Merge branch 'develop' into qt5_port

.gitlab-ci.yml

@@ -38,6 +38,7 @@ test:centos7.3:
     - module load Perl/5.22.2-goolf-1.7.20
     - module load HH-suite/2.0.16-goolf-1.7.20-Boost-1.53.0-Python-2.7.11
     - module load OpenMM/6.1-goolf-1.7.20-Python-2.7.11
+    - module load SQLite/3.9.2-goolf-1.7.20
     - echo "... done running centos7.3 'before_script'."
   script:
   - echo "Testing on CentOS 7..."
@@ -57,6 +58,8 @@ test:centos7.3:
              -DEIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include
              -DFFTW_LIBRARY=$EBROOTFFTW/lib/libfftw3f.a
              -DFFTW_INCLUDE_DIR=$EBROOTFFTW/include
+             -DSQLITE3_LIBRARY=$EBROOTSQLITE/lib/libsqlite3.so
+             -DSQLITE3_INCLUDE_DIR=$EBROOTSQLITE/include
              -DBOOST_ROOT=$EBROOTBOOST
              -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake
              -DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so

CHANGELOG.txt

+Changes in Release 1.x.x
+--------------------------------------------------------------------------------
+
+ * Use system provided SQLite3 library
+
 Changes in Release 1.9.0
 --------------------------------------------------------------------------------
 

CMakeLists.txt

@@ -234,7 +234,8 @@ else()
 endif()
 
 find_package(Eigen 3.2.0 REQUIRED)
-find_package(Python 2.7 REQUIRED)
+find_package(Python 2.4 REQUIRED)
+find_package(SQLite3 3.7.13 REQUIRED)
 
 if(USE_NUMPY)
   find_package(Numpy REQUIRED)
@@ -307,6 +308,7 @@ include_directories(${Boost_INCLUDE_DIRS}
                     ${TIFF_INCLUDE_DIR}
                     ${PNG_INCLUDE_DIRS}
                     ${OPEN_MM_INCLUDE_DIRS}
+                    ${SQLITE3_INCLUDE_DIRS}
                     )
 if(USE_NUMPY)
 include_directories(${PYTHON_NUMPY_INCLUDE_DIR})

cmake_support/FindSQLite3.cmake

+# Once done this will define
+# - Find SQLite3
+# Find the native SQLite3 includes and library
+# 
+#  SQLITE3_INCLUDE_DIRS  - SQLite3 include dir.
+#  SQLITE3_LIBRARIES     - List of libraries when using SQLite3.
+#  SQLITE3_FOUND         - True if SQLite3 found.
+
+find_path(SQLITE3_INCLUDE_DIR sqlite3.h)
+find_library(SQLITE3_LIBRARY NAMES sqlite3)
+
+# handle the QUIETLY and REQUIRED arguments and set SQLITE3_FOUND to TRUE if 
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
+
+mark_as_advanced(SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
+
+SET(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})
+SET(SQLITE3_LIBRARIES ${SQLITE3_LIBRARY})

docker/Dockerfile

@@ -47,6 +47,7 @@ RUN apt-get update -y && apt-get install -y cmake \
                                             swig \
                                             clustalw \
                                             python-virtualenv \
+                                            libsqlite3-dev \
                                             locales && \
                       # CLEANUP
                       rm -rf /var/lib/apt/lists/*

modules/conop/src/compound_lib.cc

@@ -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

@@ -22,9 +22,6 @@
 #include <map>
 #include <boost/shared_ptr.hpp>
 
-// our own local copy of sqlite3
-#include <ost/db/sqlite3.h>
-
 #include "module_config.hh"
 #include "compound.hh"
 #include "compound_lib_base.hh"
@@ -55,8 +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

modules/db/src/CMakeLists.txt

 set(OST_DB_HEADERS
 sqlite_wrap.hh
-sqlite3.h
 sqlite_conv.hh
 module_config.hh
 )
 
 set(OST_DB_SOURCES
 sqlite_wrap.cc
-sqlite3.c
 )
 
 module(NAME db SOURCES ${OST_DB_SOURCES} HEADERS ${OST_DB_HEADERS} 
-       DEPENDS_ON ost_base)
+       DEPENDS_ON ost_base sqlite3)
 if(WIN32)
   set_target_properties(ost_db PROPERTIES LINK_FLAGS "/DEF:${CMAKE_CURRENT_SOURCE_DIR}/sqlite3.def")
   add_definitions(/DSQLITE_ENABLE_COLUMN_METADATA)

modules/db/src/sqlite_conv.hh

@@ -19,7 +19,7 @@
 #ifndef OST_IO_SQLITE_CONV_HH
 #define OST_IO_SQLITE_CONV_HH
 
-#include "sqlite3.h"
+#include <sqlite3.h>
 
 #include <ost/db/module_config.hh>
 

modules/db/src/sqlite_wrap.hh

@@ -29,7 +29,7 @@
 #include <ost/base.hh>
 #include <ost/message.hh>
 
-#include "sqlite3.h"
+#include <sqlite3.h>
 #include "sqlite_conv.hh"
 
 namespace ost { namespace db {

modules/doc/install.rst

@@ -33,6 +33,7 @@ required version is given in parentheses.
 * `Boost <http://boost.org>`_ (1.53)
 * `zlib <https://zlib.net/>`_ (usually comes with Boost or system)
 * `Eigen3 <http://eigen.tuxfamily.org>`_ (3.2.0)
+* `SQLite3 <https://www3.sqlite.org>`_ (3.7.13)
 
 When you enable support for image processing, you will need:
 
@@ -215,6 +216,10 @@ can influence it.
     starting with `libtiff`)
   * `TIFF_INCLUDE_DIR` defines the include folder of libtiff (contains include
     files directly)
+  * `SQLITE3_LIBRARY` defines the location of the SQLite3 library (file name starting
+    with `libsqlite3`)
+  * `SQLITE3_INCLUDE_DIR` defines the include folder of SQLite3 (contains include
+    files directly)
   * Usually, you will receive errors for those variables when executing `cmake`
     and set them accordingly as needed.
 
@@ -300,7 +305,7 @@ All the dependencies can be installed from the package manager as follows:
 
   sudo apt-get install cmake sip-dev libtiff-dev libfftw3-dev libeigen3-dev \
                libpng-dev python-all python2.7 python-qt4 libboost-all-dev \
-               qt4-qtconfig qt4-qmake libqt4-dev libpng-dev
+               qt4-qtconfig qt4-qmake libqt4-dev libpng-dev libsqlite3-dev
 
 Now, all dependencies are located in standard locations and cmake will
 automatically find them without the need to pass any additional parameters. The
@@ -314,22 +319,6 @@ version of OpenStructure.
           -DOPTIMIZE=ON
 
 
-**Fedora 26 without GUI**
-
-All the dependencies can be installed from the package manager as follows:
-
-.. code-block:: bash
-
-  sudo dnf install cmake eigen3-devel boost-devel libpng-devel python2-devel \
-                   fftw-devel libtiff-devel
-
-Here, we compile a version without GUI as follows:
-
-.. code-block:: bash
-
-  cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF
-
-
 **macOS with Homebrew without GUI**
 
 `Homebrew <https://brew.sh/>`_ can be used to conveniently install all packages

singularity/Singularity.1.9.0

@@ -55,8 +55,9 @@ apt-get update -y && apt-get install -y cmake \
 										doxygen \
 										swig \
 										clustalw \
-                                        python-virtualenv \
-                                        locales
+                    python-virtualenv \
+                    libsqlite3-dev \
+                    locales
 
 # SET LOCALE
 ############