feat(elasticsearch): Updates to elasticsearch configuration, dao, and…

… tests (datahub-project#6269)
CybercentreCanada · Feb 1, 2023 · 4dec04f · 4dec04f
1 parent 1b0d483
commit 4dec04f
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diff --git a/build.gradle b/build.gradle
@@ -149,6 +149,7 @@ project.ext.externalDependency = [
     'springJdbc': "org.springframework:spring-jdbc:$springVersion",
     'springWeb': "org.springframework:spring-web:$springVersion",
     'springWebMVC': "org.springframework:spring-webmvc:$springVersion",
+    'springBootTest': "org.springframework.boot:spring-boot-starter-test:$springBootVersion",
     'springBoot': "org.springframework.boot:spring-boot:$springBootVersion",
     'springBootAutoconfigure': "org.springframework.boot:spring-boot-autoconfigure:$springBootVersion",
     'springBootStarterWeb': "org.springframework.boot:spring-boot-starter-web:$springBootVersion",

diff --git a/docker/datahub-gms/env/docker-without-neo4j.env b/docker/datahub-gms/env/docker-without-neo4j.env
@@ -8,6 +8,8 @@ KAFKA_BOOTSTRAP_SERVER=broker:29092
 KAFKA_SCHEMAREGISTRY_URL=http://schema-registry:8081
 ELASTICSEARCH_HOST=elasticsearch
 ELASTICSEARCH_PORT=9200
+ES_BULK_REFRESH_POLICY=WAIT_UNTIL
+GRAPH_SERVICE_DIFF_MODE_ENABLED=true
 GRAPH_SERVICE_IMPL=elasticsearch
 JAVA_OPTS=-Xms1g -Xmx1g
 ENTITY_REGISTRY_CONFIG_PATH=/datahub/datahub-gms/resources/entity-registry.yml

diff --git a/docker/datahub-gms/env/docker.env b/docker/datahub-gms/env/docker.env
@@ -8,11 +8,14 @@ KAFKA_BOOTSTRAP_SERVER=broker:29092
 KAFKA_SCHEMAREGISTRY_URL=http://schema-registry:8081
 ELASTICSEARCH_HOST=elasticsearch
 ELASTICSEARCH_PORT=9200
+ES_BULK_REFRESH_POLICY=WAIT_UNTIL
 NEO4J_HOST=http://neo4j:7474
 NEO4J_URI=bolt://neo4j
 NEO4J_USERNAME=neo4j
 NEO4J_PASSWORD=datahub
 JAVA_OPTS=-Xms1g -Xmx1g
+ES_BULK_REFRESH_POLICY=WAIT_UNTIL
+GRAPH_SERVICE_DIFF_MODE_ENABLED=true
 GRAPH_SERVICE_IMPL=neo4j
 ENTITY_REGISTRY_CONFIG_PATH=/datahub/datahub-gms/resources/entity-registry.yml
 ENTITY_SERVICE_ENABLE_RETENTION=true

diff --git a/docker/quickstart/docker-compose-without-neo4j-m1.quickstart.yml b/docker/quickstart/docker-compose-without-neo4j-m1.quickstart.yml
@@ -73,6 +73,8 @@ services:
     - KAFKA_SCHEMAREGISTRY_URL=http://schema-registry:8081
     - ELASTICSEARCH_HOST=elasticsearch
     - ELASTICSEARCH_PORT=9200
+    - ES_BULK_REFRESH_POLICY=WAIT_UNTIL
+    - GRAPH_SERVICE_DIFF_MODE_ENABLED=true
     - GRAPH_SERVICE_IMPL=elasticsearch
     - JAVA_OPTS=-Xms1g -Xmx1g
     - ENTITY_REGISTRY_CONFIG_PATH=/datahub/datahub-gms/resources/entity-registry.yml

