Before code cleanup.

CHANGELOG.md

@@ -1,6 +1,6 @@
 ## 202407.05
 
-- Ui updates.
+- Fixed issue with scrolling form potentially altering combobox values.
 
 ## 202407.04
 
@@ -74,7 +74,7 @@
 ## 202403.02
 
 - Moved functions out of submission container to submission form
-- Added submission editting functionality.
+- Added submission editing functionality.
 
 ## 202403.01
 
@@ -174,7 +174,7 @@
 
 ## 202307.03
 
-- Auto-filling of some empty cells in excel file.
+- Auto-filling of some empty cells in Excel file.
 - Better pydantic validations of missing data.
 
 ## 202307.02
@@ -211,7 +211,7 @@
 ## 202305.04
 
 - Added in hitpicking for plates with PCR results
-- Fixed error when expiry date stored as int in excel sheet.
+- Fixed error when expiry date stored as int in Excel sheet.
 
 ## 202305.03
 

README.md

@@ -142,6 +142,6 @@ This is meant to import .xlsx files created from the Design & Analysis Software
 *Download and Setup must have been performed beforehand.*
 
 1. Using pyinstaller, an exe can be created.
-2. Open a terminal in the folder with the 'src' folder.
+2. Open a terminal in the folder containing the 'src' folder.
 3. Activate the virtual environment: (Windows) ```.venv\Scripts\activate.bat```
 4. Enter the following command: ```pyinstaller .\submissions.spec --noconfirm```

src/submissions/tools/__init__.py

@@ -235,9 +235,6 @@ class Settings(BaseSettings, extra="allow"):
     database_name: str | None = None
     database_path: Path | str | None = None
     backup_path: Path | str | None = None
-    # super_users: list|None = None
-    # power_users: list|None = None
-    # rerun_regex: str
     submission_types: dict | None = None
     database_session: Session | None = None
     package: Any | None = None
@@ -272,8 +269,6 @@ class Settings(BaseSettings, extra="allow"):
                 value.mkdir(parents=True)
             except OSError:
                 value = Path(askdirectory(title="Directory for backups."))
-                # value.mkdir(parents=True)
-        # metadata.backup_path = value
         return value
 
     @field_validator('directory_path', mode="before")
@@ -302,7 +297,6 @@ class Settings(BaseSettings, extra="allow"):
             check = False
         if not check:  # and values.data['database_schema'] == "sqlite":
             # print(f"No directory found, using Documents/submissions")
-            # value = Path.home().joinpath("Documents", "submissions")
             value.mkdir(exist_ok=True)
         # print(f"Final return of directory_path: {value}")
         return value
@@ -310,17 +304,12 @@ class Settings(BaseSettings, extra="allow"):
     @field_validator('database_path', mode="before")
     @classmethod
     def ensure_database_exists(cls, value, values):
-        # if value == ":memory:":
-        #     return value
-        # and values.data['database_schema'] == "sqlite":
-        # value = values.data['directory_path']
         match values.data['database_schema']:
             case "sqlite":
                 if value is None:
                     value = values.data['directory_path']
                 if isinstance(value, str):
                     value = Path(value)
-                # db_name = f"{values.data['database_name']}.db"
             case _:
                 if value is None:
                     if check_if_app():
@@ -329,17 +318,6 @@ class Settings(BaseSettings, extra="allow"):
                         alembic_path = project_path.joinpath("alembic.ini")
                     # print(f"Getting alembic path: {alembic_path}")
                     value = cls.get_alembic_db_path(alembic_path=alembic_path, mode='path').parent
-                # value = f"{value}/{values.data['database_name']}"
-                # db_name = values.data['database_name']
-        # match value:
-        #     case str():
-        #         value = Path(value)
-        #     case None:
-        #         value = values.data['directory_path'].joinpath("submissions.db")
-        # if value.exists():
-        #     return value
-        # else:
-        #     raise FileNotFoundError(f"Couldn't find database at {value}")
         return value
 
