comparison smart_toolShed/commons/core/writer/MySqlTranscriptWriter.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

0:e0f8dcca02ed

#
# 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 os
import random
from SMART.Java.Python.mySql.MySqlTable import MySqlTable
from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable
from SMART.Java.Python.misc.Progress import Progress

class MySqlTranscriptWriter(object):
    """
    A class that writes a transcript list into a mySQL table
    @ivar name:                      name of the tables 
    @type name:                      string
    @ivar tables:                    the tables
    @type tables:                    dict of L{MySqlTranscriptTable<MySqlTranscriptTable>}
    @ivar mySqlConnection:           connection to a MySQL database
    @type mySqlConnection:           class L{MySqlConnection<MySqlConnection>}
    @ivar tmpTranscriptFileHandles:  files where transcripts are temporary stored, before copy into database
    @type tmpTranscriptFileHandles:  dict of file handles
    @ivar nbTranscriptsByChromosome: number of transcripts written
    @type nbTranscriptsByChromosome: dict of int (one for each chromosome)
    @ivar randomNumber:              a random number, used for having a unique name for the tables
    @type randomNumber:              int
    @ivar toBeWritten:               there exists transcripts to be copied into database
    @type toBeWritten:               bool                
    @ivar verbosity:                 verbosity
    @type verbosity:                 int        
    """


    def __init__(self, connection, name = None, verbosity = 0):
        """
        Constructor
        @param name:      name of the file 
        @type  name:      string
        @param verbosity: verbosity
        @type  verbosity: int
        """
        self.name                      = name
        self.verbosity                 = verbosity
        self.tables                    = {}
        self.indices                   = {}
        self.tmpTranscriptFileHandles  = {}
        self.nbTranscriptsByChromosome = {}
        self.toBeWritten               = False
        self.randomNumber              = random.randint(0, 100000)
        self.mySqlConnection           = connection
        self.nbTmpFiles                = 100
        self.transcriptValues          = {}
        self.nbTranscriptValues        = 1000
        if self.name != None:
            pos = self.name.rfind(os.sep)
            if pos != -1:
                self.name = self.name[pos+1:]
            

    def __del__(self):
        """
        Destructor
        Possibly write into into database the last transcripts
        """
        if self.toBeWritten:
            self.write()


    def addIndex(self, name, values):
        """
        Add an index to the tables
        @param name:   name of the index
        @type  name:   string
        @param values: values to index
        @type  values: list of strings
        """
        self.indices[name] = values


    def createTable(self, chromosome):
        """
        Create a table for a chromosome
        @param chromosome: a chromosome name
        @type  chromosome: string
        """
        self.tables[chromosome] = MySqlTranscriptTable(self.mySqlConnection, self.name, chromosome, self.verbosity)
        self.tables[chromosome].createTranscriptTable()
        for name, values in self.indices.iteritems():
            self.tables[chromosome].createIndex("%s_%s_%d" % (name, chromosome, self.randomNumber), values)

        
    
    def addTranscript(self, transcript):
        """
        Add a transcript to the list of transcripts to be written
        @param transcript: transcript to be written
        @type  transcript: class L{Transcript<Transcript>}
        """
        chromosome = transcript.getChromosome()
        if chromosome not in self.tables:
            self.createTable(chromosome)
            self.nbTranscriptsByChromosome[chromosome] = 1
        if chromosome not in self.transcriptValues:
            self.transcriptValues[chromosome] = []
            
        self.transcriptValues[chromosome].append(transcript.getSqlValues())

        self.nbTranscriptsByChromosome[chromosome] += 1
        self.toBeWritten                            = True
        if sum([len(transcripts) for transcripts in self.transcriptValues.values()]) > self.nbTranscriptValues:
            self.write() 


    def addElement(self, element):
        """
        Same as "addTranscript"
        @param element: transcript to be written
        @type  element: class L{Transcript<Transcript>}
        """
        self.addTranscript(element)


#   def addTranscriptList(self, transcriptListParser):
#       """
#       Add a list of transcripts to the transcripts to be written
#       @param transcriptListParser: transcripts to be written
#       @type  transcriptListParser: class L{TranscriptListParser<TranscriptListParser>}
#       """
#       progress = Progress(transcriptListParser.getNbTranscripts(), "Storing %s into database" % (transcriptListParser.fileName), self.verbosity)
#       for transcript in transcriptListParser.getIterator():
#           self.addTranscript(transcript)
#           progress.inc()
#       progress.done()
            
            
    def addTranscriptList(self, transcriptListParser):
        """
        Add a list of transcripts to the transcripts to be written
        @param transcriptListParser: transcripts to be written
        @type  transcriptListParser: class L{TranscriptListParser<TranscriptListParser>}
        """
        self.transcriptListParser = transcriptListParser
        self.mySqlConnection.executeManyQueriesIterator(self)
            
            
    def getIterator(self):
        """
        Iterator to the SQL commands to insert the list
        """
        progress = Progress(self.transcriptListParser.getNbTranscripts(), "Storing %s into database" % (self.transcriptListParser.fileName), self.verbosity)
        for transcript in self.transcriptListParser.getIterator():
            chromosome = transcript.getChromosome()
            if chromosome not in self.tables:
                self.createTable(chromosome)
            self.nbTranscriptsByChromosome[chromosome] = self.nbTranscriptsByChromosome.get(chromosome, 0) + 1
            values = transcript.getSqlValues()
            yield "INSERT INTO '%s' (%s) VALUES (%s)" % (self.tables[chromosome].name, ", ".join(self.tables[chromosome].variables), ", ".join([MySqlTable.formatSql(values[variable], self.tables[chromosome].types[variable], self.tables[chromosome].sizes[variable]) for variable in self.tables[chromosome].variables]))
            progress.inc()
        progress.done()
            
            
    def write(self):
        """
        Copy the content of the files into the database
        (May add transcripts to already created databases)
        """
        for chromosome in self.transcriptValues:
            if chromosome in self.transcriptValues:
                self.tables[chromosome].insertMany(self.transcriptValues[chromosome])
        self.transcriptValues = {}
        self.toBeWritten      = False
            
            
    def getTables(self):
        """
        Get the tables
        @return: the mySQL tables
        """
        if self.toBeWritten:
            self.write()
        return self.tables

            
            
    def removeTables(self):
        """
        Drop the tables
        """
        for chromosome in self.tables:
            self.tables[chromosome].remove()