diff --git a/docker/quickstart/docker-compose-without-neo4j.quickstart.yml b/docker/quickstart/docker-compose-without-neo4j.quickstart.yml
@@ -75,6 +75,8 @@ services:
     - KAFKA_SCHEMAREGISTRY_URL=http://schema-registry:8081
     - ELASTICSEARCH_HOST=elasticsearch
     - ELASTICSEARCH_PORT=9200
+    - ES_BULK_REFRESH_POLICY=WAIT_UNTIL
+    - GRAPH_SERVICE_DIFF_MODE_ENABLED=true
     - GRAPH_SERVICE_IMPL=elasticsearch
     - JAVA_OPTS=-Xms1g -Xmx1g
     - ENTITY_REGISTRY_CONFIG_PATH=/datahub/datahub-gms/resources/entity-registry.yml

diff --git a/docker/quickstart/docker-compose.quickstart.yml b/docker/quickstart/docker-compose.quickstart.yml
@@ -77,11 +77,13 @@ services:
     - KAFKA_SCHEMAREGISTRY_URL=http://schema-registry:8081
     - ELASTICSEARCH_HOST=elasticsearch
     - ELASTICSEARCH_PORT=9200
+    - ES_BULK_REFRESH_POLICY=WAIT_UNTIL
     - NEO4J_HOST=http://neo4j:7474
     - NEO4J_URI=bolt://neo4j
     - NEO4J_USERNAME=neo4j
     - NEO4J_PASSWORD=datahub
     - JAVA_OPTS=-Xms1g -Xmx1g
+    - GRAPH_SERVICE_DIFF_MODE_ENABLED=true
     - GRAPH_SERVICE_IMPL=neo4j
     - ENTITY_REGISTRY_CONFIG_PATH=/datahub/datahub-gms/resources/entity-registry.yml
     - ENTITY_SERVICE_ENABLE_RETENTION=true

diff --git a/entity-registry/src/main/java/com/linkedin/metadata/models/extractor/FieldExtractor.java b/entity-registry/src/main/java/com/linkedin/metadata/models/extractor/FieldExtractor.java
@@ -14,6 +14,7 @@
 import java.util.Optional;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+import javax.annotation.Nonnull;
 
 
 /**
@@ -32,7 +33,7 @@ private static long getNumArrayWildcards(PathSpec pathSpec) {
   }
 
   // Extract the value of each field in the field specs from the input record
-  public static <T extends FieldSpec> Map<T, List<Object>> extractFields(RecordTemplate record, List<T> fieldSpecs) {
+  public static <T extends FieldSpec> Map<T, List<Object>> extractFields(@Nonnull RecordTemplate record, List<T> fieldSpecs) {
     final Map<T, List<Object>> extractedFields = new HashMap<>();
     for (T fieldSpec : fieldSpecs) {
       Optional<Object> value = RecordUtils.getFieldValue(record, fieldSpec.getPath());

diff --git a/...ty-registry/src/main/java/com/linkedin/metadata/models/registry/MergedEntityRegistry.java b/...ty-registry/src/main/java/com/linkedin/metadata/models/registry/MergedEntityRegistry.java
@@ -31,8 +31,10 @@ public class MergedEntityRegistry implements EntityRegistry {
   private final Map<String, AspectSpec> _aspectNameToSpec;
 
   public MergedEntityRegistry(EntityRegistry baseEntityRegistry) {
-    entityNameToSpec = baseEntityRegistry.getEntitySpecs() != null ? baseEntityRegistry.getEntitySpecs() : new HashMap<>();
-    eventNameToSpec = baseEntityRegistry.getEventSpecs() != null ? baseEntityRegistry.getEventSpecs() : new HashMap<>();
+    // baseEntityRegistry.get*Specs() can return immutable Collections.emptyMap() which fails
+    // when this class attempts .put* operations on it.
+    entityNameToSpec = baseEntityRegistry.getEntitySpecs() != null ? new HashMap<>(baseEntityRegistry.getEntitySpecs()) : new HashMap<>();
+    eventNameToSpec = baseEntityRegistry.getEventSpecs() != null ? new HashMap<>(baseEntityRegistry.getEventSpecs()) : new HashMap<>();
     baseEntityRegistry.getAspectTemplateEngine();
     _aspectTemplateEngine = baseEntityRegistry.getAspectTemplateEngine();
     _aspectNameToSpec = baseEntityRegistry.getAspectSpecs();

diff --git a/metadata-ingestion/setup.py b/metadata-ingestion/setup.py
@@ -57,6 +57,7 @@ def get_long_description():
 
 rest_common = {
     "requests",
+    "requests_file"
 }
 
 kafka_common = {

diff --git a/metadata-ingestion/src/datahub/cli/docker_cli.py b/metadata-ingestion/src/datahub/cli/docker_cli.py
@@ -17,6 +17,7 @@
 import pydantic
 import requests
 from expandvars import expandvars
+from requests_file import FileAdapter
 
 from datahub.cli.cli_utils import DATAHUB_ROOT_FOLDER
 from datahub.cli.docker_check import (
@@ -47,16 +48,19 @@
 
