view chip.py @ 0:7f9ec5d9c4db draft default tip

Imported from capsule None

"""
Binary classes
"""

import galaxy.datatypes.data
from galaxy.datatypes.data import Data
import galaxy.datatypes.sniff
from galaxy.datatypes.sniff import *

import zipfile
from urllib import urlencode, quote_plus

log = logging.getLogger(__name__)

# Cistrome Customized Datatypes
class Eset( Data ):
    """Class describing an Expression Set"""
    file_ext = "eset"
    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
            dataset.peek  = "Expression set"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def display_peek(self, dataset):
        try:
            return dataset.peek
        except:
            return "Expression set"
    def get_mime(self):
        """Returns the mime type of the datatype"""

class XysZip( Data ):
    """Class describing a zip archive of NimbleGen XYS files"""
    file_ext = "xys.zip"
    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
            zip_file = zipfile.ZipFile( dataset.file_name, "r" )
            num_files = len( zip_file.namelist() )
            dataset.peek  = "Archive of %s NimbleGen XYS files" % ( str( num_files - 1 ) )
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def display_peek(self, dataset):
        try:
            return dataset.peek
        except:
            return "NimbleGen XYS file archive (%s)" % ( data.nice_size( dataset.get_size() ) )
    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'application/zip'

class CelZip( Data ):
    """Class describing a zip archive of Affymetrix CEL files"""
    file_ext = "cel.zip"
    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
            zip_file = zipfile.ZipFile( dataset.file_name, "r" )
            num_files = len( zip_file.namelist() )
            dataset.peek  = "Archive of %s Affymetrix CEL files" % ( str( num_files - 1 ) )
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def display_peek(self, dataset):
        try:
            return dataset.peek
        except:
            return "Affymetrix CEL file archive (%s)" % ( data.nice_size( dataset.get_size() ) )
    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'application/zip'

class Cel( Data ):
    """Class describing an binary CEL file"""
    file_ext = "cel"
    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
            export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'cel','name':'affymetrix cel file','info':'Cel file','dbkey':dataset.dbkey})
            dataset.peek  = "Binary cel sequence file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def display_peek(self, dataset):
        try:
            return dataset.peek
        except:
            return "Binary cel sequence file (%s)" % ( data.nice_size( dataset.get_size() ) )
    def sniff( self, filename ):
        """
        Determines wether the file is in cel format

        """
        parts = filename.lower().split('.')
        for p in parts:
            if p == 'cel':
                return True
        return False
    
    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'application/octet-stream'
# End