diff --git a/pyproject.toml b/pyproject.toml index acfc280..11f2ab8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,13 +11,18 @@ authors = [ dependencies = [ "berdl-notebook-utils", "biopython>=1.86", - "cdm-schema", - "click>=8.1.8", - "ruff>=0.14.8", + "click>=8.3.1", + "xmlschema>=4.2.0", + "xsdata[cli,lxml]>=25.7", + "lxml>=6.0.2", + "pytest-asyncio>=1.3.0", + "ruff>=0.14.13", ] [dependency-groups] dev = [ + "hypothesis>=6.148.9", + "mutmut>=3.4.0", "pytest>=9.0.2", "pytest-cov>=7.0.0", "pytest-env>=1.2.0", diff --git a/src/cdm_data_loader_utils/audit/__init__.py b/src/cdm_data_loader_utils/audit/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/cdm_data_loader_utils/audit/schema.py b/src/cdm_data_loader_utils/audit/schema.py new file mode 100644 index 0000000..8a5d4f0 --- /dev/null +++ b/src/cdm_data_loader_utils/audit/schema.py @@ -0,0 +1,109 @@ +"""Schema for audit tables.""" + +from pyspark.sql.types import ArrayType, IntegerType, LongType, StringType, StructField, StructType, TimestampType + +from cdm_data_loader_utils.core.pipeline_run import PipelineRun + +CHECKPOINT = "checkpoint" +METRICS = "metrics" +REJECTS = "rejects" +RUN = "run" + +RUN_ID = "run_id" +PIPELINE = "pipeline" +SOURCE = "source_path" +NAMESPACE = "namespace" + +END_TIME = "end_time" +ERROR = "error" +LAST_ENTRY_ID = "last_entry_id" +PARSED_ROW = "parsed_record" +RAW_ROW = "raw_record" +RECORDS_PROCESSED = "records_processed" +START_TIME = "start_time" +STATUS = "status" +TABLE = "table" +TIMESTAMP = "timestamp" +UPDATED = "updated" + +STATUS_ERROR = "ERROR" +STATUS_RUNNING = "RUNNING" +STATUS_SUCCESS = "SUCCESS" + +N_INVALID = "records_invalid" +N_READ = "records_read" +N_VALID = "records_valid" +ROW_ERRORS = "errors_in_record" +VALIDATION_ERRORS = "validation_errors" + + +FIELDS = { + RUN_ID: StructField(RUN_ID, StringType(), nullable=False), + PIPELINE: StructField(PIPELINE, StringType(), nullable=False), + SOURCE: StructField(SOURCE, StringType(), nullable=False), + STATUS: StructField(STATUS, StringType(), nullable=False), + UPDATED: StructField(UPDATED, TimestampType(), nullable=False), +} + +PIPELINE_FIELDS = [FIELDS[RUN_ID], FIELDS[PIPELINE], FIELDS[SOURCE]] + +AUDIT_SCHEMA = { + # represents the whole run + RUN: StructType( + [ + *PIPELINE_FIELDS, + FIELDS[STATUS], + StructField(RECORDS_PROCESSED, LongType(), nullable=True), + StructField(START_TIME, TimestampType(), nullable=False), + StructField(END_TIME, TimestampType(), nullable=True), + StructField(ERROR, StringType(), nullable=True), + ] + ), + # checkpoint during processing to allow parsing to be restarted after an error + CHECKPOINT: StructType( + [ + *PIPELINE_FIELDS, + FIELDS[STATUS], + StructField(RECORDS_PROCESSED, LongType(), nullable=True), + StructField(LAST_ENTRY_ID, StringType(), nullable=True), + FIELDS[UPDATED], + ] + ), + # per-source metrics on data ingested + METRICS: StructType( + [ + *PIPELINE_FIELDS, + StructField(N_READ, IntegerType(), nullable=False), + StructField(N_VALID, IntegerType(), nullable=False), + StructField(N_INVALID, IntegerType(), nullable=False), + StructField(VALIDATION_ERRORS, ArrayType(StringType(), containsNull=False), nullable=False), + FIELDS[UPDATED], + ] + ), + # invalid data + REJECTS: StructType( + [ + *PIPELINE_FIELDS, + StructField(RAW_ROW, StringType(), nullable=False), + StructField(PARSED_ROW, StringType(), nullable=True), + StructField(ROW_ERRORS, ArrayType(StringType()), nullable=False), + StructField(TIMESTAMP, TimestampType(), nullable=False), + ] + ), +} + + +def current_run_expr(target: str = "t", source: str = "s") -> str: + """SQL expression for matching the current run in any of the audit tables.""" + return " AND ".join([f"{target or 't'}.{param} = {source or 's'}.{param}" for param in [RUN_ID, SOURCE, PIPELINE]]) + + +def match_run(run: PipelineRun) -> str: + """SQL expression for matching the current run in any of the audit tables. + + :param run: current pipeline run + :type run: PipelineRun + :return: SQL expression string + :rtype: str + """ + return " AND ".join([f"{p} = '{getattr(run, p)}'" for p in [RUN_ID, PIPELINE, SOURCE]]) diff --git a/src/cdm_data_loader_utils/core/__init__.py b/src/cdm_data_loader_utils/core/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/cdm_data_loader_utils/core/constants.py b/src/cdm_data_loader_utils/core/constants.py new file mode 100644 index 0000000..bfcf0ea --- /dev/null +++ b/src/cdm_data_loader_utils/core/constants.py @@ -0,0 +1,4 @@ +"""Constants used in various places throughout the codebase.""" + +INVALID_DATA_FIELD_NAME = "__invalid_data__" +D = "delta" diff --git a/src/cdm_data_loader_utils/core/pipeline_run.py b/src/cdm_data_loader_utils/core/pipeline_run.py new file mode 100644 index 0000000..1f794a7 --- /dev/null +++ b/src/cdm_data_loader_utils/core/pipeline_run.py @@ -0,0 +1,13 @@ +"""Pipeline run class.""" + +from dataclasses import dataclass + + +@dataclass(frozen=True) +class PipelineRun: + """Dataclass for capturing ingestion run information.""" + + run_id: str + pipeline: str + source_path: str + namespace: str diff --git a/src/cdm_data_loader_utils/readers/__init__.py b/src/cdm_data_loader_utils/readers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/cdm_data_loader_utils/readers/dsv.py b/src/cdm_data_loader_utils/readers/dsv.py new file mode 100644 index 0000000..bcd2db0 --- /dev/null +++ b/src/cdm_data_loader_utils/readers/dsv.py @@ -0,0 +1,130 @@ +"""Generic DSV file reader with validation of incoming data.""" + +from typing import Any + +from pyspark.sql import DataFrame, SparkSession +from pyspark.sql.types import StringType, StructField, StructType + +from cdm_data_loader_utils.core.constants import INVALID_DATA_FIELD_NAME +from cdm_data_loader_utils.utils.cdm_logger import get_cdm_logger, log_and_die + +# mapping of delimiters to format names (for logging) +# spark defaults to separating on commas if nothing is specified +FORMAT_NAME = {None: "CSV", ",": "CSV", "\t": "TSV"} + +# schema field to catch input errors +INVALID_DATA_FIELD = StructField(INVALID_DATA_FIELD_NAME, StringType(), nullable=True) + +# read modes +PERMISSIVE = "PERMISSIVE" +FAILFAST = "FAILFAST" +DROP = "DROPMALFORMED" + +# default options: enforce schema, catch parse errors in INVALID_DATA_FIELD_NAME column +DEFAULT_DSV_OPTIONS = { + "inferSchema": False, + "enforceSchema": True, + "mode": PERMISSIVE, + "columnNameOfCorruptRecord": INVALID_DATA_FIELD_NAME, +} + + +logger = get_cdm_logger() + + +def get_format_name(delimiter: str | None) -> str: + """Get the nice name of the format being parsed, given the string used as delimiter.""" + return FORMAT_NAME.get(delimiter, "DSV") + + +def read( + spark: SparkSession, + path: str, + schema_fields: list[StructField], + options: dict[str, Any] | None = None, +) -> DataFrame: + """Read in a delimiter-separated file with spark. + + :param spark: spark sesh + :type spark: SparkSession + :param path: location of the file to parse + :type path: str + :param schema_fields: list of StructFields describing the expected input + :type schema_fields: list[StructField] + :param options: dictionary of options + :type options: dict[str, Any] + :return: dataframe of parsed rows + :rtype: DataFrame + """ + if not isinstance(schema_fields, list) or not all(isinstance(field, StructField) for field in schema_fields): + log_and_die("schema_fields must be specified as a list of StructFields", TypeError) + + if not options: + options = {} + + dsv_schema = StructType([*schema_fields, INVALID_DATA_FIELD]) + dsv_options = { + **DEFAULT_DSV_OPTIONS, + **options, + } + + if dsv_options["mode"] not in (PERMISSIVE, FAILFAST): + msg = "The only permitted read modes are PERMISSIVE and FAILFAST." + log_and_die(msg, ValueError) + + format_name = get_format_name(options.get("delimiter", options.get("sep"))) + + try: + df = spark.read.options(**dsv_options).csv(path, schema=dsv_schema) + except Exception: + # Log the full stack trace and re-raise to be handled by the caller + logger.exception("Failed to load %s from %s", format_name, path) + raise + + # count will not trigger an error even if in FAILFAST mode and all records are corrupt. + logger.info("Loaded %d %s records from %s", df.count(), format_name, path) + return df + + +def read_tsv( + spark: SparkSession, path: str, schema_fields: list[StructField], options: dict[str, Any] | None = None +) -> DataFrame: + """Shortcut for reading in a tab-separated file. + + :param spark: spark sesh + :type spark: SparkSession + :param path: location of the file to parse + :type path: str + :param schema_fields: list of StructFields describing the expected input + :type schema_fields: list[StructField] + :param options: dictionary of options + :type options: dict[str, Any] + :return: dataframe of parsed rows + :rtype: DataFrame + """ + if not options: + options = {} + options["separator"] = "\t" + return read(spark, path, schema_fields, options) + + +def read_csv( + spark: SparkSession, path: str, schema_fields: list[StructField], options: dict[str, Any] | None = None +) -> DataFrame: + """Shortcut for reading in a comma-separated file. + + :param spark: spark sesh + :type spark: SparkSession + :param path: location of the file to parse + :type path: str + :param schema_fields: list of StructFields describing the expected input + :type schema_fields: list[StructField] + :param options: dictionary of options + :type options: dict[str, Any] + :return: dataframe of parsed rows + :rtype: DataFrame + """ + if not options: + options = {} + options["separator"] = "," + return read(spark, path, schema_fields, options) diff --git a/src/cdm_data_loader_utils/utils/cdm_logger.py b/src/cdm_data_loader_utils/utils/cdm_logger.py new file mode 100644 index 0000000..e001f2e --- /dev/null +++ b/src/cdm_data_loader_utils/utils/cdm_logger.py @@ -0,0 +1,116 @@ +""" +Provides structured logging with contextual metadata for CDM data import pipelines. +""" + +import logging +import logging.handlers +import os +import sys +from pathlib import Path + +DEFAULT_LOGGER_NAME = "cdm_data_loader" + +GENERIC_ERROR_MESSAGE = "An error of unknown origin occurred." + +LOG_FILENAME = "cdm_data_loader.log" +MAX_LOG_FILE_SIZE = 2**30 # 1 GiB +MAX_LOG_BACKUPS = 5 + + +# TODO: adopt logging config, set just once +LOGGING_CONFIG = { + "root": {"name": "cdm_data_loader", "level": "INFO", "handlers": ["console", "file"]}, + "version": 