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diff_and_mark.py
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diff_and_mark.py
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#!/usr/bin/env python
# -*- Mode: Python; tab-width: 4; indent-tabs-mode: nil; coding: utf-8; -*-
# vim:set ft=python ts=4 sw=4 sts=4 autoindent:
# Preamble {{{
"""Mark the differences between two annotation files, creating a diff
annotation."""
try:
import annotation
except ImportError:
import os.path
from sys import path as sys_path
# Guessing that we might be in the brat tools/ directory ...
sys_path.append(os.path.join(os.path.dirname(__file__), '../server/src'))
import annotation
try:
pass
except ImportError:
import os.path
from sys import path as sys_path
# We are most likely on an old Python and need to use our internal version
sys_path.append(os.path.join(os.path.dirname(__file__), '../server/lib'))
# this seems to be necessary for annotations to find its config
sys_path.append(os.path.join(os.path.dirname(__file__), '..'))
# }}}
class Mapping: # {{{
def __init__(self):
self.first_by_second = dict()
self.second_by_first = dict()
self.only_in_second = []
def add(self, first, second, is_clone=False):
self.first_by_second[second] = first
self.second_by_first[first] = second
if is_clone:
self.only_in_second.append(second)
def get_second(self, first):
return self.second_by_first[first] if first in self.second_by_first else None
def get_first(self, second):
return self.first_by_second[second] if second in self.first_by_second else None
def is_only_in_second(self, second):
return second in self.only_in_second
def is_only_in_first(self, first):
return first in self.second_by_first
# }}}
class AnnotationDiff: # {{{
def __init__(self, first, second, result): # {{{
self.first = first
self.second = second
self.result = result
self.mapping = Mapping()
self.first_textbounds = dict(
(textbound.id, textbound) for textbound in first.get_textbounds())
# }}}
def diff(self): # {{{
# self.second_triggers = [t for t in self.second.get_triggers()]
self.diff_entities()
self.diff_triggers()
self.diff_events()
self.diff_oneline_comments()
self.diff_equivs()
self.diff_normalizations()
self.diff_attributes()
self.diff_relations()
# }}}
# Utilities for adding marks {{{
def add_mark(self, type, target, reason):
comment = annotation.OnelineCommentAnnotation(
target,
self.result.get_new_id('#'),
type,
"\t" + reason)
self.result.add_annotation(comment)
def add_missing(self, target, reason):
self.add_mark('MissingAnnotation', target, reason)
def add_added(self, target, reason):
self.add_mark('AddedAnnotation', target, reason)
def add_changed(self, target, reason):
self.add_mark('ChangedAnnotation', target, reason)
# }}}
# Entities {{{
def find_entity(self, haystack, needle):
for entity in haystack.get_entities():
if entity.same_span(needle) and entity.type == needle.type:
return entity
return None
def diff_entities(self):
found_first_ids = set()
for entity in self.second.get_entities():
found_first = self.find_entity(self.first, entity)
if found_first is None:
self.add_added(entity.id, 'Added entity')
else:
found_first_ids.add(found_first.id)
self.mapping.add(found_first.id, entity.id)
import copy
for entity in self.first.get_entities():
if entity.id not in found_first_ids:
clone = copy.copy(entity)
clone.id = self.result.get_new_id('T')
self.result.add_annotation(clone)
self.mapping.add(entity.id, clone.id, True)
self.add_missing(clone.id, 'Missing entity')
# }}}
# Triggers {{{
def find_trigger(self, haystack, needle):
for trigger in haystack.get_triggers():
if trigger.same_span(needle) and trigger.type == needle.type:
return trigger
return None
def diff_triggers(self):
found_first_ids = set()
for trigger in self.second.get_triggers():
found_first = self.find_trigger(self.first, trigger)
if found_first:
found_first_ids.add(found_first.id)
self.mapping.add(found_first.id, trigger.id)
# no `else`; the comments are handled by diff_events();
import copy
for trigger in self.first.get_triggers():
if trigger.id not in found_first_ids:
clone = copy.copy(trigger)
clone.id = self.result.get_new_id('T')
self.result.add_annotation(clone)
self.mapping.add(trigger.id, clone.id, True)
