Add more complete Capture object schemas

openflexure_microscope/api/v2/views/captures.py

@@ -14,6 +14,28 @@ from labthings.server.find import find_component
 from marshmallow import pre_dump
 
 
+class InstrumentSchema(Schema):
+    id = fields.UUID()
+    configuration = fields.Dict()
+    settings = fields.Dict()
+    state = fields.Dict()
+
+class CaptureMetadataImageSchema(Schema):
+    id = fields.UUID()
+    acquisitionDate = fields.String(format="date")
+    format = fields.String()
+    name = fields.String()
+    tags = fields.List(fields.String())
+    annotations = fields.Dict()
+
+
+class CaptureMetadataSchema(Schema):
+    experimenter = fields.Dict()  # TODO: Make schema
+    experimenterGroup = fields.Dict()  # TODO: Make schema
+    dataset = fields.Dict()  # TODO: Make schema
+    image = fields.Nested(CaptureMetadataImageSchema())
+    instrument = fields.Nested(InstrumentSchema())
+
 class CaptureSchema(Schema):
     id = fields.String()
     file = fields.String(
@@ -21,7 +43,7 @@ class CaptureSchema(Schema):
     )
     exists = fields.Bool(data_key="available")
     name = fields.String()
-    metadata = fields.Dict()
+    metadata = fields.Nested(CaptureMetadataSchema())
 
     links = fields.Dict()
 

openflexure_microscope/camera/capture.py

@@ -4,7 +4,6 @@ import os
 import shutil
 import glob
 import datetime
-import yaml
 import json
 import logging
 from PIL import Image
@@ -35,11 +34,9 @@ def pull_usercomment_dict(filepath):
         try:
             return json.loads(exif_dict["Exif"][37510].decode())
         except json.decoder.JSONDecodeError:
-            # TODO: Remove YAML support in a later version
-            logging.warning(
-                f"Capture {filepath} has metadata stored in YAML format. This is now deprecated in favour of JSON."
+            logging.error(
+                f"Capture {filepath} has old, corrupt, or missing OpenFlexure metadata. Unable to reload to server."
             )
-            return yaml.load(exif_dict["Exif"][37510].decode())
     else:
         return None
 
@@ -68,7 +65,8 @@ def build_captures_from_exif(capture_path):
         exif = pull_usercomment_dict(f)
         if exif:
             capture = capture_from_exif(f, exif)
-            captures.append(capture)
+            if capture:
+                captures.append(capture)
         else:
             logging.error("Invalid data at {}. Skipping.".format(f))
 
@@ -95,7 +93,11 @@ def capture_from_exif(path, exif_dict):
     capture.split_file_path(capture.file)
 
     # Image metadata
-    image_metadata = exif_dict.pop("image")
+    try:
+        image_metadata = exif_dict.pop("image")
+    except KeyError as e:
+        logging.error(f"Unable to obtain OpenFlexure metadata from file {path}")
+        return None
 
     # Populate capture parameters
     capture.id = image_metadata.get("id")