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b/pyproject.toml @@ -14,21 +14,17 @@ packages = [{ include = "regtech_data_validator", from = "src" }] python = ">=3.12,<4" pandas = "^2.2.2" pandera = "^0.22.1" -requests = "^2.32.3" tabulate = "^0.9.0" ujson = "^5.9.0" -fsspec = "^2024.6.1" polars-lts-cpu = "^1.21.0" pyarrow = "^19.0.0" -boto3 = "~1.36.3" -#pinning due to snyk high vulnerability find -s3fs = { version = "^2024.9.0", extras = ["aiohttp=^3.11.10"] } [tool.poetry.group.dev.dependencies] pytest = "8.3.4" pytest-cov = "6.0.0" beautifulsoup4 = "^4.12.3" lxml = "^5.3.0" +requests = "^2.32.3" [tool.poetry.group.data.dependencies] openpyxl = "^3.1.5" diff --git a/src/regtech_data_validator/cli.py b/src/regtech_data_validator/cli.py index 1ab0397..cdf5211 100644 --- a/src/regtech_data_validator/cli.py +++ b/src/regtech_data_validator/cli.py @@ -1,6 +1,5 @@ from dataclasses import dataclass from enum import StrEnum -from pathlib import Path from regtech_data_validator.data_formatters import df_to_csv, df_to_str, df_to_json, df_to_table, df_to_download from typing import Annotated, Optional @@ -8,7 +7,7 @@ import typer import typer.core -from regtech_data_validator.validator import validate_batch_csv +from regtech_data_validator.validator import validate_batch_csv, validate_lazy_frame from regtech_data_validator.validation_results import ValidationPhase # Need to do this because the latest version of typer, if the rich package exists @@ -22,6 +21,11 @@ app = typer.Typer(no_args_is_help=True, pretty_exceptions_enable=False) +class FileType(StrEnum): + CSV = 'csv' + PARQUET = 'parquet' + + @dataclass class KeyValueOpt: key: str @@ -57,7 +61,7 @@ def describe() -> None: @app.command(no_args_is_help=True) def validate( path: Annotated[ - Path, + str, typer.Argument( exists=True, dir_okay=False, @@ -77,6 +81,7 @@ def validate( ), ] = None, output: Annotated[Optional[OutputFormat], typer.Option()] = OutputFormat.TABLE, + filetype: Annotated[Optional[FileType], typer.Option()] = FileType.CSV, ) -> tuple[bool, pl.DataFrame]: """ Validate CFPB data submission @@ -87,11 +92,21 @@ def validate( final_phase = ValidationPhase.LOGICAL all_findings = [] final_df = pl.DataFrame() - # path = "s3://cfpb-devpub-regtech-sbl-filing-main/upload/2024/1234364890REGTECH006/156.csv" - for validation_results in validate_batch_csv(path, context_dict, batch_size=50000, batch_count=1): - total_findings += validation_results.error_counts.total_count + validation_results.warning_counts.total_count - final_phase = validation_results.phase - all_findings.append(validation_results) + if filetype == FileType.CSV: + for validation_results in validate_batch_csv(path, context_dict, batch_size=50000, batch_count=1): + total_findings += ( + validation_results.error_counts.total_count + validation_results.warning_counts.total_count + ) + final_phase = validation_results.phase + all_findings.append(validation_results) + elif filetype == FileType.PARQUET: + lf = pl.scan_parquet(path, allow_missing_columns=True) + for validation_results in validate_lazy_frame(lf, context_dict, batch_size=50000, batch_count=1): + total_findings += ( + validation_results.error_counts.total_count + validation_results.warning_counts.total_count + ) + final_phase = validation_results.phase + all_findings.append(validation_results) if all_findings: final_df = pl.concat([v.findings for v in all_findings], how="diagonal") diff --git a/src/regtech_data_validator/data_formatters.py b/src/regtech_data_validator/data_formatters.py index faf7864..ab34a29 100644 --- a/src/regtech_data_validator/data_formatters.py +++ b/src/regtech_data_validator/data_formatters.py @@ -1,6 +1,7 @@ import ujson import polars as pl +from typing import Dict, Any from tabulate import tabulate from functools import partial @@ -54,7 +55,7 @@ def format_findings(df: