def __init__(self, source, dtd_valid_file=None):
"""
source: File path to a BioC XML input document.
dtd_valid_file: File path to a BioC.dtd file. Using this
optional argument ensures DTD validation.
"""
self.source = source
self.collection = BioCCollection()
self.xml_tree = etree.parse(source)
if dtd_valid_file is not None:
dtd = etree.DTD(dtd_valid_file)
if dtd.validate(self.xml_tree) is False:
raise (Exception(dtd.error_log.filter_from_errors()[0]))
def __init__(self, source, dtd_valid_file=None):
"""
source: File path to a BioC XML input document.
dtd_valid_file: File path to a BioC.dtd file. Using this
optional argument ensures DTD validation.
"""
self.source = source
self.collection = BioCCollection()
self.xml_tree = etree.parse(source)
if dtd_valid_file is not None:
dtd = etree.DTD(dtd_valid_file)
if dtd.validate(self.xml_tree) is False:
raise(Exception(dtd.error_log.filter_from_errors()[0]))
class BioCReader:
"""
This class can be used to store BioC XML files in PyBioC objects,
for further manipulation.
"""
def __init__(self, source, dtd_valid_file=None):
"""
source: File path to a BioC XML input document.
dtd_valid_file: File path to a BioC.dtd file. Using this
optional argument ensures DTD validation.
"""
self.source = source
self.collection = BioCCollection()
self.xml_tree = etree.parse(source)
if dtd_valid_file is not None:
dtd = etree.DTD(dtd_valid_file)
if dtd.validate(self.xml_tree) is False:
raise (Exception(dtd.error_log.filter_from_errors()[0]))
def read(self):
"""
Invoke this method in order to read in the file provided by
the source class variable. Only after this method has been
called the BioCReader object gets populated.
"""
self._read_collection()
def _read_collection(self):
collection_elem = self.xml_tree.xpath('/collection')[0]
self.collection.source = collection_elem.xpath('source')[0].text
self.collection.date = collection_elem.xpath('date')[0].text
self.collection.key = collection_elem.xpath('key')[0].text
infon_elem_list = collection_elem.xpath('infon')
document_elem_list = collection_elem.xpath('document')
self._read_infons(infon_elem_list, self.collection)
self._read_documents(document_elem_list)
def _read_infons(self, infon_elem_list, infons_parent_elem):
for infon_elem in infon_elem_list:
infons_parent_elem.put_infon(self._get_infon_key(infon_elem),
infon_elem.text)
def _read_documents(self, document_elem_list):
for document_elem in document_elem_list:
document = BioCDocument()
document.id = document_elem.xpath('id')[0].text
self._read_infons(document_elem.xpath('infon'), document)
self._read_passages(document_elem.xpath('passage'), document)
self._read_relations(document_elem.xpath('relation'), document)
self.collection.add_document(document)
def _read_passages(self, passage_elem_list, document_parent_elem):
for passage_elem in passage_elem_list:
passage = BioCPassage()
self._read_infons(passage_elem.xpath('infon'), passage)
passage.offset = passage_elem.xpath('offset')[0].text
# Is this BioC document with <sentence>?
if len(passage_elem.xpath('sentence')) > 0:
self._read_sentences(passage_elem.xpath('sentence'), passage)
else:
# Is the (optional) text element available?
try:
passage.text = passage_elem.xpath('text')[0].text
except:
pass
self._read_annotations(passage_elem.xpath('annotation'),
passage)
self._read_relations(passage_elem.xpath('relation'), passage)
document_parent_elem.add_passage(passage)
def _read_sentences(self, sentence_elem_list, passage_parent_elem):
for sentence_elem in sentence_elem_list:
sentence = BioCSentence()
self._read_infons(sentence_elem.xpath('infon'), sentence)
sentence.offset = sentence_elem.xpath('offset')[0].text
sentence.text = sentence_elem.xpath('text')[0].text
self._read_annotations(sentence_elem.xpath('annotation'), sentence)
self._read_relations(sentence_elem.xpath('relation'), sentence)
passage_parent_elem.add_sentence(sentence)
def _read_annotations(self, annotation_elem_list, annotations_parent_elem):
for annotation_elem in annotation_elem_list:
annotation = BioCAnnotation()
# Attribute id is just #IMPLIED, not #REQUIRED
if 'id' in annotation_elem.attrib:
annotation.id = annotation_elem.attrib['id']
self._read_infons(annotation_elem.xpath('infon'), annotation)
for location_elem in annotation_elem.xpath('location'):
location = BioCLocation()
location.offset = location_elem.attrib['offset']
location.length = location_elem.attrib['length']
annotation.add_location(location)
annotation.text = annotation_elem.xpath('text')[0].text
annotations_parent_elem.add_annotation(annotation)
def _read_relations(self, relation_elem_list, relations_parent_elem):
for relation_elem in relation_elem_list:
relation = BioCRelation()
# Attribute id is just #IMPLIED, not #REQUIRED
if 'id' in relation_elem.attrib:
relation.id = relation_elem.attrib['id']
self._read_infons(relation_elem.xpath('infon'), relation)
for node_elem in relation_elem.xpath('node'):
node = BioCNode()
node.refid = node_elem.attrib['refid']
node.role = node_elem.attrib['role']
relation.add_node(node)
relations_parent_elem.add_relation(relation)
def _get_infon_key(self, elem):
return elem.attrib['key']
class BioCReader:
"""
This class can be used to store BioC XML files in PyBioC objects,
for further manipulation.
