))
{
//if(t == 14912)
//{
//cout<<"Database::readIDinfo() - get 14912"<<endl;
//}
//bp = new BlockInfo(t, this->freelist_entity);
//this->freelist_entity = bp;
tmp = new BlockInfo(t);
if (cur == NULL)
{
this->freelist_entity = cur = tmp;
}
else
{
cur->next = tmp;
cur = tmp;
}
fread(&t, sizeof(int), 1, fp);
}
fclose(fp);
fp = NULL;
fp = fopen(this->free_id_file_literal.c_str(), "r");
if (fp == NULL)
{
cout << "read literal id info error" << endl;
return;
}
fread(&(this->limitID_literal), sizeof(int), 1, fp);
fread(&t, sizeof(int), 1, fp);
while (!feof(fp))
{
bp = new BlockInfo(t, this->freelist_literal);
this->freelist_literal = bp;
fread(&t, sizeof(int), 1, fp);
}
fclose(fp);
fp = NULL;
fp = fopen(this->free_id_file_predicate.c_str(), "r");
if (fp == NULL)
{
cout << "read predicate id info error" << endl;
return;
}
fread(&(this->limitID_predicate), sizeof(int), 1, fp);
fread(&t, sizeof(int), 1, fp);
while (!feof(fp))
{
bp = new BlockInfo(t, this->freelist_predicate);
this->freelist_predicate = bp;
fread(&t, sizeof(int), 1, fp);
}
fclose(fp);
fp = NULL;
}
void
Database::writeIDinfo()
{
//cout<<"now to write the id info"<<endl;
FILE* fp = NULL;
BlockInfo *bp = NULL, *tp = NULL;
fp = fopen(this->free_id_file_entity.c_str(), "w+");
if (fp == NULL)
{
cout << "write entity id info error" << endl;
return;
}
fwrite(&(this->limitID_entity), sizeof(int), 1, fp);
bp = this->freelist_entity;
while (bp != NULL)
{
//if(bp->num == 14912)
//{
//cout<<"Database::writeIDinfo() - get 14912"<<endl;
//}
fwrite(&(bp->num), sizeof(int), 1, fp);
tp = bp->next;
delete bp;
bp = tp;
}
fclose(fp);
fp = NULL;
fp = fopen(this->free_id_file_literal.c_str(), "w+");
if (fp == NULL)
{
cout << "write literal id info error" << endl;
return;
}
fwrite(&(this->limitID_literal), sizeof(int), 1, fp);
bp = this->freelist_literal;
while (bp != NULL)
{
fwrite(&(bp->num), sizeof(int), 1, fp);
tp = bp->next;
delete bp;
bp = tp;
}
fclose(fp);
fp = NULL;
fp = fopen(this->free_id_file_predicate.c_str(), "w+");
if (fp == NULL)
{
cout << "write predicate id info error" << endl;
return;
}
fwrite(&(this->limitID_predicate), sizeof(int), 1, fp);
bp = this->freelist_predicate;
while (bp != NULL)
{
fwrite(&(bp->num), sizeof(int), 1, fp);
tp = bp->next;
delete bp;
bp = tp;
}
fclose(fp);
fp = NULL;
}
//ID alloc garbage error(LITERAL_FIRST_ID or double) add base for literal
int
Database::allocEntityID()
{
int t;
if (this->freelist_entity == NULL)
{
t = this->limitID_entity++;
if (this->limitID_entity >= Util::LITERAL_FIRST_ID)
{
cout << "fail to alloc id for entity" << endl;
return -1;
}
}
else
{
t = this->freelist_entity->num;
BlockInfo* op = this->freelist_entity;
this->freelist_entity = this->freelist_entity->next;
delete op;
}
this->entity_num++;
return t;
}
void
Database::freeEntityID(int _id)
{
if (_id == this->limitID_entity - 1)
{
this->limitID_entity--;
}
else
{
BlockInfo* p = new BlockInfo(_id, this->freelist_entity);
this->freelist_entity = p;
}
this->entity_num--;
}
int
Database::allocLiteralID()
{
int t;
if (this->freelist_literal == NULL)
{
t = this->limitID_literal++;
if (this->limitID_literal >= Util::LITERAL_FIRST_ID)
{
cout << "fail to alloc id for literal" << endl;
return -1;
}
}
else
{
t = this->freelist_literal->num;
BlockInfo* op = this->freelist_literal;
this->freelist_literal = this->freelist_literal->next;
delete op;
}
this->literal_num++;
return t + Util::LITERAL_FIRST_ID;
}
void
Database::freeLiteralID(int _id)
{
if (_id == this->limitID_literal - 1)
{
this->limitID_literal--;
}
else
{
BlockInfo* p = new BlockInfo(_id - Util::LITERAL_FIRST_ID, this->freelist_literal);
this->freelist_literal = p;
}
this->literal_num--;
}
int
Database::allocPredicateID()
{
int t;
if (this->freelist_predicate == NULL)
{
t = this->limitID_predicate++;
if (this->limitID_predicate >= Util::LITERAL_FIRST_ID)
{
cout << "fail to alloc id for predicate" << endl;
return -1;
}
}
else
{
t = this->freelist_predicate->num;
BlockInfo* op = this->freelist_predicate;
this->freelist_predicate = this->freelist_predicate->next;
delete op;
}
this->pre_num++;
return t;
}
void
Database::freePredicateID(int _id)
{
if (_id == this->limitID_predicate - 1)
{
this->limitID_predicate--;
}
else
{
BlockInfo* p = new BlockInfo(_id, this->freelist_predicate);
this->freelist_predicate = p;
}
this->pre_num--;
}
//NOTICE+QUERY:to save memory for large cases, we can consider building one tree at a time(then release)
//Or read the rdf file on separate segments
//WARN:the ID type is int, and entity/literal are just separated by a limit
//which means that entity num <= 10^9 literal num <= 10^9 predicate num <= 2*10^9
//If we use unsigned as type, then max triple can be 10^9(edge case)
//If we use long long, no more problem, but wasteful
//Or we can consider divide entity and literal totally
//In distributed gStore, each machine's graph should be based on unique encoding IDs,
//and require that triples in each graph no more than a limit(maybe 10^9)
bool
Database::build(const string& _rdf_file)
{
//manage the id for a new database
this->resetIDinfo();
string ret = Util::getExactPath(_rdf_file.c_str());
long tv_build_begin = Util::get_cur_time();
string kv_store_path = store_path + "/kv_store";
Util::create_dir(kv_store_path);
string vstree_store_path = store_path + "/vs_store";
Util::create_dir(vstree_store_path);
if (!this->encodeRDF_new(ret)) //<-- this->kvstore->id2* trees are closed
{
return false;
}
cout << "finish encode." << endl;
//cout<<"test kv"<<this->kvstore->getIDByPredicate("<contain>")<<endl;
//this->kvstore->flush();
delete this->kvstore;
this->kvstore = NULL;
//sync();
//cout << "sync kvstore" << endl;
//this->kvstore->release();
//cout<<"release kvstore"<<endl;
long before_vstree = Util::get_cur_time();
long tv_build_end = Util::get_cur_time();
cout << "after build vstree, used " << (tv_build_end - before_vstree) << "ms." << endl;
cout << "after build, used " << (tv_build_end - tv_build_begin) << "ms." << endl;
cout << "finish build VS-Tree." << endl;
//this->vstree->saveTree();
//delete this->vstree;
//this->vstree = NULL;
//sync();
