/lib/galaxy/datatypes/data.py

import logging
import metadata
import mimetypes
import os
import shutil
import sys
import tempfile
import zipfile
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

import dataproviders

from galaxy import eggs
eggs.require( "Paste" )
import paste

XSS_VULNERABLE_MIME_TYPES = [
    'image/svg+xml',  # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
    'application/xml',  # Some browsers will evalute SVG embedded JS in such XML documents.
]
DEFAULT_MIME_TYPE = 'text/plain'  # Vulnerable mime types will be replaced with this.

log = logging.getLogger(__name__)

comptypes=[]  # Is this being used anywhere, why was this here? -JohnC
try:
    import zlib
    comptypes.append( 'zip' )
except ImportError:
    pass


# Valid first column and strand column values vor bed, other formats
col1_startswith = ['chr', 'chl', 'groupun', 'reftig_', 'scaffold', 'super_', 'vcho']
valid_strand = ['+', '-', '.']

class DataMeta( type ):
    """
    Metaclass for Data class.  Sets up metadata spec.
    """
    def __init__( cls, name, bases, dict_ ):
        cls.metadata_spec = metadata.MetadataSpecCollection()
        for base in bases: #loop through bases (class/types) of cls
            if hasattr( base, "metadata_spec" ): #base of class Data (object) has no metadata
                cls.metadata_spec.update( base.metadata_spec ) #add contents of metadata spec of base class to cls
        metadata.Statement.process( cls )

@dataproviders.decorators.has_dataproviders
class Data( object ):
    """
    Base class for all datatypes.  Implements basic interfaces as well
    as class methods for metadata.

    >>> class DataTest( Data ):
    ...     MetadataElement( name="test" )
    ...
    >>> DataTest.metadata_spec.test.name
    'test'
    >>> DataTest.metadata_spec.test.desc
    'test'
    >>> type( DataTest.metadata_spec.test.param )
    <class 'galaxy.datatypes.metadata.MetadataParameter'>

    """
    # Data is not chunkable by default.
    CHUNKABLE = False

    #: dictionary of metadata fields for this datatype::
    metadata_spec = None

    __metaclass__ = DataMeta
    # Add metadata elements
    MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.DBKeyParameter, multiple=False, no_value="?" )
    # Stores the set of display applications, and viewing methods, supported by this datatype
    supported_display_apps = {}
    # If False, the peek is regenerated whenever a dataset of this type is copied
    copy_safe_peek = True
    # The dataset contains binary data --> do not space_to_tab or convert newlines, etc.
    # Allow binary file uploads of this type when True.
    is_binary = True
    # Allow user to change between this datatype and others. If False, this datatype
    # cannot be changed from or into.
    allow_datatype_change = True
    #Composite datatypes
    composite_type = None
    composite_files = odict()
    primary_file_name = 'index'
    #A per datatype setting (inherited): max file size (in bytes) for setting optional metadata
    _max_optional_metadata_filesize = None