pl.DataFrame, phase, checks): "record_no", "uid", ], - columns="field_number", + on="field_number", values=["field_name", "field_value"], aggregate_function="first", ) @@ -261,7 +262,7 @@ def process_group_data(group_df, json_results, group_size, checks): return group_df -def process_chunk(df: pl.DataFrame, validation_id: str, check: SBLCheck) -> [dict]: +def process_chunk(df: pl.DataFrame, validation_id: str, check: SBLCheck) -> Dict[str, Any]: # once we have a grouped dataframe, working with the data as a # python dict is much faster findings_json = ujson.loads(df.write_json()) diff --git a/src/regtech_data_validator/validation_results.py b/src/regtech_data_validator/validation_results.py index 40a6352..f9262f2 100644 --- a/src/regtech_data_validator/validation_results.py +++ b/src/regtech_data_validator/validation_results.py @@ -26,3 +26,4 @@ class ValidationResults(object): is_valid: bool findings: pl.DataFrame phase: ValidationPhase + record_count: int = 0 diff --git a/src/regtech_data_validator/validator.py b/src/regtech_data_validator/validator.py index a32c309..ff76173 100644 --- a/src/regtech_data_validator/validator.py +++ b/src/regtech_data_validator/validator.py @@ -1,7 +1,9 @@ """Creates two DataFrameSchema objects by rendering the schema template with validations listed in phase 1 and phase 2.""" +import logging from pathlib import Path +from typing import Dict, List import polars as pl import pandera.polars as pa from pandera import Check @@ -12,17 +14,14 @@ from regtech_data_validator.validation_results import ValidationPhase, Counts, ValidationResults from regtech_data_validator.data_formatters import format_findings -from fsspec import AbstractFileSystem, filesystem - -import shutil -import os - from regtech_data_validator.phase_validations import ( get_phase_1_schema_for_lei, get_phase_2_schema_for_lei, get_register_schema, ) +log = logging.getLogger(__name__) + # Gets all associated field names from the check def _get_check_fields(check: Check, primary_column: str) -> list[str]: @@ -55,9 +54,11 @@ def _filter_valid_records(df: pl.DataFrame, check_output: pl.Series, fields: lis def _records_to_fields(failed_records_df: pl.DataFrame) -> pl.DataFrame: - # Melts the DataFrame with columns per Check field to DataFrame with a row per field - failed_record_fields_df = failed_records_df.melt( - variable_name='field_name', value_name='field_value', id_vars=['record_no'] + # Unpivot the DataFrame with columns per Check field to DataFrame with a row per field + failed_record_fields_df = failed_records_df.unpivot( + variable_name='field_name', + value_name='field_value', + index=['record_no'], ) return failed_record_fields_df @@ -93,49 +94,50 @@ def validate( # `list[dict[str,Any]]`, but it's actually of type `SchemaError` schema_error: SchemaError - if process_errors: - for schema_error in err.schema_errors: - check = schema_error.check - column_name = schema_error.schema.name - - # CHECK_ERROR is thrown by pandera polars if the check itself has a coding error, NOT if the check data results in an error - if ( - schema_error.reason_code is SchemaErrorReason.CHECK_ERROR - or schema_error.reason_code is SchemaErrorReason.COLUMN_NOT_IN_DATAFRAME - ): - raise RuntimeError(schema_error) from schema_error - if not check: - raise RuntimeError( - f'SchemaError occurred with no associated Check for {column_name} column' - ) from schema_error - - if not isinstance(check, SBLCheck): - raise RuntimeError( - f'Check {check} type on {column_name} column not supported. Must be of type {SBLCheck}' - ) from schema_error - - schema_error = gather_errors(schema_error) - - fields = _get_check_fields(check, column_name) - check_output: pl.Series | None = schema_error.check_output - - if check_output is not None: - # Filter data not associated with failed Check, and update index for merging with findings_df - check_output = check_output.with_columns(pl.col('index').add(row_start)) + # if process_errors: + for schema_error in err.schema_errors: + check = schema_error.check + column_name = schema_error.schema.name + + # CHECK_ERROR is thrown by pandera polars if the check itself has a coding error, NOT if the check data results in an error + if ( + schema_error.reason_code is SchemaErrorReason.CHECK_ERROR + or schema_error.reason_code is SchemaErrorReason.COLUMN_NOT_IN_DATAFRAME + ): + raise RuntimeError(schema_error) from schema_error + if not check: + raise RuntimeError( + f'SchemaError occurred with no associated Check for {column_name} column' + ) from schema_error + + if not isinstance(check, SBLCheck): + raise RuntimeError( + f'Check {check} type on {column_name} column not supported. Must be of type {SBLCheck}' + ) from schema_error + + fields = _get_check_fields(check, column_name) + check_output = gather_errors(schema_error.check_output) + + if check_output is not None: + # Filter data not associated with failed Check, and update index for merging with findings_df + check_output = check_output.with_columns(pl.col('index').add(row_start)) + if process_errors: failed_records_df = _filter_valid_records(submission_df, check_output, fields) failed_record_fields_df = _records_to_fields(failed_records_df) findings = _add_validation_metadata(failed_record_fields_df, check) - check_findings.append(findings) else: - # The above exception handling _should_ prevent this from ever happenin, but...just in case. - raise RuntimeError( - f'No check output for "{check.name}" check. Pandera SchemaError: {schema_error}' + findings = _add_validation_metadata(check_output, check) + findings = findings.with_columns( + pl.lit(check.scope).alias("scope"), pl.lit(check.severity.value).alias("validation_type") ) - if check_findings: - findings_df = pl.concat(check_findings) + check_findings.append(findings) + else: + # The above exception handling _should_ prevent this from ever happenin, but...just in case. + raise RuntimeError(f'No check output for "{check.name}" check. Pandera SchemaError: {schema_error}') + if check_findings: + findings_df = pl.concat(check_findings) - updated_df = add_uid(findings_df, submission_df, row_start) - return updated_df + return add_uid(findings_df, submission_df, row_start) if process_errors else findings_df # Add the uid for the record throwing the error/warning to the error dataframe @@ -151,16 +153,14 @@ def add_uid(results_df: pl.DataFrame, submission_df: pl.DataFrame, offset: int) # This function is a Generator, and will yield the results of each batch of processing, along with the # phase (SYNTACTICAL/LOGICAL) that the findings were found. Callers of this function will want to # store or concat each iteration of findings -def validate_batch_csv( - path: Path | str, +def validate_data( + source: Path | str | pl.LazyFrame, context: dict[str, str] | None = None, batch_size: int = 50000, batch_count: int = 1, max_errors=1000000, ): has_syntax_errors = False - real_path = get_real_file_path(path) - # process the data first looking for syntax (phase 1) errors, then looking for logical (phase 2) errors/warnings syntax_schema = get_phase_1_schema_for_lei(context) syntax_checks = [check for col_schema in syntax_schema.columns.values() for check in col_schema.checks] @@ -169,8 +169,10 @@ def validate_batch_csv( all_uids = [] - for validation_results, uids in validate_chunks( - syntax_schema, real_path, batch_size, batch_count, max_errors, syntax_checks + batch_validation = validate_lazy_chunks if isinstance(source, pl.LazyFrame) else validate_chunks + + for validation_results, uids in batch_validation( + syntax_schema, source, batch_size, batch_count, max_errors, syntax_checks ): all_uids.extend(uids) # validate, and therefore validate_chunks, can return an empty dataframe for findings @@ -179,31 +181,34 @@ def validate_batch_csv( yield validation_results if not has_syntax_errors: - register_schema = get_register_schema(context) - validation_results = validate(register_schema, pl.DataFrame({"uid": all_uids}), 