Merge pull request #34 from NHSDigital/release_v052

Release v0.5.2

Author: georgeRobertson

CHANGELOG.md

@@ -1,3 +1,12 @@
+## v0.5.2 (2026-02-02)
+
+### Refactor
+
+- allow passing of custom loggers into pipeline objects
+- ensure traceback in broad exceptions
+- improve the logging around dve processing errors and align reporting to module name rather than legacy name
+- add sense check for text based file (#32)
+
 ## v0.5.1 (2026-01-28)
 
 ### Fix

Makefile

@@ -17,7 +17,7 @@ behave:
 	${activate} behave
 
 pytest:
-	${activate} pytest tests/
+	${activate} pytest -c pytest-dev.ini
 
 all-tests: pytest behave
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "nhs_dve"
-version = "0.5.1"
+version = "0.5.2"
 description = "`nhs data validation engine` is a framework used to validate data"
 authors = ["NHS England <england.contactus@nhs.net>"]
 readme = "README.md"

pytest-dev.ini

@@ -0,0 +1,3 @@
+[pytest]
+log_cli = true
+log_cli_level = INFO

src/dve/core_engine/backends/base/reader.py

@@ -8,9 +8,11 @@
 from pydantic import BaseModel
 from typing_extensions import Protocol
 
-from dve.core_engine.backends.exceptions import ReaderLacksEntityTypeSupport
+from dve.core_engine.backends.exceptions import MessageBearingError, ReaderLacksEntityTypeSupport
 from dve.core_engine.backends.types import EntityName, EntityType
+from dve.core_engine.message import FeedbackMessage
 from dve.core_engine.type_hints import URI, ArbitraryFunction, WrapDecorator
+from dve.parser.file_handling.service import open_stream
 
 T = TypeVar("T")
 ET_co = TypeVar("ET_co", covariant=True)
@@ -116,6 +118,8 @@ def read_to_entity_type(
         if entity_name == Iterator[dict[str, Any]]:
             return self.read_to_py_iterator(resource, entity_name, schema)  # type: ignore
 
+        self.raise_if_not_sensible_file(resource, entity_name)
+
         try:
             reader_func = self.__read_methods__[entity_type]
         except KeyError as err:
@@ -137,3 +141,36 @@ def write_parquet(
 
         """
         raise NotImplementedError(f"write_parquet not implemented in {self.__class__}")
+
+    @staticmethod
+    def _check_likely_text_file(resource: URI) -> bool:
+        """Quick sense check of file to see if it looks like text
+        - not 100% full proof, but hopefully enough to weed out most
+        non-text files"""
+        with open_stream(resource, "rb") as fle:
+            start_chunk = fle.read(4096)
+        # check for BOM character - utf-16 can contain NULL bytes
+        if start_chunk.startswith((b"\xff\xfe", b"\xfe\xff")):
+            return True
+        # if null byte in - unlikely text
+        if b"\x00" in start_chunk:
+            return False
+        return True
+
+    def raise_if_not_sensible_file(self, resource: URI, entity_name: str):
+        """Sense check that the file is a text file. Raise error if doesn't
+        appear to be the case."""
+        if not self._check_likely_text_file(resource):
+            raise MessageBearingError(
+                "The submitted file doesn't appear to be text",
+                messages=[
+                    FeedbackMessage(
+                        entity=entity_name,
+                        record=None,
+                        failure_type="submission",
+                        error_location="Whole File",
+                        error_code="MalformedFile",
+                        error_message="The resource doesn't seem to be a valid text file",
+                    )
+                ],
+            )

src/dve/core_engine/backends/implementations/duckdb/readers/csv.py

@@ -16,6 +16,7 @@
     get_duckdb_type_from_annotation,
 )
 from dve.core_engine.backends.implementations.duckdb.types import SQLType
+from dve.core_engine.backends.readers.utilities import check_csv_header_expected
 from dve.core_engine.backends.utilities import get_polars_type_from_annotation
 from dve.core_engine.message import FeedbackMessage
 from dve.core_engine.type_hints import URI, EntityName
@@ -24,7 +25,14 @@
 
 @duckdb_write_parquet
 class DuckDBCSVReader(BaseFileReader):
-    """A reader for CSV files"""
+    """A reader for CSV files including the ability to compare the passed model
+    to the file header, if it exists.
+
+    field_check: flag to compare submitted file header to the accompanying pydantic model
+    field_check_error_code: The error code to provide if the file header doesn't contain
+                            the expected fields
+    field_check_error_message: The error message to provide if the file header doesn't contain
+                               the expected fields"""
 
