Improve User management and crop verifier

annotation_api/app/__init__.py

@@ -10,18 +10,20 @@
 from config import s3_config
 from config import FlaskConfig, cache_config, s3_config
 
+#---------------------------------------------------------------------------------------------------------------------------#
+
 def create_app():
 	app = Flask(__name__)
 	app.config.from_object(FlaskConfig)
 
 	CORS(app, resources={
 		r'/api/*': {
-			'origins': [
-				app.config['ORIGIN_URL'],
-			],
+			'origins': app.config['ORIGIN_URLS'],
 			'supports_credentials': True     
 		}
 	})
+
+	# Register s3 service app wide
 	setattr(app, 's3', client(
         's3',
         config=s3_config,
@@ -36,26 +38,8 @@ def create_app():
 	app.errorhandler(HTTPException)(errors.handle_generic_http)
 	app.errorhandler(500)(errors.internal_service_error)
 
-	from app.routes import bp
+	from app.routers import bp
 	app.register_blueprint(bp)
 
-	from app.routers.projects import projectBp
-	app.register_blueprint(projectBp)
-
-	from app.routers.models import modelBp
-	app.register_blueprint(modelBp)
-
-	from app.routers.images import imageBp
-	app.register_blueprint(imageBp)
-
-	from app.routers.surveys import surveyBp
-	app.register_blueprint(surveyBp)
-
-	from app.routers.herdunits import herdunitBp
-	app.register_blueprint(herdunitBp)
-
-	from app.routers.schemas import schemaBp
-	app.register_blueprint(schemaBp)
-
 	return app
 

annotation_api/app/decorators.py

@@ -0,0 +1,17 @@
+from functools import wraps
+from flask import abort
+from flask_login import current_user
+
+def roles_required(*roles):
+    def wrapper(f):
+        @wraps(f)
+        def decorated_view(*args, **kwargs):
+            if not current_user.is_authenticated:
+                return abort(401)
+
+            if not any(current_user.has_role(r) for r in roles):
+                return abort(403)
+
+            return f(*args, **kwargs)
+        return decorated_view
+    return wrapper

annotation_api/app/routers/__init__.py

@@ -0,0 +1 @@
+from .router import *

annotation_api/app/routers/annotations/__init__.py

@@ -0,0 +1,2 @@
+from .annotation_validators import *
+from .annotations import *

annotation_api/app/routers/autocropper/__init__.py

@@ -0,0 +1,2 @@
+from .autocropper_validators import *
+from .autocropper import *

annotation_api/app/routers/cropverifier/__init__.py

@@ -0,0 +1,2 @@
+from .cropverifier import *
+from .cropverifier_validators import *

