Fix for unittest

combo/data/vocabulary.py

 import codecs
 import os
+import re
 import glob
-from collections import defaultdict, OrderedDict
-from typing import Dict, Union, Optional, Iterable, Callable, Any, Set, List
+from collections import defaultdict
+from typing import Dict, Optional, Iterable, Set, List
 
-from torchtext.vocab import Vocab as TorchtextVocab
-from torchtext.vocab import vocab as torchtext_vocab
 import logging
 
 from filelock import FileLock
 from transformers import PreTrainedTokenizer
 
-from combo.common import Tqdm
-from combo.data.token_embedders.embedding import EmbeddingsTextFile
+from combo.utils import ConfigurationError
+from combo.utils.file_utils import cached_path
 
 logger = logging.Logger(__name__)
 
@@ -21,6 +20,7 @@ DEFAULT_PADDING_TOKEN = "@@PADDING@@"
 DEFAULT_OOV_TOKEN = "@@UNKNOWN@@"
 NAMESPACE_PADDING_FILE = "non_padded_namespaces.txt"
 DEFAULT_NAMESPACE = "tokens"
+_NEW_LINE_REGEX = re.compile(r"\n|\r\n")
 
 
 def match_namespace(pattern: str, namespace: str):
@@ -34,24 +34,43 @@ def match_namespace(pattern: str, namespace: str):
     return False
 
 
-def _read_pretrained_tokens(embeddings_file_uri: str) -> List[str]:
-    # Moving this import to the top breaks everything (cycling import, I guess)
-
-    logger.info("Reading pretrained tokens from: %s", embeddings_file_uri)
-    tokens: List[str] = []
-    with EmbeddingsTextFile(embeddings_file_uri) as embeddings_file:
-        for line_number, line in enumerate(Tqdm.tqdm(embeddings_file), start=1):
-            token_end = line.find(" ")
-            if token_end >= 0:
-                token = line[:token_end]
-                tokens.append(token)
+class NamespaceVocabulary:
+    def __init__(self,
+                 padding_token: Optional[str] = None,
+                 oov_token: Optional[str] = None):
+        if padding_token and oov_token:
+            self._itos = {0: padding_token, 1: oov_token}
+            self._stoi = {padding_token: 0, oov_token: 1}
+        elif not padding_token and not oov_token:
+            self._itos = {}
+            self._stoi = {}
         else:
-                line_begin = line[:20] + "..." if len(line) > 20 else line
-                logger.warning("Skipping line number %d: %s", line_number, line_begin)
-    return tokens
+            raise ValueError('Padding token and OOV token must be either both None or both provided')
+
+    def append_token(self, token: str):
+        # TODO: Should I check if tokens are duplicated here?
+        vocab_size = len(self._itos)
+        self._itos[vocab_size] = token
+        self._stoi[token] = vocab_size
+
+    def append_tokens(self, tokens: Iterable[str]):
+        next_index = len(self._itos)
+        for ind, token in enumerate(tokens):
+            self._itos[next_index + ind] = token
+            self._stoi[token] = next_index + ind
+
+    def insert_token(self, token: str, index: int):
+        self._itos[index] = token
+        self._stoi[token] = index
+
+    def get_itos(self) -> Dict[int, str]:
+        return self._itos
 
+    def get_stoi(self) -> Dict[str, int]:
+        return self._stoi
 
-class _NamespaceDependentDefaultDict(defaultdict[str, TorchtextVocab]):
+
+class _NamespaceDependentDefaultDict(defaultdict[str, NamespaceVocabulary]):
     def __init__(self,
                  non_padded_namespaces: Iterable[str],
                  padding_token: str,
@@ -61,29 +80,21 @@ class _NamespaceDependentDefaultDict(defaultdict[str, TorchtextVocab]):
         self._oov_token = oov_token
         super().__init__()
 
+    def add_non_padded_namespaces(self, non_padded_namespaces: Set[str]):
+        self._non_padded_namespaces.update(non_padded_namespaces)
+
     def __missing__(self, namespace: str):
         # Non-padded _namespace
         if any([match_namespace(npn, namespace) for npn in self._non_padded_namespaces]):
-            value = torchtext_vocab(OrderedDict([]))
+            value = NamespaceVocabulary()
         else:
-            value = torchtext_vocab(
-                OrderedDict([
-                    (self._padding_token, 1),
-                    (self._oov_token, 1)
-                ])
-            )
+            value = NamespaceVocabulary(self._padding_token, self._oov_token)
         dict.__setitem__(self, namespace, value)
         return value
 