0, True) - if not validation_results.is_empty(): - validation_results = format_findings( - validation_results, - ValidationPhase.LOGICAL.value, - [check for col_schema in register_schema.columns.values() for check in col_schema.checks], - ) - error_counts, warning_counts = get_scope_counts(validation_results) - results = ValidationResults( - error_counts=error_counts, - warning_counts=warning_counts, - is_valid=((error_counts.total_count + warning_counts.total_count) == 0), - findings=validation_results, - phase=register_schema.name, - ) - yield results + yield validate_register_level(context, all_uids) - for validation_results, _ in validate_chunks( - logic_schema, real_path, batch_size, batch_count, max_errors, logic_checks + for validation_results, _ in batch_validation( + logic_schema, source, batch_size, batch_count, max_errors, logic_checks ): yield validation_results - if os.path.isdir("/tmp/s3"): - shutil.rmtree("/tmp/s3") + +def validate_batch_csv( + path: Path | str, + context: dict[str, str] | None = None, + batch_size: int = 50000, + batch_count: int = 1, + max_errors=1000000, +): + for results in validate_data(path, context, batch_size, batch_count, max_errors): + yield results + + +def validate_lazy_frame( + lf: pl.LazyFrame, + context: dict[str, str] | None = None, + batch_size: int = 50000, + batch_count: int = 1, + max_errors=1000000, +): + for results in validate_data(lf, context, batch_size, batch_count, max_errors): + yield results # Reads in a path to a csv in batches, using batch_size to determine number of rows to read into the buffer, @@ -213,55 +218,91 @@ def validate_batch_csv( # batch_count adds processing cylces (time) but can significantly reduce resources. def validate_chunks(schema, path, batch_size, batch_count, max_errors, checks): reader = pl.read_csv_batched(path, infer_schema_length=0, missing_utf8_is_empty_string=True, batch_size=batch_size) - batches = reader.next_batches(batch_count) process_errors = True total_count = 0 row_start = 0 + batches = reader.next_batches(batch_count) while batches: df = pl.concat(batches) - validation_results = validate(schema, df, row_start, process_errors) - if not validation_results.is_empty(): - - validation_results = format_findings(validation_results, schema.name.value, checks) - - error_counts, warning_counts = get_scope_counts(validation_results) - results = ValidationResults( - error_counts=error_counts, - warning_counts=warning_counts, - is_valid=((error_counts.total_count + warning_counts.total_count) == 0), - findings=validation_results, - phase=schema.name, + validation_results, total_count, process_errors = validate_chunk( + schema, df, total_count, row_start, max_errors, process_errors, checks ) + row_start += df.height + yield validation_results, df["uid"].to_list() + batches = reader.next_batches(batch_count) - total_count += results.findings.height - - if total_count > max_errors and process_errors: - process_errors = False - head_count = results.findings.height - (total_count - max_errors) - results.findings = results.findings.head(head_count) +def validate_lazy_chunks(schema, lf: pl.LazyFrame, batch_size: int, batch_count, max_errors, checks): + process_errors = True + total_count = 0 + row_start = 0 + df = lf.slice(row_start, batch_size).collect() + while df.height: + validation_results, total_count, process_errors = validate_chunk( + schema, df, total_count, row_start, max_errors, process_errors, checks + ) row_start += df.height - batches = reader.next_batches(batch_count) - yield results, df["uid"].to_list() + yield validation_results, df["uid"].to_list() + df = lf.slice(row_start, batch_size).collect() + + +def validate_chunk(schema, df: pl.DataFrame, total_count, row_start, max_errors, process_errors, checks): + log.debug("Start UID: %s, Last UID: %s", df['uid'][0], df['uid'][-1]) + validation_results = validate(schema, df, row_start, process_errors) + if