Feature/ndit 602 xsd validation

.github/workflows/ci_testing.yml

@@ -17,7 +17,7 @@ jobs:
       - name: Install extra dependencies for a python install
         run: |
           sudo apt-get update
-          sudo apt -y install --no-install-recommends liblzma-dev libbz2-dev libreadline-dev
+          sudo apt -y install --no-install-recommends liblzma-dev libbz2-dev libreadline-dev libxml2-utils
 
       - name: Install asdf cli
         uses: asdf-vm/actions/setup@v4

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

@@ -30,10 +30,12 @@ class DuckDBCSVReader(BaseFileReader):
     # TODO - stringify or not
     def __init__(
         self,
+        *,
         header: bool = True,
         delim: str = ",",
         quotechar: str = '"',
         connection: Optional[DuckDBPyConnection] = None,
+        **_,
     ):
         self.header = header
         self.delim = delim

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

@@ -20,7 +20,12 @@
 class DuckDBJSONReader(BaseFileReader):
     """A reader for JSON files"""
 
-    def __init__(self, json_format: Optional[str] = "array"):
+    def __init__(
+        self,
+        *,
+        json_format: Optional[str] = "array",
+        **_,
+    ):
         self._json_format = json_format
 
         super().__init__()

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

@@ -8,6 +8,7 @@
 from pydantic import BaseModel
 
 from dve.core_engine.backends.base.reader import read_function
+from dve.core_engine.backends.exceptions import MessageBearingError
 from dve.core_engine.backends.implementations.duckdb.duckdb_helpers import duckdb_write_parquet
 from dve.core_engine.backends.readers.xml import XMLStreamReader
 from dve.core_engine.backends.utilities import get_polars_type_from_annotation, stringify_model
@@ -18,13 +19,21 @@
 class DuckDBXMLStreamReader(XMLStreamReader):
     """A reader for XML files"""
 
-    def __init__(self, ddb_connection: Optional[DuckDBPyConnection] = None, **kwargs):
+    def __init__(self, *, ddb_connection: Optional[DuckDBPyConnection] = None, **kwargs):
         self.ddb_connection = ddb_connection if ddb_connection else default_connection
         super().__init__(**kwargs)
 
     @read_function(DuckDBPyRelation)
     def read_to_relation(self, resource: URI, entity_name: str, schema: type[BaseModel]):
         """Returns a relation object from the source xml"""
+        if self.xsd_location:
+            msg = self._run_xmllint(file_uri=resource)
+            if msg:
+                raise MessageBearingError(
+                    "Submitted file failed XSD validation.",
+                    messages=[msg],
+                )
+
         polars_schema: dict[str, pl.DataType] = {  # type: ignore
             fld.name: get_polars_type_from_annotation(fld.annotation)
             for fld in stringify_model(schema).__fields__.values()

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

@@ -31,6 +31,7 @@ def __init__(
         multi_line: bool = False,
         encoding: str = "utf-8-sig",
         spark_session: Optional[SparkSession] = None,
+        **_,
     ) -> None:
 
         self.delimiter = delimiter

src/dve/core_engine/backends/implementations/spark/readers/json.py

@@ -27,6 +27,7 @@ def __init__(
         encoding: Optional[str] = "utf-8",
         multi_line: Optional[bool] = True,
         spark_session: Optional[SparkSession] = None,
+        **_,
     ) -> None:
 
         self.encoding = encoding

src/dve/core_engine/backends/implementations/spark/readers/xml.py

@@ -12,16 +12,17 @@
 from pyspark.sql.utils import AnalysisException
 from typing_extensions import Literal
 
-from dve.core_engine.backends.base.reader import BaseFileReader, read_function
+from dve.core_engine.backends.base.reader import read_function
 from dve.core_engine.backends.exceptions import EmptyFileError
 from dve.core_engine.backends.implementations.spark.spark_helpers import (
     df_is_empty,
     get_type_from_annotation,
     spark_write_parquet,
 )
-from dve.core_engine.backends.readers.xml import XMLStreamReader
+from dve.core_engine.backends.readers.xml import BasicXMLFileReader, XMLStreamReader
+from dve.core_engine.backends.utilities import dump_errors
 from dve.core_engine.type_hints import URI, EntityName
-from dve.parser.file_handling import get_content_length
+from dve.parser.file_handling import get_content_length, get_parent
 from dve.parser.file_handling.service import open_stream
 
 SparkXMLMode = Literal["PERMISSIVE", "FAILFAST", "DROPMALFORMED"]
@@ -52,39 +53,51 @@
 
 
 @spark_write_parquet
-class SparkXMLReader(BaseFileReader):  # pylint: disable=too-many-instance-attributes
+class SparkXMLReader(BasicXMLFileReader):  # pylint: disable=too-many-instance-attributes
     """A reader for XML files built atop Spark-XML."""
 
