Removed default JSON files and submoduled JSON encoder class

openflexure_microscope/api/app.py

@@ -30,7 +30,7 @@ from labthings.extensions import find_extensions
 from openflexure_microscope.api.microscope import default_microscope as api_microscope
 from openflexure_microscope.api.utilities import init_default_extensions, list_routes
 from openflexure_microscope.api.v2 import views
-from openflexure_microscope.config import JSONEncoder
+from openflexure_microscope.json import JSONEncoder
 from openflexure_microscope.paths import (
     OPENFLEXURE_EXTENSIONS_PATH,
     OPENFLEXURE_VAR_PATH,

openflexure_microscope/captures/capture.py

@@ -12,7 +12,7 @@ import dateutil.parser
 
 from openflexure_microscope.camera import piexif
 from openflexure_microscope.camera.piexif._exceptions import InvalidImageDataError
-from openflexure_microscope.config import JSONEncoder
+from openflexure_microscope.json import JSONEncoder
 
 EXIF_FORMATS = ["JPG", "JPEG", "TIF", "TIFF"]
 THUMBNAIL_SIZE = (200, 150)

openflexure_microscope/config.py

@@ -3,18 +3,9 @@ import json
 import logging
 import os
 import shutil
-from fractions import Fraction
-from uuid import UUID
 
-import numpy as np
+from .json import JSONEncoder
-from labthings.json import LabThingsJSONEncoder
+from .paths import CONFIGURATION_FILE_PATH, SETTINGS_FILE_PATH
-
-from .paths import (
-    CONFIGURATION_FILE_PATH,
-    DEFAULT_CONFIGURATION_FILE_PATH,
-    DEFAULT_SETTINGS_FILE_PATH,
-    SETTINGS_FILE_PATH,
-)
 
 
 class OpenflexureSettingsFile:
@@ -33,7 +24,12 @@ class OpenflexureSettingsFile:
         self.path = path
 
         # Initialise basic config file with defaults if it doesn't exist
-        initialise_file(self.path, populate=defaults)
+        initialise_file(
+            self.path,
+            # Populate with default dictionary, or empty JSON if empty
+            populate=json.dumps(defaults, cls=JSONEncoder, indent=2, sort_keys=True)
+            or "{}\n",
+        )
 
     def load(self) -> dict:
         """
@@ -78,32 +74,6 @@ class OpenflexureSettingsFile:
         return settings
 
 
-class JSONEncoder(LabThingsJSONEncoder):
-    """
-    A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
-    """
-
-    def default(self, o):
-        if isinstance(o, UUID):
-            return str(o)
-        # PiCamera fractions
-        elif isinstance(o, Fraction):
-            return float(o)
-        # Numpy integers
-        elif isinstance(o, np.integer):
-            return int(o)
-        # Numpy arrays
-        elif isinstance(o, np.ndarray):
-            return o.tolist()
-        # UUIDs
-        elif isinstance(o, UUID):
-            return str(o)
-        else:
-            # call base class implementation which takes care of
-            # raising exceptions for unsupported types
-            return LabThingsJSONEncoder.default(self, o)
-
-
 # HANDLE BASIC LOADING AND SAVING OF SETTINGS FILES
 
 
@@ -184,21 +154,14 @@ def initialise_file(config_path, populate: str = "{}\n"):
             outfile.write(populate)
 
 
-# Load the default settings
-with open(DEFAULT_SETTINGS_FILE_PATH, "r") as default_settings:
-    DEFAULT_SETTINGS = default_settings.read()
-
 #: Default user settings object
-user_settings = OpenflexureSettingsFile(
+user_settings = OpenflexureSettingsFile(path=SETTINGS_FILE_PATH)
-    path=SETTINGS_FILE_PATH, defaults=DEFAULT_SETTINGS
-)
-
-
-# Load the default configuration
-with open(DEFAULT_CONFIGURATION_FILE_PATH, "r") as default_configuration:
-    DEFAULT_CONFIGURATION = default_configuration.read()
 
