mirror of
https://github.com/open-metadata/OpenMetadata.git
synced 2025-11-02 11:39:12 +00:00
Fix linting (#1958)
This commit is contained in:
Pere Miquel Brull
GitHub
parent
b11e503117
commit
1e334af89c
@ -1,6 +1,10 @@
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[BASIC]
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# W1203: logging-fstring-interpolation - f-string brings better readability and unifies style
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disable=W1203
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# W1202: logging-format-interpolation - lazy formatting in logging functions
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disable=W1203,W1202
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docstring-min-length=20
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max-args=7
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max-attributes=12
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[MASTER]
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fail-under=6.0
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@ -8,6 +8,9 @@
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""
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Generic source to build SQL connectors.
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"""
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import json
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import logging
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import re
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@ -16,7 +19,7 @@ import uuid
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from abc import abstractmethod
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from dataclasses import dataclass, field
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from datetime import datetime
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from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Type
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from typing import Dict, Iterable, List, Optional, Tuple
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from urllib.parse import quote_plus
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from pydantic import SecretStr
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@ -54,20 +57,22 @@ logger: logging.Logger = logging.getLogger(__name__)
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@dataclass
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class SQLSourceStatus(SourceStatus):
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"""
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Reports the source status after ingestion
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"""
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success: List[str] = field(default_factory=list)
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failures: List[str] = field(default_factory=list)
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warnings: List[str] = field(default_factory=list)
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filtered: List[str] = field(default_factory=list)
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def scanned(self, table_name: str) -> None:
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self.success.append(table_name)
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logger.info("Table Scanned: {}".format(table_name))
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def scanned(self, record: str) -> None:
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self.success.append(record)
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logger.info(f"Table Scanned: {record}")
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def filter(
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self, table_name: str, err: str, dataset_name: str = None, col_type: str = None
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) -> None:
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self.filtered.append(table_name)
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logger.warning("Dropped Table {} due to {}".format(table_name, err))
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def filter(self, record: str, err: str) -> None:
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self.filtered.append(record)
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logger.warning(f"Dropped Table {record} due to {err}")
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def build_sql_source_connection_url(
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@ -76,8 +81,11 @@ def build_sql_source_connection_url(
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username: Optional[str] = None,
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password: Optional[SecretStr] = None,
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database: Optional[str] = None,
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options: dict = {},
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options: Optional[dict] = None,
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) -> str:
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"""
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Helper function to prepare the db URL
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"""
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url = f"{scheme}://"
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if username is not None:
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@ -100,6 +108,12 @@ def build_sql_source_connection_url(
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class SQLConnectionConfig(ConfigModel):
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"""
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Config class containing all supported
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configurations for an SQL source, including
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data profiling and DBT generated information.
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"""
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username: Optional[str] = None
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password: Optional[SecretStr] = None
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host_port: str
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@ -144,7 +158,8 @@ def _get_table_description(schema: str, table: str, inspector: Inspector) -> str
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description = None
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try:
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table_info: dict = inspector.get_table_comment(table, schema)
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except Exception as err:
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# Catch any exception without breaking the ingestion
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except Exception as err: # pylint: disable=broad-except
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logger.error(f"Table Description Error : {err}")
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else:
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description = table_info["text"]
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@ -152,6 +167,12 @@ def _get_table_description(schema: str, table: str, inspector: Inspector) -> str
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class SQLSource(Source[OMetaDatabaseAndTable]):
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"""
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Source Connector implementation to extract
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Database & Table information and convert it
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to OpenMetadata Entities
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"""
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def __init__(
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self,
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config: SQLConnectionConfig,
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@ -174,26 +195,38 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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self.data_profiler = None
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self.data_models = {}
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if self.config.dbt_catalog_file is not None:
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self.dbt_catalog = json.load(open(self.config.dbt_catalog_file, "r"))
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with open(self.config.dbt_catalog_file, "r", encoding="utf-8") as catalog:
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self.dbt_catalog = json.load(catalog)
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if self.config.dbt_manifest_file is not None:
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self.dbt_manifest = json.load(open(self.config.dbt_manifest_file, "r"))
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with open(self.config.dbt_manifest_file, "r", encoding="utf-8") as manifest:
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self.dbt_manifest = json.load(manifest)
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def _instantiate_profiler(self):
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def _instantiate_profiler(self) -> bool:
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"""
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If the profiler is configured, load it and run.