     @field_validator('database_name', mode='before')
@@ -383,7 +361,6 @@ class Settings(BaseSettings, extra="allow"):
     @field_validator('database_session', mode="before")
     @classmethod
     def create_database_session(cls, value, values):
-
         if value is not None:
             return value
         else:
@@ -401,28 +378,6 @@ class Settings(BaseSettings, extra="allow"):
                 "{{ values['database_schema'] }}://{{ value }}/{{ db_name }}")
             database_path = template.render(values=values.data, value=value, db_name=db_name)
             # print(f"Using {database_path} for database path")
-            # database_path = values.data['database_path']
-            # if database_path is None:
-            #     # NOTE: check in user's .submissions directory for submissions.db
-            #     if Path.home().joinpath(".submissions", "submissions.db").exists():
-            #         database_path = Path.home().joinpath(".submissions", "submissions.db")
-            #     # NOTE: finally, look in the local dir
-            #     else:
-            #         database_path = project_path.joinpath("submissions.db")
-            # else:
-            #     if database_path == ":memory:":
-            #         pass
-            #     # NOTE: check if user defined path is directory
-            #     elif database_path.is_dir():
-            #         database_path = database_path.joinpath("submissions.db")
-            #     # NOTE: check if user defined path is a file
-            #     elif database_path.is_file():
-            #         database_path = database_path
-            #     else:
-            #         raise FileNotFoundError("No database file found. Exiting program.")
-            # print(f"Using {database_path} for database file.")
-            # engine = create_engine(f"sqlite:///{database_path}")  #, echo=True, future=True)
-            # engine = create_engine("postgresql+psycopg2://postgres:RE,4321q@localhost:5432/submissions")
             engine = create_engine(database_path)
             session = Session(engine)
             return session
@@ -444,8 +399,6 @@ class Settings(BaseSettings, extra="allow"):
             output = dict(power_users=['lwark', 'styson', 'ruwang'])
         else:
             print(f"Hello from database settings getter.")
-
-            # session = Session(create_engine(f"sqlite:///{db_path}"))
             # print(self.__dict__)
             session = self.database_session
             metadata = MetaData()
@@ -466,7 +419,6 @@ class Settings(BaseSettings, extra="allow"):
                     output[item[1]] = json.loads(item[2])
                 except (JSONDecodeError, TypeError):
                     output[item[1]] = item[2]
-            # config_items = {item[1]: json.loads(item[2]) for item in config_items}
         for k, v in output.items():
             if not hasattr(self, k):
                 self.__setattr__(k, v)
@@ -479,7 +431,6 @@ class Settings(BaseSettings, extra="allow"):
         url = c['alembic']['sqlalchemy.url']
         match mode:
             case 'path':
-                # path = url.replace("sqlite:///", "")
                 path = re.sub(r"^.*//", "", url)
                 path = re.sub(r"^.*@", "", path)
                 return Path(path)
@@ -523,7 +474,6 @@ class Settings(BaseSettings, extra="allow"):
                 dicto[k] = v
             with open(settings_path, 'w') as f:
                 yaml.dump(dicto, f)
-        # return settings
 
 
 def get_config(settings_path: Path | str | None = None) -> Settings:
@@ -540,16 +490,14 @@ def get_config(settings_path: Path | str | None = None) -> Settings:
     # logger.debug(f"Creating settings...")
     if isinstance(settings_path, str):
         settings_path = Path(settings_path)
-
+    # NOTE: custom pyyaml constructor to join fields
-    # custom pyyaml constructor to join fields
     def join(loader, node):
         seq = loader.construct_sequence(node)
         return ''.join([str(i) for i in seq])
 