//cout << "sync vstree" << endl;
//string cmd = "rm -rf " + _entry_file;
//system(cmd.c_str());
//cout << "signature file removed" << endl;
return true;
}
//root Path of this DB + sixTuplesFile
string
Database::getSixTuplesFile()
{
return this->getStorePath() + "/" + this->six_tuples_file;
}
/* root Path of this DB + signatureBFile */
string
Database::getSignatureBFile()
{
return this->getStorePath() + "/" + this->signature_binary_file;
}
/* root Path of this DB + DBInfoFile */
string
Database::getDBInfoFile()
{
return this->getStorePath() + "/" + this->db_info_file;
}
bool
Database::saveDBInfoFile()
{
FILE* filePtr = fopen(this->getDBInfoFile().c_str(), "wb");
if (filePtr == NULL)
{
cout << "error, can not create db info file. @Database::saveDBInfoFile" << endl;
return false;
}
fseek(filePtr, 0, SEEK_SET);
fwrite(&this->triples_num, sizeof(int), 1, filePtr);
fwrite(&this->entity_num, sizeof(int), 1, filePtr);
fwrite(&this->sub_num, sizeof(int), 1, filePtr);
fwrite(&this->pre_num, sizeof(int), 1, filePtr);
fwrite(&this->literal_num, sizeof(int), 1, filePtr);
fwrite(&this->encode_mode, sizeof(int), 1, filePtr);
fclose(filePtr);
Util::triple_num = this->triples_num;
Util::pre_num = this->pre_num;
Util::entity_num = this->entity_num;
Util::literal_num = this->literal_num;
return true;
}
bool
Database::loadDBInfoFile()
{
FILE* filePtr = fopen(this->getDBInfoFile().c_str(), "rb");
if (filePtr == NULL)
{
cout << "error, can not open db info file. @Database::loadDBInfoFile" << endl;
return false;
}
fseek(filePtr, 0, SEEK_SET);
fread(&this->triples_num, sizeof(int), 1, filePtr);
fread(&this->entity_num, sizeof(int), 1, filePtr);
fread(&this->sub_num, sizeof(int), 1, filePtr);
fread(&this->pre_num, sizeof(int), 1, filePtr);
fread(&this->literal_num, sizeof(int), 1, filePtr);
fread(&this->encode_mode, sizeof(int), 1, filePtr);
fclose(filePtr);
Util::triple_num = this->triples_num;
Util::pre_num = this->pre_num;
Util::entity_num = this->entity_num;
Util::literal_num = this->literal_num;
return true;
}
//check whether the relative 3-tuples exist usually, through sp2olist
bool
Database::exist_triple(int _sub_id, int _pre_id, int _obj_id)
{
int* _objidlist = NULL;
int _list_len = 0;
(this->kvstore)->getobjIDlistBysubIDpreID(_sub_id, _pre_id, _objidlist, _list_len);
bool is_exist = false;
// for(int i = 0; i < _list_len; i ++)
// {
// if(_objidlist[i] == _obj_id)
// {
// is_exist = true;
// break;
// }
// }
if (Util::bsearch_int_uporder(_obj_id, _objidlist, _list_len) != -1)
{
is_exist = true;
}
delete[] _objidlist;
return is_exist;
}
//NOTICE: all constants are transfered to ids in memory
//this maybe not ok when size is too large!
bool
Database::encodeRDF_new(const string _rdf_file)
{
#ifdef DEBUG
//cout<< "now to log!!!" << endl;
Util::logging("In encodeRDF_new");
//cout<< "end log!!!" << endl;
#endif
int** _p_id_tuples = NULL;
int _id_tuples_max = 0;
long t1 = Util::get_cur_time();
//map sub2id, pre2id, entity/literal in obj2id, store in kvstore, encode RDF data into signature
if (!this->sub2id_pre2id_obj2id_RDFintoSignature(_rdf_file, _p_id_tuples, _id_tuples_max))
{
return false;
}
long t2 = Util::get_cur_time();
cout << "after encode, used " << (t2 - t1) << "ms." << endl;
//NOTICE:close these trees now to save memory
this->kvstore->close_entity2id();
this->kvstore->close_id2entity();
this->kvstore->close_literal2id();
this->kvstore->close_id2literal();
this->kvstore->close_predicate2id();
this->kvstore->close_id2predicate();
this->kvstore->build_subID2values(_p_id_tuples, this->triples_num);
long t3 = Util::get_cur_time();
cout << "after s2xx, used " << (t3 - t2) << "ms." << endl;
this->kvstore->build_objID2values(_p_id_tuples, this->triples_num);
long t4 = Util::get_cur_time();
cout << "after o2xx, used " << (t4 - t3) << "ms." << endl;
this->kvstore->build_preID2values(_p_id_tuples, this->triples_num);
long t5 = Util::get_cur_time();
cout << "after p2xx, used " << (t5 - t4) << "ms." << endl;
//WARN:we must free the memory for id_tuples array
for (int i = 0; i < this->triples_num; ++i)
{
delete[] _p_id_tuples[i];
}
delete[] _p_id_tuples;
bool flag = this->saveDBInfoFile();
if (!flag)
{
return false;
}
Util::logging("finish encodeRDF_new");
return true;
}
//NOTICE:in here and there in the insert/delete, we may get the maxium tuples num first
//and so we can avoid the cost of memcpy(scan quickly or use wc -l)
//However, if use compressed RDF format, how can we do it fi not using parser?
//CONSIDER: just an estimated value is ok or use vector!!!(but vector also copy when enlarge)
//and read file line numbers are also costly!
bool
Database::sub2id_pre2id_obj2id_RDFintoSignature(const string _rdf_file, int**& _p_id_tuples, int & _id_tuples_max)
{
int _id_tuples_size;
{
//initial
_id_tuples_max = 10 * 1000 * 1000;
_p_id_tuples = new int*[_id_tuples_max];
_id_tuples_size = 0;
this->sub_num = 0;
this->pre_num = 0;
this->entity_num = 0;
this->literal_num = 0;
this->triples_num = 0;
(this->kvstore)->open_entity2id(KVstore::CREATE_MODE);
(this->kvstore)->open_id2entity(KVstore::CREATE_MODE);
(this->kvstore)->open_predicate2id(KVstore::CREATE_MODE);
(this->kvstore)->open_id2predicate(KVstore::CREATE_MODE);
(this->kvstore)->open_literal2id(KVstore::CREATE_MODE);
(this->kvstore)->open_id2literal(KVstore::CREATE_MODE);
}
//Util::logging("finish initial sub2id_pre2id_obj2id");
cout << "finish initial sub2id_pre2id_obj2id" << endl;
//BETTER?:close the stdio buffer sync??
ifstream _fin(_rdf_file.c_str());
if (!_fin)
{
cout << "sub2id&pre2id&obj2id: Fail to open : " << _rdf_file << endl;
//exit(0);
return false;
}
string _six_tuples_file = this->getSixTuplesFile();
ofstream _six_tuples_fout(_six_tuples_file.c_str());
if (!_six_tuples_fout)
{
cout << "sub2id&pre2id&obj2id: Fail to open: " << _six_tuples_file << endl;
//exit(0);
return false;
}
TripleWithObjType* triple_array = new TripleWithObjType[RDFParser::TRIPLE_NUM_PER_GROUP];
//don't know the number of entity
//pre allocate entitybitset_max EntityBitSet for storing signature, double the space until the _entity_bitset is used up.
