arekit 0.24.0__py3-none-any.whl → 0.25.1__py3-none-any.whl

arekit/contrib/source/nerel/io_utils.py

@@ -1,62 +0,0 @@
-from os import path
-
-from arekit.common.experiment.data_type import DataType
-from arekit.contrib.source.nerel.folding.fixed import create_fixed_folding
-from arekit.contrib.source.nerel.utils import iter_filename_and_splittype
-from arekit.contrib.source.zip_utils import ZipArchiveUtils
-
-
-class NerelIOUtils(ZipArchiveUtils):
-
-    splits = {
-        DataType.Train: "train",
-        DataType.Dev: "dev",
-        DataType.Test: "test"
-    }
-
-    @staticmethod
-    def get_archive_filepath(version):
-        return path.join(NerelIOUtils.get_data_root(), "nerel-{}.zip".format(version))
-
-    @staticmethod
-    def get_annotation_innerpath(folding_data_type, filename):
-        assert(isinstance(filename, str))
-        return path.join(NerelIOUtils.splits[folding_data_type], "{}.ann".format(filename))
-
-    @staticmethod
-    def get_news_innerpath(folding_data_type, filename):
-        assert(isinstance(filename, str))
-        return path.join(NerelIOUtils.splits[folding_data_type], "{}.txt".format(filename))
-
-    @staticmethod
-    def map_doc_to_fold_type(version):
-
-        it = iter_filename_and_splittype(
-            filenames_it=NerelIOUtils.iter_filenames_from_zip(version),
-            splits=NerelIOUtils.splits.items())
-
-        d2f = {}
-        for filename, split_type in it:
-            d2f[filename] = split_type
-
-        return d2f
-
-    @staticmethod
-    def read_dataset_split(version, docs_limit=None):
-
-        it = iter_filename_and_splittype(
-            filenames_it=NerelIOUtils.iter_filenames_from_zip(version),
-            splits=NerelIOUtils.splits.items())
-
-        f2d = {}
-        for filename, split_type in it:
-            if split_type not in f2d:
-                f2d[split_type] = []
-            f2d[split_type].append(filename)
-
-        filenames_by_ids, data_folding = create_fixed_folding(train_filenames=f2d[DataType.Train],
-                                                              test_filenames=f2d[DataType.Test],
-                                                              dev_filenames=f2d[DataType.Dev],
-                                                              limit=docs_limit)
-
-        return filenames_by_ids, data_folding