-    def add_non_padded_namespaces(self, non_padded_namespaces: Set[str]):
-        self._non_padded_namespaces.update(non_padded_namespaces)
-
 
 class Vocabulary:
     def __init__(self,
-                 counter: Dict[str, Dict[str, int]] = None,
-                 min_count: Dict[str, int] = None,
-                 max_vocab_size: Union[int, Dict[str, int]] = None,
                  non_padded_namespaces: Iterable[str] = DEFAULT_NON_PADDED_NAMESPACES,
                  padding_token: Optional[str] = DEFAULT_PADDING_TOKEN,
                  oov_token: Optional[str] = DEFAULT_OOV_TOKEN):
@@ -105,46 +116,7 @@ class Vocabulary:
     def _extend(self,
                 tokens_to_add: Dict[str, Dict[str, int]]):
         for namespace, tokens in tokens_to_add.items():
-            for token in tokens:
-                self._vocab[namespace].append_token(token)
-
-    @classmethod
-    def from_files(cls,
-                   directory: str,
-                   padding_token: Optional[str] = DEFAULT_PADDING_TOKEN,
-                   oov_token: Optional[str] = DEFAULT_OOV_TOKEN) -> None:
-        """
-        Adapted from https://github.com/allenai/allennlp/blob/main/allennlp/data/vocabulary.py
-
-        :param directory:
-        :param padding_token:
-        :param oov_token:
-        :return:
-        """
-        files = [file for file in glob.glob(os.path.join(directory, '*.txt'))]
-
-        if len(files) == 0:
-            logger.warning(f'Directory %s is empty' % directory)
-
-        non_padded_namespaces = []
-
-        try:
-            with codecs.open(
-                    os.path.join(directory, NAMESPACE_PADDING_FILE), "w", "utf-8"
-            ) as namespace_file:
-                non_padded_namespaces = [namespace.strip() for namespace in namespace_file]
-        except FileNotFoundError:
-            logger.warning("No file %s - all namespaces will be treated as padded namespaces." % NAMESPACE_PADDING_FILE)
-
-        for file in files:
-            if file.split('/')[-1] == NAMESPACE_PADDING_FILE:
-                # Namespaces file - already read
-                continue
-            namespace_name = file.split('/')[-1].replace('.txt', '')
-            with codecs.open(
-                    file, "w", "utf-8"
-            ) as namespace_tokens_file:
-                tokens = [token.strip() for token in namespace_tokens_file]
+            self._vocab[namespace].append_tokens(tokens)
 
     def save_to_files(self, directory: str) -> None:
         """
@@ -232,14 +204,24 @@ class Vocabulary:
 
         self._non_padded_namespaces.add(namespace)
 
+    def extend_from_vocab(self, vocab: "Vocabulary") -> None:
+        """
+        Adds all vocabulary items from all namespaces in the given vocabulary to this vocabulary.
+        Useful if you want to load a model and extends its vocabulary from new instances.
+
+        We also add all non-padded namespaces from the given vocabulary to this vocabulary.
+        """
+        self._non_padded_namespaces.update(vocab._non_padded_namespaces)
+        for namespace in vocab.get_namespaces():
+            for token in vocab.get_token_to_index_vocabulary(namespace):
+                self.add_token_to_namespace(token, namespace)
+
     def get_index_to_token_vocabulary(self, namespace: str = DEFAULT_NAMESPACE) -> Dict[int, str]:
         if not isinstance(namespace, str):
             raise ValueError(
                 "Namespace must be passed as string. Received %s with type %s" % (repr(namespace), type(namespace)))
 
-        itos: List[str] = self._vocab[namespace].get_itos()
-
-        return {i: s for i, s in enumerate(itos)}
+        return self._vocab[namespace].get_itos()
 
     def get_token_to_index_vocabulary(self, namespace: str = DEFAULT_NAMESPACE) -> Dict[str, int]:
         if not isinstance(namespace, str):
@@ -266,3 +248,108 @@ class Vocabulary:
 
