When user try to add a second tag to tagged fragment, fragment positions are incorrect

Incorrect fragment positions in Annotator "create" request about collaborative-platform HOT 2 CLOSED

providedh commented on June 9, 2024

Incorrect fragment positions in Annotator "create" request

from collaborative-platform.

Comments (2)

Janchorizo commented on June 9, 2024

I have tried replicating this issue and the following is what I found:

After loading the adhered document and annotating it, there are some cases in which the
annotation failed on me.

Having those annotations, and selecting the fourth word in the paragraph (Coppaun), I
the server fails at creating the annotation. The following screenshot shows the retrieved document
at app load, the message sent to the server, and the slice of the original document using
the sent positions:

The server-side code fails in the _add_tag method.

collaborative-platform/src/collaborative_platform/apps/close_reading/annotator.py

Lines 529 to 630 in 4f87067

 def __add_tag(self, annotated_fragment, tag, uncertainty=False, reference=False): 

 new_annotated_fragment = '' 

 annotation_ids = [] 

 while len(annotated_fragment) > 0: 

 # handle xml tag 

 if re.search(r'^\s*?<[^<>]*?>', annotated_fragment): 

 match = re.search(r'^\s*?<[^<>]*?>', annotated_fragment) 

 tag_to_move = match.group() 

 end_tag = '</' + tag 

 empty_tag = '<' + tag + '/' 

 if tag in tag_to_move and end_tag not in tag_to_move and empty_tag not in tag_to_move: 

 match = re.search(r'<[^>\s]+', tag_to_move) 

 tag_begin = match.group() 

 if uncertainty: 

 if 'xml:id="' not in tag_to_move: 

 id = f"{tag}_{self.__file.name}-{self.__tag_xml_id_number}" 

 attribute = f' xml:id="{id}"' 

 annotation_ids.append('#' + id) 

 new_tag_to_move = tag_to_move[:len(tag_begin)] + attribute + tag_to_move[len(tag_begin):] 

 self.__tag_xml_id_number += 1 

 else: 

 match = re.search(r'xml:id=".*?"', tag_to_move) 

 existing_id = match.group() 

 existing_id = existing_id.replace('xml:id="', '') 

 existing_id = existing_id.replace('"', '') 

 annotation_ids.append('#' + existing_id) 

 new_tag_to_move = tag_to_move 

 new_annotated_fragment += new_tag_to_move 

 elif reference: 

 if 'ref="' not in tag_to_move: 

 id = self.__get_id_of_list_object_to_reference() 

 attribute = f' ref="#{id}"' 

 annotation_ids.append('#' + id) 

 new_tag_to_move = tag_to_move[:len(tag_begin)] + attribute + tag_to_move[len(tag_begin):] 

 else: 

 match = re.search(r'ref=".*?"', tag_to_move) 

 existing_reference = match.group() 

 id = self.__get_id_of_list_object_to_reference() 

 if id in existing_reference: 

 raise NotModified(f"Reference to element with xml:id: {id} already exist.") 

 updated_reference = f'{existing_reference[:-1]} #{id}"' 

 annotation_ids.append('#' + id) 

 new_tag_to_move = tag_to_move.replace(existing_reference, updated_reference) 

 new_annotated_fragment += new_tag_to_move 

 else: 

 new_annotated_fragment += tag_to_move 

 annotated_fragment = annotated_fragment[len(tag_to_move):] 

 # handle text 

 else: 

 match = re.search(r'^\s*[^<>]+', annotated_fragment) 

 text_to_move = match.group() 

 if tag in self.__tags: 

 new_annotated_fragment += text_to_move 

 annotated_fragment = annotated_fragment[len(text_to_move):] 

 else: 

 attribute = "" 

 if uncertainty: 

 id = f"{tag}_{self.__file.name}-{self.__tag_xml_id_number}" 

 attribute = f' xml:id="{id}"' 

 annotation_ids.append('#' + id) 

 elif reference: 

 id = self.__get_id_of_list_object_to_reference() 

 attribute = f' ref="#{id}"' 

 annotation_ids.append('#' + id) 

 tag_open = f'<{tag}{attribute}>' 

 tag_close = f'</{tag}>' 

 new_annotated_fragment += tag_open + text_to_move + tag_close 

 annotated_fragment = annotated_fragment[len(text_to_move):] 

 if uncertainty: 

 self.__tag_xml_id_number += 1 

 return new_annotated_fragment, annotation_ids

The annotated_fragment argument is
set to a different value than what is obtained in the front-end: </date> Coppaun<gap/>

from collaborative-platform.

bug-rancher commented on June 9, 2024

I replicated your bug. The root of this bug is this same as in first message in this issue - wrong positions in request. The difference is that positions pointing to fragment with part of the tag on the end instead on the beginning ('Coppaun<' instead 'objectName ref="#object_recipe_0_xml-1">Guetten' as in first post).