     def __init__(
         self,
         *,
         record_tag: str,
         root_tag: Optional[str] = None,
         spark_session: Optional[SparkSession] = None,
         sampling_ratio: int = 1,
         exclude_attribute: bool = True,
         mode: SparkXMLMode = "PERMISSIVE",
         infer_schema: bool = False,
         ignore_namespace: bool = True,
         null_values: Collection[str] = frozenset(("NULL", "null", "")),
         sanitise_multiline: bool = True,
         namespace=None,
         trim_cells=True,
+        xsd_location: Optional[URI] = None,
+        xsd_error_code: Optional[str] = None,
+        xsd_error_message: Optional[str] = None,
+        rules_location: Optional[URI] = None,
         **_,
     ) -> None:
-        self.record_tag = record_tag
+
+        super().__init__(
+            record_tag=record_tag,
+            root_tag=root_tag,
+            trim_cells=trim_cells,
+            null_values=null_values,
+            sanitise_multiline=sanitise_multiline,
+            xsd_location=xsd_location,
+            xsd_error_code=xsd_error_code,
+            xsd_error_message=xsd_error_message,
+            rules_location=rules_location,
+        )
+
         self.spark_session = spark_session or SparkSession.builder.getOrCreate()
         self.sampling_ratio = sampling_ratio
         self.exclude_attribute = exclude_attribute
         self.mode = mode
         self.infer_schema = infer_schema
         self.ignore_namespace = ignore_namespace
-        self.root_tag = root_tag
         self.sanitise_multiline = sanitise_multiline
-        self.null_values = null_values
         self.namespace = namespace
-        self.trim_cells = trim_cells
-        super().__init__()
 
     def read_to_py_iterator(
         self, resource: URI, entity_name: EntityName, schema: type[BaseModel]
@@ -106,6 +119,14 @@
         if get_content_length(resource) == 0:
             raise EmptyFileError(f"File at {resource} is empty.")
 
+        if self.xsd_location:
+            msg = self._run_xmllint(file_uri=resource)
+            if msg:
+                working_folder = get_parent(resource)
+                dump_errors(
+                    working_folder=working_folder, step_name="file_transformation", messages=[msg]
+                )
+
         spark_schema: StructType = get_type_from_annotation(schema)
         kwargs = {
             "rowTag": self.record_tag,
@@ -143,7 +164,7 @@
                     kwargs["rowTag"] = f"{namespace}:{self.record_tag}"
                     df = (
                         self.spark_session.read.format("xml")
-                        .options(**kwargs)
+                        .options(**kwargs)  # type: ignore
                         .load(resource, schema=read_schema)
                     )
             if self.root_tag and df.columns:

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

@@ -36,6 +36,7 @@ def __init__(
         trim_cells: bool = True,
         null_values: Collection[str] = frozenset({"NULL", "null", ""}),
         encoding: str = "utf-8-sig",
+        **_,
     ):
         """Init function for the base CSV reader.
 

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

@@ -12,8 +12,10 @@
 
 from dve.core_engine.backends.base.reader import BaseFileReader
 from dve.core_engine.backends.exceptions import EmptyFileError
+from dve.core_engine.backends.readers.xml_linting import run_xmllint
 from dve.core_engine.backends.utilities import get_polars_type_from_annotation, stringify_model
 from dve.core_engine.loggers import get_logger
+from dve.core_engine.message import FeedbackMessage
 from dve.core_engine.type_hints import URI, EntityName
 from dve.parser.file_handling import NonClosingTextIOWrapper, get_content_length, open_stream
 from dve.parser.file_handling.implementations.file import (
@@ -101,7 +103,7 @@ def clear(self) -> None:
     def __iter__(self) -> Iterator["XMLElement"]: ...
 
 
-class BasicXMLFileReader(BaseFileReader):
+class BasicXMLFileReader(BaseFileReader):  # pylint: disable=R0902
     """A reader for XML files built atop LXML."""
 
     def __init__(
@@ -114,6 +116,10 @@ def __init__(
         sanitise_multiline: bool = True,
         encoding: str = "utf-8-sig",
         n_records_to_read: Optional[int] = None,
+        xsd_location: Optional[URI] = None,
+        xsd_error_code: Optional[str] = None,
+        xsd_error_message: Optional[str] = None,
+        rules_location: Optional[URI] = None,
         **_,
     ):
         """Init function for the base XML reader.
@@ -148,6 +154,15 @@ def __init__(
         """Encoding of the XML file."""
         self.n_records_to_read = n_records_to_read
         """The maximum number of records to read from a document."""
+        if rules_location is not None and xsd_location is not None:
+            self.xsd_location = rules_location + xsd_location
+        else:
+            self.xsd_location = xsd_location  # type: ignore
+            """The URI of the xsd file if wishing to perform xsd validation."""
+        self.xsd_error_code = xsd_error_code
+        """The error code to be reported if xsd validation fails (if xsd)"""
+        self.xsd_error_message = xsd_error_message
+        """The error message to be reported if xsd validation fails"""
         super().__init__()
         self._logger = get_logger(__name__)
 
@@ -259,6 +274,22 @@ def _parse_xml(
         for element in elements:
             yield self._parse_element(element, template_row)
 
+    def _run_xmllint(self, file_uri: URI) -> FeedbackMessage | None:
+        """Run xmllint package to validate against a given xsd. Requires xmlint to be installed
+        onto the system to run succesfully."""
+        if self.xsd_location is None:
+            raise AttributeError("Trying to run XML lint with no `xsd_location` provided.")
+        if self.xsd_error_code is None:
+            raise AttributeError("Trying to run XML with no `xsd_error_code` provided.")
+        if self.xsd_error_message is None:
+            raise AttributeError("Trying to run XML with no `xsd_error_message` provided.")
+        return run_xmllint(
+            file_uri=file_uri,
+            schema_uri=self.xsd_location,
+            error_code=self.xsd_error_code,
+            error_message=self.xsd_error_message,
+        )
+
     def read_to_py_iterator(
         self,
         resource: URI,