1, + "handlers": { + "console": { + "class": "logging.StreamHandler", + "formatter": "json", + "level": "INFO", + "stream": "ext://sys.stdout", + }, + "file": { + "class": "logging.handlers.RotatingFileHandler", + "formatter": "json", + "filename": LOG_FILENAME, + "maxBytes": MAX_LOG_FILE_SIZE, + "backupCount": MAX_LOG_BACKUPS, + }, + }, + "formatters": { + "json": { + "format": '{"time": "%(asctime)s", "level": "%(levelname)s", "module": "%(module)s", "msg": "%(message)s"}' + } + }, +} + + +def get_cdm_logger( + logger_name: str | None = None, log_level: str | None = None, log_dir: str | None = None +) -> logging.Logger: + """Initialise the logger for the module. + + If the logger name is not set, the default name "cdm_data_loader" will be used. + + :param logger_name: name for the logger, defaults to None + :type logger_name: str | None, optional + :param log_level: logger level, defaults to None + :type log_level: str | None, optional + :param log_dir: directory to save log files to, optional. If no directory is specified, logs will just be emitted to the console. + :type log_dir: str | None + :return: initialised logger + :rtype: logging.Logger + """ + if not logger_name: + logger_name = DEFAULT_LOGGER_NAME + # Always get the same logger by name + logger = logging.getLogger(logger_name) + + # Determine log level (argument > env var > default) + effective_log_level = (log_level or os.getenv("LOG_LEVEL", "INFO")).upper() + logger.setLevel(getattr(logging, effective_log_level, logging.DEBUG)) + + # JSON-style structured formatter + formatter = logging.Formatter( + '{"time": "%(asctime)s", "level": "%(levelname)s", "module": "%(module)s", "msg": "%(message)s"}' + ) + + # Console handler + ch = logging.StreamHandler(sys.stdout) + ch.setFormatter(formatter) + logger.addHandler(ch) + + if log_dir: + log_dir_path = Path(log_dir) + if not log_dir_path.exists() and log_dir_path.is_dir(): + msg = f"{log_dir} does not exist or is not a directory." + raise FileNotFoundError(msg) + # Add the log message handler to the logger + file_handler = logging.handlers.RotatingFileHandler( + LOG_FILENAME, maxBytes=MAX_LOG_FILE_SIZE, backupCount=MAX_LOG_BACKUPS + ) + logger.addHandler(file_handler) + + return logger + + +def log_and_die(error_msg: str, error_class: type[Exception], logger_name: str | None = None) -> None: + """Log an error message and then raise the error. + + :param error_msg: error message string + :type error_msg: str + :param error_class: class of error to throw + :type error_class: type[Exception] + :param logger_name: name of the logger to use, defaults to None + :type logger_name: str | None, optional + """ + logger = get_cdm_logger(logger_name) + + if not error_msg: + logger.warning("No error supplied to log_and_die. Using generic error message.") + error_msg = GENERIC_ERROR_MESSAGE + + if not isinstance(error_class, type) or not issubclass(error_class, BaseException): + error_class = RuntimeError + + logger.error(error_msg) + raise error_class(error_msg) diff --git a/src/cdm_data_loader_utils/utils/download/__init__.py b/src/cdm_data_loader_utils/utils/download/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/cdm_data_loader_utils/utils/download/async_client.py b/src/cdm_data_loader_utils/utils/download/async_client.py new file mode 100644 index 0000000..89e7904 --- /dev/null +++ b/src/cdm_data_loader_utils/utils/download/async_client.py @@ -0,0 +1,213 @@ +"""Asynchronous file download client. + +Usage: + +# initialise a download client that downloads files in chunks of 1024 bytes and retries the downlooad +# three times in case of connection/timeout errors +async_client = AsyncFileDownloader(max_attempts=3, chunk_size=1024) + +# output_path will be the path to the saved file +output_path = await async_client.download( + "https://example.com/file.txt", + Path("/path") / "to" / "save" / "file.txt"), + expected_checksum="some_checksum", + checksum_fn="sha512", + extra_headers={ + "If-None-Match": "abc", + "If-Modified-Since": "Wed, 21 Oct 2015 07:28:00 GMT" + }) + +""" + +import asyncio +import logging +from pathlib import Path +from typing import Any + +import httpx +from tenacity import ( + AsyncRetrying, + retry_if_exception_type, + stop_after_attempt, + wait_exponential, +) + +from cdm_data_loader_utils.utils.download.core import ( + DownloadCore, + DownloadError, + NonRetryableDownloadError, +) +from cdm_data_loader_utils.utils.cdm_logger import get_cdm_logger + +logger: logging.Logger = get_cdm_logger() + + +def get_async_httpx_client() -> httpx.AsyncClient: + """Get a basic client for executing http requests.""" + return httpx.AsyncClient( + timeout=httpx.Timeout(30.0), + limits=httpx.Limits( + max_connections=20, + max_keepalive_connections=10, + ), + follow_redirects=True, + ) + + +class AsyncFileDownloader: + """ + Asynchronous downloader interface. + """ + + RETRYABLE_EXCEPTIONS = ( + httpx.TimeoutException, + httpx.TransportError, + DownloadError, + ) + + def __init__( # noqa: PLR0913 + self, + client: httpx.AsyncClient | None = None, + max_attempts: int = 5, + min_backoff: int = 1, + max_backoff: int = 30, + chunk_size: int = 8192, + max_concurrency: int | None = None, + ) -> None: + """Initialise an async download client. + + :param client: an httpx.Client object, defaults to None + :type client: httpx.Client | None, optional + :param max_attempts: how many times to retry the request defaults to 5 + :type max_attempts: int, optional + :param min_backoff: minimum backoff for retries, defaults to 1 + :type min_backoff: int, optional + :param max_backoff: maximum backoff for retries, defaults to 30 + :type max_backoff: int, optional + :param chunk_size: chunk size for the downloader, defaults to 8192 + :type chunk_size: int, optional + :param max_concurrency: maximum concurrency for the downloader, defaults to None + :type max_concurrency: int, optional + """ + self.client = client or get_async_httpx_client() + self.chunk_size = chunk_size + self.semaphore = asyncio.Semaphore(max_concurrency) if max_concurrency else None + + self._retry = AsyncRetrying( + retry=retry_if_exception_type(self.RETRYABLE_EXCEPTIONS), + stop=stop_after_attempt(max_attempts), + wait=wait_exponential( + min=min_backoff, + max=max_backoff, + ), + reraise=True, + ) + + async def download( + self, + url: str, + destination: str | Path, + expected_checksum: str | None = None, + checksum_fn: str | None = "sha256", + extra_headers: dict[str, Any] | None = None, + ) -> Path | None: + """Download a file from ``url`` to ``destination`` on disk. + + Returns the file path if successful; None otherwise. + 304 / Not Modified responses return None. + + :param url: URL to download from + :type url: str + :param destination: where to save the file to + :type destination: str | Path + :param expected_checksum: expected checksum (if known), defaults to None + :type expected_checksum: str | None, optional + :param checksum_fn: function used for calculating the checksum, defaults to "sha256" + :type checksum_fn: str, optional + :param extra_headers: allow extra headers to be passed, defaults to None + :type last_modified: dict[str, Any | None, optional + :return: either the path to the downloaded file or None if no file was downloaded + :rtype: Path | None + """ + destination, checksum_fn, extra_headers = DownloadCore.validate_args(destination, checksum_fn, extra_headers) + + if self.semaphore: + async with self.semaphore: + return await self._download_with_retry( + url, + destination, + expected_checksum, + checksum_fn, + extra_headers, + ) + + return await self._download_with_retry( + url, + destination, + expected_checksum, + checksum_fn, + extra_headers, + ) + + async def _download_with_retry(self, *args) -> Path | None: + async for attempt in self._retry: + with attempt: + return await self._download_once(*args) + # this should never be raised under normal circumstances + # tenacity should never exhaust silently + msg = "Iterator exhausted, unreachable code reached!" + raise RuntimeError(msg) + + async def _download_once( + self, + url: str, + destination: Path, + expected_checksum: str | None, + checksum_fn: str, + extra_headers: dict[str, Any], + ) -> Path | None: + """Core download function. + + :param url: URL to download from + :type url: str + :param destination: where to save the file to + :type destination: Path + :param expected_checksum: expected checksum (if known), defaults to None + :type expected_checksum: str | None, optional + :param checksum_fn: function used for calculating the checksum + :type checksum_fn: str + :param extra_headers: any extra headers to pass to the request + :type extra_headers: dict[str, Any] + :raises DownloadError: for unrecoverable download errors + :raises ChecksumMismatchError: if the checksum does not match expected_checksum + :return: either the path to the downloaded file or None if no file was downloaded + :rtype: Path | None + """ + try: + async with self.client.stream("GET", url, headers=extra_headers) as response: + # check the response - should the download continue? + if not DownloadCore.validate_response(response): + logger.info("%s: resource has not been modified", url, extra={"url": url}) + return None + + chunks = response.aiter_bytes(chunk_size=self.chunk_size) + + await DownloadCore.write_and_hash_async( + url, + destination, + chunks, + expected_checksum=expected_checksum, + checksum_fn=checksum_fn, + ) + + except NonRetryableDownloadError as exc: + logger.exception("%s: %s; retry not possible", url, exc.args[0], extra={"url": url}) + raise + + except Exception as exc: + logger.exception("%s: %s; retry possible", url, exc.args[0], extra={"url": url}) + raise DownloadError(str(exc)) from exc + + logger.info("%s: download successful", url, extra={"path": str(destination)}) + + return destination diff --git a/src/cdm_data_loader_utils/utils/download/core.py b/src/cdm_data_loader_utils/utils/download/core.py new file mode 100644 index 0000000..819b83b --- /dev/null +++ b/src/cdm_data_loader_utils/utils/download/core.py @@ -0,0 +1,188 @@ +"""File downloader with tenacity for retry support.""" + +import hashlib +import logging +from collections.abc import AsyncIterable, Iterable +from pathlib import Path +from typing import Any + +import httpx + +from cdm_data_loader_utils.utils.cdm_logger import get_cdm_logger, log_and_die + +logger: logging.Logger = get_cdm_logger() + + +class DownloadError(Exception): + """Retryable download error.""" + + +class NonRetryableDownloadError(Exception): + """Retryable download error.""" + + +class ChecksumMismatchError(NonRetryableDownloadError): + """Checksum validation failed.""" + + +class DownloadCore: + """ + HTTP file downloader with retries and checksum testing. + """ + + RETRYABLE_EXCEPTIONS = ( + httpx.TimeoutException, + httpx.TransportError, + DownloadError, + ) + + @staticmethod + def validate_args( + destination: str | Path, + checksum_fn: str | None = None, + extra_headers: dict[str, Any] | None = None, + ) -> tuple[Path, str, dict[str, Any]]: + """Validate download arguments, apply defaults, and convert them to the appropriate format. + + If no checksum function is supplied, it will be set to "sha256". + + :param destination: location to save file to + :type destination: str | Path + :param checksum_fn: function for calculating file checksum + :type checksum_fn: str | None, optional + :param extra_headers: extra headers to add to the httpx request, defaults to None + :type extra_headers: dict[str, Any] | None, optional + :return: arguments spruced up and in shape! + :rtype: tuple[Path, str, dict[str, Any]] + """ + if not checksum_fn: + checksum_fn = "sha256" + + # shake hashing algorithms require a length for the hexdigest => too much faff, error out + if checksum_fn not in hashlib.algorithms_available or checksum_fn.startswith("shake"): + log_and_die(f"Hashing algorithm {checksum_fn} not supported.", ValueError) + + destination = Path(destination) + destination.parent.mkdir(parents=True, exist_ok=True) + + if not extra_headers: + extra_headers = {} + + return (destination, checksum_fn, extra_headers) + + @staticmethod + def validate_response(response: httpx.Response) -> bool: + """Check the response from the server and act accordingly.""" + status = response.status_code + + if status == 304: # noqa: PLR2004 + return False + + # successful response + if 200 <= status < 300: # noqa: PLR2004 + return True + + # client error + if 400 <= status < 500: # noqa: PLR2004 + msg = f"Client error: {status} {response.reason_phrase}" + raise NonRetryableDownloadError(msg) + + # server errors + msg = f"Server error: {status} {response.reason_phrase}" + raise DownloadError(msg) + + @staticmethod + def check_hash( + url: str, + expected_checksum: str, + checksum_fn: str, + hash_obj, #: hashlib._Hash, + ) -> None: + """Compare the expected to actual checksum. + + :param url: download URL + :type url: str + :param expected_checksum: expected checksum + :type expected_checksum: str + :param checksum_fn: checksum algorithm + :type checksum_fn: str + :param hash_obj: hash object for calculating checksum + :type hash_obj: bool + :raises ChecksumMismatchError: if the checksum is incorrect + """ + if hash_obj: + # check the checksum matches expectations + actual = hash_obj.hexdigest() + if actual.lower() != expected_checksum.lower(): + msg = f"{url}: Checksum mismatch: expected={expected_checksum}, actual={actual}" + raise ChecksumMismatchError(msg) + logger.info("%s: %s checksum matches", url, checksum_fn) + + @staticmethod + def write_and_hash( + url: str, + destination: Path, + chunks: Iterable[bytes], + expected_checksum: str | None, + checksum_fn: str, + ) -> None: + """Write downloaded data to disk and accrue data for calculating the checksum of the download. + + :param url: URL to download from + :type url: str + :param destination: where to save the file to + :type destination: Path + :param chunks: iterable chunks of downloaded data + :type chunks: Iterable[bytes] + :param expected_checksum: expected checksum (if known), defaults to None + :type expected_checksum: str | None, optional + :param checksum_fn: function used for calculating the checksum, defaults to "sha256" + :type checksum_fn: str, optional + :raises ChecksumMismatchError: if the checksum of the downloaded data does not match the expected checksum. + """ + hash_obj = hashlib.new(checksum_fn) if expected_checksum else None + + with destination.open("wb") as fh: + for chunk in chunks: + fh.write(chunk) + if hash_obj: + hash_obj.update(chunk) + + # include expected_checksum to stop the typechecker complaining + if hash_obj and expected_checksum: + DownloadCore.check_hash(url, expected_checksum, checksum_fn, hash_obj) + + @staticmethod + async def write_and_hash_async( + url: str, + destination: Path, + chunks: AsyncIterable[bytes], + expected_checksum: str | None, + checksum_fn: str, + ) -> None: + """Write downloaded data to disk and accrue data for calculating the checksum of the download. + + :param url: URL to download from + :type url: str + :param destination: where to save the file to + :type destination: Path + :param chunks: iterable chunks of downloaded data + :type chunks: AsyncIterable[bytes] + :param expected_checksum: expected checksum (if known), defaults to None + :type expected_checksum: str | None, optional + :param checksum_fn: function used for calculating the checksum, defaults to "sha256" + :type checksum_fn: str, optional + :raises ChecksumMismatchError: if the checksum of the downloaded data does not match the expected checksum. + """ + hash_obj = hashlib.new(checksum_fn) if expected_checksum else None + + # NOTE: file I/O is sync, but chunk iteration must be async + with destination.open("wb") as fh: + async for chunk in chunks: + fh.write(chunk) + if hash_obj: + hash_obj.update(chunk) + + # include expected_checksum to stop the typechecker complaining + if hash_obj and expected_checksum: + DownloadCore.check_hash(url, expected_checksum, checksum_fn, hash_obj) diff --git a/src/cdm_data_loader_utils/utils/download/sync_client.py b/src/cdm_data_loader_utils/utils/download/sync_client.py new file mode 100644 index 0000000..bf2192f --- /dev/null +++ b/src/cdm_data_loader_utils/utils/download/sync_client.py @@ -0,0 +1,189 @@ +"""Synchronous file download client. + +Usage: + +# initialise a download client that downloads files in chunks of 1024 bytes and retries the downlooad +# three times in case of connection/timeout errors +sync_client = FileDownloader(max_attempts=3, chunk_size=1024) + +# output_path will be the path to the saved file +output_path = sync_client.download( + "https://example.com/file.txt", + Path("/path") / "to" / "save" / "file.txt"), + expected_checksum="some_checksum", + checksum_fn="sha512", + extra_headers={ + "If-None-Match": "abc", + "If-Modified-Since": "Wed, 21 Oct 2015 07:28:00 GMT" + }) + +""" + +import logging +from pathlib import Path +from typing import Any + +import httpx +from tenacity import ( + before_sleep_log, + retry, + retry_if_exception_type, + stop_after_attempt, + wait_exponential, +) + +from cdm_data_loader_utils.utils.download.core import ( + DownloadCore, + DownloadError, + NonRetryableDownloadError, +) +from cdm_data_loader_utils.utils.cdm_logger import get_cdm_logger + +logger: logging.Logger = get_cdm_logger() + + +def get_httpx_client() -> httpx.Client: + """Get a basic client for executing http requests.""" + return httpx.Client( + timeout=httpx.Timeout(30.0), + limits=httpx.Limits( + max_connections=20, + max_keepalive_connections=10, + ), + follow_redirects=True, + ) + + +class FileDownloader: + """ + Synchronous downloader interface. + """ + + RETRYABLE_EXCEPTIONS = ( + httpx.TimeoutException, + httpx.TransportError, + DownloadError, + ) + + def __init__( + self, + client: httpx.Client | None = None, + max_attempts: int = 5, + min_backoff: int = 1, + max_backoff: int = 30, + chunk_size: int = 8192, + ) -> None: + """Initialise a synchronous download client. + + :param client: an httpx.Client object, defaults to None + :type client: httpx.Client | None, optional + :param max_attempts: how many times to retry the request defaults to 5 + :type max_attempts: int, optional + :param min_backoff: minimum backoff for retries, defaults to 1 + :type min_backoff: int, optional + :param max_backoff: maximum backoff for retries, defaults to 30 + :type max_backoff: int, optional + :param chunk_size: chunk size for the downloader, defaults to 8192 + :type chunk_size: int, optional + """ + self.client = client or get_httpx_client() + self.chunk_size = chunk_size + + self._retry = retry( + retry=retry_if_exception_type(self.RETRYABLE_EXCEPTIONS), + stop=stop_after_attempt(max_attempts), + wait=wait_exponential( + min=min_backoff, + max=max_backoff, + ), + reraise=True, + before_sleep=before_sleep_log(logger, logging.WARNING), + ) + + def download( + self, + url: str, + destination: str | Path, + expected_checksum: str | None = None, + checksum_fn: str | None = None, + extra_headers: dict[str, Any] | None = None, + ) -> Path | None: + """Download a file from ``url`` to ``destination`` on disk. + + Returns the file path if successful; None otherwise. + 304 / Not Modified responses return None. + + :param url: URL to download from + :type url: str + :param destination: where to save the file to + :type destination: str | Path + :param expected_checksum: expected checksum (if known), defaults to None + :type expected_checksum: str | None, optional + :param checksum_fn: function used for calculating the checksum. Set to "sha256" if not supplied. + :type checksum_fn: str, optional + :param extra_headers: allow extra headers to be passed, defaults to None + :type last_modified: dict[str, Any | None, optional + :return: either the path to the downloaded file or None if no file was downloaded + :rtype: Path | None + """ + destination, checksum_fn, extra_headers = DownloadCore.validate_args(destination, checksum_fn, extra_headers) + + @self._retry + def _once() -> Path | None: + return self._download_once(url, destination, expected_checksum, checksum_fn, extra_headers) + + return _once() + + def _download_once( + self, + url: str, + destination: Path, + expected_checksum: str | None, + checksum_fn: str, + extra_headers: dict[str, Any], + ) -> Path | None: + """Core synchronous download function. + + :param url: URL to download from + :type url: str + :param destination: where to save the file to + :type destination: Path + :param expected_checksum: expected checksum (if known), defaults to None + :type expected_checksum: str | None, optional + :param checksum_fn: function used for calculating the checksum, defaults to "sha256" + :type checksum_fn: str, optional + :param extra_headers: any extra headers to pass to the request, defaults to None + :type extra_headers: dict[str, Any] | None, optional + :raises DownloadError: for unrecoverable download errors + :raises ChecksumMismatchError: if the checksum does not match expected_checksum + :return: either the path to the downloaded file or None if no file was downloaded + :rtype: Path | None + """ + try: + with self.client.stream("GET", url, headers=extra_headers) as response: + continue_dl = DownloadCore.validate_response(response) + if not continue_dl: + logger.info("%s: resource has not been modified", url, extra={"url": url}) + return None + + chunks = response.iter_bytes(chunk_size=self.chunk_size) + + DownloadCore.write_and_hash( + url, + destination, + chunks, + expected_checksum=expected_checksum, + checksum_fn=checksum_fn, + ) + + except NonRetryableDownloadError as exc: + logger.exception("%s: %s; retry not possible", url, exc.args[0], extra={"url": url}) + raise + + except Exception as exc: + logger.exception("%s: %s; retry possible", url, exc.args[0], extra={"url": url}) + raise DownloadError(str(exc)) from exc + + logger.info("%s: download successful", url, extra={"path": str(destination)}) + + return destination diff --git a/src/cdm_data_loader_utils/utils/gz.py b/src/cdm_data_loader_utils/utils/gz.py new file mode 100644 index 0000000..332deb8 --- /dev/null +++ b/src/cdm_data_loader_utils/utils/gz.py @@ -0,0 +1,72 @@ +"""File compression utils.""" + +import gzip +import shutil +from pathlib import Path + +import click + +from cdm_data_loader_utils.utils.cdm_logger import get_cdm_logger + +logger = get_cdm_logger() + + +def compress_files(directory: Path | str, file_glob: str) -> None: + """Compress all files matching a certain pattern in a directory. + + :param directory: directory to look in + :type directory: Path | str + :param file_glob: pattern to match + :type file_glob: str + :raises ValueError: if the directory is not found + """ + if not isinstance(directory, Path): + directory = Path(directory) + + if not directory.exists() or not directory.is_dir(): + msg = f"Directory {directory!s} not found: check the path is correct" + raise FileNotFoundError(msg) + + to_compress = list(directory.glob(file_glob)) + logger.info("Found %d file(s) to compress", len(to_compress)) + if not to_compress: + return + + for f in to_compress: + compress_file(f) + logger.info("Work complete!") + + +def compress_file(file: Path) -> None: + """Compress a file using gzip. + + :param file: file to compress + :type file: Path + """ + if Path(f"{file!s}.gz").exists(): + logger.info("Found existing file %s: skipping gz operation", str(file) + ".gz") + return + + with file.open("rb") as f_in, gzip.open(str(file) + ".gz", "wb") as f_out: + shutil.copyfileobj(f_in, f_out) + logger.info("Created output file %s.gz", str(file)) + + +@click.command() +@click.option("--source", "-i", required=True, help="input file(s) to process") +@click.option("--file-glob", "-f", default="*", help="glob for files in a directory") +def main(source: str, file_glob: str) -> None: + """Compress a file or directory from the command line.""" + source_path = Path(source) + if not source_path.exists(): + msg = f"Path {source} does not exist" + raise RuntimeError(msg) + + if source_path.is_dir(): + compress_files(source_path, file_glob or "*") + else: + compress_file(source_path) + + +if __name__ == "__main__": + main() diff --git a/src/cdm_data_loader_utils/utils/helpers.py b/src/cdm_data_loader_utils/utils/helpers.py new file mode 100644 index 0000000..97f36b6 --- /dev/null +++ b/src/cdm_data_loader_utils/utils/helpers.py @@ -0,0 +1,38 @@ +"""Misc database-related helpers.""" + + +def _ensembl_type(xref: str) -> str: + """Given an Ensembl ID, return the likely type.""" + prefixes = { + "ENST": "transcript", + "ENSP": "protein sequence", + "ENSG": "gene sequence", + "ENSE": "exon", + "ENSFM": "protein family", + "ENSGT": "gene tree", + "ENSR": "regulatory feature", + } + + return prefixes.get(xref[0:4], prefixes.get(xref[0:5], "sequence")) + + +def _refseq_type(xref: str) -> str | None: + prefixes = { + "AC_": "Genomic: complete genomic molecule, usually alternate assembly", + "NC_": "Genomic: complete genomic molecule, usually reference assembly", + "NG_": "Genomic: incomplete genomic region", + "NT_": "Genomic: contig or scaffold, clone-based or Whole Genome Shotgun sequence data", + "NW_": "Genomic: contig or scaffold, primarily Whole Genome Shotgun sequence data", + "NZ_": "Genomic: complete genomes and unfinished WGS data; an ordered collection of WGS sequence for a genome", + "NM_": "mRNA: protein-coding transcripts (usually curated)", + "NR_": "RNA: non-protein-coding transcripts", + "XM_": "mRNA: predicted model protein-coding transcript (computed)", + "XR_": "RNA: predicted model non-protein-coding transcript (computed)", + "AP_": "Protein: annotated on AC_ alternate assembly", + "NP_": "Protein: associated with an NM_ or NC_ accession", + "YP_": "Protein: annotated on genomic molecules without an instantiated transcript record (computed)", + "XP_": "Protein: predicted model, associated with an XM_ accession (computed)", + "WP_": "Protein: non-redundant across multiple strains and species", + } + first_three_letters = xref[0:3] + return prefixes.get(first_three_letters) diff --git a/src/cdm_data_loader_utils/utils/spark_delta.py b/src/cdm_data_loader_utils/utils/spark_delta.py index f5f3e16..35e5b75 100644 --- a/src/cdm_data_loader_utils/utils/spark_delta.py +++ b/src/cdm_data_loader_utils/utils/spark_delta.py @@ -4,9 +4,9 @@ from berdl_notebook_utils.spark.database import create_namespace_if_not_exists from pyspark.sql import DataFrame, DataFrameWriter, SparkSession -from cdm_data_loader_utils.utils.logging import get_logger +from cdm_data_loader_utils.utils.cdm_logger import get_cdm_logger -logger = get_logger() +logger = get_cdm_logger() APPEND = "append" OVERWRITE = "overwrite" @@ -209,9 +209,6 @@ def write_delta(spark: SparkSession, sdf: DataFrame, delta_ns: str, table: str, raise -DELTA_METHOD = True - - def write_delta_to_file( spark: SparkSession, sdf: DataFrame, delta_ns: str, table: str, writer: DataFrameWriter, data_dir: str ) -> None: diff --git a/tests/conftest.py b/tests/conftest.py index 8c3641e..a232a83 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,48 +1,44 @@ """Global configuration settings for tests.""" +import datetime +from collections.abc import Generator +from copy import deepcopy from pathlib import Path from typing import Any import pytest +from pyspark.sql import SparkSession, DataFrame +from pyspark.sql.types import ( + ArrayType, + BooleanType, + DateType, + FloatType, + IntegerType, + StringType, + StructField, + StructType, +) -stats_output = { - "FW305-3-2-15-C-TSA1_scaffolds.fna": { - "scaffolds": 59, - "contigs": 61, - "gc_avg": 0.65985, - "gc_std": 0.02052, - "filename": "/home/runner/work/cdm-data-loader-utils/cdm-data-loader-utils/tests/data/FW305-3-2-15-C-TSA1/FW305-3-2-15-C-TSA1_scaffolds.fna", - }, - "FW305-C-112.1_scaffolds.fna": { - "scaffolds": 28, - "contigs": 31, - "gc_avg": 0.69368, - "gc_std": 0.03501, - "filename": "/home/runner/work/cdm-data-loader-utils/cdm-data-loader-utils/tests/data/FW305-C-112.1/FW305-C-112.1_scaffolds.fna", - }, -} - -checkm2_output = { - "FW305-3-2-15-C-TSA1_scaffolds": { - "checkm2_completeness": 99.99, - "checkm2_contamination": 1.09, - }, - "FW305-C-112.1_scaffolds": {"checkm2_completeness": None, "checkm2_contamination": 12.27}, -} - -RESULTS = { - "single": { - "stats": {"FW305-3-2-15-C-TSA1_scaffolds.fna": stats_output["FW305-3-2-15-C-TSA1_scaffolds.fna"]}, - "checkm2": {"FW305-3-2-15-C-TSA1_scaffolds": checkm2_output["FW305-3-2-15-C-TSA1_scaffolds"]}, - }, - "multi": {"stats": stats_output, "checkm2": checkm2_output}, -} +from cdm_data_loader_utils.audit.schema import ( + NAMESPACE, + PIPELINE, + ROW_ERRORS, + RUN_ID, + SOURCE, +) +from cdm_data_loader_utils.core.pipeline_run import PipelineRun +from cdm_data_loader_utils.readers.dsv import INVALID_DATA_FIELD +from cdm_data_loader_utils.utils.spark_delta import get_spark +SAVE_DIR = "spark.sql.warehouse.dir" -@pytest.fixture(scope="session") -def checkm2_stats_results() -> dict[str, Any]: - """Expected results from parsing checkm2 and bbmap stats files.""" - return RESULTS + +@pytest.fixture +def spark(tmp_path: Path) -> Generator[SparkSession, Any]: + """Generate a spark session with spark.sql.warehouse.dir set to the pytest temporary directory.""" + spark = get_spark("test_delta_app", local=True, delta_lake=True, override={SAVE_DIR: tmp_path}) + yield spark + spark.stop() @pytest.fixture(scope="session") @@ -51,12 +47,6 @@ def test_data_dir() -> Path: return Path("tests") / "data" -@pytest.fixture(scope="session") -def genome_paths_file() -> str: - """Input file for tests.""" - return "tests/data/genome_paths.json" - - @pytest.fixture(scope="session") def json_test_strings() -> dict[str, Any]: """A selection of JSON strings for testing.""" @@ -80,3 +70,365 @@ def json_test_strings() -> dict[str, Any]: "array_of_objects": '[{"key": "value"}]', "object": '{"key": "value"}', } + + +@pytest.fixture +def empty_df_schema() -> list[StructField]: + """List of fields corresponding to the empty dataframe.""" + return [ + StructField("name", StringType(), nullable=True), + StructField("id", IntegerType(), nullable=False), + ] + + +@pytest.fixture +def empty_df(spark: SparkSession, empty_df_schema: list[StructField]) -> Generator[DataFrame, Any]: + """Empty dataframe for testing usage.""" + df = spark.createDataFrame([], schema=StructType(empty_df_schema)) + yield df + assert df.schema == StructType(empty_df_schema) + + +# Various CSV permutations for testing +VALID = "valid_csv" +MISSING_REQUIRED = "invalid_csv_missing_required" +TYPE_MISMATCH = "invalid_csv_type_mismatch" +TOO_FEW_COLS = "invalid_csv_too_few_cols" +TOO_MANY_COLS = "invalid_csv_too_many_cols" +ALL_LINES = "all_lines" + + +@pytest.fixture(scope="session") +def csv_schema() -> list[StructField]: + """List of fields for parsing the various CSV snippets.""" + return [ + StructField("col1", IntegerType(), nullable=False), + StructField("col2", DateType(), nullable=False), + StructField("col3", FloatType(), nullable=False), + StructField("col4", BooleanType(), nullable=False), + StructField("col5", StringType(), nullable=False), + ] + + +@pytest.fixture(scope="session") +def valid_csv(test_data_dir: Path) -> Path: + """Valid CSV data. + + 1,20250301,1.2345,true,EcoCyc:EG10986-MONOMER + 2,20250201,0.2,false,MetaCyc:EG10986-MONOMER + 3,20250801,23,True,4261555 + 4,00010101,.1234,False,col5 + + """ + return test_data_dir / "dsv" / "valid.csv" + + +@pytest.fixture(scope="session") +def invalid_csv_missing_required(test_data_dir: Path) -> Path: + """CSV data with required fields missing. + + # correct number of cols, but some cols are empty + 1,,,,col5 + # missing leading cols + ,,2.345,True,col5 + # missing trailing cols + 3,20250531,23.45,, + # all missing + ,,,, + """ + return test_data_dir / "dsv" / "missing_required.csv" + + +@pytest.fixture(scope="session") +def invalid_csv_missing_required_annots() -> list[list[str]]: + """Generate the expected error annotations for the lines in invalid_csv_missing_required. + + :return: list of list of error