     def get_namespaces(self) -> Set[str]:
         return set(self._vocab.keys())
+
+    def set_from_file(self,
+                      filename: str,
+                      is_padded: bool = True,
+                      oov_token: str = DEFAULT_OOV_TOKEN,
+                      namespace: str = "tokens"):
+        if is_padded:
+            self._vocab[namespace].insert_token(self._padding_token, 0)
+        with codecs.open(filename, "r", "utf-8") as input_file:
+            lines = _NEW_LINE_REGEX.split(input_file.read())
+            # Be flexible about having final newline or not
+            if lines and lines[-1] == "":
+                lines = lines[:-1]
+            for i, line in enumerate(lines):
+                index = i + 1 if is_padded else i
+                token = line.replace("@@NEWLINE@@", "\n")
+                if token == oov_token:
+                    token = self._oov_token
+
+                self._vocab[namespace].insert_token(token, index)
+        if is_padded:
+            assert self._oov_token in self._vocab[namespace].get_itos(), "OOV token not found!"
+
+
+class PretrainedTransformerVocabulary(Vocabulary):
+    def __init__(self,
+                 model_name: str,
+                 namespace: str = "tokens",
+                 oov_token: Optional[str] = None):
+        """
+        Initialize a vocabulary from the vocabulary of a pretrained transformer model.
+        If `oov_token` is not given, we will try to infer it from the transformer tokenizer.
+        """
+        from combo.common import cached_transformers
+
+        tokenizer = cached_transformers.get_tokenizer(model_name)
+        if oov_token is None:
+            if hasattr(tokenizer, "_unk_token"):
+                oov_token = tokenizer._unk_token
+            elif hasattr(tokenizer, "special_tokens_map"):
+                oov_token = tokenizer.special_tokens_map.get("unk_token")
+
+        super().__init__(non_padded_namespaces=[namespace],
+                         oov_token=oov_token)
+        self.add_transformer_vocab(tokenizer, namespace)
+
+
+class FromFilesVocabulary(Vocabulary):
+    def __init__(self,
+                 directory: str,
+                 padding_token: Optional[str] = DEFAULT_PADDING_TOKEN,
+                 oov_token: Optional[str] = DEFAULT_OOV_TOKEN) -> None:
+        """
+        Adapted from https://github.com/allenai/allennlp/blob/main/allennlp/data/vocabulary.py
+
+        :param directory:
+        :param padding_token:
+        :param oov_token:
+        :return:
+        """
+        logger.info("Loading token dictionary from %s.", directory)
+        padding_token = padding_token if padding_token is not None else DEFAULT_PADDING_TOKEN
+        oov_token = oov_token if oov_token is not None else DEFAULT_OOV_TOKEN
+
+        if not os.path.isdir(directory):
+            base_directory = cached_path(directory, extract_archive=True)
+            # For convenience we'll check for a 'vocabulary' subdirectory of the archive.
+            # That way you can use model archives directly.
+            vocab_subdir = os.path.join(base_directory, "vocabulary")
+            if os.path.isdir(vocab_subdir):
+                directory = vocab_subdir
+            elif os.path.isdir(base_directory):
+                directory = base_directory
+            else:
+                raise ConfigurationError(f"{directory} is neither a directory nor an archive")
+
+        files = [file for file in glob.glob(os.path.join(directory, '*.txt'))]
+
+        if len(files) == 0:
+            logger.warning(f'Directory %s is empty' % directory)
+
+        with FileLock(os.path.join(directory, ".lock")):
+            with codecs.open(
+                    os.path.join(directory, NAMESPACE_PADDING_FILE), "r", "utf-8"
+            ) as namespace_file:
+                non_padded_namespaces = [namespace_str.strip() for namespace_str in namespace_file]
+
+            super().__init__(
+                non_padded_namespaces=non_padded_namespaces,
+                padding_token=padding_token,
+                oov_token=oov_token,
+            )
+
+            for namespace_filename in os.listdir(directory):
+                if namespace_filename == NAMESPACE_PADDING_FILE:
+                    continue
+                if namespace_filename.startswith("."):
+                    continue
+                namespace = namespace_filename.replace(".txt", "")
+                if any(match_namespace(pattern, namespace) for pattern in non_padded_namespaces):
+                    is_padded = False
+                else:
+                    is_padded = True
+                filename = os.path.join(directory, namespace_filename)
+                self.set_from_file(filename, is_padded, namespace=namespace, oov_token=oov_token)

tests/data/data_readers/test_conll.py

 import unittest
+import os
 
 from combo.data import ConllDatasetReader
 
@@ -6,19 +7,19 @@ from combo.data import ConllDatasetReader
 class ConllDatasetReaderTest(unittest.TestCase):
     def test_read_all_tokens(self):
         reader = ConllDatasetReader(coding_scheme='IOB2')
-        tokens = [token for token in reader('conll_test_file.txt')]
+        tokens = [token for token in reader(os.path.join(os.path.dirname(__file__), 'conll_test_file.txt'))]
         self.assertEqual(len(tokens), 6)
 
     def test_tokenize_correct_tokens(self):
         reader = ConllDatasetReader(coding_scheme='IOB2')
-        token = next(iter(reader('conll_test_file.txt')))
+        token = next(iter(reader(os.path.join(os.path.dirname(__file__), 'conll_test_file.txt'))))
         self.assertListEqual([str(t) for t in token['tokens'].tokens],
                              ['SOCCER', '-', 'JAPAN', 'GET', 'LUCKY', 'WIN', ',',
                               'CHINA', 'IN', 'SURPRISE', 'DEFEAT', '.'])
 