    # Trackster track type.
    track_type = None

    # Data sources.
    data_sources = {}

    def __init__(self, **kwd):
        """Initialize the datatype"""
        object.__init__(self, **kwd)
        self.supported_display_apps = self.supported_display_apps.copy()
        self.composite_files = self.composite_files.copy()
        self.display_applications = odict()
    def write_from_stream(self, dataset, stream):
        """Writes data from a stream"""
        fd = open(dataset.file_name, 'wb')
        while 1:
            chunk = stream.read(1048576)
            if not chunk:
                break
            os.write(fd, chunk)
        os.close(fd)
    def set_raw_data(self, dataset, data):
        """Saves the data on the disc"""
        fd = open(dataset.file_name, 'wb')
        os.write(fd, data)
        os.close(fd)
    def get_raw_data( self, dataset ):
        """Returns the full data. To stream it open the file_name and read/write as needed"""
        try:
            return file(dataset.file_name, 'rb').read(-1)
        except OSError, e:
            log.exception('%s reading a file that does not exist %s' % (self.__class__.__name__, dataset.file_name))
            return ''
    def dataset_content_needs_grooming( self, file_name ):
        """This function is called on an output dataset file after the content is initially generated."""
        return False
    def groom_dataset_content( self, file_name ):
        """This function is called on an output dataset file if dataset_content_needs_grooming returns True."""
        pass
    def init_meta( self, dataset, copy_from=None ):
        # Metadata should be left mostly uninitialized.  Dataset will
        # handle returning default values when metadata is not set.
        # copy_from allows metadata to be passed in that will be
        # copied. (although this seems ambiguous, see
        # Dataset.set_metadata.  It always copies the rhs in order to
        # flag the object as modified for SQLAlchemy.
        if copy_from:
            dataset.metadata = copy_from.metadata
    def set_meta( self, dataset, overwrite = True, **kwd ):
        """Unimplemented method, allows guessing of metadata from contents of file"""
        return True
    def missing_meta( self, dataset, check = [], skip = [] ):
        """
        Checks for empty metadata values, Returns True if non-optional metadata is missing
        Specifying a list of 'check' values will only check those names provided; when used, optionality is ignored
        Specifying a list of 'skip' items will return True even when a named metadata value is missing
        """
        if check:
            to_check = [ ( to_check, dataset.metadata.get( to_check ) ) for to_check in check ]
        else:
            to_check = dataset.metadata.items()
        for key, value in to_check:
            if key in skip or ( not check and dataset.metadata.spec[key].get( "optional" ) ):
                continue #we skip check for optional and nonrequested values here
            if not value:
                return True
        return False
    def set_max_optional_metadata_filesize( self, max_value ):
        try:
            max_value = int( max_value )
        except:
            return
        self.__class__._max_optional_metadata_filesize = max_value
    def get_max_optional_metadata_filesize( self ):
        rval = self.__class__._max_optional_metadata_filesize
        if rval is None:
            return -1
        return rval
    max_optional_metadata_filesize = property( get_max_optional_metadata_filesize, set_max_optional_metadata_filesize )
    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = ''
            dataset.blurb = 'data'
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def display_peek(self, dataset ):
        """Create HTML table, used for displaying peek"""
        out = ['<table cellspacing="0" cellpadding="3">']
        try:
            if not dataset.peek:
                dataset.set_peek()
            data = dataset.peek
            lines =  data.splitlines()
            for line in lines:
                line = line.strip()
                if not line:
                    continue
                if type( line ) is unicode:
                    out.append( '<tr><td>%s</td></tr>' % escape( line ) )
                else:
                    out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) )
            out.append( '</table>' )
            out = "".join( out )
        except Exception, exc:
            out = "Can't create peek %s" % str( exc )
        return out

    def _archive_main_file(self, archive, display_name, data_filename):
        """Called from _archive_composite_dataset to add central file to archive.

        Unless subclassed, this will add the main dataset file (argument data_filename)
        to the archive, as an HTML file with its filename derived from the dataset name
        (argument outfname).

        Returns a tuple of boolean, string, string: (error, msg, messagetype)
        """
        error, msg, messagetype = False, "", ""
        archname = '%s.html' % display_name  # fake the real nature of the html file
        try:
            archive.add(data_filename, archname)
        except IOError:
            error = True
            log.exception("Unable to add composite parent %s to temporary library download archive" % data_filename)
            msg = "Unable to create archive for download, please report this error"
            messagetype = "error"
        return error, msg, messagetype

