AdvancedAnalysisFileParser 0.1.4__cp313-cp313-win_amd64.whl

AdvancedAnalysisFileParser/AdvancedAnalysisConstants.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 Final
+
+
+class AdvancedAnalysisConstants:
+    OUTPUT_DIR: Final[str]
+    OUTPUT_JSON: Final[str]
+    INPUT_DIR: Final[str]
+    MAP_FILES: Final[str]
+    WARNING_KEY: Final[str]
+    SEQUENCE_ID: Final[str]

AdvancedAnalysisFileParser/AdvancedAnalysisParser.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 argparse
+import json
+import logging
+import os
+from typing import Optional
+from .Models import *
+from .Warnings import *
+from .Parsers import *
+from .AdvancedAnalysisConstants import AdvancedAnalysisConstants
+
+
+class AdvancedAnalysisParser:
+    """AdvancedAnalysisParser
+
+    Parses special callers outputs (TSV/JSON) into a unified JSON format.
+
+    Usage:
+        - Instantiate with a config dict (JsonDict) specifying input/output files and directories.
+        - Call run() to parse and write output JSON.
+        - Use from_cli() for command-line usage.
+
+    Parameters for constructor (json_request: JsonDict):
+        - input_files: List[str] (optional) - List of input file paths to parse.
+        - input_dir: str (optional) - Directory containing input files.
+        - output_dir: str (optional) - Directory to write output JSON.
+        - output_json: str (optional) - Output JSON filename.
+        - MAP_FILES: dict (optional) - Mapping for file-specific configs.
+
+    Returns:
+        - run(return_dict=True): Returns parsed result as JsonDict.
+        - run(return_dict=False): Writes output JSON file, returns None.
+
+    Example:
+        config = {
+            "input_files": ["file1.json", "file2.tsv"],
+            "input_dir": "./inputs",
+            "output_dir": "./outputs",
+            "output_json": "result.json"
+        }
+        parser = AdvancedAnalysisParser(config)
+        parser.run()
+    """
+    def __init__(self, json_request: JsonDict) -> None:
+        """Initialize parser with configuration.
+
+        Args:
+            json_request (JsonDict): Configuration dict. See class docstring for keys.
+        """
+        ...
+    def run(self, return_dict: bool=False) -> Optional[JsonDict]:
+        """Parse files and output unified JSON.
+
+        Args:
+            return_dict (bool): If True, returns parsed result as dict. If False, writes output file.
+
+        Returns:
+            JsonDict if return_dict is True, else None.
+        """
+        ...
+    def parse_files(self) -> JsonDict:
+        """Parse all input files specified in config.
+
+        Returns:
+            JsonDict: Unified parsed result from all files.
+        Raises:
+            ValueError: If no input files found.
+        """
+        ...
+    def parse_by_config(self, parser: IAdvancedAnalysisFileParser) -> JsonDict:
+        """Parse a single file using its parser and build result.
+
+        Args:
+            parser (IAdvancedAnalysisFileParser): Parser instance for the file.
+
+        Returns:
+            JsonDict: Parsed and formatted result for the file.
+        """
+        ...
+    @staticmethod
+    def parse_args() -> argparse.Namespace:
+        """Parse command-line arguments for CLI usage.
+
+        Returns:
+            argparse.Namespace: Parsed CLI arguments.
+        """
+        ...
+    @classmethod
+    def from_cli(cls) -> None:
+        """Entry point for command-line usage.
+        Loads config from file and/or CLI args, runs parser.
+        """
+        ...