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Return True if the profiling ran correctly
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"""
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try:
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if self.config.data_profiler_enabled:
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if self.data_profiler is None:
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# pylint: disable=import-outside-toplevel
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from metadata.profiler.dataprofiler import DataProfiler
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# pylint: enable=import-outside-toplevel
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self.data_profiler = DataProfiler(
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status=self.status, connection_str=self.connection_string
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)
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return True
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return False
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except Exception:
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# Catch any errors during profiling init and continue ingestion
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except Exception as exc: # pylint: disable=broad-except
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logger.error(
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f"Error loading profiler {exc}"
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"DataProfiler configuration is enabled. Please make sure you ran "
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"pip install 'openmetadata-ingestion[data-profiler]'"
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)
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return False
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def prepare(self):
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self._parse_data_model()
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@ -204,15 +237,15 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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):
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pass
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def type_of_column_name(self, sa_type, table_name: str, column_name: str):
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return sa_type
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def standardize_schema_table_names(
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self, schema: str, table: str
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) -> Tuple[str, str]:
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@staticmethod
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def standardize_schema_table_names(schema: str, table: str) -> Tuple[str, str]:
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return schema, table
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def fetch_sample_data(self, schema: str, table: str):
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def fetch_sample_data(self, schema: str, table: str) -> Optional[TableData]:
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"""
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Get some sample data from the source to be added
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to the Table Entities
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"""
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try:
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query = self.config.query.format(schema, table)
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logger.info(query)
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@ -221,14 +254,14 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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for col in results.keys():
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cols.append(col.replace(".", "_DOT_"))
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rows = []
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for r in results:
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row = list(r)
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for res in results:
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row = list(res)
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rows.append(row)
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return TableData(columns=cols, rows=rows)
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except Exception as err:
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logger.error(
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"Failed to generate sample data for {} - {}".format(table, err)
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)
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# Catch any errors and continue the ingestion
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except Exception as err: # pylint: disable=broad-except
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logger.error(f"Failed to generate sample data for {table} - {err}")
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return None
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def next_record(self) -> Iterable[OMetaDatabaseAndTable]:
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inspector = inspect(self.engine)
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@ -236,7 +269,7 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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if not self.sql_config.schema_filter_pattern.included(schema):
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self.status.filter(schema, "Schema pattern not allowed")
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continue
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logger.debug("total tables {}".format(inspector.get_table_names(schema)))
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logger.debug(f"Total tables {inspector.get_table_names(schema)}")
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if self.config.include_tables:
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yield from self.fetch_tables(inspector, schema)
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if self.config.include_views:
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@ -245,6 +278,10 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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def fetch_tables(
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self, inspector: Inspector, schema: str
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) -> Iterable[OMetaDatabaseAndTable]:
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"""
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Scrape an SQL schema and prepare Database and Table
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OpenMetadata Entities
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"""
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for table_name in inspector.get_table_names(schema):
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try:
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schema, table_name = self.standardize_schema_table_names(
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@ -252,13 +289,11 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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)
