atlas_search_extractor | 🎉 Initial commit.

Signed-off-by: mgorsk1 <gorskimariusz13@gmail.com>

databuilder/extractor/atlas_search_data_extractor.py

@@ -0,0 +1,278 @@
+# Copyright Contributors to the Amundsen project.
+# SPDX-License-Identifier: Apache-2.0
+
+import importlib
+import logging
+import multiprocessing.pool
+from copy import deepcopy
+from functools import reduce
+from typing import Iterator, Optional, List, Tuple, Any, Dict, Generator
+
+from atlasclient.client import Atlas
+from pyhocon import ConfigTree, ConfigFactory
+
+from databuilder.extractor.base_extractor import Extractor
+
+LOGGER = logging.getLogger(__name__)
+
+# custom types
+type_fields_mapping_spec = Dict[str, List[Tuple[str, str, Any, Any]]]
+type_fields_mapping = List[Tuple[str, str, Any, Any]]
+
+
+# @todo document classes/methods
+# @todo write tests
+
+
+class AtlasSearchDataExtractor(Extractor):
+    ATLAS_URL_CONFIG_KEY = 'atlas_url'
+    ATLAS_PORT_CONFIG_KEY = 'atlas_port'
+    ATLAS_PROTOCOL_CONFIG_KEY = 'atlas_protocol'
+    ATLAS_VALIDATE_SSL_CONFIG_KEY = 'atlas_validate_ssl'
+    ATLAS_USERNAME_CONFIG_KEY = 'atlas_auth_user'
+    ATLAS_PASSWORD_CONFIG_KEY = 'atlas_auth_pw'
+    ATLAS_SEARCH_CHUNK_SIZE_KEY = 'atlas_search_chunk_size'
+    ATLAS_DETAILS_CHUNK_SIZE_KEY = 'atlas_details_chunk_size'
+    ATLAS_TIMEOUT_SECONDS_KEY = 'atlas_timeout_seconds'
+    ATLAS_MAX_RETRIES_KEY = 'atlas_max_retries'
+
+    PROCESS_POOL_SIZE_KEY = 'process_pool_size'
+
+    ENTITY_TYPE_KEY = 'entity_type'
+
+    DEFAULT_CONFIG = ConfigFactory.from_dict({ATLAS_URL_CONFIG_KEY: "localhost",
+                                              ATLAS_PORT_CONFIG_KEY: 21000,
+                                              ATLAS_PROTOCOL_CONFIG_KEY: 'http',
+                                              ATLAS_VALIDATE_SSL_CONFIG_KEY: False,
+                                              ATLAS_SEARCH_CHUNK_SIZE_KEY: 250,
+                                              ATLAS_DETAILS_CHUNK_SIZE_KEY: 25,
+                                              ATLAS_TIMEOUT_SECONDS_KEY: 120,
+                                              ATLAS_MAX_RETRIES_KEY: 2,
+                                              PROCESS_POOL_SIZE_KEY: 10})
+
+    # @todo fill out below fields for TableESDocument
+    # tags: List[str],
+
+    # es_document field, atlas field path, modification function, default_value
+    FIELDS_MAPPING_SPEC: type_fields_mapping_spec = {
+        'Table': [
+            ('database', 'typeName', None, None),
+            ('cluster', 'attributes.qualifiedName', lambda x: x.split('@')[-1], None),
+            ('schema', 'relationshipAttributes.db.displayText', None, None),
+            ('name', 'attributes.name', None, None),
+            ('key', 'attributes.qualifiedName', None, None),
+            ('description', 'attributes.description', None, None),
+            ('last_updated_timestamp', 'updateTime', lambda x: int(x) / 1000, 0),
+            ('total_usage', 'attributes.popularityScore', lambda x: int(x), 0),
+            ('unique_usage', 'attributes.uniqueUsage', lambda x: int(x), 1),
+            ('column_names', 'relationshipAttributes.columns', lambda x: AtlasSearchDataExtractor._filter_none(
+                [c.get('attributes').get('name') for c in x if c.get('status').lower() == 'active']), []),
+            ('column_descriptions', 'relationshipAttributes.columns',
+             lambda x: AtlasSearchDataExtractor._filter_none(
+                 [c.get('attributes').get('description') for c in x if c.get('status').lower() == 'active']), []),
+            ('tags', 'tags', None, []),
+            ('badges', 'classifications',
+             lambda x: AtlasSearchDataExtractor._filter_none(
+                 [c.get('typeName') for c in x if c.get('entityStatus', '').lower() == 'active']), []),
