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Source code for galaxy.datatypes.xml

"""
XML format classes
"""
import logging
import re

from . import (
    data,
    dataproviders
)

log = logging.getLogger(__name__)


[docs]@dataproviders.decorators.has_dataproviders class GenericXml(data.Text): """Base format class for any XML file.""" edam_format = "format_2332" file_ext = "xml"
[docs] 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 = 'XML data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff(self, filename): """ Determines whether the file is XML or not >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' ) >>> GenericXml().sniff( fname ) True >>> fname = get_test_fname( 'interval.interval' ) >>> GenericXml().sniff( fname ) False """ # TODO - Use a context manager on Python 2.5+ to close handle handle = open(filename) line = handle.readline() handle.close() # TODO - Is there a more robust way to do this? return line.startswith('<?xml ')
[docs] def merge(split_files, output_file): """Merging multiple XML files is non-trivial and must be done in subclasses.""" if len(split_files) > 1: raise NotImplementedError("Merging multiple XML files is non-trivial and must be implemented for each XML type") # For one file only, use base class method (move/copy) data.Text.merge(split_files, output_file)
merge = staticmethod(merge)
[docs] @dataproviders.decorators.dataprovider_factory('xml', dataproviders.hierarchy.XMLDataProvider.settings) def xml_dataprovider(self, dataset, **settings): dataset_source = dataproviders.dataset.DatasetDataProvider(dataset) return dataproviders.hierarchy.XMLDataProvider(dataset_source, **settings)
[docs]class MEMEXml(GenericXml): """MEME XML Output data""" file_ext = "memexml"
[docs] 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 = 'MEME XML data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff(self, filename): return False
[docs]class CisML(GenericXml): """CisML XML data""" # see: http://www.ncbi.nlm.nih.gov/pubmed/15001475 file_ext = "cisml"
[docs] 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 = 'CisML data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff(self, filename): return False
[docs]class Phyloxml(GenericXml): """Format for defining phyloxml data http://www.phyloxml.org/""" edam_data = "data_0872" edam_format = "format_3159" file_ext = "phyloxml"
[docs] 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 = 'Phyloxml data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff(self, filename): """"Checking for keyword - 'phyloxml' always in lowercase in the first few lines""" f = open(filename, "r") firstlines = "".join(f.readlines(5)) f.close() if "phyloxml" in firstlines: return True return False
[docs] def get_visualizations(self, dataset): """ Returns a list of visualizations for datatype. """ return ['phyloviz']
[docs]class Owl(GenericXml): """ Web Ontology Language OWL format description http://www.w3.org/TR/owl-ref/ """ edam_format = "format_3262" file_ext = "owl"
[docs] 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) dataset.blurb = "Web Ontology Language OWL" else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disc'
[docs] def sniff(self, filename): """ Checking for keyword - '<owl' in the first 200 lines. """ owl_marker = re.compile(r'\<owl:') with open(filename) as handle: # Check first 200 lines for the string "<owl:" first_lines = handle.readlines(200) for line in first_lines: if owl_marker.search(line): return True return False