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if not self.sql_config.table_filter_pattern.included(table_name):
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self.status.filter(
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"{}.{}".format(self.config.get_service_name(), table_name),
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f"{self.config.get_service_name()}.{table_name}",
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"Table pattern not allowed",
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)
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continue
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self.status.scanned(
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"{}.{}".format(self.config.get_service_name(), table_name)
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)
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self.status.scanned(f"{self.config.get_service_name()}.{table_name}")
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description = _get_table_description(schema, table_name, inspector)
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fqn = f"{self.config.service_name}.{self.config.database}.{schema}.{table_name}"
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@ -275,7 +310,8 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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if self.sql_config.generate_sample_data:
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table_data = self.fetch_sample_data(schema, table_name)
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table_entity.sampleData = table_data
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except Exception as err:
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# Catch any errors during the ingestion and continue
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except Exception as err: # pylint: disable=broad-except
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logger.error(repr(err))
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logger.error(err)
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@ -291,16 +327,19 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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table=table_entity, database=self._get_database(schema)
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)
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yield table_and_db
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except Exception as err:
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# Catch any errors during the ingestion and continue
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except Exception as err: # pylint: disable=broad-except
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logger.error(err)
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self.status.warnings.append(
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"{}.{}".format(self.config.service_name, table_name)
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)
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self.status.warnings.append(f"{self.config.service_name}.{table_name}")
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continue
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def fetch_views(
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self, inspector: Inspector, schema: str
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) -> Iterable[OMetaDatabaseAndTable]:
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"""
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Get all views in the SQL schema and prepare
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Database & Table OpenMetadata Entities
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"""
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for view_name in inspector.get_view_names(schema):
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try:
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if self.config.scheme == "bigquery":
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@ -309,12 +348,11 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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)
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if not self.sql_config.table_filter_pattern.included(view_name):
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self.status.filter(
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"{}.{}".format(self.config.get_service_name(), view_name),
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f"{self.config.get_service_name()}.{view_name}",
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"View pattern not allowed",
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)
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continue
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try:
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if self.config.scheme == "bigquery":
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view_definition = inspector.get_view_definition(
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f"{self.config.project_id}.{schema}.{view_name}"
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@ -329,17 +367,15 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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except NotImplementedError:
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view_definition = ""
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description = _get_table_description(schema, view_name, inspector)
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table_columns = self._get_columns(schema, view_name, inspector)
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view_name = view_name.replace(".", "_DOT_")
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fqn = f"{self.config.service_name}.{self.config.database}.{schema}.{view_name}"
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table = Table(
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id=uuid.uuid4(),
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name=view_name,
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name=view_name.replace(".", "_DOT_"),
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tableType="View",
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description=description if description is not None else " ",
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fullyQualifiedName=fqn,
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columns=table_columns,
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description=_get_table_description(schema, view_name, inspector)
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or "",
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# This will be generated in the backend!! #1673
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fullyQualifiedName=view_name,
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columns=self._get_columns(schema, view_name, inspector),
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viewDefinition=view_definition,
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)
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if self.sql_config.generate_sample_data:
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@ -350,31 +386,34 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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table=table, database=self._get_database(schema)
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)
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yield table_and_db
