# Copyright (c) 2023 Cisco and/or its affiliates. # Licensed 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. """Prepare data for Plotly Dash applications. """ import logging import resource import awswrangler as wr import pandas as pd import pyarrow as pa from yaml import load, FullLoader, YAMLError from datetime import datetime, timedelta from time import time from pytz import UTC from awswrangler.exceptions import EmptyDataFrame, NoFilesFound from pyarrow.lib import ArrowInvalid, ArrowNotImplementedError from ..utils.constants import Constants as C class Data: """Gets the data from parquets and stores it for further use by dash applications. """ def __init__(self, data_spec_file: str) -> None: """Initialize the Data object. :param data_spec_file: Path to file specifying the data to be read from parquets. :type data_spec_file: str :raises RuntimeError: if it is not possible to open data_spec_file or it is not a valid yaml file. """ # Inputs: self._data_spec_file = data_spec_file # Specification of data to be read from parquets: self._data_spec = list() # Data frame to keep the data: self._data = { "statistics": pd.DataFrame(), "trending": pd.DataFrame(), "iterative": pd.DataFrame(), "coverage": pd.DataFrame() } # Read from files: try: with open(self._data_spec_file, "r") as file_read: self._data_spec = load(file_read, Loader=FullLoader) except IOError as err: raise RuntimeError( f"Not possible to open the file {self._data_spec_file,}\n{err}" ) except YAMLError as err: raise RuntimeError( f"An error occurred while parsing the specification file " f"{self._data_spec_file,}\n" f"{err}" ) @property def data(self): return self._data @staticmethod def _get_list_of_files( path, last_modified_begin=None, last_modified_end=None, days=None ) -> list: """Get list of interested files stored in S3 compatible storage and returns it. :param path: S3 prefix (accepts Unix shell-style wildcards) (e.g. s3://bucket/prefix) or list of S3 objects paths (e.g. [s3://bucket/key0, s3://bucket/key1]). :param last_modified_begin: Filter the s3 files by the Last modified date of the object. The filter is applied only after list all s3 files. :param last_modified_end: Filter the s3 files by the Last modified date of the object. The filter is applied only after list all s3 files. :param days: Number of days to filter. :type path: Union[str, List[str]] :type last_modified_begin: datetime, optional :type last_modified_end: datetime, optional :type days: integer, optional :returns: List of file names. :rtype: list """ file_list = list() if days: last_modified_begin = datetime.now(tz=UTC) - timedelta(days=days) try: file_list = wr.s3.list_objects( path=path, suffix="parquet", last_modified_begin=last_modified_begin, last_modified_end=last_modified_end ) logging.debug("\n".join(file_list)) except NoFilesFound as err: logging.error(f"No parquets found.\n{err}") except EmptyDataFrame as err: logging.error(f"No data.\n{err}") return file_list def _validate_columns(self, data_type: str) -> str: """Check if all columns are present in the dataframe. :param data_type: The data type defined in data.yaml :type data_type: str :returns: Error message if validation fails, otherwise empty string. :rtype: str """ defined_columns = set() for data_set in self._data_spec: if data_set.get("data_type", str()) == data_type: defined_columns.update(data_set.get("columns", set())) if not defined_columns: return "No columns defined in the data set(s)." if self.data[data_type].empty: return "No data." ret_msg = str() for col in defined_columns: if col not in self.data[data_type].columns: if not ret_msg: ret_msg = "Missing columns: " else: ret_msg += ", " ret_msg += f"{col}" return ret_msg @staticmethod def _write_parquet_schema( path, partition_filter=None, columns=None, validate_schema=False, last_modified_begin=None, last_modified_end=None, days=None ) -> None: """Auxiliary function to write parquet schemas. Use it instead of "_create_dataframe_from_parquet" in "read_all_data". :param path: S3 prefix (accepts Unix shell-style wildcards) (e.g. s3://bucket/prefix) or list of S3 objects paths (e.g. [s3://bucket/key0, s3://bucket/key1]). :param partition_filter: Callback Function filters to apply on PARTITION columns (PUSH-DOWN filter). This function MUST receive a single argument (Dict[str, str]) where keys are partitions names and values are partitions values. Partitions values will be always strings extracted from S3. This function MUST return a bool, True to read the partition or False to ignore it. Ignored if dataset=False. :param columns: Names of columns to read from the file(s). :param validate_schema: Check that individual file schemas are all the same / compatible. Schemas within a folder prefix should all be the same. Disable if you have schemas that are different and want to disable this check. :param last_modified_begin: Filter the s3 files by the Last modified date of the object. The filter is applied only after list all s3 files. :param last_modified_end: Filter the s3 files by the Last modified date of the object. The filter is applied only after list all s3 files. :param days: Number of days to filter. :type path: Union[str, List[str]] :type partition_filter: Callable[[Dict[str, str]], bool], optional :type columns: List[str], optional :type validate_schema: bool, optional :type last_modified_begin: datetime, optional :type last_modified_end: datetime, optional :type days: integer, optional """ if days: last_modified_begin = datetime.now(tz=UTC) - timedelta(days=days) df = wr.s3.read_parquet( path=path, path_suffix="parquet", ignore_empty=True, validate_schema=validate_schema, use_threads=True, dataset=True, columns=columns, partition_filter=partition_filter, last_modified_begin=last_modified_begin, last_modified_end=last_modified_end, chunked=1 ) for itm in df: try: # Specify the condition or remove it: if pd.api.types.is_string_dtype(itm["result_rate_unit"]): print(pa.Schema.from_pandas(itm)) pa.parquet.write_metadata( pa.Schema.from_pandas(itm), f"{C.PATH_TO_SCHEMAS}_tmp_schema" ) print(itm) break except KeyError: pass @staticmethod def _create_dataframe_from_parquet( path, partition_filter=None, columns=None, validate_schema=False, last_modified_begin=None, last_modified_end=None, days=None, schema=None ) -> pd.DataFrame: """Read parquet stored in S3 compatible storage and returns Pandas Dataframe. :param path: S3 prefix (accepts Unix shell-style wildcards) (e.g. s3://bucket/prefix) or list of S3 objects paths (e.g. [s3://bucket/key0, s3://bucket/key1]). :param partition_filter: Callback Function filters to apply on PARTITION columns (PUSH-DOWN filter). This function MUST receive a single argument (Dict[str, str]) where keys are partitions names and values are partitions values. Partitions values will be always strings extracted from S3. This function MUST return a bool, True to read the partition or False to ignore it. Ignored if dataset=False. :param columns: Names of columns to read from the file(s). :param validate_schema: Check that individual file schemas are all the same / compatible. Schemas within a folder prefix should all be the same. Disable if you have schemas that are different and want to disable this check. :param last_modified_begin: Filter the s3 files by the Last modified date of the object. The filter is applied only after list all s3 files. :param last_modified_end: Filter the s3 files by the Last modified date of the object. The filter is applied only after list all s3 files. :param days: Number of days to filter. :param schema: Path to schema to use when reading data from the parquet. :type path: Union[str, List[str]] :type partition_filter: Callable[[Dict[str, str]], bool], optional :type columns: List[str], optional :type validate_schema: bool, optional :type last_modified_begin: datetime, optional :type last_modified_end: datetime, optional :type days: integer, optional :type schema: string :returns: Pandas DataFrame or None if DataFrame cannot be fetched. :rtype: DataFrame """ df = pd.DataFrame() start = time() if days: last_modified_begin = datetime.now(tz=UTC) - timedelta(days=days) try: df = wr.s3.read_parquet( path=path, path_suffix="parquet", ignore_empty=True, schema=schema, validate_schema=validate_schema, use_threads=True, dataset=True, columns=columns, partition_filter=partition_filter, last_modified_begin=last_modified_begin, last_modified_end=last_modified_end, dtype_backend="pyarrow" ) df.info(verbose=True, memory_usage="deep") logging.debug( f"\nCreation of dataframe {path} took: {time() - start}\n" ) except (ArrowInvalid, ArrowNotImplementedError) as err: logging.error(f"Reading of data from parquets FAILED.\n{repr(err)}") except NoFilesFound as err: logging.error( f"Reading of data from parquets FAILED.\n" f"No parquets found in specified time period.\n" f"Nr of days: {days}\n" f"last_modified_begin: {last_modified_begin}\n" f"{repr(err)}" ) except EmptyDataFrame as err: logging.error( f"Reading of data from parquets FAILED.\n" f"No data in parquets in specified time period.\n" f"Nr of days: {days}\n" f"last_modified_begin: {last_modified_begin}\n" f"{repr(err)}" ) return df def read_all_data(self, days: int=None) -> dict: """Read all data necessary for all applications. :param days: Number of days to filter. If None, all data will be downloaded. :type days: int :returns: A dictionary where keys are names of parquets and values are the pandas dataframes with fetched data. :rtype: dict(str: pandas.DataFrame) """ data_lists = { "statistics": list(), "trending": list(), "iterative": list(), "coverage": list() } logging.info("\n\nReading data:\n" + "-" * 13 + "\n") for data_set in self._data_spec: logging.info( f"\n\nReading data for {data_set['data_type']} " f"{data_set['partition_name']} {data_set.get('release', '')}\n" ) schema_file = data_set.get("schema", None) if schema_file: try: schema = pa.parquet.read_schema( f"{C.PATH_TO_SCHEMAS}{schema_file}" ) except FileNotFoundError as err: logging.error(repr(err)) logging.error("Proceeding without schema.") schema = None else: schema = None partition_filter = lambda part: True \ if part[data_set["partition"]] == data_set["partition_name"] \ else False if data_set["data_type"] in ("trending", "statistics"): time_period = days else: time_period = None data = Data._create_dataframe_from_parquet( path=data_set["path"], partition_filter=partition_filter, columns=data_set.get("columns", None), days=time_period, schema=schema ) if data_set["data_type"] in ("iterative", "coverage"): data["release"] = data_set["release"] data["release"] = data["release"].astype("category") data_lists[data_set["data_type"]].append(data) logging.info( "\n\nData post-processing, validation and summary:\n" + "-" * 45 + "\n" ) for key in self._data.keys(): logging.info(f"\n\nDataframe {key}:\n") self._data[key] = pd.concat( data_lists[key], ignore_index=True, copy=False ) self._data[key].info(verbose=True, memory_usage="deep") err_msg = self._validate_columns(key) if err_msg: self._data[key] = pd.DataFrame() logging.error( f"Data validation FAILED.\n" f"{err_msg}\n" "Generated dataframe replaced by an empty dataframe." ) mem_alloc = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1000 logging.info(f"\n\nMemory allocation: {mem_alloc:.0f}MB\n") return self._data