strings + :rtype: list[list[str]] + """ + valid_invalid_fields = [[1, 0, 0, 0, 1], [0, 0, 1, 1, 1], [1, 1, 1, 0, 0], [0, 0, 0, 0, 0]] + return [[f"missing_required: col{n + 1}" for n in range(5) if not row[n]] for row in valid_invalid_fields] + + +@pytest.fixture(scope="session") +def invalid_csv_type_mismatch(test_data_dir: Path) -> Path: + """CSV data with incorrect data types. + + # Y, N, Y, N, Y + 1,2,3,4,5 + # N, N, Y, N, Y + 1.234,2.3456,3.45,4.5,5 + # N, N, N, Y, Y + true,false,true,false,true + # Y, Y, N, N, Y + 00200202,00200202,00200202,00200202,00200202 + """ + return test_data_dir / "dsv" / "type_mismatch.csv" + + +@pytest.fixture(scope="session") +def invalid_csv_too_few_cols(test_data_dir: Path) -> Path: + """CSV data containing rows with too few columns. + + # too few cols + 1 + 2,20250502,0.2345 + 3,,23.56,False + ,,, + """ + return test_data_dir / "dsv" / "too_few_cols.csv" + + +@pytest.fixture(scope="session") +def invalid_csv_too_many_cols(test_data_dir: Path) -> Path: + """CSV data containing rows with too many columns. + + # too many cols - all have 6 cols + ,,,,, + 2,20250710,col3,True,,col6 + # empty trailing + 3,20250101,,,, + # empty leading + ,,,,,col6 + """ + return test_data_dir / "dsv" / "too_many_cols.csv" + + +@pytest.fixture(scope="session") +def all_lines(test_data_dir: Path) -> Path: + """All the CSV lines in a single fixture!""" + return test_data_dir / "dsv" / "all_lines.csv" + + +@pytest.fixture(scope="session") +def annotated_df_schema(csv_schema: list[StructField]) -> StructType: + """The schema for the annotated dataframe produced by validating one of the CSV files above.""" + actual_csv_schema = list(csv_schema) + for r in actual_csv_schema: + r.nullable = True + + return StructType([*actual_csv_schema, INVALID_DATA_FIELD, StructField(ROW_ERRORS, ArrayType(StringType()))]) + + +@pytest.fixture(scope="session") +def annotated_df_data() -> list[dict[str, Any]]: + """The output of running all_lines (above) through the dsv parser and df_nullable_fields validator.""" + return deepcopy( + [ + { + "col1": 1, + "col2": datetime.date(2025, 3, 1), + "col3": 1.2345000505447388, + "col4": True, + "col5": "EcoCyc:EG10986-MONOMER", + "__invalid_data__": None, + "errors_in_record": [], + }, + { + "col1": 2, + "col2": datetime.date(2025, 2, 1), + "col3": 0.20000000298023224, + "col4": False, + "col5": "MetaCyc:EG10986-MONOMER", + "__invalid_data__": None, + "errors_in_record": [], + }, + { + "col1": 3, + "col2": datetime.date(2025, 8, 1), + "col3": 23.0, + "col4": True, + "col5": "4261555", + "__invalid_data__": None, + "errors_in_record": [], + }, + { + "col1": 4, + "col2": datetime.date(1, 1, 1), + "col3": 0.1234000027179718, + "col4": False, + "col5": "col5", + "__invalid_data__": None, + "errors_in_record": [], + }, + { + "col1": 1, + "col2": None, + "col3": None, + "col4": None, + "col5": "col5", + "__invalid_data__": None, + "errors_in_record": ["missing_required: col2", "missing_required: col3", "missing_required: col4"], + }, + { + "col1": None, + "col2": None, + "col3": 2.3450000286102295, + "col4": True, + "col5": "col5", + "__invalid_data__": None, + "errors_in_record": ["missing_required: col1", "missing_required: col2"], + }, + { + "col1": 3, + "col2": datetime.date(2025, 5, 31), + "col3": 23.450000762939453, + "col4": None, + "col5": None, + "__invalid_data__": None, + "errors_in_record": ["missing_required: col4", "missing_required: col5"], + }, + { + "col1": None, + "col2": None, + "col3": None, + "col4": None, + "col5": None, + "__invalid_data__": None, + "errors_in_record": [ + "missing_required: col1", + "missing_required: col2", + "missing_required: col3", + "missing_required: col4", + "missing_required: col5", + ], + }, + { + "col1": None, + "col2": None, + "col3": None, + "col4": None, + "col5": None, + "__invalid_data__": ",,,,,", + "errors_in_record": ["parse_error"], + }, + { + "col1": 2, + "col2": datetime.date(2025, 7, 10), + "col3": None, + "col4": True, + "col5": None, + "__invalid_data__": "2,20250710,col3,True,,col6", + "errors_in_record": ["parse_error"], + }, + { + "col1": 3, + "col2": datetime.date(2025, 1, 1), + "col3": None, + "col4": None, + "col5": None, + "__invalid_data__": "3,20250101,,,,", + "errors_in_record": ["parse_error"], + }, + { + "col1": None, + "col2": None, + "col3": None, + "col4": None, + "col5": None, + "__invalid_data__": ",,,,,col6", + "errors_in_record": ["parse_error"], + }, + { + "col1": 1, + "col2": None, + "col3": None, + "col4": None, + "col5": None, + "__invalid_data__": "1", + "errors_in_record": ["parse_error"], + }, + { + "col1": 2, + "col2": datetime.date(2025, 5, 2), + "col3": 0.2345000058412552, + "col4": None, + "col5": None, + "__invalid_data__": "2,20250502,0.2345", + "errors_in_record": ["parse_error"], + }, + { + "col1": 3, + "col2": None, + "col3": 23.559999465942383, + "col4": False, + "col5": None, + "__invalid_data__": "3,,23.56,False", + "errors_in_record": ["parse_error"], + }, + { + "col1": None, + "col2": None, + "col3": None, + "col4": None, + "col5": None, + "__invalid_data__": ",,,", + "errors_in_record": ["parse_error"], + }, + { + "col1": 1, + "col2": None, + "col3": 3.0, + "col4": None, + "col5": "5", + "__invalid_data__": "1,2,3,4,5", + "errors_in_record": ["parse_error"], + }, + { + "col1": None, + "col2": None, + "col3": 3.450000047683716, + "col4": None, + "col5": "5", + "__invalid_data__": "1.234,2.3456,3.45,4.5,5", + "errors_in_record": ["parse_error"], + }, + { + "col1": None, + "col2": None, + "col3": None, + "col4": False, + "col5": "true", + "__invalid_data__": "true,false,true,false,true", + "errors_in_record": ["parse_error"], + }, + { + "col1": 200202, + "col2": datetime.date(20, 2, 2), + "col3": 200202.0, + "col4": None, + "col5": "00200202", + "__invalid_data__": "00200202,00200202,00200202,00200202,00200202", + "errors_in_record": ["parse_error"], + }, + ] + ) + + +@pytest.fixture(scope="session") +def annotated_df_errors(annotated_df_data: list[dict[str, Any]]) -> set[str]: + """Unique errors found in annotated_df_data.""" + list_of_errors = [] + for r in annotated_df_data: + list_of_errors.extend(r[ROW_ERRORS]) + + return set(list_of_errors) + + +# Audit-related stuff + +TEST_NS = "TEST_NS" +PIPELINE_RUN = {RUN_ID: "1234-5678-90", PIPELINE: "KeystoneXL", SOURCE: "/path/to/file"} +ALT_PIPELINE_RUN = {RUN_ID: "9876-5432-10", PIPELINE: "KeystoneXXXL", SOURCE: "/path/to/dir"} + + +@pytest.fixture(scope="package") +def pipeline_run() -> PipelineRun: + """Generate a pipeline run.""" + return PipelineRun(**{**PIPELINE_RUN, NAMESPACE: TEST_NS}) + + +@pytest.fixture(scope="package") +def alt_pipeline_run() -> PipelineRun: + """Generate a different pipeline run.""" + return PipelineRun(**{**ALT_PIPELINE_RUN, NAMESPACE: TEST_NS}) diff --git a/tests/data/dsv/all_lines.csv b/tests/data/dsv/all_lines.csv new file mode 100644 index 0000000..3baae40 --- /dev/null +++ b/tests/data/dsv/all_lines.csv @@ -0,0 +1,34 @@ +# all valid +1,20250301,1.2345,true,EcoCyc:EG10986-MONOMER +2,20250201,0.2,false,MetaCyc:EG10986-MONOMER +3,20250801,23,True,4261555 +4,00010101,.1234,False,col5 +# correct number of cols, cols empty +1,,,,col5 +# missing leading cols +,,2.345,True,col5 +# missing trailing cols +3,20250531,23.45,, +# all missing +,,,, +# too many cols - all have 6 cols +,,,,, +2,20250710,col3,True,,col6 +# empty trailing +3,20250101,,,, +# empty leading +,,,,,col6 +# too few cols +1 +2,20250502,0.2345 +3,,23.56,False +,,, +# CSV with incorrect types +# Y, N, Y, N, Y +1,2,3,4,5 +# N, N, Y, N, Y +1.234,2.3456,3.45,4.5,5 +# N, N, N, Y, Y +true,false,true,false,true +# Y, Y, N, N, Y +00200202,00200202,00200202,00200202,00200202 diff --git a/tests/data/dsv/missing_required.csv b/tests/data/dsv/missing_required.csv new file mode 100644 index 0000000..82a2187 --- /dev/null +++ b/tests/data/dsv/missing_required.csv @@ -0,0 +1,8 @@ +# correct number of cols, cols empty +1,,,,col5 +# missing leading cols +,,2.345,True,col5 +# missing trailing cols +3,20250531,23.45,, +# all missing +,,,, diff --git a/tests/data/dsv/too_few_cols.csv b/tests/data/dsv/too_few_cols.csv new file mode 100644 index 0000000..b4ff10a --- /dev/null +++ b/tests/data/dsv/too_few_cols.csv @@ -0,0 +1,5 @@ +# too few cols +1 +2,20250502,0.2345 +3,,23.56,False +,,, diff --git a/tests/data/dsv/too_many_cols.csv b/tests/data/dsv/too_many_cols.csv new file mode 100644 index 0000000..ba521a8 --- /dev/null +++ b/tests/data/dsv/too_many_cols.csv @@ -0,0 +1,7 @@ +# too many cols - all have 6 cols +,,,,, +2,20250710,col3,True,,col6 +# empty trailing +3,20250101,,,, +# empty leading +,,,,,col6 diff --git a/tests/data/dsv/type_mismatch.csv b/tests/data/dsv/type_mismatch.csv new file mode 100644 index 0000000..07d59d8 --- /dev/null +++ b/tests/data/dsv/type_mismatch.csv @@ -0,0 +1,9 @@ +# CSV with incorrect types +# Y, N, Y, N, Y +1,2,3,4,5 +# N, N, Y, N, Y +1.234,2.3456,3.45,4.5,5 +# N, N, N, Y, Y +true,false,true,false,true +# Y, Y, N, N, Y +00200202,00200202,00200202,00200202,00200202 diff --git a/tests/data/dsv/valid.csv b/tests/data/dsv/valid.csv new file mode 100644 index 0000000..3fb1d42 --- /dev/null +++ b/tests/data/dsv/valid.csv @@ -0,0 +1,5 @@ +# all valid +1,20250301,1.2345,true,EcoCyc:EG10986-MONOMER +2,20250201,0.2,false,MetaCyc:EG10986-MONOMER +3,20250801,23,True,4261555 +4,00010101,.1234,False,col5 diff --git a/tests/helpers.py b/tests/helpers.py new file mode 100644 index 0000000..2dcd24a --- /dev/null +++ b/tests/helpers.py @@ -0,0 +1,17 @@ +"""Utilities for running tests.""" + +from pyspark.sql import SparkSession +from pyspark.sql.types import StructType + + +def create_empty_delta_table( + spark: SparkSession, + db: str, + table: str, + schema: StructType, +) -> None: + """Create an empty delta table, initialising the db namespace first.""" + spark.sql(f"CREATE DATABASE IF NOT EXISTS {db}") + df = spark.createDataFrame([], schema) + df.write.format("delta").mode("error").saveAsTable(f"{db}.