 #: Default user settings object
 user_configuration = OpenflexureSettingsFile(
-    path=CONFIGURATION_FILE_PATH, defaults=DEFAULT_CONFIGURATION
+    path=CONFIGURATION_FILE_PATH,
+    defaults={
+        "camera": {"type": "PiCamera"},
+        "stage": {"type": "SangaStage", "port": None},
+    },
 )

openflexure_microscope/json.py

@@ -0,0 +1,31 @@
+from fractions import Fraction
+from uuid import UUID
+
+import numpy as np
+from labthings.json import LabThingsJSONEncoder
+
+
+class JSONEncoder(LabThingsJSONEncoder):
+    """
+    A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
+    """
+
+    def default(self, o):
+        if isinstance(o, UUID):
+            return str(o)
+        # PiCamera fractions
+        elif isinstance(o, Fraction):
+            return float(o)
+        # Numpy integers
+        elif isinstance(o, np.integer):
+            return int(o)
+        # Numpy arrays
+        elif isinstance(o, np.ndarray):
+            return o.tolist()
+        # UUIDs
+        elif isinstance(o, UUID):
+            return str(o)
+        else:
+            # call base class implementation which takes care of
+            # raising exceptions for unsupported types
+            return LabThingsJSONEncoder.default(self, o)

openflexure_microscope/microscope_configuration.default.json

@@ -1,9 +0,0 @@
-{
-  "camera": {
-    "type": "PiCamera"
-  },
-  "stage": {
-    "type": "SangaStage",
-    "port": null
-  }
-}

openflexure_microscope/microscope_settings.default.json

@@ -1,7 +0,0 @@
-{
-  "fov": [
-    4100,
-    3146
-  ],
-  "jpeg_quality": 100
-}

openflexure_microscope/paths.py

@@ -38,18 +38,6 @@ def logs_file_path(filename: str):
         os.makedirs(logs_dir)
     return os.path.join(logs_dir, filename)
 
-
-# HANDLE DEFAULTS FILES STORED IN THIS APPLICATION
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-
-#: Path of default (first-run) microscope settings
-DEFAULT_SETTINGS_FILE_PATH = os.path.join(HERE, "microscope_settings.default.json")
-#: Path of default (first-run) microscope configuration
-DEFAULT_CONFIGURATION_FILE_PATH = os.path.join(
-    HERE, "microscope_configuration.default.json"
-)
-
 # BASE PATHS
 
 if os.name == "nt":

openflexure_microscope/rescue/check_settings.py

@@ -1,5 +1,6 @@
 import json
 import logging
+from .error_sources import ErrorSource
 
 ERROR_SOURCES = []
 
@@ -8,27 +9,35 @@ def trace_config_exceptions():
     error_sources = []
 
     from openflexure_microscope.paths import (
-        DEFAULT_CONFIGURATION_FILE_PATH,
+        CONFIGURATION_FILE_PATH,
         SETTINGS_FILE_PATH,
     )
 
     try:
-        default_config = json.load(DEFAULT_CONFIGURATION_FILE_PATH)
+        default_config = json.load(CONFIGURATION_FILE_PATH)
         if not default_config:
-            error_sources.append("default_config_empty")
+            error_sources.append(ErrorSource(
+                "Configuration file is missing or empty. This may occur if the server has never been started."
+            ))
     except Exception as e:  # pylint: disable=W0703
         logging.error("Error parsing config:")
         logging.error(e)
-        error_sources.append("default_config_error")
+        error_sources.append(ErrorSource(
+            f"Configuration file is malformed. You can reset to the default configuration by deleting {CONFIGURATION_FILE_PATH}."
+        ))
 
     try:
         default_settings = json.load(SETTINGS_FILE_PATH)
         if not default_settings:
-            error_sources.append("default_settings_empty")
+            error_sources.append(ErrorSource(
+                "Settings file is missing or empty. This may occur if the server has never been started."
+            ))
     except Exception as e:  # pylint: disable=W0703
         logging.error("Error parsing settings:")
         logging.error(e)
-        error_sources.append("default_settings_error")
+        error_sources.append(ErrorSource(
+            f"Settings file is malformed. You can reset to the default settings by deleting {SETTINGS_FILE_PATH}."
+        ))
 
     return error_sources
 
@@ -39,7 +48,9 @@ def main():
     try:
         from openflexure_microscope import config as _
     except Exception as e:  # pylint: disable=W0703
-        error_sources.append("config_settings_import_error")
+        error_sources.append(ErrorSource(
+            "Error importing configuration submodule. This could be an error in our code."
+        ))
         logging.error("Error importing config:")
         logging.error(e)
         error_sources.extend(trace_config_exceptions())