     def test_tokenize_correct_tags(self):
         reader = ConllDatasetReader(coding_scheme='IOB2')
-        token = next(iter(reader('conll_test_file.txt')))
+        token = next(iter(reader(os.path.join(os.path.dirname(__file__), 'conll_test_file.txt'))))
         self.assertListEqual(token['tags'].labels,
                              ['O', 'O', 'B-LOC', 'O', 'O', 'O', 'O',
                               'B-PER', 'O', 'O', 'O', 'O'])

tests/data/data_readers/test_text_classification_json_reader.py

 import unittest
+import os
 
 from combo.data.dataset_readers import TextClassificationJSONReader
 from combo.data.fields import LabelField, TextField, ListField
@@ -8,12 +9,12 @@ from combo.data.tokenizers import SpacySentenceSplitter
 class TextClassificationJSONReaderTest(unittest.TestCase):
     def test_read_two_tokens(self):
         reader = TextClassificationJSONReader()
-        tokens = [token for token in reader('text_classification_json_reader.json')]
+        tokens = [token for token in reader(os.path.join(os.path.dirname(__file__), 'text_classification_json_reader.json'))]
         self.assertEqual(len(tokens), 2)
 
     def test_read_two_examples_fields_without_sentence_splitting(self):
         reader = TextClassificationJSONReader()
-        tokens = [token for token in reader('text_classification_json_reader.json')]
+        tokens = [token for token in reader(os.path.join(os.path.dirname(__file__), 'text_classification_json_reader.json'))]
         self.assertEqual(len(tokens[0].fields.items()), 2)
         self.assertIsInstance(tokens[0].fields.get('label'), LabelField)
         self.assertEqual(tokens[0].fields.get('label').label, 'label1')
@@ -23,7 +24,7 @@ class TextClassificationJSONReaderTest(unittest.TestCase):
 
     def test_read_two_examples_tokens_without_sentence_splitting(self):
         reader = TextClassificationJSONReader()
-        tokens = [token for token in reader('text_classification_json_reader.json')]
+        tokens = [token for token in reader(os.path.join(os.path.dirname(__file__), 'text_classification_json_reader.json'))]
         self.assertEqual(len(tokens[0].fields.items()), 2)
         self.assertIsInstance(tokens[0].fields.get('tokens'), TextField)
         self.assertEqual(len(tokens[0].fields.get('tokens').tokens), 13)
@@ -33,7 +34,7 @@ class TextClassificationJSONReaderTest(unittest.TestCase):
 
     def test_read_two_examples_tokens_with_sentence_splitting(self):
         reader = TextClassificationJSONReader(sentence_segmenter=SpacySentenceSplitter())
-        tokens = [token for token in reader('text_classification_json_reader.json')]
+        tokens = [token for token in reader(os.path.join(os.path.dirname(__file__), 'text_classification_json_reader.json'))]
         self.assertEqual(len(tokens[0].fields.items()), 2)
         self.assertIsInstance(tokens[0].fields.get('tokens'), ListField)
         self.assertEqual(len(tokens[0].fields.get('tokens').field_list), 2)

tests/data/data_readers/test_universal_dependencies_dataset_reader.py

 import unittest
+import os
 
 from combo.data import UniversalDependenciesDatasetReader
 
@@ -6,24 +7,24 @@ from combo.data import UniversalDependenciesDatasetReader
 class UniversalDependenciesDatasetReaderTest(unittest.TestCase):
     def test_read_all_tokens(self):
         t = UniversalDependenciesDatasetReader()
-        tokens = [token for token in t('tl_trg-ud-test.conllu')]
+        tokens = [token for token in t(os.path.join(os.path.dirname(__file__), 'tl_trg-ud-test.conllu'))]
         self.assertEqual(len(tokens), 128)
 
     def test_read_text(self):
         t = UniversalDependenciesDatasetReader()
-        token = next(iter(t('tl_trg-ud-test.conllu')))
+        token = next(iter(t(os.path.join(os.path.dirname(__file__), 'tl_trg-ud-test.conllu'))))
         self.assertListEqual([str(t) for t in token['sentence'].tokens],
                              ['Gumising', 'ang', 'bata', '.'])
 
     def test_read_deprel(self):
         t = UniversalDependenciesDatasetReader()
-        token = next(iter(t('tl_trg-ud-test.conllu')))
+        token = next(iter(t(os.path.join(os.path.dirname(__file__), 'tl_trg-ud-test.conllu'))))
         self.assertListEqual(token['deprel'].labels,
                              ['root', 'case', 'nsubj', 'punct'])
 
     def test_read_upostag(self):
         t = UniversalDependenciesDatasetReader()
-        token = next(iter(t('tl_trg-ud-test.conllu')))
+        token = next(iter(t(os.path.join(os.path.dirname(__file__), 'tl_trg-ud-test.conllu'))))
         self.assertListEqual(token['upostag'].labels,
                              ['VERB', 'ADP', 'NOUN', 'PUNCT'])