--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/mySql/MySqlTable.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,349 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+import re
+import sys
+
+class MySqlTable(object):
+    """
+    Store a table of a mySQL database, used for transcripts or exons
+    Record a a name and a type (int, float, double) for each column
+    @ivar name:            name of the table
+    @type name:            string
+    @ivar variables:       name of the columns
+    @type variables:       list of string
+    @ivar types:           type of the columns
+    @type types:           dict of string
+    @ivar mySqlConnection: connection to a database
+    @type mySqlConnection: class L{MySqlConnection<MySqlConnection>}
+    @ivar nbLines:         number of rows
+    @type nbLines:         int
+    @ivar verbosity:       verbosity
+    @type verbosity:       int
+    """
+
+    def __init__(self, connection, name, verbosity = 0):
+        """
+        Constructor
+        Possibly retrieve column names and types if table exists
+        @param mySqlConnection: connection to a databas
+        @type  mySqlConnection: class L{MySqlConnection<MySqlConnection>}
+        @param name:            name of the table
+        @type  name:            string
+        @param verbosity:       verbosity
+        @type  verbosity:       int
+        """
+        self.name      = name
+        self.variables = []
+        self.types     = {}
+        self.sizes     = {}
+        self.nbLines   = None
+        self.verbosity = verbosity
+        self.mySqlConnection = connection
+        queryTables = self.mySqlConnection.executeQuery("SELECT name FROM sqlite_master WHERE type LIKE 'table' AND name LIKE '%s'" % (self.name))
+        self.created = not queryTables.isEmpty()
+        if self.created:
+            queryFields = self.mySqlConnection.executeQuery("PRAGMA table_info('%s')" % (name))
+            for field in queryFields.getIterator():
+                if field[1] != "id":
+                    self.variables.append(field[1])
+                    self.types[field[1]] = field[2]
+                    self.sizes[field[1]] = field[3]
+                    
+                    
+    def getName(self):
+        return self.name
+
+
+    def create(self, variables, types, sizes):
+        """
+        Create a table using give column names and types
+        @param variables: names of the columns
+        @type  variables: list of string
+        @param types:     types of the columns
+        @type  types:     dict of string
+        @param sizes:     sizes of the types
+        @type  sizes:     dict of int
+        """
+        self.variables = variables
+        self.types = types
+        self.sizes = sizes
+        if self.created:
+            self.remove()
+        query = "CREATE TABLE '%s' (id INTEGER PRIMARY KEY" % (self.name)
+        for variable in variables:
+            query = "%s, %s %s(%d)" % (query, variable, types[variable], sizes[variable])
+        query += ")"
+        self.mySqlConnection.executeQuery(query)
+        self.created = True
+
+
+    def insertMany(self, lines):
+        """
+        Insert many lines
+        @param lines: the list of values
+        @type  lines: list of lists
+        """
+        commands = []
+        for values in lines:
+            commands.append("INSERT INTO '%s' (%s) VALUES (%s)" % (self.name, ", ".join(self.variables), ", ".join([MySqlTable.formatSql(values[variable], self.types[variable], self.sizes[variable]) for variable in self.variables])))
+        self.mySqlConnection.executeManyQueries(commands)
+        
+        
+    def insertManyFormatted(self, lines):
+        """
+        Insert many lines
+        @param lines: the list of values
+        @type  lines: list of lists
+        """
+        replacer = ["?"] * len(self.variables)
+        command = "INSERT INTO '%s' (%s) VALUES (%s)" % (self.name, ", ".join(self.variables), ", ".join(replacer))
+        values  = [[line[variable] for variable in self.variables] for line in lines]
+        self.mySqlConnection.executeManyFormattedQueries(command, values)
+        
+        
+    def rename(self, name):
+        """
+        Rename the table
+        @param name: the new name
+        @type  name: string
+        """
+        self.mySqlConnection.executeQuery("RENAME TABLE '%s' TO '%s'" % (self.name, name))
+        self.name = name
+        
+    
+    def copy(self, table):
+        """
+        Copy the given table this one
+        @param table: the table to be copied
+        @type  table: class L{MySqlTable<MySqlTable>}
+        """
+        variables = []
+        types = {}
+        sizes = {}
+        fields = self.mySqlConnection.executeQuery("PRAGMA table_info(%s)" % (table.name))
+        for field in fields.getIterator():
+            if field[1] != "id":
+                variables.append(field[1])
+                m = re.search(r"(\w+)\((\d+)\)", field[2])
+                if m == None:
+                    raise Exception("\nFormat %s in table %s is strange." % (field[2], table.name))
+                types[field[1]] = m.group(1)
+                sizes[field[1]] = int(m.group(2))
+        self.create(variables, types, sizes)
+        self.mySqlConnection.executeQuery("INSERT INTO '%s' SELECT * FROM %s" % (self.name, table.name))
+        
+
+    def add(self, table):
+        """
+        Add the content of a table to this one
+        @param table: the table to be added
+        @type  table: class L{MySqlTable<MySqlTable>}
+        """
+        self.mySqlConnection.executeQuery("INSERT INTO '%s' SELECT * FROM %s" % (self.name, table.name))
+        self.created = True
+        
+        
+    def exists(self):
+        """
+        Check if the table exists in mySQL
+        @return: true if it exits
+        """
+        return self.created
+    
+
+    def remove(self):
+        """
+        Remove this table
+        """
+        if self.exists():
+            query = "DROP TABLE IF EXISTS '%s'" % (self.name)