annotation_api/app/routers/cropverifier/cropverifier.py

@@ -0,0 +1,140 @@
+# Endpoints for crop verification in the API
+# Author: Michael B. Lance
+
+#---------------------------------------------------------------------------------------------------------------------------#
+
+from uuid import UUID
+
+from botocore.exceptions import ClientError
+from flask import Blueprint, abort, request
+from flask_login import login_required, current_user
+from flask_pydantic import validate
+from psycopg.errors import DatabaseError, UniqueViolation
+
+from app.extensions import base, s3
+from database import ObjectNotFound
+
+from .cropverifier_validators import *
+
+verifierBp = Blueprint('verifier', __name__, url_prefix='/api/v1/verifier')
+
+#---------------------------------------------------------------------------------------------------------------------------#
+# GET 
+
+@verifierBp.get('/reviewed-area')
+@login_required
+@validate()
+def get(query: RAQuery):
+	'''
+	Retrieve a reviewed area
+	---
+	paramaters:
+	  - in: query
+		name: herd_unit_id
+		type: number
+	  - in: query
+		name: survey_id
+		type: number
+	responses:
+		200:
+			description: List of reviewed areas.
+		400:
+			description: Invalid UUID format.
+		404:
+			description: No reviewed areas found.
+		500:
+			description: Database error.
+	'''
+	try:
+		params = query.model_dump()
+		params['num'] = 1
+		reviewed_areas = base.get_crop_to_review(params, current_user.user_id)
+	except ObjectNotFound as e:
+		abort(404, str(e))
+	except (DatabaseError, Exception) as e:
+		print(e)
+		abort(500)
+
+	print(reviewed_areas)
+
+	return [ra.to_dict() for ra in reviewed_areas], 200
+
+@verifierBp.get('/needing-reviewed')
+@login_required
+@validate()
+def get_selection_count(query: RAQuery):
+	'''
+
+	'''
+	try:
+		count = base.get_crop_to_review_selection_count(query.model_dump())
+	except ObjectNotFound as e:
+		abort(404, str(e))
+	except (DatabaseError, Exception):
+		abort(500)
+
+	return {'count': count}, 200
+
+#---------------------------------------------------------------------------------------------------------------------------#
+# PUT
+
+@verifierBp.put('/submit')
+@login_required
+@validate()
+def approve_annotations(body: ApproveAnnotations):
+	'''
+
+	'''
+	data = body.model_dump()
+
+	# loop over incoming annotation data
+	for annot in data['annotations']:
+
+		# check if annotation in the database
+		try:
+			if base.get_annotation_exists(UUID(annot['uuid'])):
+
+				# TODO: check if annotation still inersects prediction in threshold
+				# update annotation
+				res_i = base.update_annotation(
+					annot['annotation_id'],
+					label_id=annot['label_id'],
+					box_tx=annot['dimensions']['top_left']['x'],
+					box_ty=annot['dimensions']['top_left']['y'],
+					box_bx=annot['dimensions']['bottom_right']['x'],
+					box_by=annot['dimensions']['bottom_right']['y'],	
+				)
+			# else
+			else:
+				# create annotation
+				base.create_annotation(
+					label_id = annot['label_id'],
+					image_id = annot['image_id'], 
+					herd_unit_id = annot['herd_unit_id'],
+					box_tx = annot['dimensions']['top_left']['x'],
+					box_ty = annot['dimensions']['top_left']['y'],
+					box_bx = annot['dimensions']['bottom_right']['x'],
+					box_by = annot['dimensions']['bottom_right']['y'],
+					user_id = current_user.user_id,
+					uuid = annot['uuid']
+				)
+		except ObjectNotFound as e:
+			abort(404, str(e))
+		except (DatabaseError, Exception):
+			abort(500)
+
+	# loop over deleted annotations
+	try:
+		# TODO: add method to delete multiple dicts in a single pass
+		for annot in data['deleted_annotations']:
+			base.delete_annotation(annot['annotation_id'])
+
+		# set crop reviewed 
+		base.update_reviewed_area(data['reviewed_area_id'], reviewed_by_user_id = current_user.user_id)
+
+		# set image closed
+		base.update_image(data['image_id'], {'opened_by_user_id':0})
+	except (DatabaseError, Exception):
+		abort(500)
+
+	return '', 201

annotation_api/app/routers/cropverifier/cropverifier_validators.py

@@ -0,0 +1,24 @@
+from pydantic import BaseModel, field_validator
+from typing import Union, List, Optional, Dict
+from uuid import UUID
+
+class RAQuery(BaseModel):
+	herd_unit_id: Optional[List[int]]
+	survey_id: Optional[List[int]] 
+	include_reviewed: Optional[bool] = False
+	include_opened: Optional[bool] = False
+
+	@field_validator('herd_unit_id', 'survey_id', mode='before')
+	@classmethod
+	def ensure_list(cls, value):
+		if isinstance(value, list):
+			return value
+		if value is None or value == "":
+			return []
+		return [value]
+
+class ApproveAnnotations(BaseModel):
+	reviewed_area_id: Union[int, UUID]
+	image_id: Union[int, UUID]
+	annotations: List[Dict]
+	deleted_annotations: List[Dict]

annotation_api/app/routers/herdunits/herdunits.py

@@ -43,7 +43,7 @@ def get_by_id(herd_unit_id: str):
 		abort(404, f'Herd Unit with ID {herd_unit_id} was not found!')
 
 	else:
-		return herd_unit.serialize()
+		return herd_unit.to_dict()
 
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
@@ -79,7 +79,7 @@ def get_surveys(herd_unit_id: str):
 	except (DatabaseError, Exception) as e:
 		abort(500)
 
-	return [survey.serialize() for survey in surveys], 200
+	return [survey.to_dict() for survey in surveys], 200
 
 #---------------------------------------------------------------------------------------------------------------------------#
 # POST
@@ -97,4 +97,4 @@ def create(body: CreateHerdUnit):
 		print(e)
 		abort(500)
 
-	return herd_unit.serialize(), 201
+	return herd_unit.to_dict(), 201

annotation_api/app/routers/images/__init__.py

@@ -1,3 +1,2 @@
-# images/__init__.py
 from .image_validators import *
 from .images import *