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Commit df90bac0 authored by Studer Gabriel's avatar Studer Gabriel
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Use forward declaration to avoid external dependency on SQLite3

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modules/conop/src/compound_lib.cc
+ 60
− 47
View file @ df90bac0
......@@ -28,6 +28,7 @@
#include "compound_lib.hh"
#include <ost/version.hh>
#include <ost/string_ref.hh>
#include <sqlite3.h>
using boost::format;
......@@ -105,13 +106,32 @@ const char* INSERT_CHEMLIB_INFO_STATEMENT="insert into chemlib_info
}
struct CompoundLib::Database {
Database(): ptr(NULL) { }
Database(sqlite3* p): ptr(p) { }
~Database() {
if (ptr) {
int retval = sqlite3_close(ptr);
if (retval != SQLITE_OK) {
LOG_ERROR("Problem while closing SQLite db for CompoundLib: "
<< sqlite3_errmsg(ptr));
}
}
}
sqlite3* ptr;
};
void CompoundLib::SetChemLibInfo(void){
sqlite3_stmt* stmt=NULL;
//~ if (!conn_) {
//~ if (!db_->ptr) {
//~ LOG_ERROR(sqlite3_errmsg("Connection to DB not made"));
//~ }
int retval=sqlite3_prepare_v2(conn_, INSERT_CHEMLIB_INFO_STATEMENT,
int retval=sqlite3_prepare_v2(db_->ptr, INSERT_CHEMLIB_INFO_STATEMENT,
strlen(INSERT_CHEMLIB_INFO_STATEMENT), &stmt, NULL);
time_t rawtime;
struct tm * timeinfo;
......@@ -131,10 +151,10 @@ void CompoundLib::SetChemLibInfo(void){
}
retval=sqlite3_step(stmt);
if (SQLITE_DONE!=retval) {
if (sqlite3_errcode(conn_)==SQLITE_CONSTRAINT) {
if (sqlite3_errcode(db_->ptr)==SQLITE_CONSTRAINT) {
LOG_ERROR("chemlib info already exists");
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
}
sqlite3_finalize(stmt);
......@@ -144,7 +164,7 @@ Date CompoundLib::GetCreationDate(void){
String query="SELECT creation_date FROM chemlib_info";
sqlite3_stmt* stmt;
int retval=sqlite3_prepare_v2(conn_, query.c_str(),
int retval=sqlite3_prepare_v2(db_->ptr, query.c_str(),
static_cast<int>(query.length()),
&stmt, NULL);
if (SQLITE_OK==retval) {
......@@ -174,7 +194,7 @@ String CompoundLib::GetOSTVersionUsed() {
sqlite3_stmt* stmt;
String version;
int retval=sqlite3_prepare_v2(conn_, query.c_str(),
int retval=sqlite3_prepare_v2(db_->ptr, query.c_str(),
static_cast<int>(query.length()),
&stmt, NULL);
if (SQLITE_OK==retval) {
......@@ -202,7 +222,7 @@ String CompoundLib::GetOSTVersionUsed() {
void CompoundLib::AddCompound(const CompoundPtr& compound)
{
sqlite3_stmt* stmt=NULL;
int retval=sqlite3_prepare_v2(conn_, INSERT_COMPOUND_STATEMENT,
int retval=sqlite3_prepare_v2(db_->ptr, INSERT_COMPOUND_STATEMENT,
strlen(INSERT_COMPOUND_STATEMENT), &stmt, NULL);
String crea_date_str, modi_date_str;
if (SQLITE_OK==retval) {
......@@ -233,27 +253,27 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
sqlite3_bind_text(stmt, 11, compound->GetInchiKey().c_str(),
compound->GetInchiKey().length(), NULL);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
sqlite3_finalize(stmt);
return;
}
retval=sqlite3_step(stmt);
if (SQLITE_DONE!=retval) {
if (sqlite3_errcode(conn_)==SQLITE_CONSTRAINT) {
if (sqlite3_errcode(db_->ptr)==SQLITE_CONSTRAINT) {
LOG_ERROR("Compound '" << compound->GetID() << "' already exists for the "
<< compound->GetDialectAsString() << " dialect.");
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
}
sqlite3_finalize(stmt);
sqlite3_int64 compound_id=sqlite3_last_insert_rowid(conn_);
sqlite3_int64 compound_id=sqlite3_last_insert_rowid(db_->ptr);
// insert atoms
const AtomSpecList& al=compound->GetAtomSpecs();
std::vector<sqlite3_int64> atom_ids(al.size(), 0);
for (AtomSpecList::const_iterator i=al.begin(), e=al.end(); i!=e; ++i) {
const AtomSpec& a=*i;
retval=sqlite3_prepare_v2(conn_, INSERT_ATOM_STATEMENT,
retval=sqlite3_prepare_v2(db_->ptr, INSERT_ATOM_STATEMENT,
