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Source code for galaxy.datatypes.xml

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

from galaxy import util
from galaxy.datatypes.metadata import MetadataElement
from . import (
    data,
    dataproviders,
    sniff
)

log = logging.getLogger(__name__)

OWL_MARKER = re.compile(r'\<owl:')
SBML_MARKER = re.compile(r'\<sbml')


[docs]@dataproviders.decorators.has_dataproviders @sniff.build_sniff_from_prefix 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) dataset.blurb = 'XML data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
def _has_root_element_in_prefix(self, file_prefix, root): contents = file_prefix.string_io() while True: line = contents.readline() if line is None or not line.startswith('<?'): break # pattern match <root or <ns:root for any ns string pattern = r'^<(\w*:)?%s' % root return line is not None and re.match(pattern, line) is not None
[docs] def sniff_prefix(self, file_prefix): """ 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 """ return file_prefix.startswith('<?xml ')
[docs] @staticmethod 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)
[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]@sniff.disable_parent_class_sniffing 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) dataset.blurb = 'MEME XML data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs]@sniff.disable_parent_class_sniffing 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) dataset.blurb = 'CisML data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs]class Dzi(GenericXml): """ Deep zoom image format, see https://github.com/openseadragon/openseadragon/wiki/The-DZI-File-Format """ # General elements. MetadataElement(name="base_name", desc="Base name for this dataset", default='DeepZoomImage', readonly=True, set_in_upload=True) MetadataElement(name="format", desc="File format of the tiles", default=None, readonly=True, visible=True, no_value=None) MetadataElement(name="tile_size", desc="Size of tiles", default=None, readonly=True, visible=True, no_value=None) # Collection elements. MetadataElement(name="max_level", desc="Max pyramid level", default=None, readonly=True, optional=True, visible=True, no_value=None) MetadataElement(name="quality", desc="Quality", default=None, readonly=True, optional=True, visible=True, no_value=None) # Image elements. MetadataElement(name="height", desc="Size height", default=None, readonly=True, optional=True, visible=True, no_value=None) MetadataElement(name="overlap", desc="Overlap of all four sides of tiles", default=None, readonly=True, optional=True, visible=True, no_value=None) MetadataElement(name="width", desc="Size width", default=None, readonly=True, optional=True, visible=True, no_value=None) file_ext = 'dzi'
[docs] def __init__(self, **kwd): super().__init__(**kwd)
[docs] def set_meta(self, dataset, **kwd): tree = util.parse_xml(dataset.file_name) root = tree.getroot() dataset.metadata.format = root.get('Format') dataset.metadata.tile_size = root.get('TileSize') # DeepZoom image files can include # xml namespace attributes. if root.tag.find('Collection') >= 0: dataset.metadata.max_level = root.get('MaxLevel') dataset.metadata.quality = root.get('Quality') elif root.tag.find('Image') >= 0: dataset.metadata.overlap = root.get('Overlap') for elem in root: if elem.tag.find('Size') >= 0: dataset.metadata.width = elem.get('Width') dataset.metadata.height = elem.get('Height')
[docs] def get_visualizations(self, dataset): """ Returns a list of visualizations for datatype""" return ['openseadragon']
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) dataset.blurb = "Deep Zoom Image" else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disc'
[docs] def sniff_prefix(self, file_prefix): """ Checking for keyword - 'Collection' or 'Image' in the first 200 lines. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('1.dzi') >>> Dzi().sniff(fname) True >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') >>> Dzi().sniff(fname) False """ for line in file_prefix.line_iterator(): line = line.lower() if line.find('<collection') >= 0 or line.find('<image') >= 0: return True 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) dataset.blurb = 'Phyloxml data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff_prefix(self, file_prefix): """"Checking for keyword - 'phyloxml' always in lowercase in the first few lines. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( '1.phyloxml' ) >>> Phyloxml().sniff( fname ) True >>> fname = get_test_fname( 'interval.interval' ) >>> Phyloxml().sniff( fname ) False >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' ) >>> Phyloxml().sniff( fname ) False """ return self._has_root_element_in_prefix(file_prefix, "phyloxml")
[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) dataset.blurb = "Web Ontology Language OWL" else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disc'
[docs] def sniff_prefix(self, file_prefix): """ Checking for keyword - '<owl' in the first 200 lines. """ return file_prefix.search(OWL_MARKER)
[docs]class Sbml(GenericXml): """ System Biology Markup Language http://sbml.org """ file_ext = "sbml" edam_data = "data_2024" edam_format = "format_2585"
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) dataset.blurb = "System Biology Markup Language SBML" else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disc'
[docs] def sniff_prefix(self, file_prefix): """ Checking for keyword - '<sbml' in the first 200 lines. """ return file_prefix.search(SBML_MARKER)