""" Image classes """ import data import logging from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata from galaxy.datatypes.sniff import * from urllib import urlencode, quote_plus import zipfile import os, subprocess, tempfile log = logging.getLogger(__name__) class Image( data.Data ): """Class describing an image""" def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Image in %s format' % dataset.extension dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' class Pdf( Image ): def sniff(self, filename): """Determine if the file is in pdf format. """ headers = get_headers(filename, None, 1) try: if headers[0][0].startswith("%PDF"): return True else: return False except IndexError: return False def create_applet_tag_peek( class_name, archive, params ): text = """ """ % ( class_name, archive ) for name, value in params.iteritems(): text += """""" % ( name, value ) text += """ """ % ( class_name, archive ) for name, value in params.iteritems(): text += """""" % ( name, value ) text += """ """ return """

%s

""" % text class Gmaj( data.Data ): """Class describing a GMAJ Applet""" file_ext = "gmaj.zip" copy_safe_peek = False def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: if hasattr( dataset, 'history_id' ): params = { "bundle":"display?id=%s&tofile=yes&toext=.zip" % dataset.id, "buttonlabel": "Launch GMAJ", "nobutton": "false", "urlpause" :"100", "debug": "false", "posturl": quote_plus( "history_add_to?%s" % "&".join( [ "%s=%s" % ( key, value ) for key, value in { 'history_id': dataset.history_id, 'ext': 'maf', 'name': 'GMAJ Output on data %s' % dataset.hid, 'info': 'Added by GMAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id }.items() ] ) ) } class_name = "edu.psu.bx.gmaj.MajApplet.class" archive = "/static/gmaj/gmaj.jar" dataset.peek = create_applet_tag_peek( class_name, archive, params ) dataset.blurb = 'GMAJ Multiple Alignment Viewer' else: dataset.peek = "After you add this item to your history, you will be able to launch the GMAJ applet." dataset.blurb = 'GMAJ Multiple Alignment Viewer' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek(self, dataset): try: return dataset.peek except: return "peek unavailable" def get_mime(self): """Returns the mime type of the datatype""" return 'application/zip' def sniff(self, filename): """ NOTE: the sniff.convert_newlines() call in the upload utility will keep Gmaj data types from being correctly sniffed, but the files can be uploaded (they'll be sniffed as 'txt'). This sniff function is here to provide an example of a sniffer for a zip file. """ if not zipfile.is_zipfile( filename ): return False contains_gmaj_file = False zip_file = zipfile.ZipFile(filename, "r") for name in zip_file.namelist(): if name.split(".")[1].strip().lower() == 'gmaj': contains_gmaj_file = True break zip_file.close() if not contains_gmaj_file: return False return True class Html( data.Text ): """Class describing an html file""" file_ext = "html" def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "HTML file" dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def get_mime(self): """Returns the mime type of the datatype""" return 'text/html' def sniff( self, filename ): """ Determines whether the file is in html format >>> fname = get_test_fname( 'complete.bed' ) >>> Html().sniff( fname ) False >>> fname = get_test_fname( 'file.html' ) >>> Html().sniff( fname ) True """ headers = get_headers( filename, None ) try: for i, hdr in enumerate(headers): if hdr and hdr[0].lower().find( '' ) >=0: return True return False except: return True class Laj( data.Text ): """Class describing a LAJ Applet""" file_ext = "laj" copy_safe_peek = False def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: if hasattr( dataset, 'history_id' ): params = { "alignfile1": "display?id=%s" % dataset.id, "buttonlabel": "Launch LAJ", "title": "LAJ in Galaxy", "posturl": quote_plus( "history_add_to?%s" % "&".join( [ "%s=%s" % ( key, value ) for key, value in { 'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id }.items() ] ) ), "noseq": "true" } class_name = "edu.psu.cse.bio.laj.LajApplet.class" archive = "/static/laj/laj.jar" dataset.peek = create_applet_tag_peek( class_name, archive, params ) else: dataset.peek = "After you add this item to your history, you will be able to launch the LAJ applet." dataset.blurb = 'LAJ Multiple Alignment Viewer' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek(self, dataset): try: return dataset.peek except: return "peek unavailable"