int entitybitset_max = 10000000; //set larger to avoid the copy cost
//int entitybitset_max = 10000;
EntityBitSet** _entity_bitset = new EntityBitSet*[entitybitset_max];
for (int i = 0; i < entitybitset_max; i++)
{
_entity_bitset[i] = new EntityBitSet();
_entity_bitset[i]->reset();
}
EntityBitSet _tmp_bitset;
//parse a file
RDFParser _parser(_fin);
Util::logging("==> while(true)");
while (true)
{
int parse_triple_num = 0;
_parser.parseFile(triple_array, parse_triple_num);
{
stringstream _ss;
_ss << "finish rdfparser" << this->triples_num << endl;
//Util::logging(_ss.str());
cout << _ss.str() << endl;
}
cout << "after info in sub2id_" << endl;
if (parse_triple_num == 0)
{
break;
}
//Process the Triple one by one
for (int i = 0; i < parse_triple_num; i++)
{
this->triples_num++;
//if the _id_tuples exceeds, double the space
if (_id_tuples_size == _id_tuples_max)
{
int _new_tuples_len = _id_tuples_max * 2;
int** _new_id_tuples = new int*[_new_tuples_len];
memcpy(_new_id_tuples, _p_id_tuples, sizeof(int*) * _id_tuples_max);
delete[] _p_id_tuples;
_p_id_tuples = _new_id_tuples;
_id_tuples_max = _new_tuples_len;
}
// For subject
// (all subject is entity, some object is entity, the other is literal)
string _sub = triple_array[i].getSubject();
int _sub_id = (this->kvstore)->getIDByEntity(_sub);
if (_sub_id == -1)
{
//_sub_id = this->entity_num;
_sub_id = this->allocEntityID();
//this->entity_num++;
(this->kvstore)->setIDByEntity(_sub, _sub_id);
(this->kvstore)->setEntityByID(_sub_id, _sub);
}
// For predicate
string _pre = triple_array[i].getPredicate();
int _pre_id = (this->kvstore)->getIDByPredicate(_pre);
if (_pre_id == -1)
{
//_pre_id = this->pre_num;
_pre_id = this->allocPredicateID();
//this->pre_num++;
(this->kvstore)->setIDByPredicate(_pre, _pre_id);
(this->kvstore)->setPredicateByID(_pre_id, _pre);
}
// For object
string _obj = triple_array[i].getObject();
int _obj_id = -1;
// obj is entity
if (triple_array[i].isObjEntity())
{
_obj_id = (this->kvstore)->getIDByEntity(_obj);
if (_obj_id == -1)
{
//_obj_id = this->entity_num;
_obj_id = this->allocEntityID();
//this->entity_num++;
(this->kvstore)->setIDByEntity(_obj, _obj_id);
(this->kvstore)->setEntityByID(_obj_id, _obj);
}
}
//obj is literal
if (triple_array[i].isObjLiteral())
{
_obj_id = (this->kvstore)->getIDByLiteral(_obj);
if (_obj_id == -1)
{
//_obj_id = Util::LITERAL_FIRST_ID + (this->literal_num);
_obj_id = this->allocLiteralID();
//this->literal_num++;
(this->kvstore)->setIDByLiteral(_obj, _obj_id);
(this->kvstore)->setLiteralByID(_obj_id, _obj);
//#ifdef DEBUG
//if(_obj == "\"Bob\"")
//{
//cout << "this is id for Bob: " << _obj_id << endl;
//}
//cout<<"literal should be bob: " << kvstore->getLiteralByID(_obj_id)<<endl;
//cout<<"id for bob: "<<kvstore->getIDByLiteral("\"Bob\"")<<endl;
//#endif
}
}
// For id_tuples
_p_id_tuples[_id_tuples_size] = new int[3];
_p_id_tuples[_id_tuples_size][0] = _sub_id;
_p_id_tuples[_id_tuples_size][1] = _pre_id;
_p_id_tuples[_id_tuples_size][2] = _obj_id;
_id_tuples_size++;
#ifdef DEBUG_PRECISE
// save six tuples
{
_six_tuples_fout << _sub_id << '\t'
<< _pre_id << '\t'
<< _obj_id << '\t'
<< _sub << '\t'
<< _pre << '\t'
<< _obj << endl;
}
#endif
//TODO:the memory cost maybe too larger if combine teh below process here
//we can do below after this function or after all B+trees are built and closed
//and we can decide the length of signature according to entity num then
//1. after all b+trees: empty id_tuples and only open id2string, reload rdf file and encode(using string for entity/literal)
//
//2. after thsi function or after all B+trees: close others and only use id_tuples to encode(no need to read file again, which is too costly)
//not encoded with string but all IDs(not using encode for string regex matching, then this is ok!)
//Because we encode with ID, then Signature has to be changed(and dynamic sig length)
//use same encode strategy for entity/literal/predicate, and adjust the rate of the 3 parts according to real case
//What is more, if the system memory is enough(precisely, the memory you want to assign to gstore - to vstree/entity_sig_array),
//we can also set the sig length larger(which should be included in config file)
//_entity_bitset is used up, double the space
if (this->entity_num >= entitybitset_max)
{
//cout<<"to double entity bitset num"<<endl;
EntityBitSet** _new_entity_bitset = new EntityBitSet*[entitybitset_max * 2];
//TODO+BETTER?:if use pointer for array, avoid the copy cost of entitybitset, but consumes more mmeory
//if the triple size is 1-2 billion, then the memory cost will be very large!!!
memcpy(_new_entity_bitset, _entity_bitset, sizeof(EntityBitSet*) * entitybitset_max);
delete[] _entity_bitset;
_entity_bitset = _new_entity_bitset;
int tmp = entitybitset_max * 2;
for (int i = entitybitset_max; i < tmp; i++)
{
_entity_bitset[i] = new EntityBitSet();
_entity_bitset[i]->reset();
}
entitybitset_max = tmp;
}
{
_tmp_bitset.reset();
Signature::encodePredicate2Entity(_pre_id, _tmp_bitset, Util::EDGE_OUT);
Signature::encodeStr2Entity(_obj.c_str(), _tmp_bitset);
*_entity_bitset[_sub_id] |= _tmp_bitset;
}
if (triple_array[i].isObjEntity())
{
_tmp_bitset.reset();
Signature::encodePredicate2Entity(_pre_id, _tmp_bitset, Util::EDGE_IN);
Signature::encodeStr2Entity(_sub.c_str(), _tmp_bitset);
//cout<<"objid: "<<_obj_id <<endl;
//when 15999 error
//WARN:id allocated can be very large while the num is not so much
//This means that maybe the space for the _obj_id is not allocated now
//NOTICE:we prepare the free id list in uporder and contiguous, so in build process
//this can work well
*_entity_bitset[_obj_id] |= _tmp_bitset;
}
}
}
cout<<"==> end while(true)"<<endl;
delete[] triple_array;
_fin.close();
_six_tuples_fout.close();
{
//save all entity_signature into binary file
string _sig_binary_file = this->getSignatureBFile();
FILE* _sig_fp = fopen(_sig_binary_file.c_str(), "wb");
if (_sig_fp == NULL) {
cout << "Failed to open : " << _sig_binary_file << endl;
}
//NOTICE:in build process, all IDs are continuous growing
//EntityBitSet _all_bitset;
for (int i = 0; i < this->entity_num; i++)
{
SigEntry* _sig = new SigEntry(EntitySig(*_entity_bitset[i]), i);
fwrite(_sig, sizeof(SigEntry), 1, _sig_fp);
//_all_bitset |= *_entity_bitset[i];
delete _sig;
}
fclose(_sig_fp);
for (int i = 0; i < entitybitset_max; i++)
{
delete _entity_bitset[i];
}
delete[] _entity_bitset;
}
{
stringstream _ss;
_ss << "finish sub2id pre2id obj2id" << endl;
_ss << "tripleNum is " << this->triples_num << endl;
_ss << "entityNum is " << this->entity_num << endl;