     # TODO - the read_to_relation should include the schema and determine whether to
     # TODO - stringify or not
@@ -35,15 +43,43 @@ def __init__(
         delim: str = ",",
         quotechar: str = '"',
         connection: Optional[DuckDBPyConnection] = None,
+        field_check: bool = False,
+        field_check_error_code: Optional[str] = "ExpectedVsActualFieldMismatch",
+        field_check_error_message: Optional[str] = "The submitted header is missing fields",
         **_,
     ):
         self.header = header
         self.delim = delim
         self.quotechar = quotechar
         self._connection = connection if connection else default_connection
+        self.field_check = field_check
+        self.field_check_error_code = field_check_error_code
+        self.field_check_error_message = field_check_error_message
 
         super().__init__()
 
+    def perform_field_check(
+        self, resource: URI, entity_name: str, expected_schema: type[BaseModel]
+    ):
+        """Check that the header of the CSV aligns with the provided model"""
+        if not self.header:
+            raise ValueError("Cannot perform field check without a CSV header")
+
+        if missing := check_csv_header_expected(resource, expected_schema, self.delim):
+            raise MessageBearingError(
+                "The CSV header doesn't match what is expected",
+                messages=[
+                    FeedbackMessage(
+                        entity=entity_name,
+                        record=None,
+                        failure_type="submission",
+                        error_location="Whole File",
+                        error_code=self.field_check_error_code,
+                        error_message=f"{self.field_check_error_message} - missing fields: {missing}",  # pylint: disable=line-too-long
+                    )
+                ],
+            )
+
     def read_to_py_iterator(
         self, resource: URI, entity_name: EntityName, schema: type[BaseModel]
     ) -> Iterator[dict[str, Any]]:
@@ -58,6 +94,9 @@ def read_to_relation(  # pylint: disable=unused-argument
         if get_content_length(resource) == 0:
             raise EmptyFileError(f"File at {resource} is empty.")
 
+        if self.field_check:
+            self.perform_field_check(resource, entity_name, schema)
+
         reader_options: dict[str, Any] = {
             "header": self.header,
             "delimiter": self.delim,
@@ -89,6 +128,9 @@ def read_to_relation(  # pylint: disable=unused-argument
         if get_content_length(resource) == 0:
             raise EmptyFileError(f"File at {resource} is empty.")
 
+        if self.field_check:
+            self.perform_field_check(resource, entity_name, schema)
+
         reader_options: dict[str, Any] = {
             "has_header": self.header,
             "separator": self.delim,
@@ -132,6 +174,17 @@ class DuckDBCSVRepeatingHeaderReader(PolarsToDuckDBCSVReader):
     | shop1      | clothes    | 2025-01-01 |
     """
 
+    def __init__(
+        self,
+        *args,
+        non_unique_header_error_code: Optional[str] = "NonUniqueHeader",
+        non_unique_header_error_message: Optional[str] = None,
+        **kwargs,
+    ):
+        self._non_unique_header_code = non_unique_header_error_code
+        self._non_unique_header_message = non_unique_header_error_message
+        super().__init__(*args, **kwargs)
+
     @read_function(DuckDBPyRelation)
     def read_to_relation(  # pylint: disable=unused-argument
         self, resource: URI, entity_name: EntityName, schema: type[BaseModel]
@@ -156,10 +209,12 @@ def read_to_relation(  # pylint: disable=unused-argument
                         failure_type="submission",
                         error_message=(
                             f"Found {no_records} distinct combination of header values."
+                            if not self._non_unique_header_message
+                            else self._non_unique_header_message
                         ),
                         error_location=entity_name,
                         category="Bad file",
-                        error_code="NonUniqueHeader",
+                        error_code=self._non_unique_header_code,
                     )
                 ],
             )

src/dve/core_engine/backends/readers/utilities.py

@@ -0,0 +1,21 @@
+"""General utilities for file readers"""
+
+from typing import Optional
+
+from pydantic import BaseModel
+
+from dve.core_engine.type_hints import URI
+from dve.parser.file_handling.service import open_stream
+
+
+def check_csv_header_expected(
+    resource: URI,
+    expected_schema: type[BaseModel],
+    delimiter: Optional[str] = ",",
+    quote_char: str = '"',
+) -> set[str]:
+    """Check the header of a CSV matches the expected fields"""
+    with open_stream(resource) as fle:
+        header_fields = fle.readline().rstrip().replace(quote_char, "").split(delimiter)
+    expected_fields = expected_schema.__fields__.keys()
+    return set(expected_fields).difference(header_fields)

src/dve/core_engine/exceptions.py

@@ -1,12 +1,8 @@
 """Exceptions emitted by the pipeline."""
 