 BOOTSTRAP_MCES_FILE = "metadata-ingestion/examples/mce_files/bootstrap_mce.json"
 
-GITHUB_BASE_URL = "https://raw.githubusercontent.com/datahub-project/datahub/master"
+DOCKER_COMPOSE_BASE = os.getenv(
+    "DOCKER_COMPOSE_BASE",
+    "https://raw.githubusercontent.com/datahub-project/datahub/master",
+)
 
-GITHUB_NEO4J_AND_ELASTIC_QUICKSTART_COMPOSE_URL = (
-    f"{GITHUB_BASE_URL}/{NEO4J_AND_ELASTIC_QUICKSTART_COMPOSE_FILE}"
+NEO4J_AND_ELASTIC_QUICKSTART_COMPOSE_URL = (
+    f"{DOCKER_COMPOSE_BASE}/{NEO4J_AND_ELASTIC_QUICKSTART_COMPOSE_FILE}"
 )
-GITHUB_ELASTIC_QUICKSTART_COMPOSE_URL = (
-    f"{GITHUB_BASE_URL}/{ELASTIC_QUICKSTART_COMPOSE_FILE}"
+ELASTIC_QUICKSTART_COMPOSE_URL = (
+    f"{DOCKER_COMPOSE_BASE}/{ELASTIC_QUICKSTART_COMPOSE_FILE}"
 )
-GITHUB_M1_QUICKSTART_COMPOSE_URL = f"{GITHUB_BASE_URL}/{M1_QUICKSTART_COMPOSE_FILE}"
-GITHUB_BOOTSTRAP_MCES_URL = f"{GITHUB_BASE_URL}/{BOOTSTRAP_MCES_FILE}"
+M1_QUICKSTART_COMPOSE_URL = f"{DOCKER_COMPOSE_BASE}/{M1_QUICKSTART_COMPOSE_FILE}"
+BOOTSTRAP_MCES_URL = f"{DOCKER_COMPOSE_BASE}/{BOOTSTRAP_MCES_FILE}"
 
 
 class Architectures(Enum):
@@ -630,13 +634,17 @@ def quickstart(
                 fg="red",
             )
         github_file = (
-            GITHUB_NEO4J_AND_ELASTIC_QUICKSTART_COMPOSE_URL
+            NEO4J_AND_ELASTIC_QUICKSTART_COMPOSE_URL
             if should_use_neo4j and not is_arch_m1(quickstart_arch)
-            else GITHUB_ELASTIC_QUICKSTART_COMPOSE_URL
+            else ELASTIC_QUICKSTART_COMPOSE_URL
             if not is_arch_m1(quickstart_arch)
-            else GITHUB_M1_QUICKSTART_COMPOSE_URL
+            else M1_QUICKSTART_COMPOSE_URL
         )
 
+        # also allow local files
+        request_session = requests.Session()
+        request_session.mount("file://", FileAdapter())
+
         with open(
             default_quickstart_compose_file, "wb"
         ) if default_quickstart_compose_file else tempfile.NamedTemporaryFile(
@@ -646,16 +654,16 @@ def quickstart(
             quickstart_compose_file.append(path)
             click.echo(f"Fetching docker-compose file {github_file} from GitHub")
             # Download the quickstart docker-compose file from GitHub.
-            quickstart_download_response = requests.get(github_file)
+            quickstart_download_response = request_session.get(github_file)
             quickstart_download_response.raise_for_status()
             tmp_file.write(quickstart_download_response.content)
             logger.debug(f"Copied to {path}")
 