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except Exception as err:
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# Catch any errors and continue the ingestion
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except Exception as err: # pylint: disable=broad-except
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logger.error(err)
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self.status.warnings.append(
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"{}.{}".format(self.config.service_name, view_name)
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)
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self.status.warnings.append(f"{self.config.service_name}.{view_name}")
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continue
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def _parse_data_model(self):
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"""
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Get all the DBT information and feed it to the Table Entity
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"""
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if self.config.dbt_manifest_file and self.config.dbt_catalog_file:
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logger.info("Parsing Data Models")
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manifest_nodes = self.dbt_manifest["nodes"]
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manifest_sources = self.dbt_manifest["sources"]
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manifest_entities = {**manifest_nodes, **manifest_sources}
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catalog_nodes = self.dbt_catalog["nodes"]
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catalog_sources = self.dbt_catalog["sources"]
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catalog_entities = {**catalog_nodes, **catalog_sources}
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manifest_entities = {
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**self.dbt_manifest["nodes"],
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**self.dbt_manifest["sources"],
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}
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catalog_entities = {
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**self.dbt_catalog["nodes"],
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**self.dbt_catalog["sources"],
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}
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for key, mnode in manifest_entities.items():
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name = mnode["alias"] if "alias" in mnode.keys() else mnode["name"]
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cnode = catalog_entities.get(key)
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if cnode is not None:
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columns = self._parse_data_model_columns(name, mnode, cnode)
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else:
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columns = []
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columns = (
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self._parse_data_model_columns(name, mnode, cnode) if cnode else []
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)
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if mnode["resource_type"] == "test":
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continue
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upstream_nodes = self._parse_data_model_upstream(mnode)
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@ -382,14 +421,12 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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mnode["alias"] if "alias" in mnode.keys() else mnode["name"]
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)
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model_name = model_name.replace(".", "_DOT_")
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description = mnode.get("description", "")
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schema = mnode["schema"]
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path = f"{mnode['root_path']}/{mnode['original_file_path']}"
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raw_sql = mnode.get("raw_sql", "")
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model = DataModel(
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modelType=ModelType.DBT,
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description=description,
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path=path,
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description=mnode.get("description", ""),
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path=f"{mnode['root_path']}/{mnode['original_file_path']}",
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rawSql=raw_sql,
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sql=mnode.get("compiled_sql", raw_sql),
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columns=columns,
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@ -403,12 +440,14 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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if "depends_on" in mnode and "nodes" in mnode["depends_on"]:
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for node in mnode["depends_on"]["nodes"]:
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try:
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node_type, database, table = node.split(".", 2)
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_, database, table = node.split(".", 2)
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table = table.replace(".", "_DOT_")
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table_fqn = f"{self.config.service_name}.{database}.{table}"
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upstream_nodes.append(table_fqn)
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except Exception:
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logger.error(f"Failed to parse the node {node} to capture lineage")
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except Exception as err: # pylint: disable=broad-except
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logger.error(
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f"Failed to parse the node {node} to capture lineage {err}"
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)
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continue
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return upstream_nodes
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@ -443,8 +482,8 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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ordinalPosition=ccolumn["index"],
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)
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columns.append(col)
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except Exception as e:
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logger.error(f"Failed to parse column type due to {e}")
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except Exception as err: # pylint: disable=broad-except
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logger.error(f"Failed to parse column type due to {err}")
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return columns
