from galaxy.datatypes.binary import Binary from galaxy.datatypes.xml import GenericXml class Group(Binary): """Class describing a ProteinPilot group files""" file_ext = "group" Binary.register_unsniffable_binary_ext('group') class ProteinPilotXml(GenericXml): file_ext = "proteinpilot.xml"
from galaxy.datatypes import data from galaxy.datatypes.binary import Binary class Cel(Binary): """Class for generic CEL binary format""" file_ext = "cel" Binary.register_unsniffable_binary_ext("cel")
return dataset.peek except: return "HMMER3 database (multiple files)" def __init__(self, **kwd): Binary.__init__(self, **kwd) # Binary model self.add_composite_file('model.hmm.h3m', is_binary=True) # SSI index for binary model self.add_composite_file('model.hmm.h3i', is_binary=True) # Profiles (MSV part) self.add_composite_file('model.hmm.h3f', is_binary=True) # Profiles (remained) self.add_composite_file('model.hmm.h3p', is_binary=True) Binary.register_unsniffable_binary_ext("hmmpress") class Stockholm_1_0( Text ): edam_data = "data_0863" edam_format = "format_1961" file_ext = "stockholm" MetadataElement( name="number_of_models", default=0, desc="Number of multiple alignments", readonly=True, visible=True, optional=True, no_value=0 ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if (dataset.metadata.number_of_models == 1): dataset.blurb = "1 alignment" else:
""" k-mer count and presence """ from galaxy.datatypes.binary import Binary import logging log = logging.getLogger(__name__) class Count(Binary): def __init__(self, **kwd): Binary.__init__(self, **kwd) class Presence(Binary): def __init__(self, **kwd): Binary.__init__(self, **kwd) Binary.register_unsniffable_binary_ext("ct") Binary.register_unsniffable_binary_ext("pt")
else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek( self, dataset ): try: return dataset.peek except: return "Audio (WAV) file (%s)" % ( data.nice_size( dataset.get_size() ) ) def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): if preview: return ("WAV audio files cannot be previewed.") else: return super(Wav, self).display_data( trans, dataset, preview, filename, to_ext, size, offset, **kwd) Binary.register_unsniffable_binary_ext("wav") class Mp3(Binary): file_ext = "mp3" def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "Audio (MP3) 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 ):
""" k-mer count and presence """ from galaxy.datatypes.binary import Binary import logging log = logging.getLogger(__name__) class Count(Binary): def __init__(self, **kwd): Binary.__init__(self, **kwd) class Presence(Binary): def __init__(self, **kwd): Binary.__init__(self, **kwd) Binary.register_unsniffable_binary_ext("ct") Binary.register_unsniffable_binary_ext("pt")
from galaxy.datatypes.binary import Binary class Sf3(Binary): """Class describing a Scaffold SF3 files""" file_ext = "sf3" Binary.register_unsniffable_binary_ext('sf3')
rval = ['<html><head><title>Wiff Composite Dataset </title></head><p/>'] rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems(): fn = composite_name opt_text = '' if composite_file.optional: opt_text = ' (optional)' if composite_file.get('description'): rval.append('<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text)) else: rval.append('<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text)) rval.append('</ul></div></html>') return "\n".join(rval) if hasattr(Binary, 'register_unsniffable_binary_ext'): Binary.register_unsniffable_binary_ext('wiff') class IdpDB(Binary): file_ext = "idpDB" if hasattr(Binary, 'register_unsniffable_binary_ext'): Binary.register_unsniffable_binary_ext('idpDB') class PepXmlReport(Tabular): """pepxml converted to tabular report""" file_ext = "tsv" def __init__(self, **kwd): Tabular.__init__(self, **kwd)
from galaxy.datatypes.binary import Binary from galaxy.datatypes.xml import GenericXml class Group( Binary ): """Class describing a ProteinPilot group files""" file_ext = "group" Binary.register_unsniffable_binary_ext('group') class ProteinPilotXml( GenericXml ): file_ext = "proteinpilot.xml"
if match: x = match.group('resx') y = match.group('resy') fps = match.group('fps') else: x = y = fps = 0 return x, y, fps def set_meta(self, dataset, **kwd): (x, y, fps) = self._get_resolution( dataset.file_name ) dataset.metadata.resolution_y = y dataset.metadata.resolution_x = x dataset.metadata.fps = fps class Mp4( Video ): file_ext = "mp4" def sniff(self, filename): with magic.Magic(flags=magic.MAGIC_MIME_TYPE) as m: return m.id_filename(filename) is 'video/mp4' #Binary.register_unsniffable_binary_ext("mp4") class Flv( Video ): file_ext = "flv" def sniff(self, filename): with magic.Magic(flags=magic.MAGIC_MIME_TYPE) as m: return m.id_filename(filename) is 'video/x-flv' Binary.register_unsniffable_binary_ext("flv")
if composite_file.optional: opt_text = ' (optional)' if composite_file.get('description'): rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text)) else: rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text)) rval.append('</ul></div></html>') return "\n".join(rval) if hasattr(Binary, 'register_unsniffable_binary_ext'): Binary.register_unsniffable_binary_ext('wiff') class IdpDB(Binary): file_ext = "idpDB" if hasattr(Binary, 'register_unsniffable_binary_ext'): Binary.register_unsniffable_binary_ext('idpDB') class PepXmlReport(Tabular): """pepxml converted to tabular report""" file_ext = "tsv" def __init__(self, **kwd):
from galaxy.datatypes import data from galaxy.datatypes.binary import Binary class Cel( Binary ): """Class for generic CEL binary format""" file_ext = "cel" Binary.register_unsniffable_binary_ext("cel")