Merge pull request #47 from whalebot-helmsman/master

Move annotations from GATE to WebAnnotator format

Author: kmike

.gitignore

@@ -50,8 +50,7 @@ notebooks/*.ipynb
 notebooks/*.marisa
 notebooks/*.wapiti
 notebooks/*.crfsuite
-webstruct_data/corpus/random_pages/wa/*.html
 webstruct_data/corpus/us_contact_pages/cleaned
 example/_data/*
 example/*.joblib
-example/*.html
+example/*.html

example/ner/data.py

@@ -44,11 +44,14 @@ def load_webstruct_data() -> List:
     )
 
     trees2 = webstruct.load_trees(
-        str(WEBSTRUCT_DATA / "corpus/us_contact_pages/annotated/*.xml"),
-        loader=gate_loader
+        str(WEBSTRUCT_DATA / "corpus/us_contact_pages/wa/*.html"),
+        loader=wa_loader
     )
     trees = chain(trees1, trees2)
-    return list(pages_progress(trees, desc="Loading webstruct default annotated data"))
+    return list(pages_progress(
+        trees,
+        desc="Loading webstruct default annotated data"
+        ))
 
 
 def load_countries() -> Set[str]:

webstruct/annotation_converter.py

@@ -0,0 +1,53 @@
+import logging
+import argparse
+
+import webstruct.loaders
+from webstruct.webannotator import EntityColors, to_webannotator
+
+
+def main():
+    cmdline = argparse.ArgumentParser(description=('utility '
+                                                   'to convert annotations '
+                                                   'from GATE format to '
+                                                   'WebAnnotator format'))
+    cmdline.add_argument('--GATE',
+                         help='path to file annotated in GATE format',
+                         type=str,
+                         required=True)
+    cmdline.add_argument('--sample',
+                         help=('path to file annotated in WebAnnotator format '
+                               'for colors and entities transfer'),
+                         type=str,
+                         required=True)
+    cmdline.add_argument('--WebAnnotator',
+                         help='path to result file in WebAnnotator format',
+                         type=str,
+                         required=True)
+    cmdline.add_argument('--loglevel',
+                         help='logging level',
+                         type=str,
+                         default='INFO')
+    args = cmdline.parse_args()
+
+    logging.basicConfig(level=getattr(logging, args.loglevel.upper()),
+                        format=('%(asctime)s [%(levelname)s]'
+                                '%(pathname)s:%(lineno)d %(message)s'))
+    with open(args.sample, 'rb') as sample_reader:
+        colors = EntityColors.from_htmlbytes(sample_reader.read())
+        entities = [typ for typ in colors]
+
+    logging.debug('Current entities %s', entities)
+    logging.debug('Current colors %s', colors)
+
+    gate = webstruct.loaders.GateLoader(known_entities=entities)
+    tokenizer = webstruct.HtmlTokenizer(tagset=entities)
+    with open(args.GATE, 'rb') as reader:
+        data = reader.read()
+        tree = gate.loadbytes(data)
+        tokens, annotations = tokenizer.tokenize_single(tree)
+        tree = to_webannotator(tree, entity_colors=colors)
+        with open(args.WebAnnotator, 'wb') as writer:
+            tree.write(writer, method='html', pretty_print=True)
+
+if __name__ == "__main__":
+    main()

