AdvancedAnalysisFileParser 0.1.4__cp311-cp311-win_amd64.whl

AdvancedAnalysisFileParser/Models/ConditionOperator.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from enum import Enum
+
+
+class ConditionOperator(Enum):
+    EQ: str
+    NE: str
+    GT: str
+    LT: str
+    GE: str
+    LE: str
+    CONTAINS: str

AdvancedAnalysisFileParser/Models/FieldCondition.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from typing import Any, Callable, Dict, Optional
+from .ConditionOperator import ConditionOperator
+
+
+class FieldCondition:
+    def __init__(self, operator: ConditionOperator, value: Any, message: str, field: Optional[str]=None):
+        """Create a condition to check a field value against a target value using an operator.
+
+        Args:
+            operator (ConditionOperator): The comparison operator (e.g., EQ, GT, CONTAINS).
+            value (Any): The value to compare against.
+            message (str): Message to return if the condition is met.
+            field (Optional[str]): Name of the field to check (optional, for context).
+        """
+        ...
+    def check(self, value: Any) -> bool:
+        """Check if the provided value satisfies the condition.
+
+        Args:
+            value (Any): The value to check.
+
+        Returns:
+            bool: True if the condition is met, False otherwise.
+        """
+        ...
+
+OPERATOR_FUNCS: Dict[ConditionOperator, Callable[[Any, Any], bool]]

AdvancedAnalysisFileParser/Models/FieldWarningConfig.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from typing import Optional
+from .FieldCondition import FieldCondition
+
+
+class FieldWarningConfig:
+    warning: Optional[FieldCondition]

AdvancedAnalysisFileParser/Models/JsonDict.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from typing import Any, Dict
+
+JsonDict: Any

AdvancedAnalysisFileParser/Models/SectionConfig.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from dataclasses import dataclass
+from typing import Optional, Dict
+from .FieldCondition import FieldCondition
+
+
+@dataclass
+class SectionConfig:
+    include_all_fields: bool
+    fields: Optional[Dict[str, FieldCondition]]

AdvancedAnalysisFileParser/Models/__init__.py

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+from .JsonDict import JsonDict
+from .FieldCondition import FieldCondition
+from .ConditionOperator import ConditionOperator
+from .FieldWarningConfig import FieldWarningConfig
+from .SectionConfig import SectionConfig
+
+__all__ = [
+    "JsonDict",
+    "ConditionOperator",
+    "SectionConfig",
+    "FieldCondition",
+    "FieldWarningConfig"
+]

AdvancedAnalysisFileParser/Parsers/AdvancedAnalysisFileParserFactory.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from .IAdvancedAnalysisFileParser import IAdvancedAnalysisFileParser
+from .DragenTruSightOncology500TSVParser import DragenTruSightOncology500TSVParser
+from .OneLineTsvParser import OneLineTsvParser
+from .JsonSectionParser import JsonSectionParser
+from ..Models import JsonDict
+
+
+class AdvancedAnalysisFileParserFactory:
+    """Returns the correct IParser implementation based on file path."""
+    @staticmethod
+    def get_parser(file_path: str) -> IAdvancedAnalysisFileParser:
+        ...

AdvancedAnalysisFileParser/Parsers/DragenTruSightOncology500TSVParser.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+import csv
+import logging
+from typing import Dict, Any, List, Optional, Union, Tuple
+from .IAdvancedAnalysisFileParser import IAdvancedAnalysisFileParser
+from ..Models import JsonDict, SectionConfig
+
+
+class DragenTruSightOncology500TSVParser(IAdvancedAnalysisFileParser):
+    """Parser for CombinedVariantOutput TSV.
+    Reads only configured sections and fields, streaming parse inside loader.
+    """
+    def parse(self) -> JsonDict:
+        """Entry point: prepare section configs and delegate to loader-parsing function."""
+        ...

AdvancedAnalysisFileParser/Parsers/IAdvancedAnalysisFileParser.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from abc import ABC, abstractmethod
+import os
+from pathlib import Path
+from typing import Any
+from ..Warnings import IWarning
+from AdvancedAnalysisFileParser.AdvancedAnalysisConstants import AdvancedAnalysisConstants
+from AdvancedAnalysisFileParser.Warnings.WarningFactory import WarningFactory
+from ..Models import JsonDict
+
+
+class IAdvancedAnalysisFileParser(ABC):
+    section_config: JsonDict
+    file_config: JsonDict
+    def __init__(self, section_config: JsonDict, file_path: str) -> None:
+        """Initialize a file parser for advanced analysis.
+
+        Args:
+            section_config (JsonDict): Section configuration for parsing.
+            file_path (str): Path to the file to parse (must be .json or .tsv).
+
+        Raises:
+            ValueError: If file_path is empty or not a string.
+            FileNotFoundError: If the file does not exist.
+        """
+        ...
+    def parse(self) -> JsonDict:
+        """Parse the file and return its data as a JsonDict.
+
+        Returns:
+            JsonDict: Parsed data from the file.
+        """
+        ...
+    def build_result(self, data: JsonDict) -> JsonDict:
+        """Build a result dictionary from parsed data and section config.
+
+        Args:
+            data (JsonDict): Parsed data from the file.
+
+        Returns:
+            JsonDict: Result dictionary with formatted values and warnings.
+        """
+        ...

AdvancedAnalysisFileParser/Parsers/JsonSectionParser.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+import json
+from .IAdvancedAnalysisFileParser import IAdvancedAnalysisFileParser
+from ..Models import JsonDict
+
+
+class JsonSectionParser(IAdvancedAnalysisFileParser):
+    """Parse JSON files with a specific section into a unified format.
+    The section is specified by the 'json_key' or 'caller_key' in the config.
+    """
+    def parse(self) -> JsonDict:
+        ...

AdvancedAnalysisFileParser/Parsers/OneLineTsvParser.pyi

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+# Generated by tools/generate_stubs.py - do not edit.
+# The implementation ships compiled; this file is the published surface.
+
+from typing import Any
+from .IAdvancedAnalysisFileParser import IAdvancedAnalysisFileParser
+from ..Models import JsonDict
+
+
+class OneLineTsvParser(IAdvancedAnalysisFileParser):
+    is_tsv_parser: bool
+    def parse(self) -> JsonDict:
+        ...

AdvancedAnalysisFileParser/Parsers/__init__.py

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+from .IAdvancedAnalysisFileParser import IAdvancedAnalysisFileParser
+from .AdvancedAnalysisFileParserFactory import AdvancedAnalysisFileParserFactory
+
+__all__ = [
+    "IAdvancedAnalysisFileParser",
+    "AdvancedAnalysisFileParserFactory",
+]