Resolves marshmallow_sqlalchemy.ModelSchema deprecation warning

crc/models/file.py

@@ -1,7 +1,7 @@
 import enum
 
 from marshmallow_enum import EnumField
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 from sqlalchemy import func
 from sqlalchemy.dialects.postgresql import UUID
 
@@ -81,8 +81,10 @@ class FileModel(db.Model):
     latest_version = db.Column(db.Integer, default=0)
 
 
-class FileModelSchema(ModelSchema):
+class FileModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = FileModel
+        load_instance = True
+        include_relationships = True
         include_fk = True  # Includes foreign keys
     type = EnumField(FileType)

crc/models/stats.py

@@ -1,4 +1,4 @@
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 
 from crc import db
 
@@ -16,9 +16,11 @@ class WorkflowStatsModel(db.Model):
     last_updated = db.Column(db.DateTime)
 
 
-class WorkflowStatsModelSchema(ModelSchema):
+class WorkflowStatsModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = WorkflowStatsModel
+        load_instance = True
+        include_relationships = True
         include_fk = True  # Includes foreign keys
 
 
@@ -35,7 +37,9 @@ class TaskEventModel(db.Model):
     date = db.Column(db.DateTime)
 
 
-class TaskEventModelSchema(ModelSchema):
+class TaskEventModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = TaskEventModel
+        load_instance = True
+        include_relationships = True
         include_fk = True  # Includes foreign keys

crc/models/study.py

@@ -1,6 +1,6 @@
 from marshmallow_enum import EnumField
-from marshmallow_sqlalchemy import ModelSchema
-from sqlalchemy import func, Column
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
+from sqlalchemy import func
 
 from crc import db
 from crc.models.protocol_builder import ProtocolBuilderStatus
@@ -24,9 +24,11 @@ class StudyModel(db.Model):
     status_spec_version = db.Column(db.String)
 
 
-class StudyModelSchema(ModelSchema):
+class StudyModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = StudyModel
+        load_instance = True
+        include_relationships = True
         include_fk = True  # Includes foreign keys
 
     protocol_builder_status = EnumField(ProtocolBuilderStatus)

crc/models/user.py

@@ -1,7 +1,7 @@
 import datetime
 
 import jwt
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 
 from crc import db, app
 from crc.api.common import ApiError
@@ -52,7 +52,9 @@ class UserModel(db.Model):
             raise ApiError('token_invalid', 'The Authentication token you provided.  You need a new token. ')
 
 
-class UserModelSchema(ModelSchema):
+class UserModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = UserModel
+        load_instance = True
+        include_relationships = True
 

crc/models/workflow.py

@@ -1,6 +1,6 @@
 import enum
 
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 
 from crc import db
 
@@ -11,9 +11,11 @@ class WorkflowSpecCategoryModel(db.Model):
     display_name = db.Column(db.String)
 
 
-class WorkflowSpecCategoryModelSchema(ModelSchema):
+class WorkflowSpecCategoryModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = WorkflowSpecCategoryModel
+        load_instance = True
+        include_relationships = True
 
 
 class WorkflowSpecModel(db.Model):
@@ -28,9 +30,11 @@ class WorkflowSpecModel(db.Model):
     is_status = db.Column(db.Boolean, default=False)
 
 
-class WorkflowSpecModelSchema(ModelSchema):
+class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
     class Meta:
         model = WorkflowSpecModel
+        load_instance = True
+        include_relationships = True
         include_fk = True  # Includes foreign keys
 
 

tests/test_tasks_api.py

@@ -159,7 +159,7 @@ class TestTasksApi(BaseTest):
         }
         workflow_api = self.complete_form(workflow, tasks[0], data)
         self.assertIsNotNone(workflow_api.next_task)
-        self.assertEquals("EndEvent_0evb22x", workflow_api.next_task['name'])
+        self.assertEqual("EndEvent_0evb22x", workflow_api.next_task['name'])
         self.assertTrue(workflow_api.status == WorkflowStatus.complete)
         rv = self.app.get('/v1.0/file?workflow_id=%i' % workflow.id, headers=self.logged_in_headers())
         self.assert_success(rv)

tests/test_workflow_processor.py

@@ -312,7 +312,7 @@ class TestWorkflowProcessor(BaseTest):
         workflow_model.bpmn_workflow_json = processor.serialize()
         processor2 = WorkflowProcessor(workflow_model)
         self.assertEqual("Step 1", processor2.bpmn_workflow.last_task.task_spec.description)
-        self.assertNotEquals("# This is some documentation I wanted to add.",
+        self.assertNotEqual("# This is some documentation I wanted to add.",
                           processor2.bpmn_workflow.last_task.task_spec.documentation)
 
         # You can do a soft update and get the right response.