+            ('display_name', 'attributes.qualifiedName', lambda x: x.split('@')[0], None),
+            ('schema_description', 'attributes.parameters.sourceDescription', None, None),
+            (
+                'programmatic_descriptions', 'attributes.parameters', lambda x: [str(s) for s in list(x.values())],
+                {})
+        ]
+    }
+
+    ENTITY_MODEL_BY_TYPE = {
+        'Table': 'databuilder.models.table_elasticsearch_document.TableESDocument'
+    }
+
+    REQUIRED_RELATIONSHIPS_BY_TYPE = {
+        'Table': ['columns']
+    }
+
+    def init(self, conf: ConfigTree) -> None:
+        self.conf = conf.with_fallback(AtlasSearchDataExtractor.DEFAULT_CONFIG)
+        self.driver = self._get_driver()
+
+        self._extract_iter: Optional[Iterator[Any]] = None
+
+    @property
+    def entity_type(self) -> str:
+        return self.conf.get(AtlasSearchDataExtractor.ENTITY_TYPE_KEY)
+
+    @property
+    def basic_search_query(self) -> Dict:
+        query = {
+            'typeName': self.entity_type,
+            'excludeDeletedEntities': True,
+            'query': '*'
+        }
+
+        LOGGER.debug(f'Basic Search Query: {query}')
+
+        return query
+
+    @property
+    def dsl_search_query(self) -> Dict:
+        query = {
+            'query': f'{self.entity_type} where __state = "ACTIVE"'
+        }
+
+        LOGGER.debug(f'DSL Search Query: {query}')
+
+        return query
+
+    @property
+    def model_class(self) -> Any:
+        model_class = AtlasSearchDataExtractor.ENTITY_MODEL_BY_TYPE.get(self.entity_type)
+
+        if model_class:
+            module_name, class_name = model_class.rsplit(".", 1)
+            mod = importlib.import_module(module_name)
+
+            return getattr(mod, class_name)
+
+    @property
+    def field_mappings(self) -> type_fields_mapping:
+        return AtlasSearchDataExtractor.FIELDS_MAPPING_SPEC.get(self.entity_type) or []
+
+    def extract(self) -> Any:
+        if not self._extract_iter:
+            self._extract_iter = self._get_extract_iter()
+
+        try:
+            return next(self._extract_iter)
+        except StopIteration:
+            return None
+
+    def get_scope(self) -> str:
+        return 'extractor.atlas_search_data'
+
+    @staticmethod
+    def _filter_none(input_list: List) -> List:
+        return list(filter(None, input_list))
+
+    def _get_driver(self) -> Any:
+        return Atlas(host=self.conf.get_string(AtlasSearchDataExtractor.ATLAS_URL_CONFIG_KEY),
+                     port=self.conf.get_string(AtlasSearchDataExtractor.ATLAS_PORT_CONFIG_KEY),
+                     username=self.conf.get_string(AtlasSearchDataExtractor.ATLAS_USERNAME_CONFIG_KEY),
+                     password=self.conf.get_string(AtlasSearchDataExtractor.ATLAS_PASSWORD_CONFIG_KEY),
+                     protocol=self.conf.get_string(AtlasSearchDataExtractor.ATLAS_PROTOCOL_CONFIG_KEY),
+                     validate_ssl=self.conf.get_bool(AtlasSearchDataExtractor.ATLAS_VALIDATE_SSL_CONFIG_KEY),
+                     timeout=self.conf.get_int(AtlasSearchDataExtractor.ATLAS_TIMEOUT_SECONDS_KEY),
+                     max_retries=self.conf.get_int(AtlasSearchDataExtractor.ATLAS_MAX_RETRIES_KEY))
+
+    @staticmethod
+    def split_list_to_chunks(input_list: List[Any], n: int) -> Generator:
+        """Yield successive n-sized chunks from lst."""
+        for i in range(0, len(input_list), n):
+            yield input_list[i:i + n]
+
+    def _execute_query(self, params: Dict, relationships: Optional[List[str]] = None) -> Any:
+        def get_details(guid_list: List[str]) -> List:
+            result = []
+
+            LOGGER.info(f'Processing guids chunk of size: {len(guid_list)}')
+
+            try:
