From a6e1e9f5431d8786e921a8d331fdc65a91b71712 Mon Sep 17 00:00:00 2001 From: Saipraneeth <2506664+msaipraneeth@users.noreply.github.com> Date: Tue, 9 Jan 2024 09:11:46 +0000 Subject: [PATCH] add util method to generate entities from python dict|list object (#12) * Added is_attribute to EntityPath * Added sub_schemata to EntitySchema * Added doc to sub_schemata * Fixed doc for sub_schemata * Fixed doc for sub_schemata * remove pillow dependency * add build_entities_from_data to utils method * construct sub entities * fix mypy issues * add python-ulid dependency * support bool, int, float datatypes * iterate all over the object to generate schema paths * switch to python sdk * merge sub_entities of same type * support list type * add __str__ method to EntityPath and EntitySchema * add simple test case for build_entities_from_data * fix Pep8 E501 in entity.py * fix mypy issues * add __str__ and __eq__ for EntitySchema and EntityPath * compare object instead of comparing string representations * add test case with array object in first level * fix mypy issues * refactor utils module to package * test case to validate with two level in json object * Renamed EntitySchema and EntityPath attributes. * move to python module * update EntityPath attributes * add array and empty json tests * refactor utils module * fix flake8 issue * update changelog --------- Co-authored-by: Robert Isele Co-authored-by: Sebastian Tramp --- .idea/cmem-plugin-base.iml | 2 +- .python-version | 1 + CHANGELOG.md | 7 + cmem_plugin_base/dataintegration/entity.py | 27 ++ .../{utils.py => utils/__init__.py} | 2 +- .../dataintegration/utils/entity_builder.py | 213 +++++++++++ poetry.lock | 337 ++++++++++++------ pyproject.toml | 3 +- tests/test_utils_build_entities_from_data.py | 219 ++++++++++++ 9 files changed, 693 insertions(+), 118 deletions(-) create mode 100644 .python-version rename cmem_plugin_base/dataintegration/{utils.py => utils/__init__.py} (97%) create mode 100644 cmem_plugin_base/dataintegration/utils/entity_builder.py create mode 100644 tests/test_utils_build_entities_from_data.py diff --git a/.idea/cmem-plugin-base.iml b/.idea/cmem-plugin-base.iml index 5ba7e2f..759b1b2 100644 --- a/.idea/cmem-plugin-base.iml +++ b/.idea/cmem-plugin-base.iml @@ -5,7 +5,7 @@ - + diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..371cfe3 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11.1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e4d1e3..2679539 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/) +## [Unreleased] + +### Added + +- add util method to generate entities from python dict | list object + + ## [4.4.0] 2023-11-24 ### Added diff --git a/cmem_plugin_base/dataintegration/entity.py b/cmem_plugin_base/dataintegration/entity.py index fcde0a2..256d96a 100644 --- a/cmem_plugin_base/dataintegration/entity.py +++ b/cmem_plugin_base/dataintegration/entity.py @@ -19,6 +19,19 @@ def __init__(self, path: str, self.is_relation = is_relation self.is_single_value = is_single_value + def __repr__(self): + obj = { + 'path': self.path, 'is_relation': self.is_relation, + 'is_single_value': self.is_single_value + } + return f"EntityPath({obj})" + + def __eq__(self, other): + return (isinstance(other, EntityPath) + and self.path == other.path + and self.is_relation == other.is_relation + and self.is_single_value == other.is_single_value) + class EntitySchema: """An entity schema. @@ -40,6 +53,20 @@ def __init__(self, self.path_to_root = path_to_root self.sub_schemata = sub_schemata + def __repr__(self): + obj = { + "type_uri": self.type_uri, "paths": self.paths, + "path_to_root": self.path_to_root + } + return f"EntitySchema({obj})" + + def __eq__(self, other): + return (isinstance(other, EntitySchema) + and self.type_uri == other.type_uri + and self.paths == other.paths + and self.path_to_root == other.path_to_root + and self.sub_schemata == other.sub_schemata) + class Entity: """An Entity can represent an instance of any given concept. diff --git a/cmem_plugin_base/dataintegration/utils.py b/cmem_plugin_base/dataintegration/utils/__init__.py similarity index 97% rename from cmem_plugin_base/dataintegration/utils.py rename to cmem_plugin_base/dataintegration/utils/__init__.py index fef30b3..0ce80e5 100644 --- a/cmem_plugin_base/dataintegration/utils.py +++ b/cmem_plugin_base/dataintegration/utils/__init__.py @@ -71,7 +71,7 @@ def split_task_id(task_id: str) -> tuple: def write_to_dataset( - dataset_id: str, file_resource=None, context: Optional[UserContext] = None + dataset_id: str, file_resource=None, context: Optional[UserContext] = None ): """Write to a