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WIP use the new package

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This commit is contained in:
Patrick Jentsch 2021-08-06 16:50:22 +02:00
parent a4b2fc3a65
commit 66516eeb89
5 changed files with 219 additions and 184 deletions
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80
packages/stand-off-data-py/stand_off_data/export.py Normal file
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@ -0,0 +1,80 @@
from xml.sax.saxutils import escape
class ExportMixin:
def to_vrt(self, text):
# Devide annotations into CWB's verticalized text format (.vrt) logic
p_attrs = [] # positional attributes
s_attrs = [] # structural attributes
for annotation in self.annotations:
if annotation.name == 'token':
p_attrs.append(annotation)
else:
s_attrs.append(annotation)
# Sort annotations, necessary for the next checks
p_attrs.sort()
s_attrs.sort()
# Check for p_attr<->p_attr overlap
for i, p_attr in enumerate(p_attrs[:-1]):
next_p_attr = p_attrs[i + 1]
# Check if first_p_attr starts/ends within second_p_attr
if ((p_attr.start >= next_p_attr.start) and (p_attr.start <= next_p_attr.end) # noqa
or (p_attr.end >= next_p_attr.start) and (p_attr.end <= next_p_attr.end)): # noqa
raise Exception('Positional attribute overlaps another')
# Check for s_attr<->p_attr overlap
for i, s_attr in enumerate(s_attrs):
for p_attr in p_attrs:
# Check if s_attr starts within p_attr
if s_attr.start > p_attr.start and s_attr.start < p_attr.end:
# Change s_attr start to p_attr's start
s_attrs[i].start = p_attr.start
# Check if s_attr ends within p_attr
if s_attr.end < p_attr.end and s_attr.end > p_attr.start:
# Change s_attr end to p_attr's end
s_attrs[i].end = p_attr.end
# Check if s_attr starts/ends before/after p_attr
if p_attr.start >= s_attr.end or p_attr.end <= s_attr.start:
# No further Checking needed (just because p_attrs are sorted)
break
s_attr_start_buffer = {}
s_attr_end_buffer = {}
for i, s_attr in enumerate(s_attrs):
if s_attr_start_buffer[s_attr.start]:
s_attr_start_buffer[s_attr.start].append(i)
else:
s_attr_start_buffer[s_attr.start] = [i]
if s_attr_end_buffer[s_attr.end]:
s_attr_end_buffer[s_attr.end].append(i)
else:
s_attr_end_buffer[s_attr.end] = [i]
vrt = ''
vrt += '<text>\n'
for p_attr in p_attrs:
# s_attr_starts
for k in {k: v for k, v in s_attr_start_buffer.items() if k <= p_attr.start}: # noqa
s_attrs = s_attr_start_buffer.pop(k)
for s_attr in s_attrs:
foo = ''
for property in s_attr.properties:
foo += ' {}="{}"'.format(escape(property.name),
escape(property.value))
vrt += '<{}{}>\n'.format(escape(s_attr.name), foo)
for k in {k: v for k, v in s_attr_end_buffer.items() if k <= p_attr.start}: # noqa
s_attrs = s_attr_end_buffer.pop(k)
for s_attr in s_attrs:
vrt += '</{}>\n'.format(escape(s_attr.name))
# s_attr_ends
foo = {'lemma': None, 'ner': None, 'pos': None, 'simple_pos': None, 'word': None} # noqa
for property in p_attrs.properties:
if property.name == 'lemma':
foo['lemma'] = escape(property.value)
elif property.name == 'ner':
foo['ner'] = escape(property.value)
elif property.name == 'pos':
foo['pos'] = escape(property.value)
elif property.name == 'simple_pos':
foo['simple_pos'] = escape(property.value)
foo['word'] = escape(text[p_attr.start:p_attr.end])
vrt += '{word}\t{pos}\t{lemma}\t{simple_pos}\t{ner}\n'.format(
**foo)
vrt += '</text>\n'

9
packages/stand-off-data-py/stand_off_data/models.py
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@ -1,4 +1,7 @@
class StandOffData:
from .export import ExportMixin
class StandOffData(ExportMixin):
def __init__(self, attrs):
self.meta = attrs.get('meta', {})
self.lookup = {tag_definition.id: tag_definition for tag_definition in
@ -69,7 +72,7 @@ class PropertyAnnotation:
self.tag_id = attrs['tag_id']
if self.property_id not in self.lookup[self.tag_id].properties:
raise Exception('Unknown property id: {}'.format(self.property_id))
self.value = property['value']
self.value = attrs['value']
