annotate compressed.py @ 1:ddf34b1d55c8 default tip

fix wrong Tgdb format

"""
Compressed classes
"""

import mimetypes, logging, os, os.path, sys, time, tempfile, shutil, string, glob, re, zipfile, tarfile

from galaxy.datatypes.data import Data
from galaxy.datatypes.sniff import *
from cgi import escape
from inspect import isclass
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions
from galaxy.util import inflector
from galaxy.util.bunch import Bunch
from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
from galaxy.datatypes.checkers import *
from galaxy.datatypes import data


log = logging.getLogger(__name__)

class Zip( Data ):
    file_ext = "zip"
   
    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
	    dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        if (check_zip( filename )):
            return True
        return False
	

class Tgz( Data ):
    file_ext = "tar.gz"

    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        is_gzipped, is_valid = check_gzip( filename )
        is_tar = tarfile.is_tarfile( filename )
        return (is_gzipped and is_valid and is_tar)

 
class Tbz2( Data ):
    file_ext = "tar.bz2"

    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        is_bzipped, is_valid = check_bz2( filename )
        is_tar = tarfile.is_tarfile( filename )
        return (is_bzipped and is_valid and is_tar)

    
class Fastqgz( Data ):
    file_ext = "fastq.gz"

    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        is_gzipped, is_valid = check_gzip( filename )
        is_tar = tarfile.is_tarfile( filename )
        return (is_gzipped and is_valid and not is_tar)

class Fastqbz2( Data ):
    file_ext = "fastq.bz2"

    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        is_bzipped, is_valid = check_bz2( filename )
        is_tar = tarfile.is_tarfile( filename )
        return (is_bzipped and is_valid and not is_tar)