# }}}
# Events {{{
#
# Events are a problem, since there can be multiple events for the
# same trigger which are only distinguished by their arguments.
# An additional problem is that arguments can also be events, so we
# don't necessarily know the mapping of the arguments.
# Thus, when comparing events-as-arguments, we compare only their
# triggers.
def trigger_or_self(self, target, triggers):
try:
return triggers[target]
except KeyError:
return target
def find_closest_events(
self,
second_event,
found_events_dict,
first_triggers,
second_triggers):
second_args = dict(
(role, self.trigger_or_self(
target, second_triggers)) for (
role, target) in second_event.args)
second_roles = set(second_args.keys())
for first_event in self.first.get_events():
if self.mapping.get_second(
first_event.trigger) == second_event.trigger and first_event.type == second_event.type:
first_args = dict(
(role, self.mapping.get_second(
self.trigger_or_self(
target, first_triggers))) for (
role, target) in first_event.args)
first_roles = set(first_args.keys())
only_first = set(
role for role in first_roles if first_args.get(role) != second_args.get(role))
only_second = set(
role for role in second_roles if first_args.get(role) != second_args.get(role))
match = (
first_event.id,
first_args,
second_args,
only_first,
only_second)
score = len(only_first) + len(only_second)
# XXX this is horrible; what's more Pythonic way?
try:
found_events_dict[score]
except KeyError:
found_events_dict[score] = dict()
try:
found_events_dict[score][second_event.id]
except KeyError:
found_events_dict[score][second_event.id] = []
found_events_dict[score][second_event.id].append(match)
def diff_events(self):
second_triggers = dict((event.id, event.trigger)
for event in self.second.get_events())
first_triggers = dict((event.id, event.trigger)
for event in self.first.get_events())
found_first_ids = set()
found_second_ids = set()
found_events_dict = dict()
# first pass, collect exact matches
for event in self.second.get_events():
self.find_closest_events(
event,
found_events_dict,
first_triggers,
second_triggers)
# XXX Pythonize
for score in sorted(found_events_dict.keys()):
for second_event_id in found_events_dict[score]:
if second_event_id not in found_second_ids:
for match in found_events_dict[score][second_event_id]:
first_event_id, first_args, second_args, only_first, only_second = match
if first_event_id not in found_first_ids:
found_first_ids.add(first_event_id)
found_second_ids.add(second_event_id)
self.mapping.add(first_event_id, second_event_id)
for role in only_first:
first_text = self.first_textbounds[self.mapping.get_first(
first_args[role])].get_text()
if role in only_second:
self.add_changed(
second_event_id, 'Changed role %s (from %s "%s")' %
(role, first_args[role], first_text))
else:
self.add_changed(
second_event_id, 'Missing role %s (%s "%s")' %
(role, first_args[role], first_text))
for role in only_second - only_first:
self.add_changed(
second_event_id,
'Added role %s' %
role)
for event in self.second.get_events():
if event.id not in found_second_ids:
self.add_added(event.id, 'Added event')
for event in self.first.get_events():
if event.id not in found_first_ids:
import copy
clone = copy.copy(event)
clone.id = self.result.get_new_id('E')
clone.trigger = self.mapping.get_second(event.trigger)
clone.args = [(role, self.mapping.get_second(trigger))
for (role, trigger) in clone.args]
self.result.add_annotation(clone)
self.mapping.add(event.id, clone.id, True)
self.add_missing(clone.id, 'Missing event')
# }}}
# Attributes {{{
def find_attribute(self, haystack, needle, target):
for attribute in haystack.get_attributes():
if attribute.target == target and attribute.type == needle.type:
return attribute
return None
def has_attribute(self, haystack, needle, target):
return (self.find_attribute(haystack, needle, target) is not None)
def diff_attributes(self):
for attribute in self.second.get_attributes():
target_in_first = self.mapping.get_first(attribute.target)
found_first = self.find_attribute(
self.first, attribute, target_in_first)
if found_first is None:
if target_in_first:
self.add_changed(
attribute.target,
'Added attribute %s' %
attribute.type)
elif found_first.value != attribute.value:
self.add_changed(
attribute.target, 'Changed attribute %s (from %s)' %
(attribute.type, found_first.value))
for attribute in self.first.get_attributes():
target_in_second = self.mapping.get_second(attribute.target)
if self.mapping.is_only_in_first(attribute.target):
# clone the attribute, since the event was cloned too;
# no need to note it's missing, since the whole event is
# missing
import copy
clone = copy.copy(attribute)
clone.id = self.result.get_new_id('A')
clone.target = target_in_second
self.result.add_annotation(clone)
else:
if not self.has_attribute(
self.second,
attribute,
target_in_second) and target_in_second:
self.add_changed(
attribute.target, 'Missing attribute %s (%s)' %
(attribute.type, attribute.value))
# }}}
# One-line Comments {{{
def has_oneline_comment(self, haystack, needle, target):
for oneline_comment in haystack.get_oneline_comments():
if oneline_comment.target == target and oneline_comment.get_text() == needle.get_text():
return True
return False
def diff_oneline_comments(self):
for oneline_comment in self.second.get_oneline_comments():
target_in_first = self.mapping.get_first(oneline_comment.target)
if not self.has_oneline_comment(
self.first, oneline_comment, target_in_first):
self.add_changed(
oneline_comment.target, 'Added %s: "%s"' %
(oneline_comment.type, oneline_comment.get_text()))
for oneline_comment in self.first.get_oneline_comments():
target_in_second = self.mapping.get_second(oneline_comment.target)
if not self.has_oneline_comment(
self.second, oneline_comment, target_in_second):
self.add_changed(
target_in_second, 'Missing %s: "%s"' %
(oneline_comment.type, oneline_comment.get_text()))
# }}}
# Equivs {{{
def diff_equivs(self):
# first we find out for each entity how they map between equiv
# groups in the first vs. second (like, "T1 is group 2 in second,
# but its corresponding entity in first is group 3": `"T1": [3, 2]`)
correspondence_map = dict()
second_equivs = [equiv.entities for equiv in self.second.get_equivs()]
for equiv_group, equiv in enumerate(second_equivs):
for entity in equiv:
correspondence_map[entity] = [None, equiv_group]
first_equivs = [equiv.entities for equiv in self.first.get_equivs()]
for equiv_group, equiv in enumerate(first_equivs):
for first_entity in equiv:
entity = self.mapping.get_second(first_entity)
if entity in correspondence_map:
correspondence_map[entity][0] = equiv_group
else:
correspondence_map[entity] = [equiv_group, None]
correspondence_hist = dict()
for entity in list(correspondence_map.keys()):
key = "%s-%s" % tuple(correspondence_map[entity])
if key not in correspondence_hist:
correspondence_hist[key] = [
1, correspondence_map[entity], [entity]]
else:
correspondence_hist[key][0] += 1
correspondence_hist[key][2].append(entity)
seen = []
import operator
sorted_hist = sorted(
iter(correspondence_hist.items()),
key=operator.itemgetter(1))
for key, equiv_item in sorted_hist:
count, correspondence_pair, entities = equiv_item
first_group, second_group = correspondence_pair
for entity in entities:
if first_group is None:
self.add_changed(entity, 'Added to equiv')
elif second_group is None:
rest = ["%s (%s)" % (self.mapping.get_second(other), self.first_textbounds[other].get_text(
)) for other in first_equivs[first_group] if other != entity]
self.add_changed(
entity, 'Missing from equiv with %s' %
', '.join(rest))
elif entity in seen:
rest = ["%s (%s)" % (self.mapping.get_second(other), self.first_textbounds[other].get_text(
)) for other in first_equivs[first_group] if other != entity]
self.add_changed(
entity, 'Changed from equiv %s' %
', '.join(rest))
else:
seen.append(entity)
# }}}
# Relations {{{
def diff_relations(self):
first_relations = dict(
((self.mapping.get_second(
relation.arg1),
self.mapping.get_second(
relation.arg2),
relation.type),
relation.id) for relation in self.first.get_relations())
second_relations = dict(
((relation.arg1,
relation.arg2,
relation.type),
relation.id) for relation in self.second.get_relations())
first_relations_set = set(first_relations)
second_relations_set = set(second_relations)
for relation in second_relations_set - first_relations_set:
source, target, relation_type = relation
self.add_changed(
source, 'Added relation %s to %s' %
(relation_type, target))
for relation in first_relations_set - second_relations_set:
source, target, relation_type = relation
first_text = self.first_textbounds[self.mapping.get_first(
target)].get_text()
self.add_changed(
source, 'Missing relation %s to %s "%s"' %
(relation_type, target, first_text))
# }}}
# Normalizations {{{
def has_normalization(self, haystack, needle, target):
for normalization in haystack.get_normalizations():
if normalization.target == target and normalization.refdb == needle.refdb and normalization.refid == needle.refid:
return True
return False
def diff_normalizations(self):
for normalization in self.second.get_normalizations():
target_in_first = self.mapping.get_first(normalization.target)
if not self.has_normalization(
self.first, normalization, target_in_first):
self.add_changed(
normalization.target, 'Added normalization %s:%s "%s"' %
(normalization.refdb, normalization.refid, normalization.reftext))
for normalization in self.first.get_normalizations():
target_in_second = self.mapping.get_second(normalization.target)
if not self.has_normalization(