webstruct/annotation_verifier.py

@@ -0,0 +1,171 @@
+import json
+import logging
+import argparse
+
+import webstruct.loaders
+import webstruct.webannotator
+
+DEFAULT_ENTITIES = [
+    'ORG', 'TEL', 'FAX', 'HOURS',
+    'STREET', 'CITY', 'STATE', 'ZIPCODE', 'COUNTRY',
+    'EMAIL', 'PER', 'FUNC', 'SUBJ'
+]
+
+
+def nodes_difference(l, r):
+    if l.tag != r.tag:
+        return {'tag': '"{0}" != "{1}"'.format(l.tag, r.tag)}
+
+    l_attrib = [(k, l.attrib[k]) for k in l.attrib]
+    l_attrib.sort(key=lambda x: x[0])
+    r_attrib = [(k, r.attrib[k]) for k in r.attrib]
+    r_attrib.sort(key=lambda x: x[0])
+
+    idx = 0
+    while idx < len(l_attrib) and idx < len(r_attrib):
+        l_attr = l_attrib[idx]
+        r_attr = r_attrib[idx]
+        idx = idx + 1
+
+        if l_attr != r_attr:
+            return {'attributes': '"{0}" != "{1}"'.format(l_attr, r_attr)}
+
+    if idx < len(l_attrib):
+        return {'attributes': "{0} != None".format(l_attrib[idx])}
+
+    if idx < len(r_attrib):
+        return {'attributes': "None != {0}".format(r_attrib[idx])}
+
+    l_text = ''
+    if l.text:
+        l.text = l.text.strip()
+
+    r_text = ''
+    if r.text:
+        r.text = r.text.strip()
+
+    if l_text != r_text:
+        return {'text': "{0} != {1}".format(l_text, r_text)}
+
+    l_tail = ''
+    if l.tail:
+        l.tail = l.tail.strip()
+
+    r_tail = ''
+    if r.tail:
+        r.tail = r.tail.strip()
+
+    if l_tail != r_tail:
+        return {'tail': "{0} != {1}".format(l_tail, r_tail)}
+
+    if len(l) != len(r):
+        return {'children count': "{0} != {1}".format(len(l), len(r))}
+
+    return None
+
+
+def node_path(node):
+    ret = ''
+    current = node
+    while current is not None:
+        parent = current.getparent()
+        idx = 0
+        if parent:
+            idx = parent.index(current)
+        step = '{0}:{1}'.format(idx, current.tag)
+        ret = step + '/' + ret
+        current = parent
+
+    return ret
+
+
+def tree_difference(l, r):
+    stack = [(l, r)]
+    while stack:
+        l_node, r_node = stack.pop(0)
+        diff = nodes_difference(l_node, r_node)
+
+        if diff:
+            return {"l":    node_path(l_node),
+                    "r":    node_path(r_node),
+                    "diff": diff}
+
+        for idx, l_child in enumerate(l_node):
+            stack.append((l_child, r_node[idx]))
+
+    return None
+
+
+def main():
+    cmdline = argparse.ArgumentParser(description=('utility to verify '
+                                                   'annotation conversion '
+                                                   'from GATE format '
+                                                   'to WebAnnotator format'))
+    cmdline.add_argument('--GATE',
+                         help='path to file annotated in GATE format',
+                         type=str,
+                         required=True)
+    cmdline.add_argument('--WebAnnotator',
+                         help='path to file annotated in WebAnnotator format',
+                         type=str,
+                         required=True)
+    cmdline.add_argument('--entity',
+                         help='enitity type to verify against',
+                         type=str,
+                         action='append',
+                         required=False)
+    cmdline.add_argument('--loglevel',
+                         help='logging level',
+                         type=str,
+                         default='INFO')
+    args = cmdline.parse_args()
+
+    logging.basicConfig(level=getattr(logging, args.loglevel.upper()),
+                        format=('%(asctime)s [%(levelname)s] '
+                                '%(pathname)s:%(lineno)d %(message)s'))
+
+    if args.entity:
+        entities = args.entity
+    else:
+        entities = DEFAULT_ENTITIES
+
+    logging.debug('Known entities %s', entities)
+
+    gate = webstruct.loaders.GateLoader(known_entities=entities)
+    wa = webstruct.loaders.WebAnnotatorLoader(known_entities=entities)
+
+    tokenizer = webstruct.HtmlTokenizer(tagset=entities)
+    with open(args.GATE, 'rb') as reader:
+        data = reader.read()
+        gate_tree = gate.loadbytes(data)
+        gate_tokens, gate_annotations = tokenizer.tokenize_single(gate_tree)
+
+    with open(args.WebAnnotator, 'rb') as reader:
+        data = reader.read()
+        wa_tree = wa.loadbytes(data)
+        wa_tokens, wa_annotations = tokenizer.tokenize_single(wa_tree)
+
+    is_diff = False
+    tree_diff = tree_difference(gate_tree, wa_tree)
+    if tree_diff:
+        logging.error('tree differs %s', json.dumps(tree_diff))
+        is_diff = True
+
+    annot_diff = list()
+    for idx, (gate_a, wa_a) in enumerate(zip(gate_annotations,
+                                             wa_annotations)):
+        if gate_a == wa_a:
+            continue
+
+        annot_diff.append({'idx':    idx,
+                           'gate_a': gate_a,
+                           'wa_a':   wa_a})
+
+    if annot_diff:
+        logging.error('annotation differs %s', json.dumps(annot_diff))
+        is_diff = True
+
+    return is_diff is False
+
+if __name__ == "__main__":
+    main()