{table}") + assert df.count() == 0 diff --git a/tests/parsers/conftest.py b/tests/parsers/conftest.py new file mode 100644 index 0000000..fa41f7a --- /dev/null +++ b/tests/parsers/conftest.py @@ -0,0 +1,50 @@ +"""Global configuration settings for tests.""" + +from typing import Any + +import pytest + +stats_output = { + "FW305-3-2-15-C-TSA1_scaffolds.fna": { + "scaffolds": 59, + "contigs": 61, + "gc_avg": 0.65985, + "gc_std": 0.02052, + "filename": "/home/runner/work/cdm-data-loader-utils/cdm-data-loader-utils/tests/data/FW305-3-2-15-C-TSA1/FW305-3-2-15-C-TSA1_scaffolds.fna", + }, + "FW305-C-112.1_scaffolds.fna": { + "scaffolds": 28, + "contigs": 31, + "gc_avg": 0.69368, + "gc_std": 0.03501, + "filename": "/home/runner/work/cdm-data-loader-utils/cdm-data-loader-utils/tests/data/FW305-C-112.1/FW305-C-112.1_scaffolds.fna", + }, +} + +checkm2_output = { + "FW305-3-2-15-C-TSA1_scaffolds": { + "checkm2_completeness": 99.99, + "checkm2_contamination": 1.09, + }, + "FW305-C-112.1_scaffolds": {"checkm2_completeness": None, "checkm2_contamination": 12.27}, +} + +RESULTS = { + "single": { + "stats": {"FW305-3-2-15-C-TSA1_scaffolds.fna": stats_output["FW305-3-2-15-C-TSA1_scaffolds.fna"]}, + "checkm2": {"FW305-3-2-15-C-TSA1_scaffolds": checkm2_output["FW305-3-2-15-C-TSA1_scaffolds"]}, + }, + "multi": {"stats": stats_output, "checkm2": checkm2_output}, +} + + +@pytest.fixture(scope="session") +def genome_paths_file() -> str: + """Input file for tests.""" + return "tests/data/genome_paths.json" + + +@pytest.fixture(scope="session") +def checkm2_stats_results() -> dict[str, Any]: + """Expected results from parsing checkm2 and bbmap stats files.""" + return RESULTS diff --git a/tests/parsers/test_bbmap_stats.py b/tests/parsers/test_bbmap_stats.py index 20f9d38..8557502 100644 --- a/tests/parsers/test_bbmap_stats.py +++ b/tests/parsers/test_bbmap_stats.py @@ -7,7 +7,7 @@ import pytest from cdm_data_loader_utils.parsers.bbmap_stats import get_bbmap_stats -from tests.conftest import RESULTS +from tests.parsers.conftest import RESULTS def test_get_bbmap_stats_empty(tmp_path: Path) -> None: diff --git a/tests/parsers/test_checkm2.py b/tests/parsers/test_checkm2.py index 89645e2..0365ea1 100644 --- a/tests/parsers/test_checkm2.py +++ b/tests/parsers/test_checkm2.py @@ -6,7 +6,7 @@ import pytest from cdm_data_loader_utils.parsers.checkm2 import get_checkm2_data -from tests.conftest import RESULTS +from tests.parsers.conftest import RESULTS def test_get_checkm2_data_empty(tmp_path: Path) -> None: diff --git a/tests/readers/__init__.py b/tests/readers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/readers/test_dsv.py b/tests/readers/test_dsv.py new file mode 100644 index 0000000..987f7c3 --- /dev/null +++ b/tests/readers/test_dsv.py @@ -0,0 +1,129 @@ +"""Tests for parser error handling, schema compliance, and so on.""" + +import logging +from typing import Any +from unittest.mock import MagicMock + +import pytest +from py4j.protocol import Py4JJavaError +from pyspark.errors import AnalysisException +from pyspark.sql import DataFrame, SparkSession +from pyspark.sql.types import IntegerType, StringType, StructField, StructType + +from cdm_data_loader_utils.readers.dsv import read +from tests.conftest import ALL_LINES, MISSING_REQUIRED, TOO_FEW_COLS, TOO_MANY_COLS, TYPE_MISMATCH, VALID + +PERMISSIVE = "PERMISSIVE" +DROP = "DROPMALFORMED" +FAILFAST = "FAILFAST" + +INGEST_MODES = [PERMISSIVE, DROP, FAILFAST] + +TEST_SCHEMA_FIELD = StructField("what", StringType(), nullable=False) + + +@pytest.mark.parametrize( + "schema_fields", + [ + # valid schema but not the right format + StructType([TEST_SCHEMA_FIELD, TEST_SCHEMA_FIELD]), + # not a list + TEST_SCHEMA_FIELD, + # list contains raw types + [StringType(), IntegerType(), TEST_SCHEMA_FIELD], + # completely wrong! + {"this": "str"}, + ], +) +def test_read_wrong_schema_format(schema_fields: Any, caplog: pytest.LogCaptureFixture) -> None: # noqa: ANN401 + """Ensure that the schema is in the right form.""" + err_msg = "schema_fields must be specified as a list of StructFields" + with pytest.raises(TypeError, match=err_msg): + read(MagicMock(), "/some/path", schema_fields) + + assert len(caplog.records) == 1 + assert caplog.records[0].levelno == logging.ERROR + assert caplog.records[0].message == err_msg + + +@pytest.mark.requires_spark +@pytest.mark.parametrize(("delimiter", "fmt"), [(",", "CSV"), ("\t", "TSV"), ("|", "DSV"), (None, "CSV")]) +def test_read_errors(spark: SparkSession, delimiter: str | None, fmt: str, caplog: pytest.LogCaptureFixture) -> None: + """Check error handling.""" + options = {"delimiter": delimiter} if delimiter else {} + + with pytest.raises(AnalysisException, match="Path does not exist:"): + read(spark, "/path/to/nowhere", [TEST_SCHEMA_FIELD], options) + + assert len(caplog.records) == 1 + assert caplog.records[0].levelno == logging.ERROR + assert caplog.records[0].message == f"Failed to load {fmt} from /path/to/nowhere" + + +@pytest.mark.requires_spark +@pytest.mark.parametrize("mode", INGEST_MODES) +@pytest.mark.parametrize("csv_lines", [VALID, MISSING_REQUIRED, TYPE_MISMATCH, TOO_FEW_COLS, TOO_MANY_COLS, ALL_LINES]) +def test_csv_read_modes( # noqa: PLR0913 + spark: SparkSession, + mode: str, + csv_lines: str, + csv_schema: list[StructField], + request: pytest.FixtureRequest, + caplog: pytest.LogCaptureFixture, +) -> None: + """Test ingestion of valid and invalid CSV data.""" + n_rows = 4 + csv_lines_path = request.getfixturevalue(csv_lines) + + read_options = { + "delimiter": ",", + "header": False, + "comment": "#", + "dateFormat": "yyyyMMdd", + "ignoreLeadingWhiteSpace": True, + "ignoreTrailingWhiteSpace": True, + "mode": mode, + } + + if mode == DROP: + with pytest.raises(ValueError, match="The only permitted read modes are PERMISSIVE and FAILFAST"): + read(spark, str(csv_lines_path), csv_schema, options=read_options) + return + + # spark will happily read in the data and report that it loaded the max number of lines + test_df = read(spark, str(csv_lines_path), csv_schema, options=read_options) + assert isinstance(test_df, DataFrame) + # check logging + assert len(caplog.records) == 1 + assert caplog.records[0].levelno == logging.INFO + assert ( + caplog.records[0].message + == f"Loaded {n_rows * 5 if csv_lines == ALL_LINES else n_rows} CSV records from {csv_lines_path!s}" + ) + + if mode == FAILFAST and csv_lines in (TOO_FEW_COLS, TOO_MANY_COLS, TYPE_MISMATCH, ALL_LINES): + with pytest.raises(Py4JJavaError, match="An error occurred while calling "): + test_df.collect() + return + + read(spark, str(csv_lines_path), csv_schema, options=read_options) + + data_rows = [r.asDict() for r in test_df.collect()] + + # all modes should correctly parse the valid data + # none of the modes GAF about missing required values, so all will be read + if csv_lines in (VALID, MISSING_REQUIRED): + assert len(data_rows) == n_rows + return + + if csv_lines in (TOO_FEW_COLS, TOO_MANY_COLS, TYPE_MISMATCH): + if mode == DROP: + # dropmalformed will not parse any content from these files as all lines are invalid + assert len(data_rows) == 0 + else: + # permissive will pull in all the data + assert len(data_rows) == n_rows + return + + # ALL_LINES: permissive will pull in all, DROP will just pull in the VALID + MISSING_REQUIRED lines + assert len(data_rows) == n_rows * 5 if mode == PERMISSIVE else n_rows * 2 diff --git a/tests/utils/download/__init__.py b/tests/utils/download/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/utils/download/conftest.py b/tests/utils/download/conftest.py new file mode 100644 index 0000000..2505bd6 --- /dev/null +++ b/tests/utils/download/conftest.py @@ -0,0 +1,57 @@ +"""Fixtures for testing downloads.""" + +from collections.abc import Awaitable, Callable +from dataclasses import dataclass +from pathlib import Path + +import httpx +import pytest + +from cdm_data_loader_utils.utils.download.async_client import AsyncFileDownloader +from cdm_data_loader_utils.utils.download.sync_client import FileDownloader + + +@dataclass +class DownloaderAdapter: + """Class providing a uniform API to the sync and async file downloader.""" + + name: str + make_downloader: Callable + download: Callable[..., Awaitable[Path | None]] + + +@pytest.fixture(params=["sync", "async"]) +def downloader_adapter(request: pytest.FixtureRequest) -> DownloaderAdapter: + """Fixture to generate sync or async file download clients.""" + + def make_sync(handler: Callable, **kwargs) -> FileDownloader: + client = httpx.Client(transport=httpx.MockTransport(handler)) + return FileDownloader(client, **kwargs) + + def make_async(handler: Callable, **kwargs) -> AsyncFileDownloader: + client = httpx.AsyncClient(transport=httpx.MockTransport(handler)) + return AsyncFileDownloader(client, **kwargs) + + # async def download_sync(downloader: FileDownloader, url: str, dest: Path) -> None: + # # Call sync method inside async test + # downloader.download(url, dest) + + async def download_sync(downloader: FileDownloader, *args, **kwargs) -> Path | None: + # Call sync method inside async test + return downloader.download(*args, **kwargs) + + async def download_async(downloader: AsyncFileDownloader, *args, **kwargs) -> Path | None: + return await downloader.download(*args, **kwargs) + + if request.param == "sync": + return DownloaderAdapter( + name="sync", + make_downloader=make_sync, + download=download_sync, + ) + + return DownloaderAdapter( + name="async", + make_downloader=make_async, + download=download_async, + ) diff --git a/tests/utils/download/test_async_client.py b/tests/utils/download/test_async_client.py new file mode 100644 index 0000000..f42518e --- /dev/null +++ b/tests/utils/download/test_async_client.py @@ -0,0 +1,133 @@ +"""Tests for the AsyncFileDownloader client that have no counterpart in the sync version.""" + +import asyncio +from pathlib import Path +from typing import NoReturn, Self + +import httpx +import pytest + +from cdm_data_loader_utils.utils.download.async_client import AsyncFileDownloader + +DOWNLOAD_URL = "https://example.com/file.txt" + + +@pytest.mark.asyncio +async def test_max_concurrency_is_enforced(tmp_path: Path) -> None: + """ + No more than max_concurrency downloads may run at once. + """ + max_concurrency = 2 + active = 0 + peak = 0 + lock = asyncio.Lock() + block = asyncio.Event() + + async def handler(_: httpx.Request) -> httpx.Response: + nonlocal active, peak + async with lock: + active += 1 + peak = max(peak, active) + + # Block all requests here until released + await block.wait() + async with lock: + active -= 1 + + return httpx.Response(200, content=b"ok") + + downloader = AsyncFileDownloader( + httpx.AsyncClient(transport=httpx.MockTransport(handler)), + max_concurrency=max_concurrency, + ) + + async def start_download(i: int) -> None: + dest = tmp_path / f"file_{i}.txt" + await downloader.download( + DOWNLOAD_URL, + dest, + ) + + tasks = [asyncio.create_task(start_download(i)) for i in range(5)] + + # Give tasks time to start and block + await asyncio.sleep(0.1) + # Release blocked requests + block.set() + await asyncio.gather(*tasks) + # peak concurrency should be limited by the max_concurrency value + assert peak == max_concurrency + + +@pytest.mark.asyncio +async def