         if standalone_consumers:
             consumer_github_file = (
-                f"{GITHUB_BASE_URL}/{CONSUMERS_QUICKSTART_COMPOSE_FILE}"
+                f"{DOCKER_COMPOSE_BASE}/{CONSUMERS_QUICKSTART_COMPOSE_FILE}"
                 if should_use_neo4j
-                else f"{GITHUB_BASE_URL}/{ELASTIC_CONSUMERS_QUICKSTART_COMPOSE_FILE}"
+                else f"{DOCKER_COMPOSE_BASE}/{ELASTIC_CONSUMERS_QUICKSTART_COMPOSE_FILE}"
             )
 
             default_consumer_compose_file = (
@@ -672,7 +680,7 @@ def quickstart(
                     f"Fetching consumer docker-compose file {consumer_github_file} from GitHub"
                 )
                 # Download the quickstart docker-compose file from GitHub.
-                quickstart_download_response = requests.get(consumer_github_file)
+                quickstart_download_response = request_session.get(consumer_github_file)
                 quickstart_download_response.raise_for_status()
                 tmp_file.write(quickstart_download_response.content)
                 logger.debug(f"Copied to {path}")
@@ -839,7 +847,7 @@ def ingest_sample_data(path: Optional[str], token: Optional[str]) -> None:
             path = str(pathlib.Path(tmp_file.name))
 
             # Download the bootstrap MCE file from GitHub.
-            mce_json_download_response = requests.get(GITHUB_BOOTSTRAP_MCES_URL)
+            mce_json_download_response = requests.get(BOOTSTRAP_MCES_URL)
             mce_json_download_response.raise_for_status()
             tmp_file.write(mce_json_download_response.content)
         click.echo(f"Downloaded to {path}")

diff --git a/metadata-ingestion/src/datahub/ingestion/source/state/checkpoint.py b/metadata-ingestion/src/datahub/ingestion/source/state/checkpoint.py
@@ -118,7 +118,7 @@ def create_from_checkpoint_aspect(
         except Exception as e:
             # Failure to load config is probably okay...config structure has changed.
             logger.warning(
-                "Failed to construct checkpoint's config from checkpoint aspect.", e
+                "Failed to construct checkpoint's config from checkpoint aspect. %s", e
             )
         else:
             try:

diff --git a/...-integration/java/datahub-client/src/test/java/datahub/client/kafka/KafkaEmitterTest.java b/...-integration/java/datahub-client/src/test/java/datahub/client/kafka/KafkaEmitterTest.java
@@ -15,7 +15,6 @@
 import org.apache.kafka.clients.admin.KafkaAdminClient;
 import org.apache.kafka.clients.admin.NewTopic;
 import org.apache.kafka.clients.producer.ProducerConfig;
-import org.apache.kafka.common.errors.TimeoutException;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.testcontainers.containers.Network;
@@ -106,7 +105,7 @@ private static String createTopics(Stream<String> bootstraps) {
       try {
         createAdminClient(bootstrap).createTopics(singletonList(new NewTopic(TOPIC, partitions, replicationFactor))).all().get();
         return bootstrap;
-      } catch (TimeoutException | InterruptedException | ExecutionException ex) {
+      } catch (RuntimeException | InterruptedException | ExecutionException ex) {
         return null;
       }
     }).filter(Objects::nonNull).findFirst().get();

diff --git a/...data-integration/java/spark-lineage/spark-smoke-test/golden_json/JavaHdfsIn2HdfsOut2.json b/...data-integration/java/spark-lineage/spark-smoke-test/golden_json/JavaHdfsIn2HdfsOut2.json
@@ -116,11 +116,11 @@
           {
             "com.linkedin.datajob.DataJobInputOutput": {
               "inputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hdfs,file:/opt/workspace/resources/data/in1.csv,PROD)",
-                "urn:li:dataset:(urn:li:dataPlatform:hdfs,file:/opt/workspace/resources/data/in2.csv,PROD)"
+                "urn:li:dataset:(urn:li:dataPlatform:file,file:/opt/workspace/resources/data/in1.csv,PROD)",
+                "urn:li:dataset:(urn:li:dataPlatform:file,file:/opt/workspace/resources/data/in2.csv,PROD)"
               ],
               "outputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hdfs,file:/opt/workspace/resources/data/JavaHdfsIn2HdfsOut2/out.csv,PROD)"
+                "urn:li:dataset:(urn:li:dataPlatform:file,file:/opt/workspace/resources/data/JavaHdfsIn2HdfsOut2/out.csv,PROD)"
               ]
             }
           },