strlen(INSERT_ATOM_STATEMENT), &stmt, NULL);
if (SQLITE_OK==retval) {
sqlite3_bind_int64(stmt, 1, compound_id);
......@@ -267,16 +287,16 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
sqlite3_bind_int(stmt, 8, a.ordinal);
retval=sqlite3_step(stmt);
assert(retval==SQLITE_DONE);
atom_ids[a.ordinal]=sqlite3_last_insert_rowid(conn_);
atom_ids[a.ordinal]=sqlite3_last_insert_rowid(db_->ptr);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
sqlite3_finalize(stmt);
}
const BondSpecList& bl=compound->GetBondSpecs();
for (BondSpecList::const_iterator i=bl.begin(), e=bl.end(); i!=e; ++i) {
const BondSpec& b=*i;
retval=sqlite3_prepare_v2(conn_, INSERT_BOND_STATEMENT,
retval=sqlite3_prepare_v2(db_->ptr, INSERT_BOND_STATEMENT,
strlen(INSERT_BOND_STATEMENT), &stmt, NULL);
if (SQLITE_OK==retval) {
sqlite3_bind_int64(stmt, 1, compound_id);
......@@ -287,7 +307,7 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
retval=sqlite3_step(stmt);
assert(retval==SQLITE_DONE);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
sqlite3_finalize(stmt);
}
......@@ -296,23 +316,23 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
CompoundLibPtr CompoundLib::Copy(const String& filename) const
{
CompoundLibPtr clone=CompoundLibPtr(new CompoundLib);
int retval=sqlite3_open(filename.c_str(), &clone->conn_);
int retval=sqlite3_open(filename.c_str(), &clone->db_->ptr);
if (SQLITE_OK==retval) {
sqlite3_backup* backup;
backup=sqlite3_backup_init(clone->conn_, "main", conn_, "main");
backup=sqlite3_backup_init(clone->db_->ptr, "main", db_->ptr, "main");
if (backup){
sqlite3_backup_step(backup, -1);
sqlite3_backup_finish(backup);
}
int rc=sqlite3_errcode(clone->conn_);
int rc=sqlite3_errcode(clone->db_->ptr);
if (rc!=SQLITE_OK) {
LOG_ERROR(sqlite3_errmsg(clone->conn_));
LOG_ERROR(sqlite3_errmsg(clone->db_->ptr));
return CompoundLibPtr();
}
return clone;
}
LOG_ERROR(sqlite3_errmsg(clone->conn_));
LOG_ERROR(sqlite3_errmsg(clone->db_->ptr));
return CompoundLibPtr();
}
......@@ -321,18 +341,18 @@ CompoundLibPtr CompoundLib::Copy(const String& filename) const
CompoundLibPtr CompoundLib::Create(const String& database)
{
CompoundLibPtr lib(new CompoundLib);
int retval=sqlite3_open(database.c_str(), &lib->conn_);
int retval=sqlite3_open(database.c_str(), &lib->db_->ptr);
if (SQLITE_OK==retval) {
const char** cmd=CREATE_CMD;
while (*cmd) {
sqlite3_stmt* stmt;
retval=sqlite3_prepare_v2(lib->conn_, *cmd, strlen(*cmd), &stmt, NULL);
retval=sqlite3_prepare_v2(lib->db_->ptr, *cmd, strlen(*cmd), &stmt, NULL);
if (SQLITE_OK==retval) {
retval=sqlite3_step(stmt);
sqlite3_finalize(stmt);
assert(SQLITE_DONE==retval);
} else {
LOG_ERROR(sqlite3_errmsg(lib->conn_));
LOG_ERROR(sqlite3_errmsg(lib->db_->ptr));
sqlite3_finalize(stmt);
return CompoundLibPtr();
}
......@@ -340,7 +360,7 @@ CompoundLibPtr CompoundLib::Create(const String& database)
}
return lib;
}
LOG_ERROR(sqlite3_errmsg(lib->conn_));
LOG_ERROR(sqlite3_errmsg(lib->db_->ptr));
return CompoundLibPtr();
}
......@@ -349,28 +369,28 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
{
int flags=readonly ? SQLITE_OPEN_READONLY : SQLITE_OPEN_READWRITE;
CompoundLibPtr lib(new CompoundLib);
int retval=sqlite3_open_v2(database.c_str(), &lib->conn_, flags, NULL);
int retval=sqlite3_open_v2(database.c_str(), &lib->db_->ptr, flags, NULL);
if (SQLITE_OK!=retval) {
LOG_ERROR(sqlite3_errmsg(lib->conn_));
LOG_ERROR(sqlite3_errmsg(lib->db_->ptr));
return CompoundLibPtr();
}
// check if column chem_type exists in database
String aq="SELECT chem_type FROM chem_compounds LIMIT 1";
sqlite3_stmt* stmt;
retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
retval=sqlite3_prepare_v2(lib->db_->ptr, aq.c_str(),