arekit/contrib/source/nerel/labels.py

@@ -1,241 +0,0 @@
-from arekit.common.labels.base import Label
-
-
-class OpinionBelongsTo(Label):
-    pass
-
-
-class OpinionRelatesTo(Label):
-    pass
-
-
-class NegEffectFrom(Label):
-    pass
-
-
-class NegStateFrom(Label):
-    pass
-
-
-class PosEffectFrom(Label):
-    pass
-
-
-class PosAuthorFrom(Label):
-    pass
-
-
-class NegAuthorFrom(Label):
-    pass
-
-
-class PosStateFrom(Label):
-    pass
-
-
-class NegativeTo(Label):
-    pass
-
-
-class PositiveTo(Label):
-    pass
-
-
-class STATE_BELONGS_TO(Label):
-    pass
-
-
-class ABBREVIATION(Label):
-    pass
-
-
-class HEADQUARTERED_IN(Label):
-    pass
-
-
-class AGE_DIED_AT(Label):
-    pass
-
-
-class AGE_IS(Label):
-    pass
-
-
-class AGENT(Label):
-    pass
-
-
-class IDEOLOGY_OF(Label):
-    pass
-
-
-class PLACE_RESIDES_IN(Label):
-    pass
-
-
-class POINT_IN_TIME(Label):
-    pass
-
-
-class INANIMATE_INVOLVED(Label):
-    pass
-
-
-class PRICE_OF(Label):
-    pass
-
-
-class INCOME(Label):
-    pass
-
-
-class PRODUCES(Label):
-    pass
-
-
-class ALTERNATIVE_NAME(Label):
-    pass
-
-
-class AWARDED_WITH(Label):
-    pass
-
-
-class CAUSE_OF_DEATH(Label):
-    pass
-
-
-class CONVICTED_OF(Label):
-    pass
-
-
-class DATE_DEFUNCT_IN(Label):
-    pass
-
-
-class DATE_FOUNDED_IN(Label):
-    pass
-
-
-class DATE_OF_BIRTH(Label):
-    pass
-
-
-class DATE_OF_CREATION(Label):
-    pass
-
-
-class DATE_OF_DEATH(Label):
-    pass
-
-
-class END_TIME(Label):
-    pass
-
-
-class EXPENDITURE(Label):
-    pass
-
-
-class FOUNDED_BY(Label):
-    pass
-
-
-class KNOWS(Label):
-    pass
-
-
-class RELATIVE(Label):
-    pass
-
-
-class LOCATED_IN(Label):
-    pass
-
-
-class RELIGION_OF(Label):
-    pass
-
-
-class MEDICAL_CONDITION(Label):
-    pass
-
-
-class SCHOOLS_ATTENDED(Label):
-    pass
-
-
-class MEMBER_OF(Label):
-    pass
-
-
-class SIBLING(Label):
-    pass
-
-
-class ORGANIZES(Label):
-    pass
-
-
-class SPOUSE(Label):
-    pass
-
-
-class ORIGINS_FROM(Label):
-    pass
-
-
-class START_TIME(Label):
-    pass
-
-
-class OWNER_OF(Label):
-    pass
-
-
-class SUBEVENT_OF(Label):
-    pass
-
-
-class PARENT_OF(Label):
-    pass
-
-
-class SUBORDINATE_OF(Label):
-    pass
-
-
-class PART_OF(Label):
-    pass
-
-
-class TAKES_PLACE_IN(Label):
-    pass
-
-
-class PARTICIPANT_IN(Label):
-    pass
-
-
-class WORKPLACE(Label):
-    pass
-
-
-class PENALIZED_AS(Label):
-    pass
-
-
-class WORKS_AS(Label):
-    pass
-
-
-class PLACE_OF_DEATH(Label):
-    pass
-
-
-class PLACE_OF_BIRTH(Label):
-    pass
-
-
-class HAS_CAUSE	(Label):
-    pass

arekit/contrib/source/nerel/reader.py

@@ -1,46 +0,0 @@
-from arekit.contrib.source.brat.annot import BratAnnotationParser
-from arekit.contrib.source.brat.doc import BratDocument
-from arekit.contrib.source.brat.sentences_reader import BratDocumentSentencesReader
-from arekit.contrib.source.nerel.entities import NerelEntityCollection
-from arekit.contrib.source.nerel.io_utils import NerelIOUtils
-
-
-class NerelDocReader(object):
-
-    def __init__(self, version, io_utils=NerelIOUtils()):
-        assert(isinstance(io_utils, NerelIOUtils))
-        self.__version = version
-        self.__io_utils = io_utils
-        self.__doc_fold = io_utils.map_doc_to_fold_type(version)
-
-    def read_text_relations(self, filename):
-        assert(isinstance(filename, str))
-
-        return self.__io_utils.read_from_zip(
-            inner_path=self.__io_utils.get_annotation_innerpath(
-                folding_data_type=self.__doc_fold[filename],
-                filename=filename),
-            process_func=lambda input_file: [
-                relation for relation in BratAnnotationParser.parse_annotations(
-                    input_file=input_file, encoding='utf-8-sig')["relations"]],
-            version=self.__version)
-
-    def read_document(self, filename, doc_id, entities_to_ignore=None):
-        assert(isinstance(filename, str))
-        assert(isinstance(doc_id, int))
-
-        def file_to_doc(input_file):
-            sentences = BratDocumentSentencesReader.from_file(input_file=input_file, entities=entities)
-            return BratDocument(doc_id=doc_id, sentences=sentences, text_relations=text_relations)
-
-        entities = NerelEntityCollection.read_collection(
-            filename=filename, version=self.__version,
-            entities_to_ignore=entities_to_ignore, io_utils=self.__io_utils)
-
-        text_relations = self.read_text_relations(filename=filename)
-
-        return self.__io_utils.read_from_zip(
-            inner_path=self.__io_utils.get_news_innerpath(
-                folding_data_type=self.__doc_fold[filename], filename=filename),
-            process_func=file_to_doc,
-            version=self.__version)