_ss << "preNum is " << this->pre_num << endl;
_ss << "literalNum is " << this->literal_num << endl;
Util::logging(_ss.str());
cout << _ss.str() << endl;
}
return true;
}
bool
Database::insertTriple(const TripleWithObjType& _triple, vector<int>* _vertices, vector<int>* _predicates)
{
//cout<<endl<<"the new triple is:"<<endl;
//cout<<_triple.subject<<endl;
//cout<<_triple.predicate<<endl;
//cout<<_triple.object<<endl;
//int sid1 = this->kvstore->getIDByEntity("<http://www.Department7.University0.edu/UndergraduateStudent394>");
//int sid2 = this->kvstore->getIDByEntity("<http://www.Department7.University0.edu/UndergraduateStudent395>");
//int oid1 = this->kvstore->getIDByEntity("<ub:UndergraduateStudent>");
//int oid2 = this->kvstore->getIDByEntity("<UndergraduateStudent394@Department7.University0.edu>");
//cout<<sid1<<" "<<sid2<<" "<<oid1<<" "<<oid2<<endl;
long tv_kv_store_begin = Util::get_cur_time();
int _sub_id = (this->kvstore)->getIDByEntity(_triple.subject);
bool _is_new_sub = false;
//if sub does not exist
if (_sub_id == -1)
{
_is_new_sub = true;
//_sub_id = this->entity_num++;
_sub_id = this->allocEntityID();
//cout<<"this is a new sub id"<<endl;
//if(_sub_id == 14912)
//{
//cout<<"get the error one"<<endl;
//cout<<_sub_id<<endl<<_triple.subject<<endl;
//cout<<_triple.predicate<<endl<<_triple.object<<endl;
//}
this->sub_num++;
(this->kvstore)->setIDByEntity(_triple.subject, _sub_id);
(this->kvstore)->setEntityByID(_sub_id, _triple.subject);
//update the string buffer
if (_sub_id < this->entity_buffer_size)
{
this->entity_buffer->set(_sub_id, _triple.subject);
}
if (_vertices != NULL)
_vertices->push_back(_sub_id);
}
int _pre_id = (this->kvstore)->getIDByPredicate(_triple.predicate);
bool _is_new_pre = false;
//if pre does not exist
if (_pre_id == -1)
{
_is_new_pre = true;
//_pre_id = this->pre_num++;
_pre_id = this->allocPredicateID();
(this->kvstore)->setIDByPredicate(_triple.predicate, _pre_id);
(this->kvstore)->setPredicateByID(_pre_id, _triple.predicate);
if (_predicates != NULL)
_predicates->push_back(_pre_id);
}
//object is either entity or literal
int _obj_id = -1;
bool _is_new_obj = false;
bool is_obj_entity = _triple.isObjEntity();
if (is_obj_entity)
{
_obj_id = (this->kvstore)->getIDByEntity(_triple.object);
if (_obj_id == -1)
{
_is_new_obj = true;
//_obj_id = this->entity_num++;
_obj_id = this->allocEntityID();
(this->kvstore)->setIDByEntity(_triple.object, _obj_id);
(this->kvstore)->setEntityByID(_obj_id, _triple.object);
//update the string buffer
if (_obj_id < this->entity_buffer_size)
{
this->entity_buffer->set(_obj_id, _triple.object);
}
if (_vertices != NULL)
_vertices->push_back(_obj_id);
}
}
else
{
_obj_id = (this->kvstore)->getIDByLiteral(_triple.object);
if (_obj_id == -1)
{
_is_new_obj = true;
//_obj_id = Util::LITERAL_FIRST_ID + this->literal_num;
_obj_id = this->allocLiteralID();
(this->kvstore)->setIDByLiteral(_triple.object, _obj_id);
(this->kvstore)->setLiteralByID(_obj_id, _triple.object);
//update the string buffer
int tid = _obj_id - Util::LITERAL_FIRST_ID;
if (tid < this->literal_buffer_size)
{
this->literal_buffer->set(tid, _triple.object);
}
if (_vertices != NULL)
_vertices->push_back(_obj_id);
}
}
//if this is not a new triple, return directly
bool _triple_exist = false;
if (!_is_new_sub && !_is_new_pre && !_is_new_obj)
{
_triple_exist = this->exist_triple(_sub_id, _pre_id, _obj_id);
}
//debug
// {
// stringstream _ss;
// _ss << this->literal_num << endl;
// _ss <<"ids: " << _sub_id << " " << _pre_id << " " << _obj_id << " " << _triple_exist << endl;
// Util::logging(_ss.str());
// }
if (_triple_exist)
{
cout << "this triple already exist" << endl;
return false;
}
else
{
this->triples_num++;
}
//cout<<"the triple spo ids: "<<_sub_id<<" "<<_pre_id<<" "<<_obj_id<<endl;
//update sp2o op2s s2po o2ps s2o o2s etc.
int updateLen = (this->kvstore)->updateTupleslist_insert(_sub_id, _pre_id, _obj_id);
//int* list = NULL;
//int len = 0;
//int root = this->kvstore->getIDByEntity("<root>");
//int contain = this->kvstore->getIDByPredicate("<contain>");
//this->kvstore->getobjIDlistBysubIDpreID(root, contain, list, len);
//cout<<root<<" "<<contain<<endl;
//if(len == 0)
//{
//cout<<"no result"<<endl;
//}
//for(int i = 0; i < len; ++i)
//{
//cout << this->kvstore->getEntityByID(list[i])<<" "<<list[i]<<endl;
//}
long tv_kv_store_end = Util::get_cur_time();
EntityBitSet _sub_entity_bitset;
_sub_entity_bitset.reset();
this->encodeTriple2SubEntityBitSet(_sub_entity_bitset, &_triple);
//if new entity then insert it, else update it.
if (_is_new_sub)
{
cout<<"to insert: "<<_sub_id<<" "<<this->kvstore->getEntityByID(_sub_id)<<endl;
SigEntry _sig(_sub_id, _sub_entity_bitset);
(this->vstree)->insertEntry(_sig);
}
else
{
//cout<<"to update: "<<_sub_id<<" "<<this->kvstore->getEntityByID(_sub_id)<<endl;
(this->vstree)->updateEntry(_sub_id, _sub_entity_bitset);
}
//if the object is an entity, then update or insert this entity's entry.
if (is_obj_entity)
{
EntityBitSet _obj_entity_bitset;
_obj_entity_bitset.reset();
this->encodeTriple2ObjEntityBitSet(_obj_entity_bitset, &_triple);
if (_is_new_obj)
{
//cout<<"to insert: "<<_obj_id<<" "<<this->kvstore->getEntityByID(_obj_id)<<endl;
SigEntry _sig(_obj_id, _obj_entity_bitset);
(this->vstree)->insertEntry(_sig);
}
else
{
//cout<<"to update: "<<_obj_id<<" "<<this->kvstore->getEntityByID(_obj_id)<<endl;
(this->vstree)->updateEntry(_obj_id, _obj_entity_bitset);
}
}
long tv_vs_store_end = Util::get_cur_time();
//debug
{
cout << "update kv_store, used " << (tv_kv_store_end - tv_kv_store_begin) << "ms." << endl;
cout << "update vs_store, used " << (tv_vs_store_end - tv_kv_store_end) << "ms." << endl;
}
return true;
//return updateLen;
}
bool
Database::removeTriple(const TripleWithObjType& _triple, vector<int>* _vertices, vector<int>* _predicates)
{
long tv_kv_store_begin = Util::get_cur_time();
int _sub_id = (this->kvstore)->getIDByEntity(_triple.subject);
int _pre_id = (this->kvstore)->getIDByPredicate(_triple.predicate);
int _obj_id = (this->kvstore)->getIDByEntity(_triple.object);
if (_obj_id == -1)
{
_obj_id = (this->kvstore)->getIDByLiteral(_triple.object);
}
if (_sub_id == -1 || _pre_id == -1 || _obj_id == -1)
{
return false;
}
bool _exist_triple = this->exist_triple(_sub_id, _pre_id, _obj_id);
if (!_exist_triple)
{
return false;
}
else
{
this->triples_num--;
}
cout << "triple existence checked" << endl;
//remove from sp2o op2s s2po o2ps s2o o2s
//sub2id, pre2id and obj2id will not be updated
(this->kvstore)->updateTupleslist_remove(_sub_id, _pre_id, _obj_id);