webstruct/tests/test_html_tools.py

@@ -0,0 +1,35 @@
+import unittest
+
+import lxml
+
+import webstruct.annotation_verifier
+
+html_1 = '<span style="abc" class="span">aa</span>'
+html_2 = '<span style="abd" class="span">aa</span>'
+html_3 = '<span style="abd" class="span">aa<p>s</p></span>'
+html_3 = '<span style="abd" class="span">aa<p>s</p><p>ss</p></span>'
+
+
+class SomethingTest(unittest.TestCase):
+
+    def test_is_node_equal_to_self(self):
+        tree_1 = lxml.etree.fromstring(html_1)
+        diff = webstruct.annotation_verifier.nodes_difference(tree_1, tree_1)
+        self.assertIsNone(diff)
+
+    def test_is_different_nodes_are_diffirent(self):
+        tree_1 = lxml.etree.fromstring(html_1)
+        tree_2 = lxml.etree.fromstring(html_2)
+        diff = webstruct.annotation_verifier.nodes_difference(tree_1, tree_2)
+        self.assertIsNotNone(diff)
+
+    def test_is_tree_equal_to_self(self):
+        tree_1 = lxml.etree.fromstring(html_3)
+        diff = webstruct.annotation_verifier.tree_difference(tree_1, tree_1)
+        self.assertIsNone(diff)
+
+    def test_is_different_trees_are_diffirent(self):
+        tree_1 = lxml.etree.fromstring(html_2)
+        tree_2 = lxml.etree.fromstring(html_3)
+        diff = webstruct.annotation_verifier.tree_difference(tree_1, tree_2)
+        self.assertIsNotNone(diff)

webstruct/tests/test_webannotator.py

@@ -15,6 +15,24 @@ def assertApplyWaTitle(self, source, result):
         webannotator.apply_wa_title(tree)
         self.assertHtmlTreeEqual(tree, html_document_fromstring(result))
 
+    def test_wa_title_no_attributes(self):
+        self.assertApplyWaTitle(
+            b"""
+            <html>
+                <head><title>Foo</title></head>
+                <body>contents</body>
+                <wa-title class="classy"><b>hello</b>, world</wa-title>
+            </html>
+            """,
+
+            b"""
+            <html>
+                <head><title><b>hello</b>, world</title></head>
+                <body>contents</body>
+            </html>
+            """
+        )
+
     def test_wa_title(self):
         self.assertApplyWaTitle(
             b"""

webstruct/webannotator.py

@@ -100,6 +100,8 @@ def apply_wa_title(tree):
         head.insert(head.index(title), wa_title)
         title.drop_tree()
         wa_title.tag = 'title'
+        for attr in  wa_title.attrib:
+            wa_title.attrib.pop(attr)
         return
 
 
@@ -254,7 +256,7 @@ def _ensure_head(tree):
 
 
 def _set_base(tree, baseurl):
-    """ 
+    """
     Add <base> tag to the tree. If <base> tag already exists do nothing.
     """
     if tree.xpath('//base'):