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Create package for stand-off-data-py

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This commit is contained in:
Patrick Jentsch 2021-07-22 16:59:29 +02:00
parent 4dea95a108
commit a4b2fc3a65
5 changed files with 75 additions and 35 deletions
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9
Dockerfile
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@ -38,7 +38,7 @@ RUN apt-get install --no-install-recommends --yes \
&& pip3 install "spacy==${SPACY_VERSION}"
# Only models that include the following components are compatibel:
# Only models that include the following components are compatibel:
# lemmatizer, ner, parser, senter, tagger,
ENV SPACY_MODELS="de_core_news_md,en_core_web_md,it_core_news_md,nl_core_news_md,pl_core_news_md,zh_core_web_md"
ENV SPACY_MODELS_VERSION=3.0.0
@ -51,6 +51,13 @@ RUN apt-get install --no-install-recommends --yes \
zip
COPY packages .
RUN cd stand-off-data-py \
&& python3 setup.py build \
&& python3 setup.py install \
&& cd -
## Install Pipeline ##
COPY nlp spacy-nlp vrt-creator /usr/local/bin/

14
packages/stand-off-data-py/setup.py
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@ -0,0 +1,14 @@
import setuptools
setuptools.setup(
name='stand-off-data',
author='Patrick Jentsch',
author_email='p.jentsch@uni-bielefeld.de',
description='A python library to handle stand off data.',
classifiers=[
'Programming Language :: Python :: 3',
'Operating System :: OS Independent',
],
packages=setuptools.find_packages(),
python_requires='>=3.5'
)

2
packages/stand-off-data-py/stand_off_data/__init__.py
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@ -0,0 +1,2 @@
# flake8: noqa
from .models import StandOffData

50
packages/stand-off-data-py/stand_off_data/models.py
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@ -1,33 +1,17 @@
'''
'generator': {
'name': 'nopaque NLP service',
'version': '1.0.0',
'arguments': {
'check_encoding': args.check_encoding,
'language': args.language
}
},
'file': {
'encoding': encoding,
'md5': text_md5.hexdigest(),
'name': os.path.basename(args.input)
}
'''
class StandOffData:
def __init__(self, attrs):
self.tags = {tag_definition.id: tag_definition for tag_definition in
[TagDefinition(x) for x in attrs.get('tags', [])]}
self.annotations = [TagAnnotation(x, self.tags) for x in
self.meta = attrs.get('meta', {})
self.lookup = {tag_definition.id: tag_definition for tag_definition in
[TagDefinition(x) for x in attrs.get('tags', [])]}
self.annotations = [TagAnnotation(x, self.lookup) for x in
attrs.get('annotations', [])]
class TagAnnotation:
def __init__(self, attrs, tag_lookup):
def __init__(self, attrs, lookup):
self.lookup = lookup
self.tag_id = attrs['tag_id']
self.tag_lookup = tag_lookup
if self.tag_id not in self.tag_lookup:
if self.tag_id not in self.lookup:
raise Exception('Unknown tag id: {}'.format(self.tag_id))
self.start = attrs['start']
self.end = attrs['end']
@ -35,16 +19,17 @@ class TagAnnotation:
raise Exception('start must be lower then end')
self.description = attrs.get('description', '')
self.properties = [
PropertyAnnotation(x, self.tag_lookup[self.tag_id].properties)
PropertyAnnotation({**x, 'tag_id': self.tag_id}, self.lookup)
for x in attrs.get('properties', [])
]
for required_property_id in self.tag_lookup[self.tag_id].required_properties:
for required_property_id in self.lookup[self.tag_id].required_properties:
if required_property_id not in self.properties:
raise Exception('Missing required property: {}'.format(required_property_id))
raise Exception(
'Missing required property: {}'.format(required_property_id))
@property
def name(self):
return self.tag_lookup[self.tag_id].name
return self.lookup[self.tag_id].name
def __lt__(self, other):
if self.start == other.start:
@ -78,17 +63,18 @@ class TagAnnotation:
class PropertyAnnotation:
def __init__(self, attrs, property_lookup):
self.property_id = property['property_id']
self.property_lookup = property_lookup
if self.property_id not in self.property_lookup:
def __init__(self, attrs, lookup):
self.lookup = lookup
self.property_id = attrs['property_id']
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']
# TODO: Process attrs['possibleValues'] as self.labels (no id?)
@property
def name(self):
return self.property_lookup[self.property_id].name
return self.lookup[self.tag_id].properties[self.property_id].name
class TagDefinition:

35
packages/stand-off-data-py/stand_off_data/utils.py
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@ -1,3 +1,6 @@
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
@ -42,6 +45,34 @@ def create_vrt(text, stand_off_data):
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] = [1]
s_attr_end_buffer[s_attr.end] = [i]
vrt = ''
# TODO do the work!
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'