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_molecules == 1):
dataset.blurb = "1 molecule"
else:
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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 = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
if (dataset.metadata.number_of_models == 1):
dataset.blurb = "1 alignment"
else:
dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
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_sequences == 1):
dataset.blurb = "1 sequence [%s]" % dataset.metadata.name_of_sequences[0]
else:
seq_list = ', '.join(dataset.metadata.name_of_sequences[0:10])
if len(dataset.metadata.name_of_sequences) > 10:
seq_list += ', ...'
dataset.blurb = "%s sequences [%s]" % ( dataset.metadata.number_of_sequences,
seq_list )
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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 = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
dataset.blurb = "Faces: %s, Vertices: %s" % (str(dataset.metadata.face), str(dataset.metadata.vertex))
else:
dataset.peek = 'File does not exist'
dataset.blurb = 'File purged from disc'
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)
dataset.blurb = self.get_blurb(dataset)
else:
dataset.peek = 'File does not exist'
dataset.blurb = 'File purged from disc'
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "pharmacophore"
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 = get_file_peek(dataset.file_name)
dataset.blurb = "grids for docking"
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 = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
dataset.blurb = "Open Biomedical Ontology (OBO)"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "SNAP HMM model"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
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 )
dataset.blurb = "JavaScript Object Notation (JSON)"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
def set_peek( self, dataset, 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 )
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 = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
dataset.blurb = "IPython Notebook"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "ESTScan scores matrices"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
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 )
dataset.blurb = "Attribute-Relation File Format (ARFF)"
dataset.blurb += ", %s comments, %s attributes" % ( dataset.metadata.comment_lines, dataset.metadata.columns )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
def set_peek(self, dataset, is_multi_byte=False):
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.file_name)
dataset.blurb = 'splib Spectral Library Format'
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset, 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)
dataset.blurb = 'Spectral Library without index files'
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:
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
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:
root_numbers = count_special_lines("^ROOT", dataset.file_name)
branch_numbers = count_special_lines("^BRANCH", dataset.file_name)
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = f"{root_numbers} roots and {branch_numbers} branches"
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:
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
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 = get_file_peek(dataset.file_name)
dataset.blurb = "Attribute-Relation File Format (ARFF)"
dataset.blurb += ", %s comments, %s attributes" % (
dataset.metadata.comment_lines, dataset.metadata.columns)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
def set_peek(self, dataset, 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)
dataset.blurb = self.blurb
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:
root_numbers = count_special_lines("^ROOT", dataset.file_name)
branch_numbers = count_special_lines("^BRANCH", dataset.file_name)
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "%s roots and %s branches" % (root_numbers, branch_numbers)
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 = get_file_peek(dataset.file_name,
is_multi_byte=is_multi_byte)
dataset.blurb = "Faces: %s, Vertices: %s" % (str(
dataset.metadata.face), str(dataset.metadata.vertex))
else:
dataset.peek = 'File does not exist'
dataset.blurb = 'File purged from disc'
def set_peek(self, dataset):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
if (dataset.metadata.number_comp == 1):
dataset.blurb = "1 significant component"
else:
dataset.blurb = f"{dataset.metadata.number_comp} significant components"
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:
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "%s atoms and %s HET-atoms\nchain_ids: %s" % (atom_numbers, hetatm_numbers, str(chain_ids))
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset):
if not dataset.dataset.purged:
if (dataset.metadata.number_of_models == 1):
dataset.blurb = "1 alignment"
else:
dataset.blurb = f"{dataset.metadata.number_of_models} alignments"
dataset.peek = get_file_peek(dataset.file_name)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
if (dataset.metadata.number_comp == 1):
dataset.blurb = "1 significant component"
else:
dataset.blurb = "%s significant components" % dataset.metadata.number_comp
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 = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
if (dataset.metadata.number_of_models == 1):
dataset.blurb = "1 alignment"
else:
dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
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.sequences:
dataset.blurb = "%s sequences" % util.commaify(str(dataset.metadata.sequences))
else:
dataset.blurb = nice_size(dataset.get_size())
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
if dataset.metadata.sequences:
dataset.blurb = f"{util.commaify(str(dataset.metadata.sequences))} sequences"
else:
dataset.blurb = nice_size(dataset.get_size())
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:
if (dataset.metadata.number_of_molecules == 1):
dataset.blurb = "1 molecule"
else:
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
dataset.peek = get_file_peek(dataset.file_name)
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 = get_file_peek(dataset.file_name)
if (dataset.metadata.number_comp == 1):
dataset.blurb = "1 significant component"
else:
dataset.blurb = "%s significant components" % dataset.metadata.number_comp
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek(self, dataset):
if not dataset.dataset.purged:
if dataset.metadata.block_count == 1:
dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, 1 block, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns"
else:
dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, {dataset.metadata.block_count} blocks, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns"
dataset.peek = get_file_peek(dataset.file_name)
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:
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "%s atoms and %s HET-atoms\nchain_ids: %s" % (atom_numbers, hetatm_numbers, str(chain_ids))
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 = 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 = nice_size(dataset.get_size())
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:
if dataset.metadata.block_count == 1:
dataset.blurb = "{} {}: Format {}, 1 block, {} headers and {} columns".format(
dataset.metadata.file_type,
dataset.metadata.version_number,
dataset.metadata.file_format,
dataset.metadata.number_of_optional_header_records,
dataset.metadata.number_of_data_columns)
else:
dataset.blurb = "{} {}: Format {}, {} blocks, {} headers and {} columns".format(
dataset.metadata.file_type,
dataset.metadata.version_number,
dataset.metadata.file_format, dataset.metadata.block_count,
dataset.metadata.number_of_optional_header_records,
dataset.metadata.number_of_data_columns)
dataset.peek = get_file_peek(dataset.file_name)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def test_get_file_peek():
# should get the first 5 lines of the file without a trailing newline character
assert get_file_peek(
'test-data/1.tabular', line_wrap=False
) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'
def test_get_file_peek():
# should get the first 5 lines of the file without a trailing newline character
assert get_file_peek(os.path.join(galaxy_directory(), 'test-data/1.tabular'), line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11\n'
def test_get_file_peek():
# should get the first 5 lines of the file without a trailing newline character
assert get_file_peek('test-data/1.tabular', line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'