+                bulk_collection = self.driver.entity_bulk(guid=guid_list)
+
+                for collection in bulk_collection:
+                    search_chunk = list(collection.entities_with_relationships(attributes=relationships))
+
+                    result += search_chunk
+
+                return result
+            except Exception:
+                return []
+
+        def get_guids(start_offset: int) -> List[str]:
+            result = []
+
+            batch_start = start_offset
+            batch_end = start_offset + search_chunk_size
+
+            LOGGER.info(f'Collecting guids for batch: {batch_start}-{batch_end}')
+
+            _params = {'offset': str(batch_start), 'limit': str(search_chunk_size)}
+
+            full_params = deepcopy(params)
+            full_params.update(**_params)
+
+            try:
+                results = self.driver.search_dsl(**full_params)
+
+                for hit in results:
+                    for entity in hit.entities:
+                        result.append(entity.guid)
+
+                return result
+            except Exception:
+                LOGGER.warning(f'Error processing batch: {batch_start}-{batch_end}', exc_info=True)
+
+                return []
+
+        search_chunk_size = self.conf.get_int(AtlasSearchDataExtractor.ATLAS_SEARCH_CHUNK_SIZE_KEY)
+        details_chunk_size = self.conf.get_int(AtlasSearchDataExtractor.ATLAS_DETAILS_CHUNK_SIZE_KEY)
+        process_pool_size = self.conf.get_int(AtlasSearchDataExtractor.PROCESS_POOL_SIZE_KEY)
+
+        guids = []
+
+        try:
+            # Fetch the table entities based on query terms
+            search_results = self.driver.search_basic.create(data=self.basic_search_query)
+
+            count = search_results._data.get("approximateCount")
+        except Exception as e:
+            count = 0
+
+        LOGGER.info(f'Received count: {count}')
+
+        if count > 0:
+            offsets = [i * search_chunk_size for i in range(int(count / search_chunk_size) + 1)]
+        else:
+            offsets = []
+
+        with multiprocessing.pool.ThreadPool(processes=process_pool_size) as pool:
+            guid_list = pool.map(get_guids, offsets, chunksize=1)
+
+        for sub_list in guid_list:
+            guids += sub_list
+
+        LOGGER.info(f'Received guids: {len(guids)}')
+
+        if guids:
+            guids_chunks = AtlasSearchDataExtractor.split_list_to_chunks(guids, details_chunk_size)
+
+            with multiprocessing.pool.ThreadPool(processes=process_pool_size) as pool:
+                return_list = pool.map(get_details, guids_chunks)
+
+            for sub_list in return_list:
+                for entry in sub_list:
+                    yield entry
+
+    def _get_extract_iter(self) -> Iterator[Any]:
+        relationships = AtlasSearchDataExtractor.REQUIRED_RELATIONSHIPS_BY_TYPE.get(self.entity_type)
+
+        for atlas_entity in self._execute_query(self.dsl_search_query, relationships=relationships):
+            model_dict = dict()
+
+            try:
+                data = atlas_entity.__dict__['_data']
+
+                for spec in self.field_mappings:
+                    model_field, atlas_field_path, _transform_spec, default_value = spec
+
+                    atlas_value = reduce(lambda x, y: x.get(y, dict()), atlas_field_path.split('.'),
+                                         data) or default_value
+
+                    transform_spec = _transform_spec or (lambda x: x)
+
+                    es_entity_value = transform_spec(atlas_value)
+                    model_dict[model_field] = es_entity_value
+
+                result = self.model_class(**model_dict)
+
+                yield result
+            except Exception:
+                LOGGER.warning(f'Error building model object.', exc_info=True)