cout << "11 trees updated" << endl;
long tv_kv_store_end = Util::get_cur_time();
int sub_degree = (this->kvstore)->getEntityDegree(_sub_id);
//if subject become an isolated point, remove its corresponding entry
if (sub_degree == 0)
{
cout<<"to remove entry for sub"<<endl;
cout<<_sub_id << " "<<this->kvstore->getEntityByID(_sub_id)<<endl;
this->kvstore->subEntityByID(_sub_id);
this->kvstore->subIDByEntity(_triple.subject);
(this->vstree)->removeEntry(_sub_id);
this->freeEntityID(_sub_id);
this->sub_num--;
//update the string buffer
if (_sub_id < this->entity_buffer_size)
{
this->entity_buffer->del(_sub_id);
}
if (_vertices != NULL)
_vertices->push_back(_sub_id);
}
//else re-calculate the signature of subject & replace that in vstree
else
{
//cout<<"to replace entry for sub"<<endl;
//cout<<_sub_id << " "<<this->kvstore->getEntityByID(_sub_id)<<endl;
EntityBitSet _entity_bitset;
_entity_bitset.reset();
this->calculateEntityBitSet(_sub_id, _entity_bitset);
//NOTICE:can not use updateEntry as insert because this is in remove
//In insert we can add a OR operation and all is ok
(this->vstree)->replaceEntry(_sub_id, _entity_bitset);
}
//cout<<"subject dealed"<<endl;
bool is_obj_entity = _triple.isObjEntity();
int obj_degree;
if (is_obj_entity)
{
obj_degree = this->kvstore->getEntityDegree(_obj_id);
if (obj_degree == 0)
{
//cout<<"to remove entry for obj"<<endl;
//cout<<_obj_id << " "<<this->kvstore->getEntityByID(_obj_id)<<endl;
this->kvstore->subEntityByID(_obj_id);
this->kvstore->subIDByEntity(_triple.object);
this->vstree->removeEntry(_obj_id);
this->freeEntityID(_obj_id);
//update the string buffer
if (_obj_id < this->entity_buffer_size)
{
this->entity_buffer->del(_obj_id);
}
if (_vertices != NULL)
_vertices->push_back(_obj_id);
}
else
{
//cout<<"to replace entry for obj"<<endl;
//cout<<_obj_id << " "<<this->kvstore->getEntityByID(_obj_id)<<endl;
EntityBitSet _entity_bitset;
_entity_bitset.reset();
this->calculateEntityBitSet(_obj_id, _entity_bitset);
this->vstree->replaceEntry(_obj_id, _entity_bitset);
}
}
else
{
obj_degree = this->kvstore->getLiteralDegree(_obj_id);
if (obj_degree == 0)
{
this->kvstore->subLiteralByID(_obj_id);
this->kvstore->subIDByLiteral(_triple.object);
this->freeLiteralID(_obj_id);
//update the string buffer
int tid = _obj_id - Util::LITERAL_FIRST_ID;
if (tid < this->literal_buffer_size)
{
this->literal_buffer->del(tid);
}
if (_vertices != NULL)
_vertices->push_back(_obj_id);
}
}
//cout<<"object dealed"<<endl;
int pre_degree = this->kvstore->getPredicateDegree(_pre_id);
if (pre_degree == 0)
{
this->kvstore->subPredicateByID(_pre_id);
this->kvstore->subIDByPredicate(_triple.predicate);
this->freePredicateID(_pre_id);
if (_predicates != NULL)
_predicates->push_back(_pre_id);
}
//cout<<"predicate dealed"<<endl;
long tv_vs_store_end = Util::get_cur_time();
//debug
{
cout << "update kv_store, used " << (tv_kv_store_end - tv_kv_store_begin) << "ms." << endl;
cout << "update vs_store, used " << (tv_vs_store_end - tv_kv_store_end) << "ms." << endl;
}
return true;
}
bool
Database::insert(std::string _rdf_file)
{
bool flag = this->load();
if (!flag)
{
return false;
}
cout << "finish loading" << endl;
long tv_load = Util::get_cur_time();
int success_num = 0;
ifstream _fin(_rdf_file.c_str());
if (!_fin)
{
cout << "fail to open : " << _rdf_file << ".@insert_test" << endl;
//exit(0);
return false;
}
//NOTICE+WARN:we can not load all triples into memory all at once!!!
//the parameter in build and insert must be the same, because RDF parser also use this
//for build process, this one can be big enough if memory permits
//for insert/delete process, this can not be too large, otherwise too costly
TripleWithObjType* triple_array = new TripleWithObjType[RDFParser::TRIPLE_NUM_PER_GROUP];
//parse a file
RDFParser _parser(_fin);
int triple_num = 0;
#ifdef DEBUG
Util::logging("==> while(true)");
#endif
while (true)
{
int parse_triple_num = 0;
_parser.parseFile(triple_array, parse_triple_num);
#ifdef DEBUG
stringstream _ss;
//NOTICE:this is not same as others, use parse_triple_num directly
_ss << "finish rdfparser" << parse_triple_num << endl;
Util::logging(_ss.str());
cout << _ss.str() << endl;
#endif
if (parse_triple_num == 0)
{
break;
}
//Process the Triple one by one
success_num += this->insert(triple_array, parse_triple_num);
//some maybe invalid or duplicate
//triple_num += parse_triple_num;
}
delete[] triple_array;
long tv_insert = Util::get_cur_time();
cout << "after insert, used " << (tv_insert - tv_load) << "ms." << endl;
//BETTER:update kvstore and vstree separately, to lower the memory cost
//flag = this->vstree->saveTree();
//if (!flag)
//{
//return false;
//}
//flag = this->saveDBInfoFile();
//if (!flag)
//{
//return false;
//}
cout << "insert rdf triples done." << endl;
cout<<"inserted triples num: "<<success_num<<endl;
//int* list = NULL;
//int len = 0;
//int root = this->kvstore->getIDByEntity("<root>");
//int contain = this->kvstore->getIDByPredicate("<contain>");
//this->kvstore->getobjIDlistBysubIDpreID(root, contain, list, len);
//cout<<root<<" "<<contain<<endl;
//if(len == 0)
//{
//cout<<"no result"<<endl;
//}
//for(int i = 0; i < len; ++i)
//{
//cout << this->kvstore->getEntityByID(list[i])<<" "<<list[i]<<endl;
//}
//cout<<endl;
//int t = this->kvstore->getIDByEntity("<node5>");
//cout<<t<<endl;
//cout<<this->kvstore->getEntityByID(0)<<endl;
return true;
}
bool
Database::remove(std::string _rdf_file)
{
bool flag = this->load();
if (!flag)
{
return false;
}
cout << "finish loading" << endl;
long tv_load = Util::get_cur_time();
int success_num = 0;
ifstream _fin(_rdf_file.c_str());
if (!_fin)
{
cout << "fail to open : " << _rdf_file << ".@remove_test" << endl;
return false;
}
//NOTICE+WARN:we can not load all triples into memory all at once!!!
TripleWithObjType* triple_array = new TripleWithObjType[RDFParser::TRIPLE_NUM_PER_GROUP];
//parse a file
RDFParser _parser(_fin);
//int triple_num = 0;
#ifdef DEBUG
Util::logging("==> while(true)");
#endif
while (true)
{
int parse_triple_num = 0;
_parser.parseFile(triple_array, parse_triple_num);
#ifdef DEBUG
stringstream _ss;
//NOTICE:this is not same as others, use parse_triple_num directly
_ss << "finish rdfparser" << parse_triple_num << endl;
Util::logging(_ss.str());
cout << _ss.str() << endl;
#endif
if (parse_triple_num == 0)
{
break;
}
success_num += this->remove(triple_array, parse_triple_num);
//some maybe invalid or duplicate
//triple_num -= parse_triple_num;
}
//TODO:better to free this just after id_tuples are ok
//(only when using group insertion/deletion)
//or reduce the array size
