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 set_peek(self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=True):
"""
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, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap)
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 set_peek( self, dataset, line_count=None ):
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek( dataset.file_name )
if line_count is None:
dataset.blurb = "%s regions" % util.commaify( str( data.get_line_count( dataset.file_name ) ) )
else:
dataset.blurb = "%s regions" % util.commaify( str( line_count ) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_multi_byte_peek( self, dataset, line_count=None ):
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=True )
if line_count is None:
dataset.blurb = "%s lines" % util.commaify( str( get_line_count( dataset.file_name ) ) )
else:
dataset.blurb = "%s lines" % util.commaify( str( line_count ) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset, line_count=None, is_multi_byte=False):
super(Tabular, self).set_peek(dataset,
line_count=line_count,
is_multi_byte=is_multi_byte)
if dataset.metadata.comment_lines:
dataset.blurb = "%s, %s comments" % (
dataset.blurb,
util.commaify(str(dataset.metadata.comment_lines)))
def set_peek( self, dataset, line_count=None, 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 )
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
dataset.blurb = "%s regions" % util.commaify( str( dataset.metadata.data_lines ) )
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
dataset.blurb = "? regions"
else:
dataset.blurb = "%s regions" % util.commaify( str( line_count ) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
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 )
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
dataset.blurb = "%s lines" % util.commaify( str( dataset.metadata.data_lines ) )
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
dataset.blurb = "? lines"
else:
dataset.blurb = "%s lines" % util.commaify( str( line_count ) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
if dataset.metadata.sequences:
dataset.blurb = "%s sequences" % util.commaify( str( dataset.metadata.sequences ) )
else:
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset ):
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek( dataset.file_name )
dataset.blurb = util.commaify( str( data.get_line_count( dataset.file_name ) ) ) + " rows"
#i don't think set_meta should not be called here, it should be called separately
self.set_meta( dataset )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset, line_count=None, is_multi_byte=False):
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)
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
dataset.blurb = "%s lines" % util.commaify(
str(dataset.metadata.data_lines))
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
dataset.blurb = "? lines"
else:
dataset.blurb = "%s lines" % util.commaify(str(line_count))
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
if dataset.metadata.sequences:
dataset.blurb = "%s sequences" % util.commaify( str( dataset.metadata.sequences ) )
else:
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, line_count=None ):
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek( dataset.file_name )
if line_count is None:
dataset.blurb = data.nice_size( dataset.get_size() )
else:
dataset.blurb = "%s lines, 454 Quality score file" % util.commaify( str( line_count ) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
if dataset.metadata.blocks:
dataset.blurb = "%s blocks" % util.commaify( str( dataset.metadata.blocks ) )
else:
# Number of blocks is not known ( this should not happen ), and auto-detect is
# needed to set metadata
dataset.blurb = "? blocks"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
if dataset.metadata.blocks:
dataset.blurb = "%s blocks" % util.commaify( str( dataset.metadata.blocks ) )
else:
# Number of blocks is not known ( this should not happen ), and auto-detect is
# needed to set metadata
dataset.blurb = "? blocks"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset):
dataset.peek = data.get_file_peek(dataset.file_name)
## dataset.peek = self.make_html_table( dataset.peek )
dataset.blurb = util.commaify(
str(data.get_line_count(dataset.file_name))) + " regions"
self.set_meta(dataset)
def set_peek( self, dataset ):
dataset.peek = data.get_file_peek( dataset.file_name )
## dataset.peek = self.make_html_table( dataset.peek )
dataset.blurb = util.commaify( str( data.get_line_count( dataset.file_name ) ) ) + " regions"
self.set_meta( dataset )
def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None ):
super(TabularData, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False )
if dataset.metadata.comment_lines:
dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) )
def set_peek(self, dataset):
dataset.peek = get_file_peek( dataset.file_name )
dataset.blurb = util.commaify( str( get_line_count( dataset.file_name ) ) ) + " lines"
def set_peek( self, dataset, line_count=None, is_multi_byte=False):
super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte)
if dataset.metadata.comment_lines:
dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) )
def set_peek(self, dataset):
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = util.commaify(str(get_line_count(
dataset.file_name))) + " lines"