# TODO: Process attrs['possibleValues'] as self.labels (no id?)
@property
@ -91,7 +94,7 @@ class TagDefinition:
@property
def required_properties(self):
return {property.id: property for property in self.properties
return {property.id: property for property in self.properties.values()
if property.is_required}

78
packages/stand-off-data-py/stand_off_data/utils.py
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@ -1,78 +0,0 @@
from xml.sax.saxutils import escape
def create_vrt(text, stand_off_data):
# Devide annotations into CWB's verticalized text format (.vrt) logic
p_attrs = [] # positional attributes
s_attrs = [] # structural attributes
for annotation in stand_off_data.annotations:
if annotation.name == 'token':
p_attrs.append(annotation)
else:
s_attrs.append(annotation)
# Sort annotations, necessary for the next checks
p_attrs.sort()
s_attrs.sort()
# Check for p_attr<->p_attr overlap
for i, p_attr in enumerate(p_attrs[:-1]):
next_p_attr = p_attrs[i + 1]
# Check if first_p_attr starts/ends within second_p_attr
if ((p_attr.start >= next_p_attr.start) and (p_attr.start <= next_p_attr.end) # noqa
or (p_attr.end >= next_p_attr.start) and (p_attr.end <= next_p_attr.end)): # noqa
raise Exception('Positional attribute overlaps another')
# Check for s_attr<->p_attr overlap
for i, s_attr in enumerate(s_attrs):
for p_attr in p_attrs:
# Check if s_attr starts within p_attr
if s_attr.start > p_attr.start and s_attr.start < p_attr.end:
# Change s_attr start to p_attr's start
s_attrs[i].start = p_attr.start
# Check if s_attr ends within p_attr
if s_attr.end < p_attr.end and s_attr.end > p_attr.start:
# Change s_attr end to p_attr's end
s_attrs[i].end = p_attr.end
# Check if s_attr starts/ends before/after p_attr
if p_attr.start >= s_attr.end or p_attr.end <= s_attr.start:
# No further Checking needed (just because p_attrs are sorted)
break
s_attr_start_buffer = {}
s_attr_end_buffer = {}
for i, s_attr in enumerate(s_attrs):
if s_attr_start_buffer[s_attr.start]:
s_attr_start_buffer[s_attr.start].append(i)
else:
s_attr_start_buffer[s_attr.start] = [i]
if s_attr_end_buffer[s_attr.end]:
s_attr_end_buffer[s_attr.end].append(i)
else:
s_attr_end_buffer[s_attr.end] = [i]
vrt = ''
vrt += '<text>\n'
for p_attr in p_attrs:
# s_attr_starts
for k in {k: v for k, v in s_attr_start_buffer.items() if k <= p_attr.start}: # noqa
s_attrs = s_attr_start_buffer.pop(k)
for s_attr in s_attrs:
foo = ''
for property in s_attr.properties:
foo += ' {}="{}"'.format(escape(property.name),
escape(property.value))
vrt += '<{}{}>\n'.format(escape(s_attr.name), foo)
for k in {k: v for k, v in s_attr_end_buffer.items() if k <= p_attr.start}: # noqa
s_attrs = s_attr_end_buffer.pop(k)
for s_attr in s_attrs:
vrt += '</{}>\n'.format(escape(s_attr.name))
# s_attr_ends
foo = {'lemma': None, 'ner': None, 'pos': None, 'simple_pos': None, 'word': None} # noqa
for property in p_attrs.properties:
if property.name == 'lemma':
foo['lemma'] = escape(property.value)
elif property.name == 'ner':
foo['ner'] = escape(property.value)
elif property.name == 'pos':
foo['pos'] = escape(property.value)
elif property.name == 'simple_pos':
foo['simple_pos'] = escape(property.value)
foo['word'] = escape(text[p_attr.start:p_attr.end])
vrt += '{word}\t{pos}\t{lemma}\t{simple_pos}\t{ner}\n'.format(**foo)
vrt += '</text>\n'

106
vrt-creator
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@ -2,96 +2,12 @@
# coding=utf-8
from argparse import ArgumentParser
from xml.sax.saxutils import escape
from stand_off_data import StandOffData
import hashlib
import json
# Two global ressources - Not very elegant but it works for now
stand_off_data = None
text = None
def meta_to_string():
string = ''
string += '<generator software="{} ({})" arguments="check_encoding: {}; language: {}"/>\n'.format( # noqa
stand_off_data['meta']['generator']['name'],
stand_off_data['meta']['generator']['version'],
stand_off_data['meta']['generator']['arguments']['check_encoding'],
stand_off_data['meta']['generator']['arguments']['language']
)
string += '<file encoding="{}" name="{}" md5="{}"/>\n'.format(
stand_off_data['meta']['file']['encoding'],
stand_off_data['meta']['file']['name'],
stand_off_data['meta']['file']['md5']