I added a validation to check for that exceptions, and now, if this exception will occur, backend will return a proper message with included fragment of xml based on positions from request. This will stop WebSockets from disconnecting in this cases and I hope this will help you to figure out why positions in request sometimes are wrong.

from collaborative-platform.

Incorrect fragment positions in Annotator "create" request about collaborative-platform HOT 2 CLOSED

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	def __add_tag(self, annotated_fragment, tag, uncertainty=False, reference=False):
	new_annotated_fragment = ''
	annotation_ids = []

	while len(annotated_fragment) > 0:
	# handle xml tag
	if re.search(r'^\s?<[^<>]?>', annotated_fragment):
	match = re.search(r'^\s?<[^<>]?>', annotated_fragment)
	tag_to_move = match.group()

	end_tag = '</' + tag
	empty_tag = '<' + tag + '/'

	if tag in tag_to_move and end_tag not in tag_to_move and empty_tag not in tag_to_move:
	match = re.search(r'<[^>\s]+', tag_to_move)
	tag_begin = match.group()

	if uncertainty:
	if 'xml:id="' not in tag_to_move:
	id = f"{tag}_{self.__file.name}-{self.__tag_xml_id_number}"
	attribute = f' xml:id="{id}"'

	annotation_ids.append('#' + id)

	new_tag_to_move = tag_to_move[:len(tag_begin)] + attribute + tag_to_move[len(tag_begin):]

	self.__tag_xml_id_number += 1
	else:
	match = re.search(r'xml:id=".*?"', tag_to_move)
	existing_id = match.group()
	existing_id = existing_id.replace('xml:id="', '')
	existing_id = existing_id.replace('"', '')

	annotation_ids.append('#' + existing_id)
	new_tag_to_move = tag_to_move

	new_annotated_fragment += new_tag_to_move

	elif reference:
	if 'ref="' not in tag_to_move:
	id = self.__get_id_of_list_object_to_reference()
	attribute = f' ref="#{id}"'

	annotation_ids.append('#' + id)
	new_tag_to_move = tag_to_move[:len(tag_begin)] + attribute + tag_to_move[len(tag_begin):]

	else:
	match = re.search(r'ref=".*?"', tag_to_move)
	existing_reference = match.group()

	id = self.__get_id_of_list_object_to_reference()

	if id in existing_reference:
	raise NotModified(f"Reference to element with xml:id: {id} already exist.")

	updated_reference = f'{existing_reference[:-1]} #{id}"'

	annotation_ids.append('#' + id)
	new_tag_to_move = tag_to_move.replace(existing_reference, updated_reference)

	new_annotated_fragment += new_tag_to_move
	else:
	new_annotated_fragment += tag_to_move

	annotated_fragment = annotated_fragment[len(tag_to_move):]

	# handle text
	else:
	match = re.search(r'^\s*[^<>]+', annotated_fragment)
	text_to_move = match.group()

	if tag in self.__tags:
	new_annotated_fragment += text_to_move

	annotated_fragment = annotated_fragment[len(text_to_move):]

	else:
	attribute = ""

	if uncertainty:
	id = f"{tag}_{self.__file.name}-{self.__tag_xml_id_number}"
	attribute = f' xml:id="{id}"'

	annotation_ids.append('#' + id)

	elif reference:
	id = self.__get_id_of_list_object_to_reference()
	attribute = f' ref="#{id}"'

	annotation_ids.append('#' + id)

	tag_open = f'<{tag}{attribute}>'
	tag_close = f'</{tag}>'

	new_annotated_fragment += tag_open + text_to_move + tag_close

	annotated_fragment = annotated_fragment[len(text_to_move):]

	if uncertainty:
	self.__tag_xml_id_number += 1

	return new_annotated_fragment, annotation_ids