delete[] triple_array;
long tv_remove = Util::get_cur_time();
cout << "after remove, used " << (tv_remove - tv_load) << "ms." << endl;
//flag = this->vstree->saveTree();
//if (!flag)
//{
//return false;
//}
//flag = this->saveDBInfoFile();
//if (!flag)
//{
//return false;
//}
cout << "remove rdf triples done." << endl;
cout<<"removed triples num: "<<success_num<<endl;
return true;
}
int
Database::insert(const TripleWithObjType* _triples, int _triple_num)
{
vector<int> vertices, predicates;
int valid_num = 0;
#ifdef USE_GROUP_INSERT
//NOTICE:this is called by insert(file) or query()(but can not be too large),
//assume that db is loaded already
int** id_tuples = new int*[_triple_num];
int i = 0;
//for(i = 0; i < _triple_num; ++i)
//{
//id_tuples[i] = new int[3];
//}
map<int, EntityBitSet> old_sigmap;
map<int, EntityBitSet> new_sigmap;
set<int> new_entity;
map<int, EntityBitSet>::iterator it;
EntityBitSet tmpset;
tmpset.reset();
int subid, objid, preid;
bool is_obj_entity;
for (i = 0; i < _triple_num; ++i)
{
bool is_new_sub = false, is_new_pre = false, is_new_obj = false;
string sub = _triples[i].getSubject();
subid = this->kvstore->getIDByEntity(sub);
if (subid == -1)
{
is_new_sub = true;
subid = this->allocEntityID();
cout << "this is a new subject: " << sub << " " << subid << endl;
this->sub_num++;
this->kvstore->setIDByEntity(sub, subid);
this->kvstore->setEntityByID(subid, sub);
new_entity.insert(subid);
//add info and update buffer
vertices.push_back(subid);
if (subid < this->entity_buffer_size)
{
this->entity_buffer->set(subid, sub);
}
}
string pre = _triples[i].getPredicate();
preid = this->kvstore->getIDByPredicate(pre);
if (preid == -1)
{
is_new_pre = true;
preid = this->allocPredicateID();
this->kvstore->setIDByPredicate(pre, preid);
this->kvstore->setPredicateByID(preid, pre);
predicates.push_back(preid);
}
is_obj_entity = _triples[i].isObjEntity();
string obj = _triples[i].getObject();
if (is_obj_entity)
{
objid = this->kvstore->getIDByEntity(obj);
if (objid == -1)
{
is_new_obj = true;
objid = this->allocEntityID();
cout << "this is a new object: " << obj << " " << objid << endl;
//this->obj_num++;
this->kvstore->setIDByEntity(obj, objid);
this->kvstore->setEntityByID(objid, obj);
new_entity.insert(objid);
//add info and update
vertices.push_back(objid);
if (objid < this->entity_buffer_size)
{
this->entity_buffer->set(objid, obj);
}
}
}
else //isObjLiteral
{
objid = this->kvstore->getIDByLiteral(obj);
if (objid == -1)
{
is_new_obj = true;
objid = this->allocLiteralID();
//this->obj_num++;
this->kvstore->setIDByLiteral(obj, objid);
this->kvstore->setLiteralByID(objid, obj);
//add info and update
vertices.push_back(objid);
int tid = objid - Util::LITERAL_FIRST_ID;
if (tid < this->literal_buffer_size)
{
this->literal_buffer->set(tid, obj);
}
}
}
bool triple_exist = false;
if (!is_new_sub && !is_new_pre && !is_new_obj)
{
triple_exist = this->exist_triple(subid, preid, objid);
}
if (triple_exist)
{
#ifdef DEBUG
cout << "this triple exist" << endl;
#endif
continue;
}
#ifdef DEBUG
cout << "this triple not exist" << endl;
#endif
id_tuples[valid_num] = new int[3];
id_tuples[valid_num][0] = subid;
id_tuples[valid_num][1] = preid;
id_tuples[valid_num][2] = objid;
this->triples_num++;
valid_num++;
tmpset.reset();
Signature::encodePredicate2Entity(preid, tmpset, Util::EDGE_OUT);
Signature::encodeStr2Entity(obj.c_str(), tmpset);
if (new_entity.find(subid) != new_entity.end())
{
it = new_sigmap.find(subid);
if (it != new_sigmap.end())
{
it->second |= tmpset;
}
else
{
new_sigmap[subid] = tmpset;
}
}
else
{
it = old_sigmap.find(subid);
if (it != old_sigmap.end())
{
it->second |= tmpset;
}
else
{
old_sigmap[subid] = tmpset;
}
}
if (is_obj_entity)
{
tmpset.reset();
Signature::encodePredicate2Entity(preid, tmpset, Util::EDGE_IN);
Signature::encodeStr2Entity(sub.c_str(), tmpset);
if (new_entity.find(objid) != new_entity.end())
{
it = new_sigmap.find(objid);
if (it != new_sigmap.end())
{
it->second |= tmpset;
}
else
{
new_sigmap[objid] = tmpset;
}
}
else
{
it = old_sigmap.find(objid);
if (it != old_sigmap.end())
{
it->second |= tmpset;
}
else
{
old_sigmap[objid] = tmpset;
}
}
}
}
#ifdef DEBUG
cout << "old sigmap size: " << old_sigmap.size() << endl;
cout << "new sigmap size: " << new_sigmap.size() << endl;
cout << "valid num: " << valid_num << endl;
#endif
//NOTICE:need to sort and remove duplicates, update the valid num
//Notice that duplicates in a group can csuse problem
//We finish this by spo cmp
//this->kvstore->updateTupleslist_insert(_sub_id, _pre_id, _obj_id);
//sort and update kvstore: 11 indexes
//
//BETTER:maybe also use int* here with a size to start
//NOTICE:all kvtrees are opened now, one by one if memory is bottleneck
//
//spo cmp: s2p s2o s2po sp2o
{
#ifdef DEBUG
cout << "INSRET PROCESS: to spo cmp and update" << endl;
#endif
qsort(id_tuples, valid_num, sizeof(int*), KVstore::_spo_cmp);
//To remove duplicates
//int ti = 1, tj = 1;
//while(tj < valid_num)
//{
//if(id_tuples[tj][0] != id_tuples[tj-1][0] || id_tuples[tj][1] != id_tuples[tj-1][1] || id_tuples[tj][2] != id_tuples[tj-1][2])
//{
//id_tuples[ti][0] = id_tuples[tj][0];
//id_tuples[ti][1] = id_tuples[tj][1];
//id_tuples[ti][2] = id_tuples[tj][2];
//ti++;
//}
//tj++;
//}
//for(tj = ti; tj < valid_num; ++tj)
//{
//delete[] id_tuples[tj];
//id_tuples[tj] = NULL;
//}
//valid_num = ti;
//
//Notice that below already consider duplicates in loop
vector<int> oidlist_s;
vector<int> pidlist_s;
vector<int> oidlist_sp;
vector<int> pidoidlist_s;
bool _sub_change = true;
bool _sub_pre_change = true;
bool _pre_change = true;
for (int i = 0; i < valid_num; ++i)
if (i + 1 == valid_num || (id_tuples[i][0] != id_tuples[i + 1][0] || id_tuples[i][1] != id_tuples[i + 1][1] || id_tuples[i][2] != id_tuples[i + 1][2]))
{
int _sub_id = id_tuples[i][0];
int _pre_id = id_tuples[i][1];
int _obj_id = id_tuples[i][2];
oidlist_s.push_back(_obj_id);
oidlist_sp.push_back(_obj_id);
pidoidlist_s.push_back(_pre_id);
pidoidlist_s.push_back(_obj_id);
pidlist_s.push_back(_pre_id);
_sub_change = (i + 1 == valid_num) || (id_tuples[i][0] != id_tuples[i + 1][0]);
_pre_change = (i + 1 == valid_num) || (id_tuples[i][1] != id_tuples[i + 1][1]);
_sub_pre_change = _sub_change || _pre_change;
if (_sub_pre_change)
{
#ifdef DEBUG
cout << "update sp2o: " << _sub_id << " " << _pre_id << " " << oidlist_sp.size() << endl;
#endif
cout << this->kvstore->getEntityByID(_sub_id) << endl;
cout << this->kvstore->getPredicateByID(_pre_id) << endl;
//this->kvstore->updateInsert_sp2o(_sub_id, _pre_id, oidlist_sp);