)
return string
def tags_to_string():
return ''
def annotations_to_string(end=float('inf')):
string = ''
while stand_off_data['annotations']:
if stand_off_data['annotations'][0]['start'] >= end:
break
annotation = stand_off_data['annotations'].pop(0)
#######################################################################
# Check for malformed annotations #
#######################################################################
if 'tag' not in annotation:
raise Exception('Annotation tag is missing')
if annotation['tag'] not in stand_off_data['tags']:
raise Exception('Unknown annotation tag: ' + annotation['tag'])
tag_model = stand_off_data['tags'][annotation['tag']]
if 'properties' in tag_model:
properties_model = tag_model['properties']
if properties_model is not None:
required_properties = filter(lambda x: 'flags' in x and 'required' in x['flags'], properties_model) # noqa
if required_properties and annotation['properties'] is None:
raise Exception('There are required properties but the "Properties" attribute is missing') # noqa
for property in required_properties:
if property not in annotation['properties']:
raise Exception('Required property is missing: ' + property) # noqa
#######################################################################
# Process tokens ~ cwb's positional attributes #
#######################################################################
if annotation['tag'] == 'token':
string += '{}\t{}\t{}\t{}\t{}\n'.format(
escape(text[annotation['start']:annotation['end']]),
escape(annotation['properties']['pos']),
escape(annotation['properties']['lemma']),
escape(annotation['properties']['simple_pos']),
escape(annotation['properties']['ner'] if 'ner' in annotation['properties'] else 'None') # noqa
)
#######################################################################
# Process other tags ~ cwb's structural attributes #
#######################################################################
else:
properties = ''
if 'properties' in annotation and annotation['properties'] is not None: # noqa
for property, value in annotation['properties'].items():
if not value:
continue
if properties_model and property in properties_model:
if 'flags' in properties_model and 'multiple' in properties_model['flags']: # noqa
properties += ' {}="|{}|"'.format(property, '|'.join(value)) # noqa
else:
properties += ' {}="{}"'.format(property, value)
string += '<' + annotation['tag'] + properties + '>\n'
string += annotations_to_string(end=min(annotation['end'], end))
string += '</' + annotation['tag'] + '>\n'
return string
def main():
global stand_off_data
global text
# Parse the given arguments
parser = ArgumentParser(description='Create a vrt from JSON and txt')
parser.add_argument('text', help='Path to txt file')
@ -100,31 +16,15 @@ def main():
args = parser.parse_args()
with open(args.stand_off_data) as stand_of_data_file:
stand_off_data = json.load(stand_of_data_file)
stand_off_data = StandOffData(json.load(stand_of_data_file))
with open(args.text, "rb") as text_file:
text_md5 = hashlib.md5()
for chunk in iter(lambda: text_file.read(128 * text_md5.block_size), b''): # noqa
text_md5.update(chunk)
if text_md5.hexdigest() != stand_off_data['meta']['file']['md5']:
if text_md5.hexdigest() != stand_off_data.meta['file']['md5']:
raise Exception('md5 not equal')
with open(args.text, encoding=stand_off_data['meta']['file']['encoding']) as text_file: # noqa
text = text_file.read()
vrt = ''
vrt += '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
vrt += '<corpus>\n'
vrt += '<text>\n'
vrt += meta_to_string()
vrt += tags_to_string()
vrt += annotations_to_string()
vrt += '</text>\n'
vrt += '</corpus>'
with open(args.output, 'w') as vrt_file:
vrt_file.write(vrt)
if __name__ == '__main__':
main()

130
vrt-creator.bak Normal file
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@ -0,0 +1,130 @@
#!/usr/bin/env python3.7
# coding=utf-8
from argparse import ArgumentParser
from xml.sax.saxutils import escape
import hashlib
import json
# Two global ressources - Not very elegant but it works for now
stand_off_data = None
text = None
def meta_to_string():
string = ''