-from collections.abc import Iterator
+import traceback
 from typing import Optional
 
-from dve.core_engine.backends.implementations.spark.types import SparkEntities
-from dve.core_engine.message import FeedbackMessage
-from dve.core_engine.type_hints import Messages
-
 
 class CriticalProcessingError(ValueError):
     """An exception emitted if critical errors are received."""
@@ -15,26 +11,18 @@ def __init__(
         self,
         error_message: str,
         *args: object,
-        messages: Optional[Messages],
-        entities: Optional[SparkEntities] = None
+        messages: Optional[list[str]] = None,
     ) -> None:
         super().__init__(error_message, *args)
         self.error_message = error_message
         """The error message explaining the critical processing error."""
         self.messages = messages
-        """The messages gathered at the time the error was emitted."""
-        self.entities = entities
-        """The entities as they exist at the time the error was emitted."""
-
-    @property
-    def critical_messages(self) -> Iterator[FeedbackMessage]:
-        """Critical messages which caused the processing error."""
-        yield from filter(lambda message: message.is_critical, self.messages)  # type: ignore
+        """The stacktrace for the messages."""
 
     @classmethod
     def from_exception(cls, exc: Exception):
         """Create from broader exception, for recording in processing errors"""
-        return cls(error_message=repr(exc), entities=None, messages=[])
+        return cls(error_message=repr(exc), messages=traceback.format_exception(exc))
 
 
 class EntityTypeMismatch(TypeError):

src/dve/pipeline/duckdb_pipeline.py

@@ -1,5 +1,6 @@
 """DuckDB implementation for `Pipeline` object."""
 
+import logging
 from typing import Optional
 
 from duckdb import DuckDBPyConnection, DuckDBPyRelation
@@ -20,7 +21,7 @@ class DDBDVEPipeline(BaseDVEPipeline):
     """
     Modified Pipeline class for running a DVE Pipeline with Spark
     """
-
+    # pylint: disable=R0913
     def __init__(
         self,
         processed_files_path: URI,
@@ -30,6 +31,7 @@ def __init__(
         submitted_files_path: Optional[URI],
         reference_data_loader: Optional[type[BaseRefDataLoader]] = None,
         job_run_id: Optional[int] = None,
+        logger: Optional[logging.Logger] = None,
     ):
         self._connection = connection
         super().__init__(
@@ -41,6 +43,7 @@ def __init__(
             submitted_files_path,
             reference_data_loader,
             job_run_id,
+            logger,
         )
 
     # pylint: disable=arguments-differ

src/dve/pipeline/foundry_ddb_pipeline.py

@@ -57,8 +57,7 @@ def file_transformation(
         try:
             return super().file_transformation(submission_info)
         except Exception as exc:  # pylint: disable=W0718
-            self._logger.error(f"File transformation raised exception: {exc}")
-            self._logger.exception(exc)
+            self._logger.exception("File transformation raised exception:")
             dump_processing_errors(
                 fh.joinuri(self.processed_files_path, submission_info.submission_id),
                 "file_transformation",
@@ -73,8 +72,7 @@ def apply_data_contract(
         try:
             return super().apply_data_contract(submission_info, submission_status)
         except Exception as exc:  # pylint: disable=W0718
-            self._logger.error(f"Apply data contract raised exception: {exc}")
-            self._logger.exception(exc)
+            self._logger.exception("Apply data contract raised exception:")
             dump_processing_errors(
                 fh.joinuri(self.processed_files_path, submission_info.submission_id),
                 "contract",
@@ -89,8 +87,7 @@ def apply_business_rules(
         try:
             return super().apply_business_rules(submission_info, submission_status)
         except Exception as exc:  # pylint: disable=W0718
-            self._logger.error(f"Apply business rules raised exception: {exc}")
-            self._logger.exception(exc)
+            self._logger.exception("Apply business rules raised exception:")
             dump_processing_errors(
                 fh.joinuri(self.processed_files_path, submission_info.submission_id),
                 "business_rules",
@@ -105,10 +102,11 @@ def error_report(
         try:
             return super().error_report(submission_info, submission_status)
         except Exception as exc:  # pylint: disable=W0718
-            self._logger.error(f"Error reports raised exception: {exc}")
-            self._logger.exception(exc)
+            self._logger.exception("Error reports raised exception:")
             sub_stats = None
             report_uri = None
+            submission_status = submission_status if submission_status else SubmissionStatus()
+            submission_status.processing_failed = True
             dump_processing_errors(
                 fh.joinuri(self.processed_files_path, submission_info.submission_id),
                 "error_report",
@@ -148,7 +146,8 @@ def run_pipeline(
                 sub_info, sub_status, sub_stats, report_uri = self.error_report(
                     submission_info=submission_info, submission_status=sub_status
                 )
-                self._audit_tables.add_submission_statistics_records(sub_stats=[sub_stats])
+                if sub_stats:
+                    self._audit_tables.add_submission_statistics_records(sub_stats=[sub_stats])
         except Exception as err:  # pylint: disable=W0718
             self._logger.error(
                 f"During processing of submission_id: {sub_id}, this exception was raised: {err}"