[WIP] profiler

ingestion/examples/workflows/redshift.json

@@ -2,9 +2,9 @@
   "source": {
     "type": "redshift",
     "config": {
-      "host_port": "cluster.name.region.redshift.amazonaws.com:5439",
+      "host_port": "redshift-cluster-1.clot5cqn1cnb.us-west-2.redshift.amazonaws.com:5439",
-      "username": "username",
+      "username": "awsuser",
-      "password": "strong_password",
+      "password": "focguC-kaqqe5-nepsok",
       "database": "warehouse",
       "service_name": "aws_redshift",
       "filter_pattern": {

ingestion/pipelines/mysql.json

@@ -4,9 +4,10 @@
     "config": {
       "username": "openmetadata_user",
       "password": "openmetadata_password",
+      "database": "openmetadata_db",
       "service_name": "local_mysql",
       "filter_pattern": {
-        "excludes": ["mysql.*", "information_schema.*"]
+        "excludes": ["mysql.*", "information_schema.*", "performance_schema.*", "sys.*"]
       }
     }
   },

ingestion/requirements.txt

@@ -17,3 +17,4 @@ fastavro>=1.2.0
 google~=3.0.0
 okta~=2.0.0
 PyMySQL~=1.0.2
+great-expectations>=0.13.31

ingestion/setup.py

@@ -64,6 +64,7 @@ base_requirements = {
     "sql-metadata~=2.0.0",
     "spacy==3.0.5",
     "requests~=2.25.1",
+    "great-expectations>=0.13.31",
     "en_core_web_sm@https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.0.0/en_core_web_sm-3.0.0.tar.gz#egg=en_core_web"
 }
 base_plugins = {

ingestion/src/metadata/ingestion/models/table_metadata.py

@@ -258,3 +258,50 @@ class Dashboard(BaseModel):
     charts: List[str]
     service: EntityReference
     lastModified: int = None
+
+
+class ValueFrequency(BaseModel):
+    """Profiler ValueFrequency"""
+    value: str
+    frequency: int
+
+
+class Histogram(BaseModel):
+    """Histogram"""
+    boundaries: List[str]
+    heights: List[str]
+
+
+class Quantile(BaseModel):
+    """Quantile"""
+    quantile: str
+    value: str
+
+
+class DatasetColumnProfile(BaseModel):
+    """Dataset Column Profile stats """
+    fqdn: str
+    unique_count: int = None
+    unique_proportion: int = None
+    null_count: int = None
+    null_proportion: int = None
+    min: str = None
+    max: str = None
+    mean: str = None
+    median: str = None
+    stddev: str = None
+    quantiles: List[Quantile] = None
+    distinct_value_frequencies: List[ValueFrequency] = None
+    histogram: List[Histogram] = None
+    sample_values: List[str] = None
+
+
+class DatasetProfile(BaseModel):
+    """Dataset(table) stats"""
+    timestamp: int
+    table_name: str
+    row_count: int = None
+    col_count: int = None
+    col_profiles: List[DatasetColumnProfile] = None
+
+

ingestion/src/metadata/ingestion/source/sql_source.py

@@ -29,7 +29,7 @@ from metadata.generated.schema.type.entityReference import EntityReference
 from metadata.generated.schema.entity.data.database import Database
 
 from metadata.generated.schema.entity.data.table import Table, Column, ColumnConstraint, TableType, TableData
-from sqlalchemy import create_engine, inspect
+from sqlalchemy import create_engine
 from sqlalchemy.engine.reflection import Inspector
 from sqlalchemy.sql import sqltypes as types
 from sqlalchemy.inspection import inspect
@@ -37,8 +37,10 @@ from sqlalchemy.inspection import inspect
 from metadata.ingestion.api.common import IncludeFilterPattern, ConfigModel, Record
 from metadata.ingestion.api.common import WorkflowContext
 from metadata.ingestion.api.source import Source, SourceStatus
+from metadata.ingestion.models.table_metadata import DatasetProfile
 from metadata.ingestion.ometa.openmetadata_rest import MetadataServerConfig
 from metadata.utils.helpers import get_database_service_or_create
+from metadata.utils.dataprofiler import DataProfiler
 
 logger: logging.Logger = logging.getLogger(__name__)
 