string += '<generator software="{} ({})" arguments="check_encoding: {}; language: {}"/>\n'.format( # noqa
stand_off_data['meta']['generator']['name'],
stand_off_data['meta']['generator']['version'],
stand_off_data['meta']['generator']['arguments']['check_encoding'],
stand_off_data['meta']['generator']['arguments']['language']
)
string += '<file encoding="{}" name="{}" md5="{}"/>\n'.format(
stand_off_data['meta']['file']['encoding'],
stand_off_data['meta']['file']['name'],
stand_off_data['meta']['file']['md5']
)
return string
def tags_to_string():
return ''
def annotations_to_string(end=float('inf')):
string = ''
while stand_off_data['annotations']:
if stand_off_data['annotations'][0]['start'] >= end:
break
annotation = stand_off_data['annotations'].pop(0)
#######################################################################
# Check for malformed annotations #
#######################################################################
if 'tag' not in annotation:
raise Exception('Annotation tag is missing')
if annotation['tag'] not in stand_off_data['tags']:
raise Exception('Unknown annotation tag: ' + annotation['tag'])
tag_model = stand_off_data['tags'][annotation['tag']]
if 'properties' in tag_model:
properties_model = tag_model['properties']
if properties_model is not None:
required_properties = filter(lambda x: 'flags' in x and 'required' in x['flags'], properties_model) # noqa
if required_properties and annotation['properties'] is None:
raise Exception('There are required properties but the "Properties" attribute is missing') # noqa
for property in required_properties:
if property not in annotation['properties']:
raise Exception('Required property is missing: ' + property) # noqa
#######################################################################
# Process tokens ~ cwb's positional attributes #
#######################################################################
if annotation['tag'] == 'token':
string += '{}\t{}\t{}\t{}\t{}\n'.format(
escape(text[annotation['start']:annotation['end']]),
escape(annotation['properties']['pos']),
escape(annotation['properties']['lemma']),
escape(annotation['properties']['simple_pos']),
escape(annotation['properties']['ner'] if 'ner' in annotation['properties'] else 'None') # noqa
)
#######################################################################
# Process other tags ~ cwb's structural attributes #
#######################################################################
else:
properties = ''
if 'properties' in annotation and annotation['properties'] is not None: # noqa
for property, value in annotation['properties'].items():
if not value:
continue
if properties_model and property in properties_model:
if 'flags' in properties_model and 'multiple' in properties_model['flags']: # noqa
properties += ' {}="|{}|"'.format(property, '|'.join(value)) # noqa
else:
properties += ' {}="{}"'.format(property, value)
string += '<' + annotation['tag'] + properties + '>\n'
string += annotations_to_string(end=min(annotation['end'], end))
string += '</' + annotation['tag'] + '>\n'
return string
def main():
global stand_off_data
global text
# Parse the given arguments
parser = ArgumentParser(description='Create a vrt from JSON and txt')
parser.add_argument('text', help='Path to txt file')
parser.add_argument('stand_off_data', help='Path to JSON file')
parser.add_argument('output', help='Path to vrt output file')
args = parser.parse_args()
with open(args.stand_off_data) as stand_of_data_file:
stand_off_data = json.load(stand_of_data_file)
with open(args.text, "rb") as text_file:
text_md5 = hashlib.md5()
for chunk in iter(lambda: text_file.read(128 * text_md5.block_size), b''): # noqa
text_md5.update(chunk)
if text_md5.hexdigest() != stand_off_data['meta']['file']['md5']:
raise Exception('md5 not equal')
with open(args.text, encoding=stand_off_data['meta']['file']['encoding']) as text_file: # noqa
text = text_file.read()
vrt = ''
vrt += '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
vrt += '<corpus>\n'
vrt += '<text>\n'
vrt += meta_to_string()
vrt += tags_to_string()
vrt += annotations_to_string()
vrt += '</text>\n'
vrt += '</corpus>'
with open(args.output, 'w') as vrt_file:
vrt_file.write(vrt)
if __name__ == '__main__':
main()