Create package for stand-off-data-py

Dockerfile

@@ -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/
 

packages/stand-off-data-py/setup.py

@@ -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'
+)

packages/stand-off-data-py/stand_off_data/__init__.py

@@ -0,0 +1,2 @@
+# flake8: noqa
+from .models import StandOffData

packages/stand-off-data-py/stand_off_data/models.py

@@ -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
+        self.meta = attrs.get('meta', {})
-                     [TagDefinition(x) for x in attrs.get('tags', [])]}
+        self.lookup = {tag_definition.id: tag_definition for tag_definition in
-        self.annotations = [TagAnnotation(x, self.tags) for x 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.lookup:
-        if self.tag_id not in self.tag_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):
+    def __init__(self, attrs, lookup):
-        self.property_id = property['property_id']
+        self.lookup = lookup
-        self.property_lookup = property_lookup
+        self.property_id = attrs['property_id']
-        if self.property_id not in self.property_lookup:
+        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:

packages/stand-off-data-py/stand_off_data/utils.py

@@ -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'