    def _archive_composite_dataset( self, trans, data=None, **kwd ):
        # save a composite object into a compressed archive for downloading
        params = util.Params( kwd )
        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
        outfname = data.name[0:150]
        outfname = ''.join(c in valid_chars and c or '_' for c in outfname)
        if (params.do_action == None):
            params.do_action = 'zip' # default
        msg = util.restore_text( params.get( 'msg', ''  ) )
        messagetype = params.get( 'messagetype', 'done' )
        if not data:
            msg = "You must select at least one dataset"
            messagetype = 'error'
        else:
            error = False
            try:
                if (params.do_action == 'zip'):
                    # Can't use mkstemp - the file must not exist first
                    tmpd = tempfile.mkdtemp()
                    util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, trans.app.config.gid )
                    tmpf = os.path.join( tmpd, 'library_download.' + params.do_action )
                    archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
                    archive.add = lambda x, y: archive.write( x, y.encode('CP437') )
                elif params.do_action == 'tgz':
                    archive = util.streamball.StreamBall( 'w|gz' )
                elif params.do_action == 'tbz':
                    archive = util.streamball.StreamBall( 'w|bz2' )
            except (OSError, zipfile.BadZipFile):
                error = True
                log.exception( "Unable to create archive for download" )
                msg = "Unable to create archive for %s for download, please report this error" % outfname
                messagetype = 'error'
            if not error:
                current_user_roles = trans.get_current_user_roles()
                ext = data.extension
                path = data.file_name
                fname = os.path.split(path)[-1]
                efp = data.extra_files_path
                #Add any central file to the archive,

                display_name = os.path.splitext(outfname)[0]
                if not display_name.endswith(ext):
                    display_name = '%s_%s' % (display_name, ext)

                error, msg, messagetype = self._archive_main_file(archive, display_name, path)
                if not error:
                    #Add any child files to the archive,
                    for root, dirs, files in os.walk(efp):
                        for fname in files:
                            fpath = os.path.join(root,fname)
                            rpath = os.path.relpath(fpath,efp)
                            try:
                                archive.add( fpath,rpath )
                            except IOError:
                                error = True
                                log.exception( "Unable to add %s to temporary library download archive" % rpath)
                                msg = "Unable to create archive for download, please report this error"
                                messagetype = 'error'
                                continue
                if not error:
                    if params.do_action == 'zip':
                        archive.close()
                        tmpfh = open( tmpf )
                        # CANNOT clean up - unlink/rmdir was always failing because file handle retained to return - must rely on a cron job to clean up tmp
                        trans.response.set_content_type( "application/x-zip-compressed" )
                        trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.zip"' % outfname
                        return tmpfh
                    else:
                        trans.response.set_content_type( "application/x-tar" )
                        outext = 'tgz'
                        if params.do_action == 'tbz':
                            outext = 'tbz'
                        trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (outfname,outext)
                        archive.wsgi_status = trans.response.wsgi_status()
                        archive.wsgi_headeritems = trans.response.wsgi_headeritems()
                        return archive.stream
        return trans.show_error_message( msg )

    def _serve_raw(self, trans, dataset, to_ext):
        trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size )
        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
        fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150]
        trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename
        trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
        return open( dataset.file_name )

    def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
        """ Old display method, for transition - though still used by API and
        test framework. Datatypes should be very careful if overridding this
        method and this interface between datatypes and Galaxy will likely
        change.

        TOOD: Document alternatives to overridding this method (data
        providers?).
        """
        #Relocate all composite datatype display to a common location.
        composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
        composite_extensions.append('html') # for archiving composite datatypes
        #Prevent IE8 from sniffing content type since we're explicit about it.  This prevents intentionally text/plain
        #content from being rendered in the browser
        trans.response.headers['X-Content-Type-Options'] = 'nosniff'
        if isinstance( data, basestring ):
            return data
        if filename and filename != "index":
            # For files in extra_files_path
            file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename)
            if os.path.exists( file_path ):
                if os.path.isdir( file_path ):
                    return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories?
                mime, encoding = mimetypes.guess_type( file_path )
                if not mime:
                    try:
                        mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] )
                    except:
                        mime = "text/plain"
                self._clean_and_set_mime_type( trans, mime )
                return open( file_path )
            else:
                return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) )
        self._clean_and_set_mime_type( trans, data.get_mime() )