@@ -72,6 +74,7 @@ class SQLConnectionConfig(ConfigModel):
     include_views: Optional[bool] = True
     include_tables: Optional[bool] = True
     generate_sample_data: Optional[bool] = True
+    data_profiler_enabled: Optional[bool] = True
     filter_pattern: IncludeFilterPattern = IncludeFilterPattern.allow_all()
 
     @abstractmethod
@@ -152,8 +155,10 @@ def get_column_type(status: SQLSourceStatus, dataset_name: str, column_type: Any
     return type_class
 
 
-class SQLSource(Source):
 
+
+
+class SQLSource(Source):
     def __init__(self, config: SQLConnectionConfig, metadata_config: MetadataServerConfig,
                  ctx: WorkflowContext):
         super().__init__(ctx)
@@ -172,6 +177,9 @@ class SQLSource(Source):
     def create(cls, config_dict: dict, metadata_config_dict: dict, ctx: WorkflowContext):
         pass
 
+    def _get_profiler_instance(self, inspector: Inspector) -> DataProfiler:
+        return DataProfiler(conn=inspector.bind, status=self.status)
+
     def standardize_schema_table_names(
             self, schema: str, table: str
     ) -> Tuple[str, str]:
@@ -211,7 +219,7 @@ class SQLSource(Source):
                 schema, table_name = self.standardize_schema_table_names(schema, table_name)
                 if not self.sql_config.filter_pattern.included(table_name):
                     self.status.filter('{}.{}'.format(self.config.get_service_name(), table_name),
-                                         "Table pattern not allowed")
+                                       "Table pattern not allowed")
                     continue
                 self.status.scanned('{}.{}'.format(self.config.get_service_name(), table_name))
 
@@ -227,6 +235,11 @@ class SQLSource(Source):
                     table_data = self.fetch_sample_data(schema, table_name)
                     table_entity.sampleData = table_data
 
+                if self.config.data_profiler_enabled:
+                    data_profiler = self._get_profiler_instance(inspector)
+                    profile = self.run_data_profiler(data_profiler, table_name, schema)
+                    logger.info(profile.json())
+
                 table_and_db = OMetaDatabaseAndTable(table=table_entity, database=self._get_database(schema))
                 yield table_and_db
             except ValidationError as err:
@@ -241,7 +254,7 @@ class SQLSource(Source):
             try:
                 if not self.sql_config.filter_pattern.included(view_name):
                     self.status.filter('{}.{}'.format(self.config.get_service_name(), view_name),
-                                         "View pattern not allowed")
+                                       "View pattern not allowed")
                     continue
                 try:
                     view_definition = inspector.get_view_definition(view_name, schema)
@@ -324,6 +337,24 @@ class SQLSource(Source):
             description = table_info["text"]
         return description
 
+    def run_data_profiler(
+            self,
+            profiler: DataProfiler,
+            table: str,
+            schema: str
+    ) -> DatasetProfile:
+        dataset_name = f"{schema}.{table}"
+        self.status.scanned(f"profile of {dataset_name}")
+        logger.info(f"Profiling {dataset_name} (this may take a while)")
+        profile = profiler.generate_profile(
+                    pretty_name=dataset_name,
+                    schema=schema,
+                    table=table,
+                    limit=50000,
+                    offset=0)
+        logger.debug(f"Finished profiling {dataset_name}")
+        return profile
+
     def close(self):
         if self.connection is not None:
             self.connection.close()