dataset. diff --git a/cmem_plugin_base/dataintegration/utils/entity_builder.py b/cmem_plugin_base/dataintegration/utils/entity_builder.py new file mode 100644 index 0000000..b830f22 --- /dev/null +++ b/cmem_plugin_base/dataintegration/utils/entity_builder.py @@ -0,0 +1,213 @@ +"""utils module for building entities from python objects dict|list.""" +from typing import Optional, Union + +from ulid import ULID + +from cmem_plugin_base.dataintegration.entity import ( + Entities, Entity, EntityPath +) +from cmem_plugin_base.dataintegration.entity import EntitySchema + + +def merge_path_values(paths_map1, paths_map2): + """ + Merge two dictionaries representing paths and values. + + This function takes two dictionaries, `paths_map1` and `paths_map2`, + each representing paths and corresponding values. It merges these dictionaries + by combining values for common paths and returns the merged dictionary. + + Args: + paths_map1 (dict): The first dictionary containing paths and values. + paths_map2 (dict): The second dictionary containing paths and values. + + Returns: + dict: A merged dictionary containing combined values for common paths. + """ + for key, value in paths_map2.items(): + current_path_map = {} + if paths_map1.get(key) is not None: + current_path_map = paths_map1[key] + current_path_map = current_path_map | value + paths_map1[key] = current_path_map + return paths_map1 + + +def generate_paths_from_data(data, path='root'): + """ + Generate a dictionary representing paths and data types from a nested JSON + structure. + + This function recursively traverses a nested JSON structure ('data') and builds + a dictionary ('paths_map') where keys are paths and values are dictionaries + containing keys and their corresponding data types. + + Args: + data (dict or list): The nested JSON structure to traverse. + path (str, optional): The current path (used for recursion). Default is 'root'. + + Returns: + dict: A dictionary representing paths and data types. + """ + paths_map = {} + if isinstance(data, list): + for _ in data: + paths_map = merge_path_values(paths_map, + generate_paths_from_data(_, path=path)) + if isinstance(data, dict): + key_to_type_map = {} + for key, value in data.items(): + key_to_type_map[key] = type(value).__name__ + if key_to_type_map[key] == 'dict': + sub_path = f"{path}/{key}" + paths_map = merge_path_values(paths_map, + generate_paths_from_data(data=value, + path=sub_path)) + if key_to_type_map[key] == 'list': + for _ in value: + if isinstance(_, dict): + key_to_type_map[key] = 'list_dict' + sub_path = f"{path}/{key}" + paths_map = merge_path_values(paths_map, + generate_paths_from_data( + data=_, + path=sub_path)) + paths_map[path] = key_to_type_map + return paths_map + + +def _get_schema(data: Union[dict, list]): + """Get the schema of an entity.""" + if not data: + return None + paths_map = generate_paths_from_data(data=data) + path_to_schema_map = {} + for path, key_to_type_map in paths_map.items(): + schema_paths = [] + for _key, _type in key_to_type_map.items(): + schema_paths.append( + EntityPath( + path=_key, + is_relation=_type in ('dict', 'list_dict'), + is_single_value=_type not in ('list', 'list_dict') + ) + ) + schema = EntitySchema( + type_uri="", + paths=schema_paths, + ) + path_to_schema_map[path] = schema + return path_to_schema_map + + +def extend_path_list(path_to_entities, sub_path_to_entities): + """ + Extend a dictionary of paths to entities by merging with another. + + This function takes two dictionaries, `path_to_entities` and `sub_path_to_entities`, + representing paths and lists of entities. It extends the lists of entities for each + path in `path_to_entities` by combining them with corresponding lists in + `sub_path_to_entities`. + + Args: + path_to_entities (dict): The main dictionary of paths to entities. + sub_path_to_entities (dict): The dictionary of additional paths to entities. + + Returns: + None: The result is modified in-place. `path_to_entities` is extended with + entities from `sub_path_to_entities`. + """ + for key, sub_entities in sub_path_to_entities.items(): + entities = path_to_entities.get(key, []) + entities.extend(sub_entities) + path_to_entities[key] = entities + + +def _get_entity( + path_from_root, + path_to_schema_map, + data, +): + """Get an entity based on the schema and data.""" + path_to_entities = {} + entity_uri = f"urn:x-ulid:{ULID()}" + values = [] + schema = path_to_schema_map[path_from_root] + for _ in schema.paths: + if data.get(_.path) is None: + values.append(['']) + elif not _.is_relation: + values.append( + [f"{data.get(_.path)}"] + if _.is_single_value + else + [f"{_v}" for _v in data.get(_.path)] + ) + else: + _data = [data.get(_.path)] if _.is_single_value else data.get(_.path) + sub_entities_uri = [] + for _v in _data: + sub_entity_path = f"{path_from_root}/{_.path}" + sub_path_to_entities = _get_entity( + path_from_root=sub_entity_path, + path_to_schema_map=path_to_schema_map, + data=_v, + ) + sub_entity = sub_path_to_entities[sub_entity_path].pop() + sub_entities_uri.append(sub_entity.uri) + sub_path_to_entities[sub_entity_path].append(sub_entity) + extend_path_list(path_to_entities, sub_path_to_entities) + values.append(sub_entities_uri) + entity = Entity(uri=entity_uri, values=values) + entities = path_to_entities.get(path_from_root, []) + entities.append(entity) + path_to_entities[path_from_root] = entities + return path_to_entities + + +def _get_entities( + data: Union[dict, list], + path_to_schema_map: dict[str, EntitySchema], +) -> dict[str, list[Entity]]: + """ + Get entities based on the schema, data, and sub-entities. + """ + path_to_entities: dict[str, list[Entity]] = {} + if isinstance(data, list): + for _ in data: + sub_path_to_entities = _get_entity( + path_from_root="root", + path_to_schema_map=path_to_schema_map, + data=_ + ) + extend_path_list(path_to_entities, sub_path_to_entities) + else: + path_to_entities = _get_entity( + path_from_root="root", + path_to_schema_map=path_to_schema_map, + data=data, + ) + return path_to_entities + + +def build_entities_from_data(data: Union[dict, list]) -> Optional[Entities]: + """ + Get entities from a data object. + """ + path_to_schema_map = _get_schema(data) + if not path_to_schema_map: + return None + path_to_entities = _get_entities( + data=data, + path_to_schema_map=path_to_schema_map, + ) + return Entities( + entities=iter(path_to_entities.get('root')), # type: ignore[arg-type] + schema=path_to_schema_map['root'], + sub_entities=[ + Entities( + entities=iter(value), + schema=path_to_schema_map[key] + ) for key, value in path_to_entities.items() if key != 'root' + ] + ) diff --git a/poetry.lock b/poetry.lock index dd4aa52..39fdcdb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -425,15 +425,34 @@ test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre [[package]] name = "idna" -version = "3.4" +version = "3.6" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.5" files = [ - {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"}, - {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, + {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"}, + {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"}, ] +[[package]] +name = "importlib-metadata" +version = "7.0.0" +description = "Read 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(>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "736c8e7226e1adb41e86572ccf10e7030fb9f58837c523cc33ba63f09729c991" +content-hash = "e6a5dcc43b6248d8cf2ba91e3f8131d17596fb1df989cf16cc4129749a706549" diff --git a/pyproject.toml b/pyproject.toml index 77b81a3..4d7b7d9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ keywords = [ [tool.poetry.dependencies] python = "^3.11" cmem-cmempy = ">=23.3.0" +python-ulid = "^2.2.0" [tool.poetry.group.dev.dependencies] bandit = "^1.7.5" @@ -31,8 +32,6 @@ defusedxml = "^0.7.1" flake8-formatter-junit-xml = "^0.0.6" genbadge = "^1.1.0" mypy = "^1.4.1" -# https://github.com/smarie/python-genbadge/issues/31 -pillow = "9.5.0" # https://github.com/rasjani/pylint-junit/issues/1 pylint = "^2" pylint-junit = "^0.3.2" diff --git a/tests/test_utils_build_entities_from_data.py b/tests/test_utils_build_entities_from_data.py new file mode 100644 index 0000000..c7b34d5 --- /dev/null +++ b/tests/test_utils_build_entities_from_data.py @@ -0,0 +1,219 @@ +"""Tests for `utils.build_entities_from_data`""" +import json + +from cmem_plugin_base.dataintegration.entity import EntitySchema, EntityPath +from cmem_plugin_base.dataintegration.utils.entity_builder import ( + build_entities_from_data +) + + +def test_single_object(): + """test generation of entities and schema for a simple JSON object.""" + test_data = """ +{ + "name": "sai", + "email": "saipraneeth@example.com" +}""" + data = json.loads(test_data) + entities = build_entities_from_data(data) + assert len(list(entities.entities)) == 1 + for _ in entities.entities: + assert len(_.values) == 2 + assert _.values == [["sai"], ["saipraneeth@example.com"]] + assert len(entities.schema.paths) == 2 + assert entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("email", False, is_single_value=True), + ] + ) + + +def test_single_object_one_level(): + """test generation of entities and