        trans.log_event( "Display dataset id: %s" % str( data.id ) )
        from galaxy import datatypes #DBTODO REMOVE THIS AT REFACTOR
        if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file
            if data.extension in composite_extensions:
                return self._archive_composite_dataset( trans, data, **kwd )
            else:
                trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size )
                if not to_ext:
                    to_ext = data.extension
                valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
                fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
                trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename
                trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, fname, to_ext)
                return open( data.file_name )
        if not os.path.exists( data.file_name ):
            raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name )
        max_peek_size = 1000000 # 1 MB
        if isinstance(data.datatype, datatypes.images.Html):
            max_peek_size = 10000000 # 10 MB for html
        preview = util.string_as_bool( preview )
        if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size:
            if trans.app.config.sanitize_all_html and trans.response.get_content_type() == "text/html":
                # Sanitize anytime we respond with plain text/html content.
                return sanitize_html(open( data.file_name ).read())
            return open( data.file_name )
        else:
            trans.response.set_content_type( "text/html" )
            return trans.stream_template_mako( "/dataset/large_file.mako",
                                            truncated_data = open( data.file_name ).read(max_peek_size),
                                            data = data)

    def display_name(self, dataset):
        """Returns formatted html of dataset name"""
        try:
            if type ( dataset.name ) is unicode:
                return escape( dataset.name )
            else:
                return escape( unicode( dataset.name, 'utf-8 ') )
        except:
            return "name unavailable"
    def display_info(self, dataset):
        """Returns formatted html of dataset info"""
        try:
            # Change new line chars to html
            info = escape( dataset.info )
            if info.find( '\r\n' ) >= 0:
                info = info.replace( '\r\n', '<br/>' )
            if info.find( '\r' ) >= 0:
                info = info.replace( '\r', '<br/>' )
            if info.find( '\n' ) >= 0:
                info = info.replace( '\n', '<br/>' )

            # Convert to unicode to display non-ascii characters.
            if type( info ) is not unicode:
                info = unicode( info, 'utf-8')

            return info
        except:
            return "info unavailable"
    def validate(self, dataset):
        """Unimplemented validate, return no exceptions"""
        return list()
    def repair_methods(self, dataset):
        """Unimplemented method, returns dict with method/option for repairing errors"""
        return None
    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'application/octet-stream'
    def add_display_app ( self, app_id, label, file_function, links_function ):
        """
        Adds a display app to the datatype.
        app_id is a unique id
        label is the primary display label, e.g., display at 'UCSC'
        file_function is a string containing the name of the function that returns a properly formatted display
        links_function is a string containing the name of the function that returns a list of (link_name,link)
        """
        self.supported_display_apps = self.supported_display_apps.copy()
        self.supported_display_apps[app_id] = {'label':label,'file_function':file_function,'links_function':links_function}
    def remove_display_app (self, app_id):
        """Removes a display app from the datatype"""
        self.supported_display_apps = self.supported_display_apps.copy()
        try:
            del self.supported_display_apps[app_id]
        except:
            log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.' % ( type, self.__class__.__name__ ) )
    def clear_display_apps( self ):
        self.supported_display_apps = {}
    def add_display_application( self, display_application ):
        """New style display applications"""
        assert display_application.id not in self.display_applications, 'Attempted to add a display application twice'
        self.display_applications[ display_application.id ] = display_application
    def get_display_application( self, key, default = None ):
        return self.display_applications.get( key, default )
    def get_display_applications_by_dataset( self, dataset, trans ):
        rval = odict()
        for key, value in self.display_applications.iteritems():
            value = value.filter_by_dataset( dataset, trans )
            if value.links:
                rval[key] = value
        return rval
    def get_display_types(self):
        """Returns display types available"""
        return self.supported_display_apps.keys()
    def get_display_label(self, type):
        """Returns primary label for display app"""
        try:
            return self.supported_display_apps[type]['label']
        except:
            return 'unknown'
    def as_display_type(self, dataset, type, **kwd):
        """Returns modified file contents for a particular display type """
        try:
            if type in self.get_display_types():
                return getattr (self, self.supported_display_apps[type]['file_function']) (dataset, **kwd)
        except:
            log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible' % (self.supported_display_apps[type]['file_function'], self.__class__.__name__, type) )
        return "This display type (%s) is not implemented for this datatype (%s)." % ( type, dataset.ext)
    def get_display_links( self, dataset, type, app, base_url, target_frame='_blank', **kwd ):
        """
        Returns a list of tuples of (name, link) for a particular display type.  No check on
        'access' permissions is done here - if you can view the dataset, you can also save it
        or send it to a destination outside of Galaxy, so Galaxy security restrictions do not
        apply anyway.
        """
        try:
            if app.config.enable_old_display_applications and type in self.get_display_types():
                return target_frame, getattr ( self, self.supported_display_apps[type]['links_function'] ) ( dataset, type, app, base_url, **kwd )
        except:
            log.exception( 'Function %s is referred to in datatype %s for generating links for type %s, but is not accessible' \
                           % ( self.supported_display_apps[type]['links_function'], self.__class__.__name__, type ) )
        return target_frame, []
    def get_converter_types(self, original_dataset, datatypes_registry):
        """Returns available converters by type for this dataset"""
        return datatypes_registry.get_converters_by_datatype(original_dataset.ext)
    def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ):
        """Returns ( target_ext, existing converted dataset )"""
        return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd )
    def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, set_output_history=True):
        """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure."""
        converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type )