test_no_concurrency_limit_when_none(tmp_path: Path) -> None: + """ + When max_concurrency is None, all downloads may run concurrently. + """ + active = 0 + peak = 0 + lock = asyncio.Lock() + block = asyncio.Event() + + async def handler(_: httpx.Request) -> httpx.Response: + nonlocal active, peak + async with lock: + active += 1 + peak = max(peak, active) + + await block.wait() + async with lock: + active -= 1 + + return httpx.Response(200, content=b"ok") + + client = httpx.AsyncClient(transport=httpx.MockTransport(handler)) + + downloader = AsyncFileDownloader( + client, + max_concurrency=None, + ) + + async def start_download(i: int) -> None: + dest = tmp_path / f"file_{i}.txt" + await downloader.download( + DOWNLOAD_URL, + dest, + ) + + n_tasks = 5 + tasks = [asyncio.create_task(start_download(i)) for i in range(n_tasks)] + + await asyncio.sleep(0.1) + block.set() + await asyncio.gather(*tasks) + + # All tasks should have entered concurrently + assert peak == n_tasks + + +class EmptyAsyncRetry: + """Async iterator that yields no retry attempts.""" + + def __aiter__(self) -> Self: + """Iterator.""" + return self + + async def __anext__(self) -> NoReturn: + """Next.""" + raise StopAsyncIteration + + +@pytest.mark.asyncio +async def test_async_client_unreachable_code(monkeypatch: pytest.MonkeyPatch) -> None: + """Test that the unreachable code is reached if the retry iterator yields no attempts. + + Defensive test, should never occur IRL. + """ + downloader = AsyncFileDownloader(client=None) + + # Replace the retry mechanism with an empty async iterator + monkeypatch.setattr(downloader, "_retry", EmptyAsyncRetry()) + + with pytest.raises(RuntimeError, match="Iterator exhausted, unreachable code reached!"): + await downloader._download_with_retry(DOWNLOAD_URL, "file.txt") # noqa: SLF001 diff --git a/tests/utils/download/test_clients.py b/tests/utils/download/test_clients.py new file mode 100644 index 0000000..f65e302 --- /dev/null +++ b/tests/utils/download/test_clients.py @@ -0,0 +1,324 @@ +"""Tests for the FileDownloader and AsyncFileDownloader modules.""" + +import hashlib +import logging +from pathlib import Path + +import httpx +import pytest + +from cdm_data_loader_utils.utils.download.async_client import AsyncFileDownloader +from cdm_data_loader_utils.utils.download.core import ( + ChecksumMismatchError, + DownloadError, + NonRetryableDownloadError, +) +from cdm_data_loader_utils.utils.download.sync_client import FileDownloader +from tests.utils.download.conftest import DownloaderAdapter + +DOWNLOAD_URL = "https://example.com/file.txt" + + +@pytest.fixture +def sample_content() -> bytes: + """Generate some extremely interesting sample content.""" + return b"Hello world!" + + +@pytest.fixture +def sample_checksum(sample_content: bytes) -> str: + """Generate a checksum for the sample content.""" + return hashlib.sha256(sample_content).hexdigest() + + +@pytest.mark.parametrize("save_loc", [Path("file.txt"), Path("path") / "to" / "file.txt"]) +@pytest.mark.asyncio +async def test_download_to_file_system_success( + save_loc: Path, tmp_path: Path, sample_content: bytes, sample_checksum: str, downloader_adapter: DownloaderAdapter +) -> None: + """Simple happy path test of a successful download.""" + + def handler(_: httpx.Request) -> httpx.Response: + return httpx.Response( + 200, + content=sample_content, + ) + + downloader = downloader_adapter.make_downloader(handler) + destination = tmp_path / save_loc + + result = await downloader_adapter.download( + downloader, + DOWNLOAD_URL, + destination, + expected_checksum=sample_checksum, + ) + assert result == destination + assert destination.is_file() + assert destination.read_bytes() == sample_content + + +@pytest.mark.asyncio +async def test_chunked_streaming(tmp_path: Path, downloader_adapter: DownloaderAdapter) -> None: + """Ensure that chunked downloads work correctly.""" + content = b"a" * 10_000 + + def handler(_: httpx.Request) -> httpx.Response: + return httpx.Response(200, content=content) + + downloader = downloader_adapter.make_downloader(handler, chunk_size=1024) + + destination = tmp_path / "file.txt" + await downloader_adapter.download(downloader, DOWNLOAD_URL, destination) + + # TODO: add in count of number of times fh.write is called by _download_once? + assert destination.read_bytes() == content + + +@pytest.mark.parametrize( + ("status", "status_text", "error", "msg"), + [ + (200, None, None, None), + (302, "Found", DownloadError, "Server"), + (304, None, None, None), + (404, "Not Found", NonRetryableDownloadError, "Client"), + (400, "Bad Request", NonRetryableDownloadError, "Client"), + (503, "Service Unavailable", DownloadError, "Server"), + ], +) +@pytest.mark.asyncio +async def test_download_validate_response( # noqa: PLR0913 + status: int, + status_text: str | None, + error: type[Exception] | None, + msg: str | None, + tmp_path: Path, + caplog: pytest.LogCaptureFixture, + downloader_adapter: DownloaderAdapter, +) -> None: + """Check that responses of various types emit the correct errors.""" + + def handler(_: httpx.Request) -> httpx.Response: + return httpx.Response(status) + + downloader = downloader_adapter.make_downloader(handler, max_attempts=1) + destination = tmp_path / "file.txt" + + if error: + with pytest.raises(error, match=f"{msg} error: {status} {status_text}"): + await downloader_adapter.download(downloader, DOWNLOAD_URL, destination) + + last_log_msg = caplog.records[-1] + assert last_log_msg.levelno == logging.ERROR + assert ( + last_log_msg.message + == f"{DOWNLOAD_URL}: {msg} error: {status} {status_text}; retry{' not ' if msg == 'Client' else ' '}possible" + ) + return + + result = await downloader_adapter.download( + downloader, + DOWNLOAD_URL, + destination, + ) + last_log_msg = caplog.records[-1] + assert last_log_msg.levelno == logging.INFO + + if status == 304: # noqa: PLR2004 + assert result is None + assert last_log_msg.message.startswith(f"{DOWNLOAD_URL}: resource has not been modified") + else: + assert result == destination + assert last_log_msg.message == f"{DOWNLOAD_URL}: download successful" + + +@pytest.mark.asyncio +async def test_extra_headers( + tmp_path: Path, caplog: pytest.LogCaptureFixture, downloader_adapter: DownloaderAdapter +) -> None: + """Test that appropriate headers are added to a request. + + Also tests the 304 response, where a resource is not downloaded as it has not been modified. + """ + extra_headers = { + "If-Modified-Since": "Wed, 21 Oct 2015 07:28:00 GMT", + "X-Sender": "my-user-name", + "Some-Other-Header": "some value", + } + + def handler(request: httpx.Request) -> httpx.Response: + for header, val in extra_headers.items(): + assert request.headers[header] == val + return httpx.Response(304) + + downloader = downloader_adapter.make_downloader(handler) + + result = await downloader_adapter.download( + downloader, + DOWNLOAD_URL, + tmp_path / "file.txt", + extra_headers=extra_headers, + ) + + assert result is None + last_log_msg = caplog.records[-1] + assert last_log_msg.levelno == logging.INFO + assert last_log_msg.message.startswith(f"{DOWNLOAD_URL}: resource has not been modified") + + +@pytest.mark.parametrize("checksum_fn", [None, *hashlib.algorithms_available]) +@pytest.mark.parametrize("content", [b"Hello, world!", b"a" * 256]) +@pytest.mark.asyncio +async def test_checksum_success( + tmp_path: Path, + content: bytes, + checksum_fn: str | None, + caplog: pytest.LogCaptureFixture, + downloader_adapter: DownloaderAdapter, +) -> None: + """Test that a correct checksum does not throw an error.""" + checksum_fn_used = checksum_fn or "sha256" + if checksum_fn_used.startswith("shake"): + pytest.skip("shake algorithms not supported") + + def handler(_: httpx.Request) -> httpx.Response: + return httpx.Response(200, content=content) + + downloader = downloader_adapter.make_downloader(handler, chunk_size=16) + destination = tmp_path / "file.txt" + + hl = hashlib.new(checksum_fn_used) + hl.update(content) + expected_checksum = hl.hexdigest() + + result = await downloader_adapter.download( + downloader, DOWNLOAD_URL, destination, expected_checksum=expected_checksum, checksum_fn=checksum_fn + ) + assert result == destination + assert destination.read_bytes() == content + assert f"{DOWNLOAD_URL}: {checksum_fn_used} checksum matches" in [m.message for m in caplog.records] + + +@pytest.mark.parametrize("checksum_fn", ["shake128", " shake256", "shake-n-vac"]) +def test_checksum_invalid_sync_downloader(checksum_fn: str, tmp_path: Path) -> None: + """Ensure that invalid checksums throw an error.""" + downloader = FileDownloader() + with pytest.raises(ValueError, match=f"Hashing algorithm {checksum_fn} not supported"): + downloader.download(DOWNLOAD_URL, tmp_path, checksum_fn=checksum_fn) + + +@pytest.mark.parametrize("checksum_fn", ["shake128", " shake256", "shake-n-vac"]) +@pytest.mark.asyncio +async def test_checksum_invalid_async_downloader(checksum_fn: str, tmp_path: Path) -> None: + """Ensure that invalid checksums throw an error.""" + downloader = AsyncFileDownloader() + with pytest.raises(ValueError, match=f"Hashing algorithm {checksum_fn} not supported"): + await downloader.download(DOWNLOAD_URL, tmp_path, checksum_fn=checksum_fn) + + +@pytest.mark.asyncio +async def test_checksum_mismatch(tmp_path: Path, sample_content: bytes, downloader_adapter: DownloaderAdapter) -> None: + """Test checksum checking!""" + + def handler(_: httpx.Request) -> httpx.Response: + return httpx.Response(200, content=sample_content) + + downloader = downloader_adapter.make_downloader(handler) + destination = tmp_path / "file.txt" + + with pytest.raises(ChecksumMismatchError): + await downloader_adapter.download( + downloader, + DOWNLOAD_URL, + destination, + expected_checksum="some_checksum_or_other", + ) + # N.b. file still exists, even though checksum validation failed. + assert destination.read_bytes() == sample_content + + +@pytest.mark.parametrize("max_attempts", range(1, 5)) +@pytest.mark.parametrize("response_type", ["error", "timeout"]) +@pytest.mark.asyncio +async def test_timeout_and_server_error_retries( # noqa: PLR0913 + tmp_path: Path, + sample_content: bytes, + max_attempts: int, + response_type: str, + caplog: pytest.LogCaptureFixture, + downloader_adapter: DownloaderAdapter, +) -> None: + """Test retry functionality with different numbers of retries. Server errors are retried.""" + calls = {"n": 0} + # the attempt where the download will succeed + successful_attempt = 3 + + def handler_503(_: httpx.Request) -> httpx.Response: + calls["n"] += 1 + if calls["n"] < successful_attempt: + return httpx.Response(503) + return