arekit/contrib/source/nerel/utils.py

@@ -1,24 +0,0 @@
-from os.path import basename
-
-
-def __iter_filtered_filenames(filenames_iter):
-    for filename in filenames_iter:
-        extension = filename[-4:]
-        # Crop extension.
-        filename = filename[:-4]
-        if extension != ".txt":
-            continue
-        yield filename, basename(filename)
-
-
-def iter_filename_and_splittype(filenames_it, splits):
-    for doc_id, data in enumerate(__iter_filtered_filenames(filenames_it)):
-        filepath, filename = data
-        for split_type, split_name in splits:
-            if split_name in filepath:
-                yield filename, split_type
-
-
-def iter_collection_filenames(filenames_it):
-    for doc_id, filename in enumerate(__iter_filtered_filenames(filenames_it)):
-        yield doc_id, filename

arekit/contrib/source/nerel/versions.py

@@ -1,12 +0,0 @@
-import enum
-
-
-class NerelVersions(enum.Enum):
-    """ List of the supported version of this collection
-    """
-
-    V1 = "v1_0"
-    V11 = "v1_1"
-
-
-DEFAULT_VERSION = NerelVersions.V1

arekit/contrib/source/nerelbio/io_utils.py

@@ -1,62 +0,0 @@
-from os import path
-
-from arekit.common.experiment.data_type import DataType
-from arekit.contrib.source.nerel.folding.fixed import create_fixed_folding
-from arekit.contrib.source.nerel.io_utils import NerelIOUtils
-from arekit.contrib.source.nerel.utils import iter_filename_and_splittype
-
-
-class NerelBioIOUtils(NerelIOUtils):
-
-    splits = {
-        DataType.Train: "train",
-        DataType.Dev: "dev",
-        DataType.Test: "test"
-    }
-
-    @staticmethod
-    def get_archive_filepath(version):
-        return path.join(NerelBioIOUtils.get_data_root(), "nerel-bio-{}.zip".format(version))
-
-    @staticmethod
-    def get_annotation_innerpath(folding_data_type, filename):
-        assert(isinstance(filename, str))
-        return path.join(NerelBioIOUtils.splits[folding_data_type], "{}.ann".format(filename))
-
-    @staticmethod
-    def get_news_innerpath(folding_data_type, filename):
-        assert(isinstance(filename, str))
-        return path.join(NerelBioIOUtils.splits[folding_data_type], "{}.txt".format(filename))
-
-    @staticmethod
-    def map_doc_to_fold_type(version):
-
-        it = iter_filename_and_splittype(
-            filenames_it=NerelBioIOUtils.iter_filenames_from_zip(version),
-            splits=NerelBioIOUtils.splits.items())
-
-        d2f = {}
-        for filename, split_type in it:
-            d2f[filename] = split_type
-
-        return d2f
-
-    @staticmethod
-    def read_dataset_split(version, docs_limit=None):
-
-        it = iter_filename_and_splittype(
-            filenames_it=NerelBioIOUtils.iter_filenames_from_zip(version),
-            splits=NerelBioIOUtils.splits.items())
-
-        f2d = {}
-        for filename, split_type in it:
-            if split_type not in f2d:
-                f2d[split_type] = []
-            f2d[split_type].append(filename)
-
-        filenames_by_ids, data_folding = create_fixed_folding(train_filenames=f2d[DataType.Train],
-                                                              test_filenames=f2d[DataType.Test],
-                                                              dev_filenames=f2d[DataType.Dev],
-                                                              limit=docs_limit)
-
-        return filenames_by_ids, data_folding