        if converter is None:
            raise Exception( "A converter does not exist for %s to %s." % ( original_dataset.ext, target_type ) )
        #Generate parameter dictionary
        params = {}
        #determine input parameter name and add to params
        input_name = 'input1'
        for key, value in converter.inputs.items():
            if deps and value.name in deps:
                params[value.name] = deps[value.name]
            elif value.type == 'data':
                input_name = key

        params[input_name] = original_dataset
        #Run converter, job is dispatched through Queue
        converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1]
        if len(params) > 0:
            trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id )
        if not visible:
            for name, value in converted_dataset.iteritems():
                value.visible = False
        if return_output:
            return converted_dataset
        return "The file conversion of %s on data %s has been added to the Queue." % (converter.name, original_dataset.hid)
    #We need to clear associated files before we set metadata
    #so that as soon as metadata starts to be set, e.g. implicitly converted datasets are deleted and no longer available 'while' metadata is being set, not just after
    #We'll also clear after setting metadata, for backwards compatibility
    def after_setting_metadata( self, dataset ):
        """This function is called on the dataset after metadata is set."""
        dataset.clear_associated_files( metadata_safe = True )
    def before_setting_metadata( self, dataset ):
        """This function is called on the dataset before metadata is set."""
        dataset.clear_associated_files( metadata_safe = True )
    def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, to_posix_lines = True, space_to_tab = False, **kwds ):
        kwds[ 'name' ] = name
        kwds[ 'optional' ] = optional
        kwds[ 'mimetype' ] = mimetype
        kwds[ 'description' ] = description
        kwds[ 'substitute_name_with_metadata' ] = substitute_name_with_metadata
        kwds[ 'is_binary' ] = is_binary
        kwds[ 'to_posix_lines' ] = to_posix_lines
        kwds[ 'space_to_tab' ] = space_to_tab
        return Bunch( **kwds )
    def add_composite_file( self, name, **kwds ):
        #self.composite_files = self.composite_files.copy()
        self.composite_files[ name ] = self.__new_composite_file( name, **kwds )
    def __substitute_composite_key( self, key, composite_file, dataset = None ):
        if composite_file.substitute_name_with_metadata:
            if dataset:
                meta_value = str( dataset.metadata.get( composite_file.substitute_name_with_metadata ) )
            else:
                meta_value = self.spec[composite_file.substitute_name_with_metadata].default
            return key % meta_value
        return key
    @property
    def writable_files( self, dataset = None ):
        files = odict()
        if self.composite_type != 'auto_primary_file':
            files[ self.primary_file_name ] = self.__new_composite_file( self.primary_file_name )
        for key, value in self.get_composite_files( dataset = dataset ).iteritems():
            files[ key ] = value
        return files
    def get_composite_files( self, dataset = None ):
        def substitute_composite_key( key, composite_file ):
            if composite_file.substitute_name_with_metadata:
                if dataset:
                    meta_value = str( dataset.metadata.get( composite_file.substitute_name_with_metadata ) )
                else:
                    meta_value = self.metadata_spec[ composite_file.substitute_name_with_metadata ].default
                return key % meta_value
            return key
        files = odict()
        for key, value in self.composite_files.iteritems():
            files[ substitute_composite_key( key, value ) ] = value
        return files
    def generate_auto_primary_file( self, dataset = None ):
        raise Exception( "generate_auto_primary_file is not implemented for this datatype." )
    @property
    def has_resolution(self):
        return False

