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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 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)