self.second, normalization, target_in_second):
self.add_changed(
target_in_second, 'Missing normalization %s:%s "%s"' %
(normalization.refdb, normalization.refid, normalization.reftext))
# }}}
# }}}
# Diff invocation {{{
KNOWN_FILE_SUFF = [annotation.TEXT_FILE_SUFFIX] + annotation.KNOWN_FILE_SUFF
EXTENSIONS_RE = '\\.(%s)$' % '|'.join(KNOWN_FILE_SUFF)
def name_without_extension(file_name):
import re
return re.sub(EXTENSIONS_RE, '', file_name)
def copy_annotations(original_name, new_name):
import shutil
for extension in KNOWN_FILE_SUFF:
try:
shutil.copyfile(
'%s.%s' %
(original_name, extension), '%s.%s' %
(new_name, extension))
except IOError as e:
pass # that extension file does not exist
return annotation.TextAnnotations(new_name)
def delete_annotations(name):
name_without_extension(name)
for extension in KNOWN_FILE_SUFF:
try:
os.remove('%s.%s' % (name, extension))
except OSError as e:
pass # that extension file does not exist
def diff_files(first_name, second_name, result_name):
first_bare = name_without_extension(first_name)
second_bare = name_without_extension(second_name)
result_bare = name_without_extension(result_name)
first = annotation.TextAnnotations(first_bare)
second = annotation.TextAnnotations(second_bare)
result = copy_annotations(second_bare, result_bare)
with result:
AnnotationDiff(first, second, result).diff()
def is_dir(name):
import os.path
if os.path.exists(name):
return os.path.isdir(name)
else:
bare_name = name_without_extension(name)
for ext in annotation.KNOWN_FILE_SUFF:
if os.path.isfile('%s.%s' % (bare_name, ext)):
return False
return None
def add_files(files, dir_or_file, errors):
import glob
import re
is_a_dir = is_dir(dir_or_file)
if is_a_dir is None:
errors.append('Error: no annotation files found in %s' % dir_or_file)
elif not is_a_dir:
files.append(dir_or_file)
else:
subfiles = glob.glob(os.path.join(dir_or_file, '*'))
matching_subfiles = [
subfile for subfile in subfiles if re.search(
EXTENSIONS_RE, subfile)]
bare_subfiles = set([name_without_extension(subfile)
for subfile in matching_subfiles])
found = False
for subfile in bare_subfiles:
if is_dir(subfile) == False:
files.append(subfile)
found = True
if not found:
errors.append(
'Error: no annotation files found in %s' %
dir_or_file)
def diff_files_and_dirs(firsts, second, result, force=False, verbose=False):
import os.path
errors = []
fatal_errors = []
second_dir = is_dir(second)
result_dir = is_dir(result)
single_first = len(firsts) == 1 and is_dir(firsts[0]) == False
first_files = []
for first in firsts:
add_files(first_files, first, errors)
if first_files == []:
fatal_errors.append(
'Error: no annotation files found in %s' %
', '.join(firsts))
if second_dir is None:
fatal_errors.append('Error: no annotation files found in %s' % second)
if not single_first and len(first_files) > 1 and result_dir is False:
fatal_errors.append(
'Error: result of comparison of multiple files doesn\'t fit in %s' %
result)
errors.extend(fatal_errors)
if fatal_errors == []:
if not single_first and second_dir and result_dir is None:
os.mkdir(result)
result_dir = True
for first_name in first_files:
basename = os.path.basename(first_name)
if verbose:
print("Comparing", basename)
if second_dir:
second_name = os.path.join(second, basename)
if is_dir(second_name):
errors.append(
'Error: No annotation files found corresponding to %s' %
second_name)
continue
else:
second_name = second
result_name = os.path.join(
result, basename) if result_dir else result
real_result_dir = is_dir(result_name)
if real_result_dir:
errors.append('Error: %s is a directory' % result_name)
continue
if not real_result_dir:
if force:
delete_annotations(result_name)
else:
errors.append(
'Error: %s already exists (use --force to overwrite)' %
result_name)
continue
diff_files(first_name, second_name, result_name)
if errors != []:
sys.stderr.write("\n".join(errors) + "\n")
exit(1)
# }}}
# Command-line invocation {{{
def argparser():
import argparse
ap = argparse.ArgumentParser(
description="Diff two annotation files, creating a diff annotation file")
ap.add_argument(
"-v",
"--verbose",
default=False,
action="store_true",
help="Verbose output.")
ap.add_argument("firsts", metavar="<first>", nargs="+",
help="Original (or gold standard) directories/files")
ap.add_argument(
"second",
metavar="<second>",
help="Changed (or tested) directory/file")
ap.add_argument("result", metavar="<result>", help="Output file/directory")
ap.add_argument(
"-f",
"--force",
action="store_true",
help="Force overwrite")
return ap
def main(argv=None):
if argv is None:
argv = sys.argv
args = argparser().parse_args(argv[1:])
diff_files_and_dirs(
args.firsts,
args.second,
args.result,
args.force,
args.verbose)
if __name__ == "__main__":
import sys
sys.exit(main(sys.argv))
# }}}