    def matches_any( self, target_datatypes ):
        """
        Check if this datatype is of any of the target_datatypes or is
        a subtype thereof.
        """
        datatype_classes = tuple( [ datatype if isclass( datatype ) else datatype.__class__ for datatype in target_datatypes ] )
        return isinstance( self, datatype_classes )
    def merge( split_files, output_file):
        """
            Merge files with copy.copyfileobj() will not hit the
            max argument limitation of cat. gz and bz2 files are also working.
        """
        if not split_files:
            raise ValueError('Asked to merge zero files as %s' % output_file)
        elif len(split_files) == 1:
            shutil.copyfileobj(open(split_files[0], 'rb'), open(output_file, 'wb'))
        else:
            fdst = open(output_file, 'wb')
            for fsrc in split_files:
                shutil.copyfileobj(open(fsrc, 'rb'), fdst)
            fdst.close()

    merge = staticmethod(merge)

    def get_visualizations( self, dataset ):
        """
        Returns a list of visualizations for datatype.
        """

        if self.track_type:
            return [ 'trackster', 'circster' ]
        return []

    # ------------- Dataproviders
    def has_dataprovider( self, data_format ):
        """
        Returns True if `data_format` is available in `dataproviders`.
        """
        return ( data_format in self.dataproviders )

    def dataprovider( self, dataset, data_format, **settings ):
        """
        Base dataprovider factory for all datatypes that returns the proper provider
        for the given `data_format` or raises a `NoProviderAvailable`.
        """
        if self.has_dataprovider( data_format ):
            return self.dataproviders[ data_format ]( self, dataset, **settings )
        raise dataproviders.exceptions.NoProviderAvailable( self, data_format )

    @dataproviders.decorators.dataprovider_factory( 'base' )
    def base_dataprovider( self, dataset, **settings ):
        dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
        return dataproviders.base.DataProvider( dataset_source, **settings )

    @dataproviders.decorators.dataprovider_factory( 'chunk', dataproviders.chunk.ChunkDataProvider.settings )
    def chunk_dataprovider( self, dataset, **settings ):
        dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
        return dataproviders.chunk.ChunkDataProvider( dataset_source, **settings )

    @dataproviders.decorators.dataprovider_factory( 'chunk64', dataproviders.chunk.Base64ChunkDataProvider.settings )
    def chunk64_dataprovider( self, dataset, **settings ):
        dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
        return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings )

    def _clean_and_set_mime_type(self, trans, mime):
        if mime.lower() in XSS_VULNERABLE_MIME_TYPES:
            if not getattr( trans.app.config, "serve_xss_vulnerable_mimetypes", True ):
                mime = DEFAULT_MIME_TYPE
        trans.response.set_content_type( mime )


@dataproviders.decorators.has_dataproviders
class Text( Data ):
    file_ext = 'txt'
    line_class = 'line'

    """Add metadata elements"""
    MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 )