process_errors and not validation_results.is_empty(): + validation_results = format_findings(validation_results, schema.name.value, checks) + + error_counts, warning_counts = get_scope_counts(validation_results) + results = ValidationResults( + record_count=df.height, + error_counts=error_counts, + warning_counts=warning_counts, + is_valid=((error_counts.total_count + warning_counts.total_count) == 0), + findings=validation_results if process_errors else pl.DataFrame(), + phase=schema.name, + ) + + total_count += error_counts.total_count + warning_counts.total_count + log.debug("Counts: %d %d", error_counts, warning_counts) + if total_count > max_errors and process_errors: + log.debug("Reached max errors, adjusting results") + process_errors = False + head_count = results.findings.height - (total_count - max_errors) + log.debug( + "Results height: %d, total count: %d, head count: %d", results.findings.height, total_count, head_count + ) + results.findings = results.findings.head(head_count) + log.debug("Results height after heading %d", results.findings.height) + + return results, total_count, process_errors -def get_real_file_path(path): - path = str(path) - if path.startswith("s3://"): - fs: AbstractFileSystem = filesystem(protocol="filecache", target_protocol="s3", cache_storage="/tmp/s3") - path = fs.unstrip_protocol(path) - with fs.open(path, "r") as f: - return f.name - return path +def validate_register_level(context: Dict[str, str] | None, all_uids: List[str]): + log.debug("Processing register logic errors") + register_schema = get_register_schema(context) + validation_results = validate(register_schema, pl.DataFrame({"uid": all_uids}), 0, True) + if not validation_results.is_empty(): + validation_results = format_findings( + validation_results, + ValidationPhase.LOGICAL.value, + [check for col_schema in register_schema.columns.values() for check in col_schema.checks], + ) + error_counts, warning_counts = get_scope_counts(validation_results) + results = ValidationResults( + error_counts=error_counts, + warning_counts=warning_counts, + is_valid=((error_counts.total_count + warning_counts.total_count) == 0), + findings=validation_results, + phase=register_schema.name, + ) + log.debug("Register counts: %d %d", error_counts, warning_counts) + return results # This function adds an index column (polars dataframes do not normally have one), and filters out # any row that did not fail a check. -def gather_errors(schema_error: SchemaError): - schema_error.check_output = schema_error.check_output.with_row_index() - error_indices = schema_error.check_output.filter(~pl.col("check_output"))["index"].to_list() - schema_error.check_output = schema_error.check_output.filter(pl.col("index").is_in(error_indices)) - return schema_error +def gather_errors(check_output: pl.DataFrame): + return check_output.with_row_index().filter(~pl.col("check_output")) def get_scope_counts(error_frame: pl.DataFrame): diff --git a/tests/test_schema_functions.py b/tests/test_schema_functions.py index d0b10b0..f824da4 100644 --- a/tests/test_schema_functions.py +++ b/tests/test_schema_functions.py @@ -2,6 +2,7 @@ import pytest import tempfile from pathlib import Path +from polars.exceptions import ColumnNotFoundError from regtech_data_validator.validator import validate_batch_csv from regtech_data_validator.validation_results import ValidationPhase @@ -271,9 +272,9 @@ def test_with_non_matching_lei(self, csv_df_file): assert results[2].phase == ValidationPhase.LOGICAL def test_column_not_found_in_df(self, csv_df_mission_column_file): - with pytest.raises(RuntimeError) as re: + with pytest.raises(ColumnNotFoundError) as re: list(validate_batch_csv(csv_df_mission_column_file)) - assert "column 'uid' not in dataframe" in str(re.value) + assert '"uid" not found' in str(re.value) def test_same_uids(self, csv_df_same_uids_file): results = list(validate_batch_csv(csv_df_same_uids_file))