+            self.mySqlConnection.executeQuery(query)
+        self.created = False
+        
+        
+    def clear(self):
+        """
+        Clear the content of this table
+        """
+        self.mySqlConnection.executeQuery("DELETE FROM '%s'" % (self.name))
+        
+        
+    def getNbElements(self):
+        """
+        Count the number of rows in the table
+        """
+        command = "SELECT COUNT(id) FROM '%s'" % (self.name)
+        query = self.mySqlConnection.executeQuery(command)
+        return int(query.getLine()[0])
+
+
+    def formatSql(self, value, type, size):
+        """
+        Format a value using MySQL encapsulation
+        """
+        if type.find("int") != -1:
+            return "%d" % value
+        if type.find("float") != -1:
+            return "%.10f" % value
+        if type.find("double") != -1:
+            return "%.20f" % value
+        if type.find("varchar") != -1:
+            if len(value) > size:
+                return "'%s'" % value[0:size]
+            return "'%s'" % value
+        raise Exception("Do not understand type %s" % (type))
+    formatSql = classmethod(formatSql)
+
+
+    def addLine(self, values):
+        """
+        Add a row to this table
+        @param values: the values of the row
+        @type  values: dict
+        @return:       the id of the added row
+        """
+        sqlValues = [values[variable] for variable in self.variables]
+        command = "INSERT INTO '%s' (%%s) VALUES (%s)" % (self.name, ", ".join(self.variables))
+        id = self.mySqlConnection.executeFormattedQueryQuery(command, sqlValues, True)
+        return id
+        sqlValues = []
+        for variable in self.variables:
+            sqlValues.append(self.formatSql(values[variable], self.types[variable], self.sizes[variable]))
+        command = "INSERT INTO '%s' (%s) VALUES (%s)" % (self.name, ", ".join(self.variables), ", ".join(sqlValues))
+        id = self.mySqlConnection.executeQuery(command, True)
+        return id
+    
+    
+    def retrieveFromId(self, id):
+        """
+        Retrieve a row from its id
+        @param id: the id of the row
+        @type  id: int
+        @return:   the row
+        """
+        query = self.mySqlConnection.executeQuery("SELECT * FROM '%s' WHERE id = %d" % (self.name, id))
+        result = query.getLine()
+        if result == None:
+            raise Exception("Error! Id %d is not in the table %s!" % (id, self.name))
+        return result
+
+
+    def retrieveBulkFromId(self, ids):
+        """
+        Retrieve a row from its id
+        @param id: the ids of the row
+        @type  id: list of int
+        @return:   the row
+        """
+        if not ids:
+            return []
+        MAXSIZE = 1000
+        results = []
+        for batch in range(len(ids) / MAXSIZE + 1):
+            theseIds = ids[batch * MAXSIZE : (batch+1) * MAXSIZE]
+            if theseIds:
+                query = self.mySqlConnection.executeQuery("SELECT * FROM '%s' WHERE id IN (%s)" % (self.name, ", ".join(["%d" % (id) for id in theseIds])))
+                lines = query.getLines()
+                if len(lines) != len(theseIds):
+                    raise Exception("Error! Some Ids of (%s) is are missing in the table '%s' (got %d instead of %d)!" % (", ".join(["%d" % (id) for id in theseIds]), self.name, len(lines)), len(theseIds))
+                results.extend(lines)
+        return results
+
+
+    def removeFromId(self, id):
+        """
+        Remove a row from its id
+        @param id: the id of the row
+        @type  id: int
+        """
+        self.mySqlConnection.executeQuery("DELETE FROM '%s' WHERE id = %d" % (self.name, id))
+    
+    
+    def getIterator(self):
+        """
+        Iterate on the content of table
+        @return: iterator to the rows of the table
+        """
+        if not self.created:
+            return
+        MAXSIZE = 1000
+        query = self.mySqlConnection.executeQuery("SELECT count(id) FROM '%s'" % (self.name))
+        nbRows = int(query.getLine()[0])
+        for chunk in range((nbRows / MAXSIZE) + 1):
+            query = self.mySqlConnection.executeQuery("SELECT * FROM '%s' LIMIT %d, %d" % (self.name, chunk * MAXSIZE, MAXSIZE))
+            for line in query.getIterator():
+                yield line
+
+
+    def createIndex(self, indexName, values, unique = False, fullText = False):
+        """
+        Add an index on the table
+        @param indexName: name of the index
+        @type  indexName: string
+        @param values:    values to be indexed
+        @type  values:    string
+        @param unique:    if the index is unique
+        @type  unique:    boolean
+        @param fullText:  whether full text should be indexed
+        @type  fullText:  boolean
+        """
+        self.mySqlConnection.executeQuery("CREATE %s%sINDEX '%s' ON '%s' (%s)" % ("UNIQUE " if unique else "", "FULLTEXT " if fullText else "", indexName, self.name, ", ".join(values)))
+
+
+    def setDefaultTagValue(self, field, name, value):
+        """
+        Add a tag value
+        @param name:  name of the tag
+        @type  name:  string
+        @param value: value of the tag
+        @type  value: string or int
+        """
+        newData = {}
+        for line in MySqlTable.getIterator(self):
+            id = line[0]
+            tags = line[field]
+            if tags == '':
+                newTag = "%s=%s" % (name, value)
+            else:
+                newTag = "%s;%s=%s" % (tags, name, value)
+            if name not in [tag.split("=")[0] for tag in tags.split(";")]:
+                newData[id] = newTag
+        for id, tag in newData.iteritems():
+            query = self.mySqlConnection.executeQuery("UPDATE '%s' SET tags = '%s' WHERE id = %i" % (self.name, tag, id))
+
+
+
+    def show(self):
+        """
+        Drop the content of the current table
+        """
+        query = self.mySqlConnection.executeQuery("SELECT * FROM '%s'" % (self.name))
+        print query.getLines()
+