sapiopycommons 2025.7.14a610__py3-none-any.whl → 2025.7.15a611__py3-none-any.whl

sapiopycommons/callbacks/callback_util.py

@@ -780,7 +780,7 @@ class CallbackUtil:
         # FR-47690: Set default values for fields that aren't present.
         for row in values:
             for field in fields:
-                if field.data_field_name not in values:
+                if field.data_field_name not in row:
                     row[field.data_field_name] = field.default_value
 
         # Convert the group_by parameter to a field name.
@@ -1812,7 +1812,8 @@ class CallbackUtil:
         return response
 
     def request_file(self, title: str, exts: Iterable[str] | None = None,
-                     show_image_editor: bool = False, show_camera_button: bool = False) -> tuple[str, bytes]:
+                     show_image_editor: bool = False, show_camera_button: bool = False,
+                     *, enforce_file_extensions: bool = True) -> tuple[str, bytes]:
         """
         Request a single file from the user.
 
@@ -1822,6 +1823,8 @@ class CallbackUtil:
         :param show_image_editor: Whether the user will see an image editor when image is uploaded in this file prompt.
         :param show_camera_button: Whether the user will be able to use camera to take a picture as an upload request,
             rather than selecting an existing file.
+        :param enforce_file_extensions: If true, then the file extensions provided in the exts parameter will be
+            enforced. If false, then the user may upload any file type.
         :return: The file name and bytes of the uploaded file.
         """
         # If no extensions were provided, use an empty list for the extensions instead.
@@ -1841,11 +1844,12 @@ class CallbackUtil:
             file_path: str = self.__send_dialog(request, self.callback.show_file_dialog, data_sink=do_consume)
 
         # Verify that each of the file given matches the expected extension(s).
-        self.__verify_file(file_path, sink.data, exts)
+        self.__verify_file(file_path, sink.data, exts if enforce_file_extensions else None)
         return file_path, sink.data
 
     def request_files(self, title: str, exts: Iterable[str] | None = None,
-                      show_image_editor: bool = False, show_camera_button: bool = False) -> dict[str, bytes]:
+                      show_image_editor: bool = False, show_camera_button: bool = False,
+                      *, enforce_file_extensions: bool = True) -> dict[str, bytes]:
         """
         Request multiple files from the user.
 
@@ -1855,6 +1859,8 @@ class CallbackUtil:
         :param show_image_editor: Whether the user will see an image editor when image is uploaded in this file prompt.
         :param show_camera_button: Whether the user will be able to use camera to take a picture as an upload request,
             rather than selecting an existing file.
+        :param enforce_file_extensions: If true, then the file extensions provided in the exts parameter will be
+            enforced. If false, then the user may upload any file type.
         :return: A dictionary of file name to file bytes for each file the user uploaded.
         """
         # If no extensions were provided, use an empty list for the extensions instead.
@@ -1870,7 +1876,7 @@ class CallbackUtil:
         for file_path in file_paths:
             sink = InMemoryRecordDataSink(self.user)
             sink.consume_client_callback_file_path_data(file_path)
-            self.__verify_file(file_path, sink.data, exts)
+            self.__verify_file(file_path, sink.data, exts if enforce_file_extensions else None)
             ret_dict.update({file_path: sink.data})
 
         return ret_dict
@@ -1887,16 +1893,17 @@ class CallbackUtil:
         """
         if file_path is None or len(file_path) == 0 or file_bytes is None or len(file_bytes) == 0:
             raise SapioUserErrorException("Empty file provided or file unable to be read.")
-        if allowed_extensions:
-            matches: bool = False
-            for ext in allowed_extensions:
-                # FR-47690: Changed to a case-insensitive match.
-                if file_path.casefold().endswith("." + ext.lstrip(".").casefold()):
-                    matches = True
-                    break
-            if matches is False:
-                raise SapioUserErrorException("Unsupported file type. Expecting the following extension(s): "
-                                              + (",".join(allowed_extensions)))
+        if not allowed_extensions:
+            return
+        matches: bool = False
+        for ext in allowed_extensions:
+            # FR-47690: Changed to a case-insensitive match.
+            if file_path.casefold().endswith("." + ext.lstrip(".").casefold()):
+                matches = True
+                break
+        if not matches:
+            raise SapioUserErrorException("Unsupported file type. Expecting the following extension(s): "
+                                          + (",".join(allowed_extensions)))
 
     def write_file(self, file_name: str, file_data: str | bytes) -> None:
         """

sapiopycommons/chem/IndigoMolecules.py

@@ -6,8 +6,6 @@ indigo = Indigo()
 renderer = IndigoRenderer(indigo)
 indigo.setOption("render-output-format", "svg")
 indigo.setOption("ignore-stereochemistry-errors", True)
-# Ignore only if loading as non-query object. That is the meaning of this flag. Does nothing if it's query molecule.
-indigo.setOption("ignore-noncritical-query-features", True)
 indigo.setOption("render-stereo-style", "ext")
 indigo.setOption("aromaticity-model", "generic")
 indigo.setOption("render-coloring", True)

sapiopycommons/files/file_text_converter.py

@@ -0,0 +1,207 @@
+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)