oidlist_sp.clear();
}
if (_sub_change)
{
#ifdef DEBUG
cout << "update s2p: " << _sub_id << " " << pidlist_s.size() << endl;
#endif
//this->kvstore->updateInsert_s2p(_sub_id, pidlist_s);
pidlist_s.clear();
#ifdef DEBUG
cout << "update s2po: " << _sub_id << " " << pidoidlist_s.size() << endl;
#endif
this->kvstore->updateInsert_s2values(_sub_id, pidoidlist_s);
pidoidlist_s.clear();
#ifdef DEBUG
cout << "update s2o: " << _sub_id << " " << oidlist_s.size() << endl;
#endif
sort(oidlist_s.begin(), oidlist_s.end());
//this->kvstore->updateInsert_s2o(_sub_id, oidlist_s);
oidlist_s.clear();
}
}
#ifdef DEBUG
cout << "INSERT PROCESS: OUT s2po..." << endl;
#endif
}
//ops cmp: o2p o2s o2ps op2s
{
#ifdef DEBUG
cout << "INSRET PROCESS: to ops cmp and update" << endl;
#endif
qsort(id_tuples, valid_num, sizeof(int**), KVstore::_ops_cmp);
vector<int> sidlist_o;
vector<int> sidlist_op;
vector<int> pidsidlist_o;
vector<int> pidlist_o;
bool _obj_change = true;
bool _pre_change = true;
bool _obj_pre_change = true;
for (int i = 0; i < valid_num; ++i)
if (i + 1 == valid_num || (id_tuples[i][0] != id_tuples[i + 1][0] || id_tuples[i][1] != id_tuples[i + 1][1] || id_tuples[i][2] != id_tuples[i + 1][2]))
{
int _sub_id = id_tuples[i][0];
int _pre_id = id_tuples[i][1];
int _obj_id = id_tuples[i][2];
sidlist_o.push_back(_sub_id);
sidlist_op.push_back(_sub_id);
pidsidlist_o.push_back(_pre_id);
pidsidlist_o.push_back(_sub_id);
pidlist_o.push_back(_pre_id);
_obj_change = (i + 1 == valid_num) || (id_tuples[i][2] != id_tuples[i + 1][2]);
_pre_change = (i + 1 == valid_num) || (id_tuples[i][1] != id_tuples[i + 1][1]);
_obj_pre_change = _obj_change || _pre_change;
if (_obj_pre_change)
{
#ifdef DEBUG
cout << "update op2s: " << _obj_id << " " << _pre_id << " " << sidlist_op.size() << endl;
#endif
//this->kvstore->updateInsert_op2s(_obj_id, _pre_id, sidlist_op);
sidlist_op.clear();
}
if (_obj_change)
{
#ifdef DEBUG
cout << "update o2s: " << _obj_id << " " << sidlist_o.size() << endl;
#endif
sort(sidlist_o.begin(), sidlist_o.end());
//this->kvstore->updateInsert_o2s(_obj_id, sidlist_o);
sidlist_o.clear();
#ifdef DEBUG
cout << "update o2ps: " << _obj_id << " " << pidsidlist_o.size() << endl;
#endif
this->kvstore->updateInsert_o2values(_obj_id, pidsidlist_o);
pidsidlist_o.clear();
#ifdef DEBUG
cout << "update o2p: " << _obj_id << " " << pidlist_o.size() << endl;
#endif
//this->kvstore->updateInsert_o2p(_obj_id, pidlist_o);
pidlist_o.clear();
}
}
#ifdef DEBUG
cout << "INSERT PROCESS: OUT o2ps..." << endl;
#endif
}
//pso cmp: p2s p2o p2so
{
#ifdef DEBUG
cout << "INSRET PROCESS: to pso cmp and update" << endl;
#endif
qsort(id_tuples, valid_num, sizeof(int*), KVstore::_pso_cmp);
vector<int> sidlist_p;
vector<int> oidlist_p;
vector<int> sidoidlist_p;
bool _pre_change = true;
bool _sub_change = true;
//bool _pre_sub_change = true;
for (int i = 0; i < valid_num; i++)
if (i + 1 == valid_num || (id_tuples[i][0] != id_tuples[i + 1][0] || id_tuples[i][1] != id_tuples[i + 1][1] || id_tuples[i][2] != id_tuples[i + 1][2]))
{
int _sub_id = id_tuples[i][0];
int _pre_id = id_tuples[i][1];
int _obj_id = id_tuples[i][2];
oidlist_p.push_back(_obj_id);
sidoidlist_p.push_back(_sub_id);
sidoidlist_p.push_back(_obj_id);
sidlist_p.push_back(_sub_id);
_pre_change = (i + 1 == valid_num) || (id_tuples[i][1] != id_tuples[i + 1][1]);
_sub_change = (i + 1 == valid_num) || (id_tuples[i][0] != id_tuples[i + 1][0]);
//_pre_sub_change = _pre_change || _sub_change;
if (_pre_change)
{
#ifdef DEBUG
cout << "update p2s: " << _pre_id << " " << sidlist_p.size() << endl;
#endif
//this->kvstore->updateInsert_p2s(_pre_id, sidlist_p);
sidlist_p.clear();
#ifdef DEBUG
cout << "update p2o: " << _pre_id << " " << oidlist_p.size() << endl;
#endif
sort(oidlist_p.begin(), oidlist_p.end());
//this->kvstore->updateInsert_p2o(_pre_id, oidlist_p);
oidlist_p.clear();
#ifdef DEBUG
cout << "update p2so: " << _pre_id << " " << sidoidlist_p.size() << endl;
#endif
this->kvstore->updateInsert_p2values(_pre_id, sidoidlist_p);
sidoidlist_p.clear();
}
}
#ifdef DEBUG
cout << "INSERT PROCESS: OUT p2so..." << endl;
#endif
}
for (int i = 0; i < valid_num; ++i)
{
delete[] id_tuples[i];
}
delete[] id_tuples;
for (it = old_sigmap.begin(); it != old_sigmap.end(); ++it)
{
this->vstree->updateEntry(it->first, it->second);
}
for (it = new_sigmap.begin(); it != new_sigmap.end(); ++it)
{
SigEntry _sig(it->first, it->second);
this->vstree->insertEntry(_sig);
}
#else
//NOTICE:we deal with insertions one by one here
//Callers should save the vstree(node and info) after calling this function
for (int i = 0; i < _triple_num; ++i)
{
bool ret = this->insertTriple(_triples[i], &vertices, &predicates);
if(ret)
{
valid_num++;
}
}
#endif
return valid_num;
}
int
Database::remove(const TripleWithObjType* _triples, int _triple_num)
{
vector<int> vertices, predicates;
int valid_num = 0;
#ifdef USE_GROUP_DELETE
//NOTICE:this is called by remove(file) or query()(but can not be too large),
//assume that db is loaded already
int** id_tuples = new int*[_triple_num];
int i = 0;
//for(i = 0; i < _triple_num; ++i)
//{
//id_tuples[i] = new int[3];
//}
//map<int, EntityBitSet> sigmap;
//map<int, EntityBitSet>::iterator it;
EntityBitSet tmpset;
tmpset.reset();
int subid, objid, preid;
bool is_obj_entity;
for (i = 0; i < _triple_num; ++i)
{
string sub = _triples[i].getSubject();
subid = this->kvstore->getIDByEntity(sub);
if(subid == -1)
{
continue;
}
string pre = _triples[i].getPredicate();
preid = this->kvstore->getIDByPredicate(pre);
if(preid == -1)
{
continue;
}
is_obj_entity = _triples[i].isObjEntity();
string obj = _triples[i].getObject();
if (is_obj_entity)
{
objid = this->kvstore->getIDByEntity(obj);
}
else //isObjLiteral
{
objid = this->kvstore->getIDByLiteral(obj);
}
if(objid == -1)
{
continue;
}
//if (subid == -1 || preid == -1 || objid == -1)
//{
//continue;
//}
bool _exist_triple = this->exist_triple(subid, preid, objid);
if (!_exist_triple)
{
continue;
}
id_tuples[valid_num] = new int[3];
id_tuples[valid_num][0] = subid;
id_tuples[valid_num][1] = preid;
id_tuples[valid_num][2] = objid;
this->triples_num--;
valid_num++;
}
//NOTICE:sort and remove duplicates, update the valid num
//Notice that duplicates in a group can cause problem
int sub_degree, obj_degree, pre_degree;
string tmpstr;
//sort and update kvstore: 11 indexes
//
//BETTER:maybe also use int* here with a size to start
//NOTICE:all kvtrees are opened now, one by one if memory is bottleneck
//
//spo cmp: s2p s2o s2po sp2o
{
#ifdef DEBUG
cout << "INSRET PROCESS: to spo cmp and update" << endl;
#endif