diff --git a/metadata-integration/java/spark-lineage/spark-smoke-test/golden_json/JavaHiveInHiveOut.json b/metadata-integration/java/spark-lineage/spark-smoke-test/golden_json/JavaHiveInHiveOut.json
@@ -200,42 +200,6 @@
               "jobId": "QueryExecId_11",
               "flow": "urn:li:dataFlow:(spark,JavaHiveInHiveOut,spark_spark-master_7077)"
             }
-          },
-          {
-            "com.linkedin.common.DataPlatformInstance": {
-              "platform": "urn:li:dataPlatform:spark"
-            }
-          },
-          {
-            "com.linkedin.datajob.DataJobInfo": {
-              "name": "insertInto at HiveInHiveOut.java:44",
-              "type": {
-                "string": "sparkJob"
-              },
-              "customProperties": {
-                "SQLQueryId": "11",
-                "appName": "JavaHiveInHiveOut",
-                "description": "insertInto at HiveInHiveOut.java:44",
-                "queryPlan": "InsertIntoHiveTable `javahiveinhiveout`.`hivetab`, org.apache.hadoop.hive.serde2.lazy.LazySimpleSerDe, false, false, [a, b, c, d]\n+- HiveTableRelation `javahiveinhiveout`.`foo5`, org.apache.hadoop.hive.serde2.lazy.LazySimpleSerDe, [a#90, b#91, c#92, d#93]\n"
-              }
-            }
-          },
-          {
-            "com.linkedin.datajob.DataJobInputOutput": {
-              "inputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hive,javahiveinhiveout.foo5,PROD)"
-              ],
-              "outputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hive,javahiveinhiveout.hivetab,PROD)"
-              ]
-            }
-          },
-          {
-            "com.linkedin.common.BrowsePaths": {
-              "paths": [
-                "/spark/spark_spark-master_7077"
-              ]
-            }
           }
         ]
       }

diff --git a/...ta-integration/java/spark-lineage/spark-smoke-test/golden_json/PythonHdfsIn2HdfsOut2.json b/...ta-integration/java/spark-lineage/spark-smoke-test/golden_json/PythonHdfsIn2HdfsOut2.json
@@ -50,11 +50,11 @@
           {
             "com.linkedin.datajob.DataJobInputOutput": {
               "inputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hdfs,file:/opt/workspace/resources/data/in1.csv,PROD)",
-                "urn:li:dataset:(urn:li:dataPlatform:hdfs,file:/opt/workspace/resources/data/in2.csv,PROD)"
+                "urn:li:dataset:(urn:li:dataPlatform:file,file:/opt/workspace/resources/data/in1.csv,PROD)",
+                "urn:li:dataset:(urn:li:dataPlatform:file,file:/opt/workspace/resources/data/in2.csv,PROD)"
               ],
               "outputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hdfs,file:/opt/workspace/resources/data/PythonHdfsIn2HdfsOut2/out1.csv,PROD)"
+                "urn:li:dataset:(urn:li:dataPlatform:file,file:/opt/workspace/resources/data/PythonHdfsIn2HdfsOut2/out1.csv,PROD)"
               ]
             }
           },

