sapiopycommons 2025.8.14a703__py3-none-any.whl → 2025.8.15a704__py3-none-any.whl

sapiopycommons/files/assay_plate_reader.py

@@ -1,93 +0,0 @@
-import base64
-import dataclasses
-from typing import Any
-
-from databind.core.dataclasses import dataclass
-from databind.json import loads
-from sapiopylib.rest.utils.singletons import SapioContextManager
-
-
-@dataclasses.dataclass
-class ProcessAssayPlateRequest:
-    """
-    A request to process the results of assay plate reader with a configuration set in Sapio.
-
-    Attributes:
-        num_rows (int): The number of rows in the plate.
-        num_columns (int): The number of columns in the plate.
-        plate_ids_in_context (list[str]): List of plate IDs that are in context for this request.
-        filename (str): The name of the file containing the assay data.
-        file_data (bytes): The binary content of the file.
-        plate_reader_config_name (str): The name of the plate reader configuration to use.
-    """
-    num_rows: int
-    num_columns: int
-    plate_ids_in_context: list[str] | None
-    filename: str
-    file_data: bytes
-    plate_reader_config_name: str
-
-    def to_json(self) -> dict[str, Any]:
-        return {
-            "numRows": self.num_rows,
-            "numCols": self.num_columns,
-            "plateIdsInContext": self.plate_ids_in_context,
-            "fileName": self.filename,
-            "fileDataBase64": base64.b64encode(self.file_data).decode('utf-8'),
-            "plateReaderName": self.plate_reader_config_name
-        }
-
-
-@dataclass
-class AssayPlateResultIdent:
-    plateId: str
-    channelIdOrBlock: str
-    kineticAssaySeconds: float | None
-
-
-@dataclass
-class AssayResultDatum:
-    """
-    Describes the data received from an assay plate reader.
-    Most of the time, the data is a single value, but sometimes it can be multiple values, especially for kinetic data.
-    """
-    DEFAULT_PROPERTY_NAME: str = "read"
-    rowPosition: str
-    columnPosition: str
-    valueByPropertyName: dict[str, float]
-    textValueByPropertyName: dict[str, str]
-
-
-@dataclass
-class AssayPlateResult:
-    """
-    Assay plate load result for a single plate in a file. A file can have more than one of this result if it has multiple plate of data in a single file.
-    """
-    resultIdent: AssayPlateResultIdent
-    numRows: int
-    numColumns: int
-    resultDatum: list[AssayResultDatum]
-
-
-@dataclass
-class AssayFileLoadResult:
-    """
-    The entire top-level file loading result for an assay plate reader file.
-    """
-    filename: str
-    plateResultList: list[AssayPlateResult]
-
-
-class AssayPlateReader(SapioContextManager):
-    """
-    This class contains services for Sapio Assay Plate Reader.
-    """
-
-    def process_plate_reader_data(self, request: ProcessAssayPlateRequest) -> AssayFileLoadResult:
-        """
-        Processes the assay plate reader data using provided request into a structured result using configuration defined in Sapio.
-        """
-        payload = request.to_json()
-        response = self.user.plugin_post("assayplatereader/process", payload=payload)
-        self.user.raise_for_status(response)
-        return loads(response.text, AssayFileLoadResult)