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@ -454,33 +493,58 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
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service=EntityReference(id=self.service.id, type=self.config.service_type),
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)
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def parse_raw_data_type(self, raw_data_type):
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return raw_data_type
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@staticmethod
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def _get_column_constraints(
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column, pk_columns, unique_columns
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) -> Optional[Constraint]:
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"""
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Prepare column constraints for the Table Entity
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"""
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constraint = None
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if column["nullable"]:
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constraint = Constraint.NULL
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elif not column["nullable"]:
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constraint = Constraint.NOT_NULL
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if column["name"] in pk_columns:
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constraint = Constraint.PRIMARY_KEY
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elif column["name"] in unique_columns:
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constraint = Constraint.UNIQUE
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return constraint
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def _get_columns(
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self, schema: str, table: str, inspector: Inspector
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) -> List[Column]:
|
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) -> Optional[List[Column]]:
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"""
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Get columns types and constraints information
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"""
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# Get inspector information:
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pk_constraints = inspector.get_pk_constraint(table, schema)
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try:
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unique_constraints = inspector.get_unique_constraints(table, schema)
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except NotImplementedError:
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logger.warning("Cannot obtain constraints - NotImplementedError")
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unique_constraints = []
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pk_columns = (
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pk_constraints["column_constraints"]
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if len(pk_constraints) > 0 and "column_constraints" in pk_constraints.keys()
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else {}
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||||
)
|
||||
unique_constraints = []
|
||||
try:
|
||||
unique_constraints = inspector.get_unique_constraints(table, schema)
|
||||
except NotImplementedError:
|
||||
pass
|
||||
unique_columns = []
|
||||
for constraint in unique_constraints:
|
||||
if "column_names" in constraint.keys():
|
||||
unique_columns = constraint["column_names"]
|
||||
|
||||
unique_columns = [
|
||||
constraint["column_names"]
|
||||
for constraint in unique_constraints
|
||||
if "column_names" in constraint.keys()
|
||||
]
|
||||
|
||||
dataset_name = f"{schema}.{table}"
|
||||
columns = inspector.get_columns(table, schema)
|
||||
table_columns = []
|
||||
row_order = 1
|
||||
try:
|
||||
for column in columns:
|
||||
for row_order, column in enumerate(inspector.get_columns(table, schema)):
|
||||
if "." in column["name"]:
|
||||
logger.info(f"Found '.' in {column['name']}")
|
||||
column["name"] = column["name"].replace(".", "_DOT_")
|
||||
@ -489,9 +553,6 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
|
||||
col_data_length = None
|
||||
arr_data_type = None
|
||||
if "raw_data_type" in column and column["raw_data_type"] is not None:
|
||||
column["raw_data_type"] = self.parse_raw_data_type(
|
||||
column["raw_data_type"]
|
||||
)
|
||||
(
|
||||
col_type,
|
||||
data_type_display,
|
||||
@ -514,26 +575,16 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
|
||||
r"(?:\w*)(?:[(]*)(\w*)(?:.*)", str(column["type"])
|
||||
).groups()
|
||||
data_type_display = column["type"]
|
||||
col_constraint = None
|
||||
if column["nullable"]:
|
||||
col_constraint = Constraint.NULL
|
||||
elif not column["nullable"]:
|
||||
col_constraint = Constraint.NOT_NULL
|
||||
if column["name"] in pk_columns:
|
||||
col_constraint = Constraint.PRIMARY_KEY
|
||||
elif column["name"] in unique_columns:
|
||||
col_constraint = Constraint.UNIQUE
|
||||
if col_type.upper() in ["CHAR", "VARCHAR", "BINARY", "VARBINARY"]:
|
||||
|
||||
col_constraint = self._get_column_constraints(
|
||||
column, pk_columns, unique_columns
|
||||
)
|
||||
|
||||
if col_type.upper() in {"CHAR", "VARCHAR", "BINARY", "VARBINARY"}:
|
||||
col_data_length = column["type"].length
|
||||
if col_data_length is None:
|
||||
col_data_length = 1
|
||||
try:
|
||||
if col_type == "NULL":
|
||||
col_type = self.type_of_column_name(
|
||||
col_type,
|
||||
column_name=column["name"],
|
||||
table_name=dataset_name,
|
||||
)
|
||||
if col_type == "NULL":
|
||||
col_type = "VARCHAR"
|
||||
data_type_display = "varchar"
|
||||
@ -544,27 +595,32 @@ class SQLSource(Source[OMetaDatabaseAndTable]):
|
||||
name=column["name"],
|
||||
description=column.get("comment", None),
|
||||
dataType=col_type,
|
||||
dataTypeDisplay="{}({})".format(col_type, col_data_length)
|
||||
dataTypeDisplay=f"{col_type}({col_data_length})"
|
||||
if data_type_display is None
|
||||
else f"{data_type_display}",
|
||||
dataLength=col_data_length,
|
||||
constraint=col_constraint,
|
||||
ordinalPosition=row_order,
|
||||
children=children if children is not None else None,
|
||||
ordinalPosition=row_order + 1, # enumerate starts at 0
|
||||
children=children,
|
||||
arrayDataType=arr_data_type,
|
||||
)
|
||||
except Exception as err:
|
||||
except Exception as err: # pylint: disable=broad-except
|
||||
logger.error(traceback.format_exc())
|
||||
logger.error(traceback.print_exc())
|
||||
logger.error(f"{err} : {column}")
|
||||
continue
|
||||
table_columns.append(om_column)
|
||||
row_order = row_order + 1
|
||||
return table_columns
|
||||
except Exception as err:
|
||||
logger.error("{}: {} {}".format(repr(err), table, err))
|
||||
except Exception as err: # pylint: disable=broad-except
|
||||
logger.error(f"{repr(err)}: {table} {err}")
|
||||
return None
|
||||
|
||||
def run_data_profiler(self, table: str, schema: str) -> TableProfile:
|
||||
"""
|
||||
Run the profiler for a table in a schema.
|
||||
|
||||
Prepare specific namings for different sources, e.g. bigquery
|
||||
"""
|
||||
dataset_name = f"{schema}.{table}"
|
||||
self.status.scanned(f"profile of {dataset_name}")
|
||||
logger.info(
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user