diff --git a/...data-integration/java/spark-lineage/spark-smoke-test/golden_json/PythonHiveInHiveOut.json b/...data-integration/java/spark-lineage/spark-smoke-test/golden_json/PythonHiveInHiveOut.json
@@ -200,42 +200,6 @@
               "jobId": "QueryExecId_11",
               "flow": "urn:li:dataFlow:(spark,PythonHiveInHiveOut,spark_spark-master_7077)"
             }
-          },
-          {
-            "com.linkedin.common.DataPlatformInstance": {
-              "platform": "urn:li:dataPlatform:spark"
-            }
-          },
-          {
-            "com.linkedin.datajob.DataJobInputOutput": {
-              "inputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hive,pythonhiveinhiveout.foo5,PROD)"
-              ],
-              "outputDatasets": [
-                "urn:li:dataset:(urn:li:dataPlatform:hive,pythonhiveinhiveout.hivetab,PROD)"
-              ]
-            }
-          },
-          {
-            "com.linkedin.common.BrowsePaths": {
-              "paths": [
-                "/spark/spark_spark-master_7077"
-              ]
-            }
-          },
-          {
-            "com.linkedin.datajob.DataJobInfo": {
-              "name": "insertInto at NativeMethodAccessorImpl.java:0",
-              "type": {
-                "string": "sparkJob"
-              },
-              "customProperties": {
-                "SQLQueryId": "11",
-                "appName": "PythonHiveInHiveOut",
-                "description": "insertInto at NativeMethodAccessorImpl.java:0",
-                "queryPlan": "InsertIntoHiveTable `pythonhiveinhiveout`.`hivetab`, org.apache.hadoop.hive.serde2.lazy.LazySimpleSerDe, false, false, [a, b, c, d]\n+- HiveTableRelation `pythonhiveinhiveout`.`foo5`, org.apache.hadoop.hive.serde2.lazy.LazySimpleSerDe, [a#90, b#91, c#92, d#93]\n"
-              }
-            }
           }
         ]
       }

diff --git a/metadata-integration/java/spark-lineage/spark-smoke-test/test_e2e.py b/metadata-integration/java/spark-lineage/spark-smoke-test/test_e2e.py
@@ -1,19 +1,10 @@
 import json
-import time
-# import urllib
-# from typing import Any, Dict, Optional, cast
 
 import pytest
 import requests
 import os
 from jsoncomparison import Compare, NO_DIFF
 
-# from datahub.ingestion.run.pipeline import Pipeline
-# from datahub.ingestion.source.sql.mysql import MySQLConfig, MySQLSource
-# from datahub.ingestion.source.sql.sql_common import BaseSQLAlchemyCheckpointState
-# from datahub.ingestion.source.state.checkpoint import Checkpoint
-# from tests.utils import ingest_file_via_rest
-
 GMS_ENDPOINT = "http://localhost:8080"
 GOLDEN_FILES_PATH = "./spark-smoke-test/golden_json/"
 golden_files = os.listdir(GOLDEN_FILES_PATH)
@@ -23,7 +14,6 @@
 restli_default_headers = {
     "X-RestLi-Protocol-Version": "2.0.0",
 }
-kafka_post_ingestion_wait_sec = 60
 
 JSONDIFF_CONFIG = {
     'output': {

diff --git a/metadata-io/build.gradle b/metadata-io/build.gradle
@@ -55,6 +55,7 @@ dependencies {
   testCompile externalDependency.testContainersCassandra
   testCompile externalDependency.lombok
   testCompile project(':test-models')
+  testImplementation externalDependency.springBootTest
 
   testAnnotationProcessor externalDependency.lombok
 

diff --git a/metadata-io/src/main/java/com/linkedin/metadata/graph/GraphService.java b/metadata-io/src/main/java/com/linkedin/metadata/graph/GraphService.java
@@ -32,6 +32,12 @@ public interface GraphService {
    */
   void addEdge(final Edge edge);
 
+  /**
+   * Remove an edge from the graph.
+   * @param edge the edge to delete
+   */
+  void removeEdge(final Edge edge);
+
   /**
    * Find related entities (nodes) connected to a source entity via edges of given relationship types. Related entities
    * can be filtered by source and destination type (use `null` for any type), by source and destination entity filter

diff --git a/metadata-io/src/main/java/com/linkedin/metadata/graph/dgraph/DgraphGraphService.java b/metadata-io/src/main/java/com/linkedin/metadata/graph/dgraph/DgraphGraphService.java
@@ -385,6 +385,11 @@ protected static String getQueryForRelatedEntities(@Nullable List<String> source
                 relationships);
     }
 
+    @Override
+    public void removeEdge(final Edge edge) {
+        throw new UnsupportedOperationException("Remove edge not supported by DgraphGraphService at this time.");
+    }
+
     @Nonnull
     @Override
     public RelatedEntitiesResult findRelatedEntities(@Nullable List<String> sourceTypes,