    def write_from_stream(self, dataset, stream):
        """Writes data from a stream"""
        # write it twice for now
        fd, temp_name = tempfile.mkstemp()
        while 1:
            chunk = stream.read(1048576)
            if not chunk:
                break
            os.write(fd, chunk)
        os.close(fd)
        # rewrite the file with unix newlines
        fp = open(dataset.file_name, 'wt')
        for line in file(temp_name, "U"):
            line = line.strip() + '\n'
            fp.write(line)
        fp.close()
    def set_raw_data(self, dataset, data):
        """Saves the data on the disc"""
        fd, temp_name = tempfile.mkstemp()
        os.write(fd, data)
        os.close(fd)
        # rewrite the file with unix newlines
        fp = open(dataset.file_name, 'wt')
        for line in file(temp_name, "U"):
            line = line.strip() + '\n'
            fp.write(line)
        fp.close()
        os.remove( temp_name )
    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'text/plain'
    def set_meta( self, dataset, **kwd ):
        """
        Set the number of lines of data in dataset.
        """
        dataset.metadata.data_lines = self.count_data_lines(dataset)
    def estimate_file_lines( self, dataset ):
        """
        Perform a rough estimate by extrapolating number of lines from a small read.
        """
        sample_size = 1048576
        dataset_fh = open( dataset.file_name )
        dataset_read = dataset_fh.read(sample_size)
        dataset_fh.close()
        sample_lines = dataset_read.count('\n')
        est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
        return est_lines
    def count_data_lines(self, dataset):
        """
        Count the number of lines of data in dataset,
        skipping all blank lines and comments.
        """
        data_lines = 0
        for line in file( dataset.file_name ):
            line = line.strip()
            if line and not line.startswith( '#' ):
                data_lines += 1
        return data_lines
    def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ):
        """
        Set the peek.  This method is used by various subclasses of Text.
        """
        if not dataset.dataset.purged:
            # The file must exist on disk for the get_file_peek() method
            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars )
            if line_count is None:
                # See if line_count is stored in the metadata
                if dataset.metadata.data_lines:
                    dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, self.line_class) )
                else:
                    # Number of lines is not known ( this should not happen ), and auto-detect is
                    # needed to set metadata
                    # This can happen when the file is larger than max_optional_metadata_filesize.
                    if int(dataset.get_size()) <= 1048576:
                        #Small dataset, recount all lines and reset peek afterward.
                        lc = self.count_data_lines(dataset)
                        dataset.metadata.data_lines = lc
                        dataset.blurb = "%s %s" % ( util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) )
                    else:
                        est_lines = self.estimate_file_lines(dataset)
                        dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) )
            else:
                dataset.blurb = "%s %s" % ( util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def split( cls, input_datasets, subdir_generator_function, split_params):
        """
        Split the input files by line.
        """
        if split_params is None:
            return

        if len(input_datasets) > 1:
            raise Exception("Text file splitting does not support multiple files")
        input_files = [ds.file_name for ds in input_datasets]

        lines_per_file = None
        chunk_size = None
        if split_params['split_mode'] == 'number_of_parts':
            lines_per_file = []
            # Computing the length is expensive!
            def _file_len(fname):
                i = 0
                f = open(fname)
                for i, l in enumerate(f):
                    pass
                f.close()
                return i + 1
            length = _file_len(input_files[0])
            parts = int(split_params['split_size'])
            if length < parts:
                parts = length
            len_each, remainder = divmod(length, parts)
            while length > 0:
                chunk = len_each
                if remainder > 0:
                    chunk += 1
                lines_per_file.append(chunk)
                remainder=- 1
                length -= chunk
        elif split_params['split_mode'] == 'to_size':
            chunk_size = int(split_params['split_size'])
        else:
            raise Exception('Unsupported split mode %s' % split_params['split_mode'])

        f = open(input_files[0], 'rt')
        try:
            chunk_idx = 0
            file_done = False
            part_file = None
            while not file_done:
                if lines_per_file is None:
                    this_chunk_size = chunk_size
                elif chunk_idx < len(lines_per_file):
                    this_chunk_size = lines_per_file[chunk_idx]
                    chunk_idx += 1
                lines_remaining = this_chunk_size
                part_file = None
                while lines_remaining > 0:
                    a_line = f.readline()
                    if a_line == '':
                        file_done = True
                        break
                    if part_file is None:
                        part_dir = subdir_generator_function()
                        part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
                        part_file = open(part_path, 'w')
                    part_file.write(a_line)
                    lines_remaining -= 1
                if part_file is not None:
                    part_file.close()
        except Exception,  e:
            log.error('Unable to split files: %s' % str(e))
            f.close()
            if part_file is not None:
                part_file.close()
            raise
        f.close()
    split = classmethod(split)