     # register the tag handler
     yaml.add_constructor('!join', join)
-
+    # NOTE: make directories
-    # make directories
     try:
         CONFIGDIR.mkdir(parents=True)
     except FileExistsError:
@@ -574,10 +522,8 @@ def get_config(settings_path: Path | str | None = None) -> Settings:
                 settings_path = project_path.joinpath('src', 'config.yml')
             with open(settings_path, "r") as dset:
                 default_settings = yaml.load(dset, Loader=yaml.Loader)
-
             # NOTE: Tell program we need to copy the config.yml to the user directory
             # NOTE: copy settings to config directory
-            # settings = Settings(**copy_settings(settings_path=CONFIGDIR.joinpath("config.yml"), settings=default_settings))
             settings = Settings(**default_settings)
             settings.save(settings_path=CONFIGDIR.joinpath("config.yml"))
             # print(f"Default settings: {pprint.pprint(settings.__dict__)}")
@@ -593,7 +539,6 @@ def get_config(settings_path: Path | str | None = None) -> Settings:
             logger.error("No config.yml file found. Writing to directory.")
             with open(settings_path, "r") as dset:
                 default_settings = yaml.load(dset, Loader=yaml.Loader)
-            # return Settings(**copy_settings(settings_path=settings_path, settings=default_settings))
             settings = Settings(**default_settings)
             settings.save(settings_path=settings_path)
     # logger.debug(f"Using {settings_path} for config file.")
@@ -623,7 +568,7 @@ class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
         """
         Override base class method to make the new log file group writable.
         """
-        # Rotate the file first.
+        # NOTE: Rotate the file first.
         handlers.RotatingFileHandler.doRollover(self)
         # NOTE: Add group write to the current permissions.
         currMode = os.stat(self.baseFilename).st_mode
@@ -692,6 +637,11 @@ def setup_logger(verbosity: int = 3):
     Returns:
         logger: logger object
     """
+    def handle_exception(exc_type, exc_value, exc_traceback):
+        if issubclass(exc_type, KeyboardInterrupt):
+            sys.__excepthook__(exc_type, exc_value, exc_traceback)
+            return
+        logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback))
     logger = logging.getLogger("submissions")
     logger.setLevel(logging.DEBUG)
     # NOTE: create file handler which logs even debug messages
@@ -700,10 +650,6 @@ def setup_logger(verbosity: int = 3):
     except FileExistsError:
         logger.warning(f"Logging directory {LOGDIR} already exists.")
     # NOTE: logging to file turned off due to repeated permission errors
-    # fh = GroupWriteRotatingFileHandler(LOGDIR.joinpath('submissions.log'), mode='a', maxBytes=100000, backupCount=3, encoding=None, delay=False)
-    # file logging will always be debug
-    # fh.setLevel(logging.DEBUG)
-    # fh.name = "File"
     # NOTE: create console handler with a higher log level
     # NOTE: create custom logger with STERR -> log
     ch = logging.StreamHandler(stream=sys.stdout)
@@ -718,19 +664,10 @@ def setup_logger(verbosity: int = 3):
     ch.name = "Stream"
     # NOTE: create formatter and add it to the handlers
     formatter = CustomFormatter()
-    # fh.setFormatter(formatter)
     ch.setFormatter(formatter)
     # NOTE: add the handlers to the logger
-    # logger.addHandler(fh)
     logger.addHandler(ch)
-
     # NOTE: Output exception and traceback to logger
-    def handle_exception(exc_type, exc_value, exc_traceback):
-        if issubclass(exc_type, KeyboardInterrupt):
-            sys.__excepthook__(exc_type, exc_value, exc_traceback)
-            return
-        logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback))
-
     sys.excepthook = handle_exception
     return logger
 
@@ -746,11 +683,6 @@ def copy_settings(settings_path: Path, settings: dict) -> dict:
     Returns:
         dict: output dictionary for use in first run
     """
-    # NOTE: if the current user is not a superuser remove the superusers entry
-    # if not getpass.getuser() in settings['super_users']:
-    #     del settings['super_users']
-    # if not getpass.getuser() in settings['power_users']:
-    #     del settings['power_users']
     if not settings_path.exists():
         with open(settings_path, 'w') as f:
             yaml.dump(settings, f)