example/scripts/sample_atlas_search_extractor.py

@@ -0,0 +1,88 @@
+# Copyright Contributors to the Amundsen project.
+# SPDX-License-Identifier: Apache-2.0
+
+import uuid
+
+from elasticsearch import Elasticsearch
+from pyhocon import ConfigFactory
+
+from databuilder.extractor.atlas_search_data_extractor import AtlasSearchDataExtractor
+from databuilder.job.job import DefaultJob
+from databuilder.loader.file_system_elasticsearch_json_loader import FSElasticsearchJSONLoader
+from databuilder.publisher.elasticsearch_publisher import ElasticsearchPublisher
+from databuilder.task.task import DefaultTask
+from databuilder.transformer.base_transformer import NoopTransformer
+
+entity_type = 'Table'
+extracted_search_data_path = '/tmp/search_data.json'
+process_pool_size = 5
+
+# atlas config
+atlas_url = 'localhost'
+atlas_port = 21000
+atlas_protocol = 'http'
+atlas_verify_ssl = False
+atlas_username = 'admin'
+atlas_password = 'admin'
+atlas_search_chunk_size = 200
+atlas_details_chunk_size = 10
+
+# elastic config
+es = Elasticsearch([
+    {'host': 'localhost'},
+])
+
+elasticsearch_client = es
+elasticsearch_new_index_key = 'tables-' + str(uuid.uuid4())
+elasticsearch_new_index_key_type = 'table'
+elasticsearch_index_alias = 'table_search_index'
+
+job_config = ConfigFactory.from_dict({
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_URL_CONFIG_KEY):
+        atlas_url,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_PORT_CONFIG_KEY):
+        atlas_port,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_PROTOCOL_CONFIG_KEY):
+        atlas_protocol,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_VALIDATE_SSL_CONFIG_KEY):
+        atlas_verify_ssl,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_USERNAME_CONFIG_KEY):
+        atlas_username,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_PASSWORD_CONFIG_KEY):
+        atlas_password,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_SEARCH_CHUNK_SIZE_KEY):
+        atlas_search_chunk_size,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ATLAS_DETAILS_CHUNK_SIZE_KEY):
+        atlas_details_chunk_size,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.PROCESS_POOL_SIZE_KEY):
+        process_pool_size,
+    'extractor.atlas_search_data.{}'.format(AtlasSearchDataExtractor.ENTITY_TYPE_KEY):
+        entity_type,
+    'loader.filesystem.elasticsearch.{}'.format(FSElasticsearchJSONLoader.FILE_PATH_CONFIG_KEY):
+        extracted_search_data_path,
+    'loader.filesystem.elasticsearch.{}'.format(FSElasticsearchJSONLoader.FILE_MODE_CONFIG_KEY):
+        'w',
+    'publisher.elasticsearch.{}'.format(ElasticsearchPublisher.FILE_PATH_CONFIG_KEY):
+        extracted_search_data_path,
+    'publisher.elasticsearch.{}'.format(ElasticsearchPublisher.FILE_MODE_CONFIG_KEY):
+        'r',
+    'publisher.elasticsearch.{}'.format(ElasticsearchPublisher.ELASTICSEARCH_CLIENT_CONFIG_KEY):
+        elasticsearch_client,
+    'publisher.elasticsearch.{}'.format(ElasticsearchPublisher.ELASTICSEARCH_NEW_INDEX_CONFIG_KEY):
+        elasticsearch_new_index_key,
+    'publisher.elasticsearch.{}'.format(ElasticsearchPublisher.ELASTICSEARCH_DOC_TYPE_CONFIG_KEY):
+        elasticsearch_new_index_key_type,
+    'publisher.elasticsearch.{}'.format(ElasticsearchPublisher.ELASTICSEARCH_ALIAS_CONFIG_KEY):
+        elasticsearch_index_alias
+})
+
+if __name__ == "__main__":
+    task = DefaultTask(extractor=AtlasSearchDataExtractor(),
+                       transformer=NoopTransformer(),
+                       loader=FSElasticsearchJSONLoader())
+
+    job = DefaultJob(conf=job_config,
+                     task=task,
+                     publisher=ElasticsearchPublisher())
+
+    job.launch()

requirements.txt

@@ -57,3 +57,5 @@ pandas>=0.21.0,<1.2.0
 
 requests==2.23.0,<3.0
 responses==0.10.6
+
+pyatlasclient==1.1.2

setup.py

@@ -65,6 +65,10 @@
     'feast==0.8.0'
 ]
 
+atlas = [
+    'pyatlasclient==1.1.2'
+]
+
 all_deps = requirements + kafka + cassandra + glue + snowflake + athena + \
     bigquery + jsonpath + db2 + dremio + druid + spark + feast
 
@@ -93,6 +97,7 @@
         'druid': druid,
         'delta-lake': spark,
         'feast': feast,
+        'atlas': atlas
     },
     classifiers=[
         'Programming Language :: Python :: 3.6',