    # ------------- Dataproviders
    @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings )
    def line_dataprovider( self, dataset, **settings ):
        """
        Returns an iterator over the dataset's lines (that have been `strip`ed)
        optionally excluding blank lines and lines that start with a comment character.
        """
        dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
        return dataproviders.line.FilteredLineDataProvider( dataset_source, **settings )

    @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings )
    def regex_line_dataprovider( self, dataset, **settings ):
        """
        Returns an iterator over the dataset's lines
        optionally including/excluding lines that match one or more regex filters.
        """
        dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
        return dataproviders.line.RegexLineDataProvider( dataset_source, **settings )


class GenericAsn1( Text ):
    """Class for generic ASN.1 text format"""
    file_ext = 'asn1'


class LineCount( Text ):
    """
    Dataset contains a single line with a single integer that denotes the
    line count for a related dataset. Used for custom builds.
    """
    pass


class Newick( Text ):
    """New Hampshire/Newick Format"""
    file_ext = "nhx"

    def __init__(self, **kwd):
        """Initialize foobar datatype"""
        Text.__init__( self, **kwd )

    def init_meta( self, dataset, copy_from=None ):
        Text.init_meta( self, dataset, copy_from=copy_from )

    def sniff( self, filename ):
        """ Returning false as the newick format is too general and cannot be sniffed."""
        return False

    def get_visualizations( self, dataset ):
        """
        Returns a list of visualizations for datatype.
        """

        return [ 'phyloviz' ]


class Nexus( Text ):
    """Nexus format as used By Paup, Mr Bayes, etc"""
    file_ext = "nex"

    def __init__(self, **kwd):
        """Initialize foobar datatype"""
        Text.__init__( self, **kwd )

    def init_meta( self, dataset, copy_from=None ):
        Text.init_meta( self, dataset, copy_from=copy_from )

    def sniff( self, filename ):
        """All Nexus Files Simply puts a '#NEXUS' in its first line"""
        f = open( filename, "r" )
        firstline = f.readline().upper()
        f.close()

        if "#NEXUS" in firstline:
            return True
        else:
            return False

    def get_visualizations( self, dataset ):
        """
        Returns a list of visualizations for datatype.
        """

        return [ 'phyloviz' ]


# ------------- Utility methods --------------

# nice_size used to be here, but to resolve cyclical dependencies it's been
# moved to galaxy.util.  It belongs there anyway since it's used outside
# datatypes.
nice_size = util.nice_size

def get_test_fname( fname ):
    """Returns test data filename"""
    path, name = os.path.split(__file__)
    full_path = os.path.join( path, 'test', fname )
    return full_path

def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=[] ):
    """
    Returns the first LINE_COUNT lines wrapped to WIDTH

    ## >>> fname = get_test_fname('4.bed')
    ## >>> get_file_peek(fname)
    ## 'chr22    30128507    31828507    uc003bnx.1_cds_2_0_chr22_29227_f    0    +\n'

    """
    # Set size for file.readline() to a negative number to force it to
    # read until either a newline or EOF.  Needed for datasets with very
    # long lines.
    if WIDTH == 'unlimited':
        WIDTH = -1
    lines = []
    count = 0
    file_type = None
    data_checked = False
    temp = open( file_name, "U" )
    while count <= LINE_COUNT:
        line = temp.readline( WIDTH )
        if line and not is_multi_byte and not data_checked:
            # See if we have a compressed or binary file
            if line[0:2] == util.gzip_magic:
                file_type = 'gzipped'
                break
            else:
                for char in line:
                    if ord( char ) > 128:
                        file_type = 'binary'
                        break
            data_checked = True
        if file_type in [ 'gzipped', 'binary' ]:
            break
        skip_line = False
        for skipchar in skipchars:
            if line.startswith( skipchar ):
                skip_line = True
                break
        if not skip_line:
            lines.append( line )
            count += 1
    temp.close()
    if file_type in [ 'gzipped', 'binary' ]:
        text = "%s file" % file_type
    else:
        try:
            text = util.unicodify( '\n'.join( lines ) )
        except UnicodeDecodeError:
            text = "binary/unknown file"
    return text