sapiopycommons/files/file_text_converter.py

@@ -1,207 +0,0 @@
-import io
-import os
-import tempfile
-from enum import Enum, auto
-
-class FileType(Enum):
-    """Supported file types for conversion."""
-    TXT = auto()
-    MD = auto()
-    CSV = auto()
-    DOC = auto()
-    DOCX = auto()
-    XLS = auto()
-    XLSX = auto()
-    PPT = auto()
-    PPTX = auto()
-    PDF = auto()
-    UNKNOWN = auto()
-
-
-class FileToTextConverter:
-    """
-    A class for converting various file types to raw text.
-    """
-    @staticmethod
-    def mime_type_to_enum(mime_type: str) -> FileType:
-        """
-        Converts a MIME type to a FileType enum.
-
-        :param mime_type: The MIME type string to convert.
-        :return: The corresponding FileType enum, or UNKNOWN if not recognized.
-        """
-        if not mime_type or not mime_type.strip():
-            return FileType.UNKNOWN
-
-        mime_map = {
-            "text/plain": FileType.TXT,
-            "text/markdown": FileType.MD,
-            "text/csv": FileType.CSV,
-            "application/msword": FileType.DOC,
-            "application/vnd.openxmlformats-officedocument.wordprocessingml.document": FileType.DOCX,
-            "application/vnd.ms-excel": FileType.XLS,
-            "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": FileType.XLSX,
-            "application/vnd.ms-powerpoint": FileType.PPT,
-            "application/vnd.openxmlformats-officedocument.presentationml.presentation": FileType.PPTX,
-            "application/pdf": FileType.PDF,
-        }
-        return mime_map.get(mime_type, FileType.UNKNOWN)
-
-    @staticmethod
-    def file_extension_to_enum(file_path: str) -> FileType:
-        """
-        Converts a file path or extension to a FileType enum.
-
-        :param file_path: The file path or extension to convert.
-        :return: The corresponding FileType enum, or UNKNOWN if not recognized.
-        """
-        if not file_path or not file_path.strip():
-            return FileType.UNKNOWN
-
-        # Extract the file extension, removing the leading dot and making it lowercase
-        file_extension = os.path.splitext(file_path)[1].lstrip('.').lower()
-
-        ext_map = {
-            "txt": FileType.TXT,
-            "md": FileType.MD,
-            "csv": FileType.CSV,
-            "doc": FileType.DOC,
-            "docx": FileType.DOCX,
-            "xls": FileType.XLS,
-            "xlsx": FileType.XLSX,
-            "ppt": FileType.PPT,
-            "pptx": FileType.PPTX,
-            "pdf": FileType.PDF,
-        }
-        return ext_map.get(file_extension, FileType.UNKNOWN)
-
-    @classmethod
-    def parse_file(cls, file_type: FileType, file_bytes: bytes) -> str | None:
-        """
-        Parses file bytes based on the FileType and returns the text content.
-
-        :param file_type: The type of the file to parse.
-        :param file_bytes: The raw bytes of the file to parse.
-        :return: The text content of the file, or None if the file type is not supported or parsing fails.
-        """
-        if file_type is None or file_bytes is None:
-            return None
-        if not file_bytes:
-            return ""
-
-        # Dispatch to the correct parser method
-        parser_map = {
-            FileType.TXT: cls._parse_plain_text,
-            FileType.MD: cls._parse_plain_text,
-            FileType.CSV: cls._parse_plain_text,
-            FileType.DOC: cls._parse_doc,
-            FileType.DOCX: cls._parse_docx,
-            FileType.XLS: cls._parse_xls,
-            FileType.XLSX: cls._parse_xlsx,
-            FileType.PPT: cls._parse_ppt,
-            FileType.PPTX: cls._parse_pptx,
-            FileType.PDF: cls._parse_pdf,
-        }
-
-        parser_func = parser_map.get(file_type)
-
-        if parser_func:
-            return parser_func(file_bytes)
-
-        return None
-
-    @staticmethod
-    def _parse_plain_text(file_bytes: bytes) -> str:
-        return file_bytes.decode('utf-8')
-
-    @staticmethod
-    def _run_textract(file_bytes: bytes, extension: str) -> str:
-        """
-        Helper to run textract on in-memory bytes by writing to a temp file.
-        Note: textract may require external system dependencies.
-        """
-        import textract
-        with tempfile.NamedTemporaryFile(suffix=f".{extension}", delete=True) as temp_file:
-            temp_file.write(file_bytes)
-            temp_file.flush()  # Ensure all bytes are written to disk
-            text = textract.process(temp_file.name).decode('utf-8')
-        return text
-
-    @classmethod
-    def _parse_doc(cls, file_bytes: bytes) -> str:
-        return cls._run_textract(file_bytes, 'doc')
-
-    @staticmethod
-    def _parse_docx(file_bytes: bytes) -> str:
-        import docx
-        with io.BytesIO(file_bytes) as stream:
-            document = docx.Document(stream)
-            return "\n".join(para.text for para in document.paragraphs if para.text.strip())
-
-    @staticmethod
-    def _parse_xls(file_bytes: bytes) -> str:
-        import xlrd
-        workbook = xlrd.open_workbook(file_contents=file_bytes)
-        text_parts = []
-        for sheet in workbook.sheets():
-            text_parts.append(f"Sheet: {sheet.name}\n")
-            for row_idx in range(sheet.nrows):
-                row_cells = []
-                for col_idx in range(sheet.ncols):
-                    cell_text = str(sheet.cell_value(row_idx, col_idx))
-                    if cell_text.strip():
-                        row_cells.append(cell_text + "\t")
-                if row_cells:
-                    text_parts.append("".join(row_cells))
-                text_parts.append("\n")
-            text_parts.append("\n")
-        return "".join(text_parts)
-
-    @staticmethod
-    def _parse_xlsx(file_bytes: bytes) -> str:
-        import openpyxl
-        with io.BytesIO(file_bytes) as stream:
-            workbook = openpyxl.load_workbook(stream, read_only=True)
-            text_parts = []
-            for sheet in workbook.worksheets:
-                text_parts.append(f"Sheet: {sheet.title}\n")
-                for row in sheet.iter_rows():
-                    row_cells = []
-                    for cell in row:
-                        cell_text = str(cell.value) if cell.value is not None else ""
-                        if cell_text.strip():
-                            row_cells.append(cell_text + "\t")
-                    if row_cells:
-                        text_parts.append("".join(row_cells))
-                    text_parts.append("\n")
-                text_parts.append("\n")
-            return "".join(text_parts)
-
-    @classmethod
-    def _parse_ppt(cls, file_bytes: bytes) -> str:
-        return cls._run_textract(file_bytes, 'ppt')
-
-    @staticmethod
-    def _parse_pptx(file_bytes: bytes) -> str:
-        import pptx
-        with io.BytesIO(file_bytes) as stream:
-            presentation = pptx.Presentation(stream)
-            text_parts = []
-            for slide in presentation.slides:
-                for shape in slide.shapes:
-                    if shape.has_text_frame:
-                        text = shape.text_frame.text
-                        if text and text.strip():
-                            text_parts.append(text)
-            return "\n".join(text_parts)
-
-    @staticmethod
-    def _parse_pdf(file_bytes: bytes) -> str:
-        """Parses a PDF file's bytes and extracts text using PyMuPDF."""
-        import pymupdf
-        text_parts = []
-        with io.BytesIO(file_bytes) as stream:
-            with pymupdf.open(stream=stream) as doc:
-                for page in doc:
-                    text_parts.append(page.get_text())
-        return "\n".join(text_parts)