ingestion/src/metadata/utils/dataprofiler.py

@@ -0,0 +1,270 @@
+#  Licensed to the Apache Software Foundation (ASF) under one or more
+#  contributor license agreements. See the NOTICE file distributed with
+#  this work for additional information regarding copyright ownership.
+#  The ASF licenses this file to You under the Apache License, Version 2.0
+#  (the "License"); you may not use this file except in compliance with
+#  the License. You may obtain a copy of the License at
+#
+#  http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+import collections
+import contextlib
+import dataclasses
+import logging
+import unittest.mock
+import time
+from typing import Any, Iterable, Optional, Callable, Tuple, TypeVar
+
+from great_expectations.core.expectation_validation_result import (
+    ExpectationSuiteValidationResult,
+    ExpectationValidationResult,
+)
+from great_expectations.data_context import BaseDataContext
+from great_expectations.data_context.types.base import (
+    DataContextConfig,
+    DatasourceConfig,
+    InMemoryStoreBackendDefaults,
+)
+from great_expectations.datasource.sqlalchemy_datasource import SqlAlchemyDatasource
+
+from metadata.ingestion.api.source import SourceStatus
+from metadata.ingestion.models.table_metadata import DatasetProfile, DatasetColumnProfile, Quantile, \
+    Histogram, ValueFrequency
+
+logger: logging.Logger = logging.getLogger(__name__)
+
+T = TypeVar("T")
+K = TypeVar("K")
+
+
+def groupby_unsorted(
+        iterable: Iterable[T], key: Callable[[T], K]
+) -> Iterable[Tuple[K, Iterable[T]]]:
+    """The default itertools.groupby() requires that the iterable is already sorted by the key.
+    This method is similar to groupby() but without the pre-sorted requirement."""
+
+    values = collections.defaultdict(list)
+    for v in iterable:
+        values[key(v)].append(v)
+    return values.items()
+
+
+@contextlib.contextmanager
+def _properly_init_datasource(conn):
+    underlying_datasource_init = SqlAlchemyDatasource.__init__
+
+    def sqlalchemy_datasource_init(
+            self: SqlAlchemyDatasource, *args: Any, **kwargs: Any
+    ) -> None:
+        underlying_datasource_init(self, *args, **kwargs, engine=conn)
+        self.drivername = conn.dialect.name
+        del self._datasource_config["engine"]
+
+    with unittest.mock.patch(
+            "great_expectations.datasource.sqlalchemy_datasource.SqlAlchemyDatasource.__init__",
+            sqlalchemy_datasource_init,
+    ), unittest.mock.patch(
+        "great_expectations.data_context.store.validations_store.ValidationsStore.set"
+    ):
+        yield
+
+
+@dataclasses.dataclass
+class DataProfiler:
+    data_context: BaseDataContext
+    status: SourceStatus
+    datasource_name: str = "om_sqlalchemy_datasource"
+
+    def __init__(self, conn, status):
+        self.conn = conn
+        self.status = status
+
+        data_context_config = DataContextConfig(
+            datasources={
+                self.datasource_name: DatasourceConfig(
+                    class_name="SqlAlchemyDatasource",
+                    credentials={
+                        "url": self.conn.engine.url,
+                    },
+                )
+            },
+            store_backend_defaults=InMemoryStoreBackendDefaults(),
+            anonymous_usage_statistics={
+                "enabled": False,
+            },
+        )
+
+        with _properly_init_datasource(self.conn):
+            self.data_context = BaseDataContext(project_config=data_context_config)
+
+    def generate_profile(
+            self,
+            pretty_name: str,
+            schema: str = None,
+            table: str = None,
+            limit: int = None,
+            offset: int = None,
+            **kwargs: Any,
+    ) -> DatasetProfile:
+        with _properly_init_datasource(self.conn):
+            evrs = self._profile_data_asset(
+                {
+                    "schema": schema,
+                    "table": table,
+                    "limit": limit,
+                    "offset": offset,
+                    **kwargs,
+                },
+                pretty_name=pretty_name,
+            )
+        profile = self._convert_evrs_to_profile(evrs, pretty_name=pretty_name)
+        return profile
+
+    def _profile_data_asset(
+            self,
+            batch_kwargs: dict,
+            pretty_name: str,
+    ) -> ExpectationSuiteValidationResult:
+        # Internally, this uses the GE dataset profiler:
+        # great_expectations.profile.basic_dataset_profiler.BasicDatasetProfiler
+
+        profile_results = self.data_context.profile_data_asset(
+            self.datasource_name,
+            batch_kwargs={
+                "datasource": self.datasource_name,
+                **batch_kwargs,
+            },
+        )
+        assert profile_results["success"]
+
+        assert len(profile_results["results"]) == 1
+        _suite, evrs = profile_results["results"][0]
+        return evrs
+
+    @staticmethod
+    def _get_column_from_evr(evr: ExpectationValidationResult) -> Optional[str]:
+        return evr.expectation_config.kwargs.get("column")
+
+    def _convert_evrs_to_profile(
+            self, evrs: ExpectationSuiteValidationResult, pretty_name: str
+    ) -> DatasetProfile:
+        profile = None
+        column_profiles = []
+        for col, evrs_for_col in groupby_unsorted(
+                evrs.results, key=self._get_column_from_evr
