Replace remaining 'mdoc_for_reading' variables with 'self._mdoc_for_reading'; move functions called from 'self._context' into if-blocks to satisfy type checking

Author: tieneupin

src/murfey/client/analyser.py

@@ -402,13 +402,14 @@ def _analyse(self, transferred_file: Path):
                         )
                     except KeyError as e:
                         logger.error(
-                            f"Metadata gathering failed with a key error for key: {e.args[0]}"
+                            "Metadata gathering failed with a key error for key: "
+                            f"{e.args[0]}"
                         )
                         raise e
                     if not dc_metadata:
-                        mdoc_for_reading = None
+                        self._mdoc_for_reading = None
                 elif transferred_file.suffix == ".mdoc":
-                    mdoc_for_reading = transferred_file
+                    self._mdoc_for_reading = transferred_file
             if not self._context:
                 if not self._find_extension(transferred_file):
                     logger.debug(f"No extension found for {transferred_file}")
@@ -446,7 +447,8 @@ def _analyse(self, transferred_file: Path):
                                 dc_metadata = {}
                             except KeyError as e:
                                 logger.error(
-                                    f"Metadata gathering failed with a key error for key: {e.args[0]}"
+                                    "Metadata gathering failed with a key error for key: "
+                                    f"{e.args[0]}"
                                 )
                                 raise e
                             except ValueError as e:
@@ -468,7 +470,8 @@ def _analyse(self, transferred_file: Path):
                                 self.notify(dc_metadata)
                             else:
                                 logger.warning(
-                                    "Could not determine acquisition software as context is not set"
+                                    "Could not determine acquisition software as context "
+                                    "is not set"
                                 )
 
             # Contexts that can be immediately posted without additional work
@@ -495,36 +498,55 @@ def _analyse(self, transferred_file: Path):
                 if self._extension:
                     logger.info(f"Extension found successfully for {transferred_file}")
                     try:
-                        self._context.post_first_transfer(
-                            transferred_file,
-                            environment=self._environment,
-                        )
+                        if self._context is not None:
+                            self._context.post_first_transfer(
+                                transferred_file,
+                                environment=self._environment,
+                            )
+                        else:
+                            logger.warning(
+                                "Could not post first transfer as context is not set"
+                            )
                     except Exception as e:
                         logger.error(f"Exception encountered: {e}")
                     if not dc_metadata:
                         try:
-                            dc_metadata = self._context.gather_metadata(
-                                mdoc_for_reading or self._xml_file(transferred_file),
-                                environment=self._environment,
-                            )
+                            if self._context is not None:
+                                dc_metadata = self._context.gather_metadata(
+                                    self._mdoc_for_reading
+                                    or self._xml_file(transferred_file),
+                                    environment=self._environment,
+                                )
+                            else:
+                                logger.warning(
+                                    "Could not gather metadata as context is not set"
+                                )
                         except KeyError as e:
                             logger.error(
-                                f"Metadata gathering failed with a key error for key: {e.args[0]}"
+                                "Metadata gathering failed with a key error for key: "
+                                f"{e.args[0]}"
                             )
                             raise e
                     if not dc_metadata or not self._force_mdoc_metadata:
-                        mdoc_for_reading = None
+                        self._mdoc_for_reading = None
                         self._unseen_xml.append(transferred_file)
                     if dc_metadata:
                         self._unseen_xml = []
                         if dc_metadata.get("file_extension"):
                             self._extension = dc_metadata["file_extension"]
                         else:
                             dc_metadata["file_extension"] = self._extension
-                        dc_metadata["acquisition_software"] = (
-                            self._context._acquisition_software
-                        )
-                        self.notify(dc_metadata)
+                        if self._context is not None:
+                            dc_metadata["acquisition_software"] = (
+                                self._context._acquisition_software
+                            )
+                            self.notify(dc_metadata)
+                        else:
+                            logger.warning(
+                                "Could not assign acquisition software to data collection "
+                                "metadata as context is not set"
+                            )
+
             elif any(
                 context in str(self._context)
                 for context in (