qsort(id_tuples, valid_num, sizeof(int*), KVstore::_spo_cmp);
vector<int> oidlist_s;
vector<int> pidlist_s;
vector<int> oidlist_sp;
vector<int> pidoidlist_s;
bool _sub_change = true;
bool _sub_pre_change = true;
bool _pre_change = true;
for (int i = 0; i < valid_num; ++i)
if (i + 1 == valid_num || (id_tuples[i][0] != id_tuples[i + 1][0] || id_tuples[i][1] != id_tuples[i + 1][1] || id_tuples[i][2] != id_tuples[i + 1][2]))
{
int _sub_id = id_tuples[i][0];
int _pre_id = id_tuples[i][1];
int _obj_id = id_tuples[i][2];
oidlist_s.push_back(_obj_id);
oidlist_sp.push_back(_obj_id);
pidoidlist_s.push_back(_pre_id);
pidoidlist_s.push_back(_obj_id);
pidlist_s.push_back(_pre_id);
_sub_change = (i + 1 == valid_num) || (id_tuples[i][0] != id_tuples[i + 1][0]);
_pre_change = (i + 1 == valid_num) || (id_tuples[i][1] != id_tuples[i + 1][1]);
_sub_pre_change = _sub_change || _pre_change;
if (_sub_pre_change)
{
this->kvstore->updateRemove_sp2o(_sub_id, _pre_id, oidlist_sp);
oidlist_sp.clear();
}
if (_sub_change)
{
this->kvstore->updateRemove_s2p(_sub_id, pidlist_s);
pidlist_s.clear();
this->kvstore->updateRemove_s2po(_sub_id, pidoidlist_s);
pidoidlist_s.clear();
sort(oidlist_s.begin(), oidlist_s.end());
this->kvstore->updateRemove_s2o(_sub_id, oidlist_s);
oidlist_s.clear();
sub_degree = (this->kvstore)->getEntityDegree(_sub_id);
if (sub_degree == 0)
{
tmpstr = this->kvstore->getEntityByID(_sub_id);
this->kvstore->subEntityByID(_sub_id);
this->kvstore->subIDByEntity(tmpstr);
(this->vstree)->removeEntry(_sub_id);
this->freeEntityID(_sub_id);
this->sub_num--;
//add info and update buffer
vertices.push_back(_sub_id);
if (_sub_id < this->entity_buffer_size)
{
this->entity_buffer->del(_sub_id);
}
}
else
{
tmpset.reset();
this->calculateEntityBitSet(_sub_id, tmpset);
this->vstree->replaceEntry(_sub_id, tmpset);
}
}
}
#ifdef DEBUG
cout << "INSERT PROCESS: OUT s2po..." << endl;
#endif
}
//ops cmp: o2p o2s o2ps op2s
{
#ifdef DEBUG
cout << "INSRET PROCESS: to ops cmp and update" << endl;
#endif
qsort(id_tuples, valid_num, sizeof(int**), KVstore::_ops_cmp);
vector<int> sidlist_o;
vector<int> sidlist_op;
vector<int> pidsidlist_o;
vector<int> pidlist_o;
bool _obj_change = true;
bool _pre_change = true;
bool _obj_pre_change = true;
for (int i = 0; i < valid_num; ++i)
if (i + 1 == valid_num || (id_tuples[i][0] != id_tuples[i + 1][0] || id_tuples[i][1] != id_tuples[i + 1][1] || id_tuples[i][2] != id_tuples[i + 1][2]))
{
int _sub_id = id_tuples[i][0];
int _pre_id = id_tuples[i][1];
int _obj_id = id_tuples[i][2];
sidlist_o.push_back(_sub_id);
sidlist_op.push_back(_sub_id);
pidsidlist_o.push_back(_pre_id);
pidsidlist_o.push_back(_sub_id);
pidlist_o.push_back(_pre_id);
_obj_change = (i + 1 == valid_num) || (id_tuples[i][2] != id_tuples[i + 1][2]);
_pre_change = (i + 1 == valid_num) || (id_tuples[i][1] != id_tuples[i + 1][1]);
_obj_pre_change = _obj_change || _pre_change;
if (_obj_pre_change)
{
this->kvstore->updateRemove_op2s(_obj_id, _pre_id, sidlist_op);
sidlist_op.clear();
}
if (_obj_change)
{
sort(sidlist_o.begin(), sidlist_o.end());
this->kvstore->updateRemove_o2s(_obj_id, sidlist_o);
sidlist_o.clear();
this->kvstore->updateRemove_o2ps(_obj_id, pidsidlist_o);
pidsidlist_o.clear();
this->kvstore->updateRemove_o2p(_obj_id, pidlist_o);
pidlist_o.clear();
is_obj_entity = this->objIDIsEntityID(_obj_id);
if (is_obj_entity)
{
obj_degree = this->kvstore->getEntityDegree(_obj_id);
if (obj_degree == 0)
{
tmpstr = this->kvstore->getEntityByID(_obj_id);
this->kvstore->subEntityByID(_obj_id);
this->kvstore->subIDByEntity(tmpstr);
(this->vstree)->removeEntry(_obj_id);
this->freeEntityID(_obj_id);
//add info and update buffer
vertices.push_back(_obj_id);
if (_obj_id < this->entity_buffer_size)
{
this->entity_buffer->del(_obj_id);
}
}
else
{
tmpset.reset();
this->calculateEntityBitSet(_obj_id, tmpset);
this->vstree->replaceEntry(_obj_id, tmpset);
}
}
else
{
obj_degree = this->kvstore->getLiteralDegree(_obj_id);
if (obj_degree == 0)
{
tmpstr = this->kvstore->getLiteralByID(_obj_id);
this->kvstore->subLiteralByID(_obj_id);
this->kvstore->subIDByLiteral(tmpstr);
this->freeLiteralID(_obj_id);
//add info and update buffer
vertices.push_back(_obj_id);
int tid = _obj_id - Util::LITERAL_FIRST_ID;
if (tid < this->literal_buffer_size)
{
this->literal_buffer->del(tid);
}
}
}
}
}
#ifdef DEBUG
cout << "INSERT PROCESS: OUT o2ps..." << endl;
#endif
}
//pso cmp: p2s p2o p2so
{
#ifdef DEBUG
cout << "INSRET PROCESS: to pso cmp and update" << endl;
#endif
qsort(id_tuples, valid_num, sizeof(int*), KVstore::_pso_cmp);
vector<int> sidlist_p;
vector<int> oidlist_p;
vector<int> sidoidlist_p;
bool _pre_change = true;
bool _sub_change = true;
//bool _pre_sub_change = true;
for (int i = 0; i < valid_num; i++)
if (i + 1 == valid_num || (id_tuples[i][0] != id_tuples[i + 1][0] || id_tuples[i][1] != id_tuples[i + 1][1] || id_tuples[i][2] != id_tuples[i + 1][2]))
{
int _sub_id = id_tuples[i][0];
int _pre_id = id_tuples[i][1];
int _obj_id = id_tuples[i][2];
oidlist_p.push_back(_obj_id);
sidoidlist_p.push_back(_sub_id);
sidoidlist_p.push_back(_obj_id);
sidlist_p.push_back(_sub_id);
_pre_change = (i + 1 == valid_num) || (id_tuples[i][1] != id_tuples[i + 1][1]);
_sub_change = (i + 1 == valid_num) || (id_tuples[i][0] != id_tuples[i + 1][0]);
//_pre_sub_change = _pre_change || _sub_change;
if (_pre_change)
{
this->kvstore->updateRemove_p2s(_pre_id, sidlist_p);
sidlist_p.clear();
sort(oidlist_p.begin(), oidlist_p.end());
this->kvstore->updateRemove_p2o(_pre_id, oidlist_p);
oidlist_p.clear();
this->kvstore->updateRemove_p2so(_pre_id, sidoidlist_p);
sidoidlist_p.clear();
pre_degree = this->kvstore->getPredicateDegree(_pre_id);
if (pre_degree == 0)
{
tmpstr = this->kvstore->getPredicateByID(_pre_id);
this->kvstore->subPredicateByID(_pre_id);
this->kvstore->subIDByPredicate(tmpstr);
this->freePredicateID(_pre_id);
//add pre info
predicates.push_back(_pre_id);
}
}
}
#ifdef DEBUG
cout << "INSERT PROCESS: OUT p2so..." << endl;
#endif
}
for (int i = 0; i < valid_num; ++i)
{
delete[] id_tuples[i];
}
delete[] id_tuples;
#else
//NOTICE:we deal with deletions one by one here
//Callers should save the vstree(node and info) after calling this function
for (int i = 0; i < _triple_num; ++i)
{
bool ret = this->removeTriple(_triples[i], &vertices, &predicates);
if(ret)
{
valid_num++;
}
}
#endif
return valid_num;
}
bool
Database::objIDIsEntityID(int _id)
{
return _id < Util::LITERAL_FIRST_ID;
}
int
main(int argc, char * argv[])
{
//chdir(dirname(argv[0]));
#ifdef DEBUG
Util util;
#endif
return 0;
}
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