scipion-pyworkflow 3.7.0__py3-none-any.whl

pyworkflow/mapper/sqlite_db.py

@@ -0,0 +1,145 @@
+# **************************************************************************
+# *
+# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address 'scipion@cnb.csic.es'
+# *
+# **************************************************************************
+
+
+"""
+This module contains some sqlite basic tools to handle Databases.
+"""
+
+import logging
+logger = logging.getLogger(__name__)
+from sqlite3 import dbapi2 as sqlite
+from sqlite3 import OperationalError as OperationalError
+from pyworkflow.utils import STATUS, getExtraLogInfo, Config
+
+
+class SqliteDb:
+    """Class to handle a Sqlite database.
+    It will create connection, execute queries and commands.
+    """
+    OPEN_CONNECTIONS = {}  # Store all connections made
+
+    def __init__(self):
+        self._reuseConnections = False
+
+    def _createConnection(self, dbName, timeout):
+        """Establish db connection"""
+        self._dbName = dbName
+        if self._reuseConnections and dbName in self.OPEN_CONNECTIONS:
+            self.connection = self.OPEN_CONNECTIONS[dbName]
+        else:
+            # self.closeConnection(dbName)  # Close the connect if exists for this db
+            self.connection = sqlite.Connection(dbName, timeout, check_same_thread=False)
+            self.connection.row_factory = sqlite.Row
+            self.OPEN_CONNECTIONS[dbName] = self.connection
+            logger.debug("Connection open for %s" % dbName, extra=getExtraLogInfo(
+                "CONNECTIONS",
+                STATUS.START,
+                dbfilename=dbName))
+
+        self.cursor = self.connection.cursor()
+        # Define some shortcuts functions
+        if Config.debugSQLOn():
+            self.executeCommand = self._debugExecute
+        else:
+            self.executeCommand = self.cursor.execute
+        self.commit = self.connection.commit
+        
+    @classmethod
+    def closeConnection(cls, dbName):
+        if dbName in cls.OPEN_CONNECTIONS:
+            connection = cls.OPEN_CONNECTIONS[dbName]
+            del cls.OPEN_CONNECTIONS[dbName]
+            connection.close()
+            logger.debug("Connection closed for %s" % dbName,
+                         extra=getExtraLogInfo('CONNECTIONS', STATUS.STOP, dbfilename=dbName))
+
+    def getDbName(self):
+        return self._dbName
+    
+    def close(self):
+        self.connection.close()
+        logger.debug("Connection closed for %s" % self._dbName,
+                     extra=getExtraLogInfo(
+                                        "CONNECTIONS",
+                                        STATUS.STOP,
+                                        dbfilename=self._dbName))
+        if self._dbName in self.OPEN_CONNECTIONS:
+            del self.OPEN_CONNECTIONS[self._dbName]
+        
+    def _debugExecute(self, *args):
+        try:
+            logger.debug("COMMAND: %s; %s" %(args[0] , self._dbName),
+                extra=getExtraLogInfo("QUERY", STATUS.EVENT, dbfilename=self._dbName)
+            )
+            logger.debug("ARGUMENTS: " + str(args[1:]))
+            return self.cursor.execute(*args)
+        except Exception as ex:
+            print(">>>> FAILED cursor.execute on db: '%s'" % self._dbName)
+            raise ex
+
+    def _iterResults(self):
+        row = self.cursor.fetchone()
+        while row is not None:
+            yield row
+            row = self.cursor.fetchone()
+        
+    def _results(self, iterate=False):
+        """ Return the results to which cursor, point to. 
+        If iterates=True, iterate yielding each result independently"""
+        if not iterate:
+            return self.cursor.fetchall()
+        else:
+            return self._iterResults()
+        
+    def getTables(self, tablePattern=None):
+        """ Return the table names existing in the Database.
+        If  tablePattern is not None, only tables matching 
+        the pattern will be returned.
+        """
+        self.executeCommand("SELECT name FROM sqlite_master "
+                            "WHERE type='table' "
+                            "AND name NOT LIKE 'sqlite_%';")
+        return [str(row['name']) for row in self._iterResults()]
+    
+    def hasTable(self, tableName):
+        return tableName in self.getTables()
+    
+    def getTableColumns(self, tableName):
+        self.executeCommand('PRAGMA table_info(%s)' % tableName)
+        return self.cursor.fetchall()
+    
+    def getVersion(self):
+        """ Return the database 'version' that is used.
+        Internally it make use of the SQLite PRAGMA database.user_version;
+        """
+        self.executeCommand('PRAGMA user_version')
+        return self.cursor.fetchone()[0]
+    
+    def setVersion(self, version):
+        self.executeCommand('PRAGMA user_version=%d' % version)
+        self.commit()
+