static_cast<int>(aq.length()),
&stmt, NULL);
lib->chem_type_available_ = retval==SQLITE_OK;
sqlite3_finalize(stmt);
aq="SELECT name FROM chem_compounds LIMIT 1";
retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
retval=sqlite3_prepare_v2(lib->db_->ptr, aq.c_str(),
static_cast<int>(aq.length()),
&stmt, NULL);
lib->name_available_ = retval==SQLITE_OK;
sqlite3_finalize(stmt);
// check if InChIs are available
aq="SELECT inchi_code FROM chem_compounds LIMIT 1";
retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
retval=sqlite3_prepare_v2(lib->db_->ptr, aq.c_str(),
static_cast<int>(aq.length()),
&stmt, NULL);
lib->inchi_available_ = retval==SQLITE_OK;
......@@ -386,7 +406,7 @@ void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) const {
"FROM atoms WHERE compound_id=%d "
"ORDER BY ordinal ASC") % pk);
sqlite3_stmt* stmt;
int retval=sqlite3_prepare_v2(conn_, aq.c_str(),
int retval=sqlite3_prepare_v2(db_->ptr, aq.c_str(),
static_cast<int>(aq.length()),
&stmt, NULL);
if (SQLITE_OK==retval) {
......@@ -401,7 +421,7 @@ void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) const {
comp->AddAtom(atom_sp);
}
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
sqlite3_finalize(stmt);
}
......@@ -416,7 +436,7 @@ void CompoundLib::LoadBondsFromDB(CompoundPtr comp, int pk) const {
"LEFT JOIN atoms AS a1 ON b.atom_one=a1.id "
"LEFT JOIN atoms as a2 ON b.atom_two=a2.id "
"WHERE b.compound_id=%d") % pk);
int retval=sqlite3_prepare_v2(conn_, aq.c_str(),
int retval=sqlite3_prepare_v2(db_->ptr, aq.c_str(),
static_cast<int>(aq.length()),
&stmt, NULL);
if (SQLITE_OK==retval) {
......@@ -429,7 +449,7 @@ void CompoundLib::LoadBondsFromDB(CompoundPtr comp, int pk) const {
comp->AddBond(bond_sp);
}
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
sqlite3_finalize(stmt);
}
......@@ -457,7 +477,7 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
query+=" FROM chem_compounds"
" WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
sqlite3_stmt* stmt;
int retval=sqlite3_prepare_v2(conn_, query.c_str(),
int retval=sqlite3_prepare_v2(db_->ptr, query.c_str(),
static_cast<int>(query.length()),
&stmt, NULL);
if (SQLITE_OK==retval) {
......@@ -503,7 +523,7 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
}
assert(SQLITE_DONE==sqlite3_step(stmt));
} else {
LOG_ERROR("ERROR: " << sqlite3_errmsg(conn_));
LOG_ERROR("ERROR: " << sqlite3_errmsg(db_->ptr));
sqlite3_finalize(stmt);
return CompoundPtr();
}
......@@ -513,23 +533,16 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
CompoundLib::CompoundLib():
CompoundLibBase(),
db_(new Database),
compound_cache_(),
conn_(NULL),
chem_type_available_(false),
name_available_(),
inchi_available_(),
creation_date_(),
ost_version_used_()
{
}
ost_version_used_() { }
CompoundLib::~CompoundLib() {
if (conn_) {
int retval = sqlite3_close(conn_);
if (retval != SQLITE_OK) {
LOG_ERROR("Problem while closing SQLite db for CompoundLib: "
<< sqlite3_errmsg(conn_));
}
}
delete db_;
}
}}
modules/conop/src/compound_lib.hh
+ 2
− 3
View file @ df90bac0
......@@ -22,8 +22,6 @@
#include <map>
#include <boost/shared_ptr.hpp>
#include <sqlite3.h>
#include "module_config.hh"
#include "compound.hh"
#include "compound_lib_base.hh"
......@@ -54,8 +52,9 @@ private:
void LoadAtomsFromDB(CompoundPtr comp, int pk) const;
void LoadBondsFromDB(CompoundPtr comp, int pk) const;
private:
struct Database;
Database* db_;
mutable CompoundMap compound_cache_;
sqlite3* conn_;
bool chem_type_available_; // wether pdbx_type is available in db
bool name_available_; // wether name is available in db
bool inchi_available_; //whether inchi is available in db
......
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