schema for a JSON object with one level of + hierarchy""" + test_data = """ +{ + "name": "sai", + "email": "saipraneeth@example.com", + "city": { + "name": "San Francisco", + "country": "United States" + } +}""" + data = json.loads(test_data) + entities = build_entities_from_data(data) + assert len(list(entities.entities)) == 1 + for _ in entities.entities: + assert len(_.values) == 3 + assert _.values[0:2] == [["sai"], ["saipraneeth@example.com"]] + assert _.values[2][0].startswith("urn:x-ulid:") + assert len(entities.schema.paths) == 3 + assert entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("email", False, is_single_value=True), + EntityPath("city", True, is_single_value=True), + ] + ) + # Validate sub entities + for _ in entities.sub_entities: + for _entity in _.entities: + assert len(_entity.values) == 2 + assert _entity.values == [["San Francisco"], ["United States"]] + assert _.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("country", False, is_single_value=True) + ] + ) + + +def test_single_object_one_level_array(): + """test generation of entities and schema for a JSON object with array object in + first level of hierarchy""" + test_data = """ +{ + "name": "sai", + "email": "saipraneeth@example.com", + "city": [{ + "name": "San Francisco", + "country": "United States" + }, + { + "name": "New York", + "country": "United States" + }] +}""" + data = json.loads(test_data) + entities = build_entities_from_data(data) + assert len(list(entities.entities)) == 1 + for _ in entities.entities: + assert len(_.values) == 3 + assert _.values[0:2] == [["sai"], ["saipraneeth@example.com"]] + assert _.values[2][0].startswith("urn:x-ulid:") + assert len(entities.schema.paths) == 3 + assert entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("email", False, is_single_value=True), + EntityPath("city", True, is_single_value=False), + ] + ) + # Validate sub entities + for _ in entities.sub_entities: + assert len(list(_.entities)) == 2 + for _entity in _.entities: + assert len(_entity.values) == 2 + assert _.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("country", False, is_single_value=True) + ] + ) + + +def test_single_object_two_level_array(): + """test generation of entities and schema for a JSON object with two levels of + hierarchy""" + test_data = """ +{ + "name": "sai", + "email": "saipraneeth@example.com", + "city": [ + { + "name": "San Francisco", + "country": "United States", + "geo_location": { + "lat": "37.773972", + "long": "-122.431297" + } + }, + { + "name": "New York", + "country": "United States", + "geo_location": { + "lat": "40.730610", + "long": "-73.935242" + } + } + ] +}""" + data = json.loads(test_data) + entities = build_entities_from_data(data) + assert len(list(entities.entities)) == 1 + for _ in entities.entities: + assert len(_.values) == 3 + assert _.values[0:2] == [["sai"], ["saipraneeth@example.com"]] + assert _.values[2][0].startswith("urn:x-ulid:") + assert len(entities.schema.paths) == 3 + assert entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("email", False, is_single_value=True), + EntityPath("city", True, is_single_value=False), + ] + ) + # Validate sub entities + location_entities = entities.sub_entities[0] + city_entities = entities.sub_entities[1] + assert len(list(city_entities.entities)) == 2 + assert len(list(location_entities.entities)) == 2 + + assert city_entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("country", False, is_single_value=True), + EntityPath("geo_location", True, is_single_value=True), + ] + ) + + assert location_entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("lat", False, is_single_value=True), + EntityPath("long", False, is_single_value=True), + ] + ) + + +def test_array_object(): + """test generation of entities and schema for a simple array JSON object.""" + test_data = """ +[{ + "name": "seebi" +}, +{ + "name": "sai", + "email": "saipraneeth@example.com" +}]""" + data = json.loads(test_data) + entities = build_entities_from_data(data) + _ = next(entities.entities) + assert len(_.values) == 2 + assert _.values == [["seebi"], [""]] + _ = next(entities.entities) + assert len(_.values) == 2 + assert _.values == [["sai"], ["saipraneeth@example.com"]] + assert len(entities.schema.paths) == 2 + assert entities.schema == EntitySchema( + type_uri="", + paths=[ + EntityPath("name", False, is_single_value=True), + EntityPath("email", False, is_single_value=True), + ] + ) + + +def test_empty_object(): + """test empty json object input""" + test_data = """[]""" + data = json.loads(test_data) + assert build_entities_from_data(data) is None