refactor: add sense check for text based file (#32)

* feat: Added new option to check csv headers in duckdb csv readers

* refactor: small changes to foundry pipeline and duckdb csv to fix header check

* feat: Added new check to base reader for sense check of whether processing a text file - applied for all reads via read_to_entity_type

* refactor: Address review comments

Author: stevenhsd

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/pipeline/foundry_ddb_pipeline.py

@@ -109,6 +109,8 @@ def error_report(
             self._logger.exception(exc)
             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 +150,8 @@ 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}"

tests/test_core_engine/test_backends/test_implementations/test_duckdb/test_ddb_utils.py

@@ -1,4 +1,3 @@
-from typing import Dict, List
 import pytest
 
 from dve.core_engine.backends.implementations.duckdb.utilities import (
@@ -16,7 +15,7 @@
         ),
     ],
 )
-def test_expr_mapping_to_columns(expressions: Dict[str, str], expected: list[str]):
+def test_expr_mapping_to_columns(expressions: dict[str, str], expected: list[str]):
     observed = expr_mapping_to_columns(expressions)
     assert observed == expected
 
@@ -51,6 +50,7 @@ def test_expr_mapping_to_columns(expressions: Dict[str, str], expected: list[str
         ),
     ],
 )
-def test_expr_array_to_columns(expressions: Dict[str, str], expected: list[str]):
+def test_expr_array_to_columns(expressions: dict[str, str], expected: list[str]):
     observed = expr_array_to_columns(expressions)
     assert observed == expected
+

tests/test_core_engine/test_backends/test_readers/test_ddb_json.py

@@ -57,7 +57,7 @@ def test_ddb_json_reader_all_str(temp_json_file):
     expected_fields = [fld for fld in mdl.__fields__]
     reader = DuckDBJSONReader()
     rel: DuckDBPyRelation = reader.read_to_entity_type(
-        DuckDBPyRelation, uri, "test", stringify_model(mdl)
+        DuckDBPyRelation, uri.as_posix(), "test", stringify_model(mdl)
     )
     assert rel.columns == expected_fields
     assert dict(zip(rel.columns, rel.dtypes)) == {fld: "VARCHAR" for fld in expected_fields}
@@ -68,7 +68,7 @@ def test_ddb_json_reader_cast(temp_json_file):
     uri, data, mdl = temp_json_file
     expected_fields = [fld for fld in mdl.__fields__]
     reader = DuckDBJSONReader()
-    rel: DuckDBPyRelation = reader.read_to_entity_type(DuckDBPyRelation, uri, "test", mdl)
+    rel: DuckDBPyRelation = reader.read_to_entity_type(DuckDBPyRelation, uri.as_posix(), "test", mdl)
 
     assert rel.columns == expected_fields
     assert dict(zip(rel.columns, rel.dtypes)) == {
@@ -82,7 +82,7 @@ def test_ddb_csv_write_parquet(temp_json_file):
     uri, _, mdl = temp_json_file
     reader = DuckDBJSONReader()
     rel: DuckDBPyRelation = reader.read_to_entity_type(
-        DuckDBPyRelation, uri, "test", stringify_model(mdl)
+        DuckDBPyRelation, uri.as_posix(), "test", stringify_model(mdl)
     )
     target_loc: Path = uri.parent.joinpath("test_parquet.parquet").as_posix()
     reader.write_parquet(rel, target_loc)

tests/test_core_engine/test_backends/test_readers/test_utilities.py

@@ -0,0 +1,55 @@
+import datetime as dt
+from pathlib import Path
+import tempfile
+from uuid import uuid4
+
+import pytest
+from pydantic import BaseModel, create_model
+
+from dve.core_engine.backends.readers.utilities import check_csv_header_expected
+
+@pytest.mark.parametrize(
+    ["header_row", "delim", "schema", "expected"],
+    [
+        (
+            "field1,field2,field3",
+            ",",
+            {"field1": (str, ...), "field2": (int, ...), "field3": (float, 1.2)},
+            set(),
+        ),
+        (
+            "field2,field3,field1",
+            ",",
+            {"field1": (str, ...), "field2": (int, ...), "field3": (float, 1.2)},
+            set(),
+        ),
+        (
+            "str_field|int_field|date_field|",
+            ",",
+            {"str_field": (str, ...), "int_field": (int, ...), "date_field": (dt.date, dt.date.today())},
+            {"str_field","int_field","date_field"},
+        ),
+        (
+            '"str_field"|"int_field"|"date_field"',
+            "|",
+            {"str_field": (str, ...), "int_field": (int, ...), "date_field": (dt.date, dt.date.today())},
+            set(),
+        ),
+        (
+            'str_field,int_field,date_field\n',
+            ",",
+            {"str_field": (str, ...), "int_field": (int, ...), "date_field": (dt.date, dt.date.today())},
+            set(),
+        ),
+        
+    ],
+)
+def test_check_csv_header_expected(
+    header_row: str, delim: str, schema: type[BaseModel], expected: set[str]
+):
+    mdl = create_model("TestModel", **schema)
+    with tempfile.TemporaryDirectory() as tmpdir:
+        fle = Path(tmpdir).joinpath(f"test_file_{uuid4().hex}.csv")
+        fle.open("w+").write(header_row)
+        res = check_csv_header_expected(fle.as_posix(), mdl, delim)
+    assert res == expected