httpx.Response(200, content=sample_content) + + def handler_timeout(_: httpx.Request) -> httpx.Response: + calls["n"] += 1 + if calls["n"] < successful_attempt: + msg = "Connection has timed out" + raise httpx.ConnectTimeout(msg) + return httpx.Response(200, content=sample_content) + + downloader = downloader_adapter.make_downloader( + handler_503 if response_type == "error" else handler_timeout, max_attempts=max_attempts + ) + destination = tmp_path / "file.txt" + + if max_attempts < successful_attempt: + expected_match = ( + "Server error: 503 Service Unavailable" if response_type == "error" else "Connection has timed out" + ) + with pytest.raises(DownloadError, match=expected_match): + await downloader_adapter.download( + downloader, + DOWNLOAD_URL, + tmp_path / "file.txt", + ) + assert calls["n"] == max_attempts + else: + # successful download + result = await downloader_adapter.download(downloader, DOWNLOAD_URL, destination) + assert result == destination + assert calls["n"] == successful_attempt + + # check the logs: we should have messages for each error/timeout until the successful download + retry_possible_msgs = [r for r in caplog.records if r.message.endswith("retry possible")] + if max_attempts < successful_attempt: + assert len(retry_possible_msgs) == max_attempts + else: + assert len(retry_possible_msgs) == successful_attempt - 1 + + +@pytest.mark.parametrize("max_attempts", range(1, 5)) +@pytest.mark.asyncio +async def test_client_error_retries( + tmp_path: Path, sample_content: bytes, max_attempts: int, downloader_adapter: DownloaderAdapter +) -> None: + """Test retry functionality with different numbers of retries. Client errors are not retried.""" + calls = {"n": 0} + # the attempt where the download will succeed + successful_attempt = 3 + + def handler(_: httpx.Request) -> httpx.Response: + calls["n"] += 1 + if calls["n"] < successful_attempt: + return httpx.Response(404) + return httpx.Response(200, content=sample_content) + + downloader = downloader_adapter.make_downloader(handler, max_attempts=max_attempts) + + with pytest.raises(NonRetryableDownloadError, match="Client error: 404 Not Found"): + await downloader_adapter.download( + downloader, + DOWNLOAD_URL, + tmp_path / "file.txt", + ) + # there will only ever be one retry + assert calls["n"] == 1 diff --git a/tests/utils/test_gz.py b/tests/utils/test_gz.py new file mode 100644 index 0000000..dcd4567 --- /dev/null +++ b/tests/utils/test_gz.py @@ -0,0 +1,173 @@ +"""Tests for the gz module.""" + +import gzip +import logging +from pathlib import Path + +import pytest +from click.testing import CliRunner + +from cdm_data_loader_utils.utils.gz import compress_file, compress_files, main + + +@pytest.fixture +def temporary_file(tmp_path: Path) -> Path: + """Create a temporary text file and return its path.""" + file_path = tmp_path / "sample.txt" + content = b"Hello, world!\nThis is a test." + file_path.write_bytes(content) + return file_path + + +def read_gz(path: Path) -> bytes: + """Utility function to read a ``.gz`` file and return its decompressed bytes.""" + with gzip.open(path, "rb") as f: + return f.read() + + +def test_compress_file_creates_gzip(temporary_file: Path, caplog: pytest.LogCaptureFixture) -> None: + """Test that running compress file actually compresses a file.""" + # Ensure no .gz exists initially + gz_path = temporary_file.with_suffix(temporary_file.suffix + ".gz") + if gz_path.exists(): + gz_path.unlink() + + compress_file(temporary_file) + + # Verify the .gz file was created + assert gz_path.exists() + + # Decompress and compare content + decompressed = read_gz(gz_path) + original = temporary_file.read_bytes() + assert decompressed == original + + assert len(caplog.records) == 1 + assert caplog.records[0].levelno == logging.INFO + assert f"Created output file {gz_path!s}" in caplog.records[0].message + + +def test_compress_file_skips_existing_gzip(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None: + """Ensure that an existing gz file prevents compress_file from running compression.""" + file_path = tmp_path / "data.bin" + file_path.write_bytes(b"binary\x00data") + # fake gzip file + gz_path = file_path.with_suffix(file_path.suffix + ".gz") + gz_path.write_bytes(b"some old crap") + original_mtime = gz_path.stat().st_mtime + + # attempt to compress data.bin + compress_file(file_path) + + # Ensure the .gz file was not overwritten (mtime unchanged) + assert gz_path.stat().st_mtime == original_mtime + assert gz_path.read_bytes() == b"some old crap" + + assert len(caplog.records) == 1 + assert caplog.records[0].levelno == logging.INFO + assert f"Found existing file {file_path!s}.gz: skipping gz operation" in caplog.records[0].message + + +def test_compress_files_multiple(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None: + """Test that compressing a directory with a glob pattern to match works.""" + # Create three files matching the glob pattern + n_files = 3 + for i in range(n_files): + (tmp_path / f"file{i}.txt").write_text(f"content {i}") + # Create a non-matching file + (tmp_path / "ignore.md").write_text("should be ignored") + + compress_files(tmp_path, "*.txt") + + # Verify .gz files were created for the three txt files only + for i in range(n_files): + gz = tmp_path / f"file{i}.txt.gz" + assert gz.exists() + with gzip.open(gz, "rt") as f: + assert f.read() == f"content {i}" + # Ensure the non-matching file was not gzipped + assert not (tmp_path / "ignore.md.gz").exists() + + assert len(caplog.records) == n_files + 2 + for r in caplog.records: + assert r.levelno == logging.INFO + assert "Found 3 file(s) to compress" in caplog.records[0].message + for r in caplog.records[1:4]: + assert f"Created output file {tmp_path!s}/file" in r.message + assert caplog.records[-1].message == "Work complete!" + + +def test_compress_files_no_matches(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None: + """Test that nothing happens (no error, etc.) if a directory doesn't contain matching files.""" + compress_files(tmp_path, "*.doesnotexist") + # No .gz files should be present + assert list(tmp_path.rglob("*.gz")) == [] + + assert len(caplog.records) == 1 + assert caplog.records[0].levelno == logging.INFO + assert "Found 0 file(s) to compress" in caplog.records[0].message + + +def test_compress_files_accepts_str_path(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None: + """The `directory` argument can be a plain string.""" + f = tmp_path / "x.txt" + f.write_text("payload") + + # Pass directory as a string + compress_files(str(tmp_path), "*.txt") + + # Verify outcome is the same as when a Path is supplied + gz = f.with_name(f.name + ".gz") + assert gz.exists() + assert read_gz(gz) == b"payload" + # Logger should still contain the expected messages + assert len(caplog.records) == 3 + msgs = [rec.message for rec in caplog.records] + assert msgs[0] == "Found 1 file(s) to compress" + assert f"Created output file {f!s}.gz" in msgs[1] + assert msgs[-1] == "Work complete!" + + +def test_compress_files_invalid_directory(tmp_path: Path) -> None: + """Check the appropriate error is thrown if the directory is not valid.""" + non_existent = tmp_path / "no_such_dir" + with pytest.raises(FileNotFoundError, match=f"Directory {non_existent!s} not found"): + compress_files(non_existent, "*") + + +@pytest.mark.skip("CliRunner conflicts with logging, causing a ValueError") +def test_cli_single_file(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None: + """Test the CLI with a valid file.""" + # ensure that the logger does not produce any output + caplog.set_level(logging.CRITICAL) + runner = CliRunner() + # Create a single file and test CLI compression of a file + file_path = tmp_path / "single.txt" + file_path.write_text("single file content") + result = runner.invoke(main, ["--source", str(file_path)]) + assert result.exit_code == 0 + assert (file_path.with_suffix(file_path.suffix + ".gz")).exists() + + +@pytest.mark.skip("CliRunner conflicts with logging, causing a ValueError") +def test_cli_directory_with_glob(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None: + """Test the CLI with a directory and some globbery action.""" + caplog.set_level(logging.CRITICAL) + sub_dir = tmp_path / "sub" + sub_dir.mkdir() + for name in ["a.txt", "b.log"]: + (sub_dir / name).write_text(name) + runner = CliRunner() + result = runner.invoke(main, ["--source", str(sub_dir), "--file-glob", "*.txt"]) + assert result.exit_code == 0 + # Only the .txt file should be gzipped + assert (sub_dir / "a.txt.gz").exists() + assert not (sub_dir / "b.log.gz").exists() + + +def test_cli_main_nonexistent_source(tmp_path: Path) -> None: + """Test the CLI interface with a missing source.""" + runner = CliRunner() + result = runner.invoke(main, ["--source", str(tmp_path / "doesnotexist")]) + assert result.exit_code != 0 + assert isinstance(result.exception, RuntimeError) diff --git a/tests/utils/test_spark_delta.py b/tests/utils/test_spark_delta.py index 86abcc8..88a1b59 100644 --- a/tests/utils/test_spark_delta.py +++ b/tests/utils/test_spark_delta.py @@ -29,14 +29,6 @@ TENANT_NAME = "The_Breakers" -@pytest.fixture -def spark(tmp_path: Path) -> Generator[SparkSession, Any]: - """Generate a spark session with spark.sql.warehouse.dir set to the pytest temporary directory.""" - spark = get_spark("test_delta_app", local=True, delta_lake=True, override={SAVE_DIR: tmp_path}) - yield spark - spark.stop() - - def gen_ns_save_dir(current_save_dir: str, namespace: str, tenant_name: str | None) -> tuple[str, str]: """Generate the projected namespace and save directory, given a file path, a namespace, and a tenant name.""" db_location = f"tenant/{tenant_name}/{namespace}.db" if tenant_name else f"user/some_user/{namespace}.db" diff --git a/uv.lock b/uv.lock index ad945bf..f1608b0 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,5 @@ version = 1 -revision = 2 +revision = 3 requires-python = ">=3.13" resolution-markers = [ "python_full_version >= '3.14'", @@ -17,7 +17,7 @@ wheels = [ [[package]] name = "aiohttp" -version = "3.13.2" +version = "3.13.3" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "aiohappyeyeballs" }, @@ -28,59 +28,59 @@ dependencies = [ { name = "propcache" }, { name = "yarl" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/1c/ce/3b83ebba6b3207a7135e5fcaba49706f8a4b6008153b4e30540c982fae26/aiohttp-3.13.2.tar.gz", hash = "sha256:40176a52c186aefef6eb3cad2cdd30cd06e3afbe88fe8ab2af9c0b90f228daca", size = 7837994, upload-time = "2025-10-28T20:59:39.937Z" } -wheels = [ - { url = 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