"""
def __init__(self, source, dtd_valid_file=None):
"""
source: File path to a BioC XML input document.
dtd_valid_file: File path to a BioC.dtd file. Using this
optional argument ensures DTD validation.
"""
self.source = source
self.collection = BioCCollection()
self.xml_tree = etree.parse(source)
if dtd_valid_file is not None:
dtd = etree.DTD(dtd_valid_file)
if dtd.validate(self.xml_tree) is False:
raise(Exception(dtd.error_log.filter_from_errors()[0]))
def read(self):
"""
Invoke this method in order to read in the file provided by
the source class variable. Only after this method has been
called the BioCReader object gets populated.
"""
self._read_collection()
def _read_collection(self):
collection_elem = self.xml_tree.xpath('/collection')[0]
self.collection.source = collection_elem.xpath('source')[0].text
self.collection.date = collection_elem.xpath('date')[0].text
self.collection.key = collection_elem.xpath('key')[0].text
infon_elem_list = collection_elem.xpath('infon')
document_elem_list = collection_elem.xpath('document')
self._read_infons(infon_elem_list, self.collection)
self._read_documents(document_elem_list)
def _read_infons(self, infon_elem_list, infons_parent_elem):
for infon_elem in infon_elem_list:
infons_parent_elem.put_infon(self._get_infon_key(infon_elem),
infon_elem.text)
def _read_documents(self, document_elem_list):
for document_elem in document_elem_list:
document = BioCDocument()
document.id = document_elem.xpath('id')[0].text
self._read_infons(document_elem.xpath('infon'), document)
self._read_passages(document_elem.xpath('passage'),
document)
self._read_relations(document_elem.xpath('relation'),
document)
self.collection.add_document(document)
def _read_passages(self, passage_elem_list, document_parent_elem):
for passage_elem in passage_elem_list:
passage = BioCPassage()
self._read_infons(passage_elem.xpath('infon'), passage)
passage.offset = passage_elem.xpath('offset')[0].text
# Is this BioC document with <sentence>?
if len(passage_elem.xpath('sentence')) > 0:
self._read_sentences(passage_elem.xpath('sentence'),
passage)
else:
# Is the (optional) text element available?
try:
passage.text = passage_elem.xpath('text')[0].text
except:
pass
self._read_annotations(passage_elem.xpath('annotation'),
passage)
self._read_relations(passage_elem.xpath('relation'),
passage)
document_parent_elem.add_passage(passage)
def _read_sentences(self, sentence_elem_list, passage_parent_elem):
for sentence_elem in sentence_elem_list:
sentence = BioCSentence()
self._read_infons(sentence_elem.xpath('infon'), sentence)
sentence.offset = sentence_elem.xpath('offset')[0].text
sentence.text = sentence_elem.xpath('text')[0].text
self._read_annotations(sentence_elem.xpath('annotation'),
sentence)
self._read_relations(sentence_elem.xpath('relation'),
sentence)
passage_parent_elem.add_sentence(sentence)
def _read_annotations(self, annotation_elem_list,
annotations_parent_elem):
for annotation_elem in annotation_elem_list:
annotation = BioCAnnotation()
# Attribute id is just #IMPLIED, not #REQUIRED
if 'id' in annotation_elem.attrib:
annotation.id = annotation_elem.attrib['id']
self._read_infons(annotation_elem.xpath('infon'),
annotation)
for location_elem in annotation_elem.xpath('location'):
location = BioCLocation()
location.offset = location_elem.attrib['offset']
location.length = location_elem.attrib['length']
annotation.add_location(location)
annotation.text = annotation_elem.xpath('text')[0].text
annotations_parent_elem.add_annotation(annotation)
def _read_relations(self, relation_elem_list, relations_parent_elem):
for relation_elem in relation_elem_list:
relation = BioCRelation()
# Attribute id is just #IMPLIED, not #REQUIRED
if 'id' in relation_elem.attrib:
relation.id = relation_elem.attrib['id']
self._read_infons(relation_elem.xpath('infon'), relation)
for node_elem in relation_elem.xpath('node'):
node = BioCNode()
node.refid = node_elem.attrib['refid']
node.role = node_elem.attrib['role']
relation.add_node(node)
relations_parent_elem.add_relation(relation)
def _get_infon_key(self, elem):
return elem.attrib['key']