arekit/contrib/source/nerelbio/labels.py

@@ -1,265 +0,0 @@
-from arekit.common.labels.base import Label
-
-
-class ABBREVIATION(Label):
-    pass
-
-
-class ALTERNATIVE_NAME(Label):
-    pass
-
-
-class KNOWS(Label):
-    pass
-
-
-class AGE_IS(Label):
-    pass
-
-
-class AGE_DIED_AT(Label):
-    pass
-
-
-class AWARDED_WITH(Label):
-    pass
-
-
-class PLACE_OF_BIRTH(Label):
-    pass
-
-
-class DATE_DEFUNCT_IN(Label):
-    pass
-
-
-class DATE_FOUNDED_IN(Label):
-    pass
-
-
-class DATE_OF_BIRTH(Label):
-    pass
-
-
-class DATE_OF_CREATION(Label):
-    pass
-
-
-class DATE_OF_DEATH(Label):
-    pass
-
-
-class POINT_IN_TIME(Label):
-    pass
-
-
-class PLACE_OF_DEATH(Label):
-    pass
-
-
-class FOUNDED_BY(Label):
-    pass
-
-
-class HEADQUARTERED_IN(Label):
-    pass
-
-
-class IDEOLOGY_OF(Label):
-    pass
-
-
-class SPOUSE(Label):
-    pass
-
-
-class MEMBER_OF(Label):
-    pass
-
-
-class ORGANIZES(Label):
-    pass
-
-
-class OWNER_OF(Label):
-    pass
-
-
-class PARENT_OF(Label):
-    pass
-
-
-class PARTICIPANT_IN(Label):
-    pass
-
-
-class PLACE_RESIDES_IN(Label):
-    pass
-
-
-class PRICE_OF(Label):
-    pass
-
-
-class PRODUCES(Label):
-    pass
-
-
-class RELATIVE(Label):
-    pass
-
-
-class RELIGION_OF(Label):
-    pass
-
-
-class SCHOOLS_ATTENDED(Label):
-    pass
-
-
-class SIBLING(Label):
-    pass
-
-
-class SUBEVENT_OF(Label):
-    pass
-
-
-class SUBORDINATE_OF(Label):
-    pass
-
-
-class TAKES_PLACE_IN(Label):
-    pass
-
-
-class WORKPLACE(Label):
-    pass
-
-
-class WORKS_AS(Label):
-    pass
-
-
-class CONVICTED_OF(Label):
-    pass
-
-
-class PENALIZED_AS(Label):
-    pass
-
-
-class START_TIME(Label):
-    pass
-
-
-class END_TIME(Label):
-    pass
-
-
-class EXPENDITURE(Label):
-    pass
-
-
-class AGENT(Label):
-    pass
-
-
-class INANIMATE_INVOLVED(Label):
-    pass
-
-
-class INCOME(Label):
-    pass
-
-
-class SUBCLASS_OF(Label):
-    pass
-
-
-class PART_OF(Label):
-    pass
-
-
-class LOCATED_IN(Label):
-    pass
-
-
-class TREATED_USING(Label):
-    pass
-
-
-class ORIGINS_FROM(Label):
-    pass
-
-
-class TO_DETECT_OR_STUDY(Label):
-    pass
-
-
-class AFFECTS(Label):
-    pass
-
-
-class HAS_CAUSE(Label):
-    pass
-
-
-class APPLIED_TO(Label):
-    pass
-
-
-class USED_IN(Label):
-    pass
-
-
-class ASSOCIATED_WITH(Label):
-    pass
-
-
-class HAS_ADMINISTRATION_ROUTE(Label):
-    pass
-
-
-class HAS_STRENGTH(Label):
-    pass
-
-
-class DURATION_OF(Label):
-    pass
-
-
-class VALUE_IS(Label):
-    pass
-
-
-class PHYSIOLOGY_OF(Label):
-    pass
-
-
-class PROCEDURE_PERFORMED(Label):
-    pass
-
-
-class MENTAL_PROCESS_OF(Label):
-    pass
-
-
-class MEDICAL_CONDITION(Label):
-    pass
-
-
-class DOSE_IS(Label):
-    pass
-
-
-class FINDING_OF(Label):
-    pass
-
-
-class CAUSE_OF_DEATH(Label):
-    pass
-
-
-class CONSUME(Label):
-    pass

arekit/contrib/source/nerelbio/reader.py

@@ -1,8 +0,0 @@
-from arekit.contrib.source.nerel.reader import NerelDocReader
-from arekit.contrib.source.nerelbio.io_utils import NerelBioIOUtils
-
-
-class NerelBioDocReader(NerelDocReader):
-
-    def __init__(self, version):
-        super(NerelBioDocReader, self).__init__(version=version, io_utils=NerelBioIOUtils())