view SMART/Java/Python/mySql/ @ 46:169d364ddd91

author m-zytnicki
date Mon, 30 Sep 2013 03:19:26 -0400
parents 44d5973c188c
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# 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
# "".
# 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 random
import sys
from SMART.Java.Python.structure.TranscriptList import TranscriptList
from SMART.Java.Python.mySql.MySqlExonTable import MySqlExonTable
from SMART.Java.Python.mySql.MySqlTable import MySqlTable
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.misc.Progress import Progress

class MySqlTranscriptTable(MySqlTable):
    """A table of transcripts in a mySQL database"""

    def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
        if chromosome == None:
            chromosome = ""
            chromosome = "_%s" % chromosome
        if name == None:
            name = "TmpTable_%d" % (random.randint(0, 100000))
        name = "%s%s" % (name, chromosome)
        super(MySqlTranscriptTable, self).__init__(connection, "%s_transcripts" % name, verbosity)

    def createTranscriptTable(self):
        self.create(Transcript.getSqlVariables(), Transcript.getSqlTypes(), Transcript.getSqlSizes())

    def rename(self, name):
        super(MySqlTranscriptTable, self).rename("%s_transcripts" % name)

    def remove(self):
        super(MySqlTranscriptTable, self).remove()
    def clear(self):
        super(MySqlTranscriptTable, self).clear()

    def copy(self, transcriptTable):
        super(MySqlTranscriptTable, self).copy(transcriptTable)

    def add(self, transcriptTable):
        super(MySqlTranscriptTable, self).add(transcriptTable)

    def addTranscript(self, transcript):
        id = self.addLine(transcript.getSqlValues()) = id
    def addTranscriptList(self, transcriptList):
        progress = Progress(transcriptList.getNbTranscript(), "Storing list to %s" % (, self.verbosity)
        for transcript in transcriptList.getIterator():

    def removeTranscript(self, transcript):
    def retrieveTranscriptFromId(self, id):
        transcript = Transcript()
        return transcript
    def retrieveBulkTranscriptFromId(self, ids):
        if not ids:
            return []
        transcripts = self.retrieveBulkFromId(ids)
        idsToTranscripts = {}
        for values in transcripts:
            transcript = Transcript()
            idsToTranscripts[values[0]] = transcript
        return idsToTranscripts.values()
    def selectTranscripts(self, command, simple = False):
        MAXSIZE = 100000
        found   = True
        cpt     = 0
        while found:
            found = False
            if simple:
                thisCommand = command
                thisCommand = "%s LIMIT %d OFFSET %d" % (command, MAXSIZE, MAXSIZE * cpt)
            query = self.mySqlConnection.executeQuery(thisCommand)
            for line in query.getIterator():
                found      = True
                id         = int(line[0])
                transcript = Transcript()
                yield (id, transcript)
            cpt += 1
            if simple:

    def getIterator(self):
        for id, transcript in self.selectTranscripts("SELECT * FROM '%s'" % (
            yield transcript

    def retrieveTranscriptList(self):
        transcriptList = TranscriptList()
        for transcriptLine in self.getLines():
            transcript = Transcript()
        return transcriptList

    def setDefaultTagValue(self, name, value):
        super(MySqlTranscriptTable, self).setDefaultTagValue(Transcript.getSqlVariables().index("tags")+1, name, value)