+        ):
+            if col is None:
+                profile = self._handle_convert_table_evrs(evrs_for_col, pretty_name=pretty_name)
+            else:
+                column_profile = self._handle_convert_column_evrs(col, evrs_for_col, pretty_name=pretty_name)
+                column_profiles.append(column_profile)
+
+        if profile is not None:
+            profile.col_profiles = column_profiles
+        return profile
+
+    def _handle_convert_table_evrs(
+            self,
+            table_evrs: Iterable[ExpectationValidationResult],
+            pretty_name: str,
+    ) -> DatasetProfile:
+        logger.info("generating table stats")
+        profile = DatasetProfile(timestamp=round(time.time() * 1000), table_name=pretty_name)
+        for evr in table_evrs:
+            exp: str = evr.expectation_config.expectation_type
+            res: dict = evr.result
+            if exp == "expect_table_row_count_to_be_between":
+                profile.row_count = res["observed_value"]
+            elif exp == "expect_table_columns_to_match_ordered_list":
+                profile.col_count = len(res["observed_value"])
+            else:
+                self.status.warning(
+                    f"profile of {pretty_name}", f"unknown table mapper {exp}"
+                )
+        return profile
+
+    def _handle_convert_column_evrs(
+            self,
+            column: str,
+            col_evrs: Iterable[ExpectationValidationResult],
+            pretty_name: str,
+    ) -> DatasetColumnProfile:
+        logger.info(f"Generating Column Stats for {column}")
+        column_profile = DatasetColumnProfile(fqdn=column)
+        for evr in col_evrs:
+            exp: str = evr.expectation_config.expectation_type
+            res: dict = evr.result
+            if not res:
+                self.status.warning(
+                    f"profile of {pretty_name}", f"{exp} did not yield any results"
+                )
+                continue
+
+            if exp == "expect_column_unique_value_count_to_be_between":
+                column_profile.unique_count = res["observed_value"]
+            elif exp == "expect_column_proportion_of_unique_values_to_be_between":
+                column_profile.unique_proportion = res["observed_value"]
+            elif exp == "expect_column_values_to_not_be_null":
+                column_profile.null_count = res["unexpected_count"]
+                if (
+                        "unexpected_percent" in res
+                        and res["unexpected_percent"] is not None
+                ):
+                    column_profile.null_proportion = res["unexpected_percent"] / 100
+            elif exp == "expect_column_values_to_not_match_regex":
+                pass
+            elif exp == "expect_column_mean_to_be_between":
+                column_profile.mean = str(res["observed_value"])
+            elif exp == "expect_column_min_to_be_between":
+                column_profile.min = str(res["observed_value"])
+            elif exp == "expect_column_max_to_be_between":
+                column_profile.max = str(res["observed_value"])
+            elif exp == "expect_column_median_to_be_between":
+                column_profile.median = str(res["observed_value"])
+            elif exp == "expect_column_stdev_to_be_between":
+                column_profile.stddev = str(res["observed_value"])
+            elif exp == "expect_column_quantile_values_to_be_between":
+                if "observed_value" in res:
+                    column_profile.quantiles = [
+                        Quantile(quantile=str(quantile), value=str(value))
+                        for quantile, value in zip(
+                            res["observed_value"]["quantiles"],
+                            res["observed_value"]["values"],
+                        )
+                    ]
+            elif exp == "expect_column_values_to_be_in_set":
+                column_profile.sample_values = [
+                    str(v) for v in res["partial_unexpected_list"]
+                ]
+            elif exp == "expect_column_kl_divergence_to_be_less_than":
+                if "details" in res and "observed_partition" in res["details"]:
+                    partition = res["details"]["observed_partition"]
+                    column_profile.histogram = Histogram(
+                        [str(v) for v in partition["bins"]],
+                        [
+                            partition["tail_weights"][0],
+                            *partition["weights"],
+                            partition["tail_weights"][1],
+                        ],
+                    )
+            elif exp == "expect_column_distinct_values_to_be_in_set":
+                if "details" in res and "value_counts" in res["details"]:
+                    column_profile.distinct_value_frequencies = [
+                        ValueFrequency(value=str(value), frequency=count)
+                        for value, count in res["details"]["value_counts"].items()
+                    ]
+            elif exp == "expect_column_values_to_be_in_type_list":
+                pass
+            elif exp == "expect_column_values_to_be_unique":
+                pass
+            else:
+                self.status.warning(
+                    f"profile of {pretty_name}",
+                    f"warning: unknown column mapper {exp} in col {column}",
+                )
+        return column_profile