sapiopycommons 2025.8.20a714__py3-none-any.whl → 2025.8.22a716__py3-none-any.whl

sapiopycommons/callbacks/callback_util.py

@@ -1815,7 +1815,8 @@ 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.
 
@@ -1825,6 +1826,8 @@ 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.
@@ -1844,11 +1847,12 @@ 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.
 
@@ -1858,6 +1862,8 @@ 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.
@@ -1873,7 +1879,7 @@ 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
@@ -1890,16 +1896,17 @@ 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

@@ -6,11 +6,15 @@ 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)
 indigo.setOption("molfile-saving-mode", "3000")
 indigo.setOption("dearomatize-verification", False)
+#YQ: Sapio-Only Option, this is my modification.
+indigo.setOption("rpe-bypass-saturation-check", True)
 indigo_inchi = IndigoInchi(indigo)
 
 
@@ -22,17 +26,15 @@ def get_aromatic_dearomatic_forms(m: IndigoObject):
     :return: pair of indigo objects, first is aromatic, second is dearomatic.
     """
     try:
-        aromatic_reaction = m.clone()
-        aromatic_reaction.aromatize()
-        dearomatic_reaction = aromatic_reaction.clone()
+        # Note: there are problems with aromatization being applied more than once, because it can crash.
+        # This is because an implicit assumption made on consequence of a particular perception may cause further
+        # aromatization to fail to find next steps and also fails to find termination.
+        # So, to ensure we only apply aromatization once, we dearomatize first, then aromatize.
+        dearomatic_reaction = m.clone()
         dearomatic_reaction.dearomatize()
-        second_aromatic_reaction = dearomatic_reaction.clone()
-        second_aromatic_reaction.aromatize()
-        match = indigo.exactMatch(aromatic_reaction, second_aromatic_reaction)
-        if match:
-            return aromatic_reaction, dearomatic_reaction
-        else:
-            return m, dearomatic_reaction
+        aromatic_reaction = dearomatic_reaction.clone()
+        aromatic_reaction.aromatize()
+        return aromatic_reaction, dearomatic_reaction
     except (Exception):
         # If aromatization then following deromatization fails, we just skip it.
         dearomatic_reaction = m.clone()