Supporting study status update

crc/api.yml

@@ -1046,22 +1046,24 @@ components:
           example: dhf8r
         protocol_builder_status:
           type: string
-          enum: [INCOMPLETE, ACTIVE, HOLD, OPEN, ABANDONED]
+          enum: [incomplete, active, hold, open, abandoned]
           example: done
         sponsor:
           type: string
+          x-nullable: true
           example: "Sartography Pharmaceuticals"
         ind_number:
           type: string
+          x-nullable: true
           example: "27b-6-42"
         hsr_number:
           type: string
           x-nullable: true
           example: "27b-6-1212"
-        categories:
-          type: array
-          items:
-            $ref: "#/components/schemas/WorkflowSpecCategory"
+        # categories:
+        #   type: array
+        #   items:
+        #     $ref: "#/components/schemas/WorkflowSpecCategory"
     WorkflowSpec:
       properties:
         id:

crc/api/study.py

@@ -6,7 +6,7 @@ from sqlalchemy.exc import IntegrityError
 from crc import session
 from crc.api.common import ApiError, ApiErrorSchema
 from crc.models.protocol_builder import ProtocolBuilderStatus
-from crc.models.study import StudySchema, StudyModel, Study
+from crc.models.study import StudySchema, StudyForUpdateSchema, StudyModel, Study
 from crc.services.study_service import StudyService
 
 
@@ -40,10 +40,12 @@ def update_study(study_id, body):
     if study_model is None:
         raise ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
 
-    study: Study = StudySchema().load(body)
+    study: Study = StudyForUpdateSchema().load(body)
     study.update_model(study_model)
     session.add(study_model)
     session.commit()
+    # Need to reload the full study to return it to the frontend
+    study = StudyService.get_study(study_id)
     return StudySchema().dump(study)
 
 

crc/models/protocol_builder.py

@@ -23,10 +23,10 @@ class ProtocolBuilderStatus(enum.Enum):
     # • Open To Enrollment: has start date and HSR number?
     # • Abandoned: deleted in PB
     INCOMPLETE = 'incomplete' # Found in PB but not ready to start (not q_complete)
-    ACTIVE = 'active', # found in PB, marked as "q_complete" and no HSR number and not hold
-    HOLD = 'hold', # CR Connect side, if the Study ias marked as "hold".
-    OPEN = 'open', # Open To Enrollment: has start date and HSR number?
-    ABANDONED = 'Abandoned'  # Not found in PB
+    ACTIVE = 'active' # found in PB, marked as "q_complete" and no HSR number and not hold
+    HOLD = 'hold' # CR Connect side, if the Study ias marked as "hold".
+    OPEN = 'open' # Open To Enrollment: has start date and HSR number?
+    ABANDONED = 'abandoned'  # Not found in PB
 
 
     #DRAFT = 'draft',                      # !Q_COMPLETE

crc/models/study.py

@@ -133,9 +133,7 @@ class Study(object):
         return instance
 
     def update_model(self, study_model: StudyModel):
-        for k,v in  self.__dict__.items():
-            if not k.startswith('_'):
-                study_model.__dict__[k] = v
+        study_model.protocol_builder_status = ProtocolBuilderStatus(self.protocol_builder_status)
 
     def model_args(self):
         """Arguments that can be passed into the Study Model to update it."""
@@ -145,6 +143,27 @@ class Study(object):
         return self_dict
 
 
+class StudyForUpdateSchema(ma.Schema):
+
+    id = fields.Integer(required=False, allow_none=True)
+    protocol_builder_status = EnumField(ProtocolBuilderStatus, by_value=True)
+    hsr_number = fields.String(allow_none=True)
+    sponsor = fields.String(allow_none=True)
+    ind_number = fields.String(allow_none=True)
+    enrollment_date = fields.Date(allow_none=True)
+
+    class Meta:
+        model = Study
+        # additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
+        #               "sponsor", "ind_number", "approvals", "files", "enrollment_date"]
+        unknown = INCLUDE
+
+    @marshmallow.post_load
+    def make_study(self, data, **kwargs):
+        """Can load the basic study data for updates to the database, but categories are write only"""
+        return Study(**data)
+
+
 class StudySchema(ma.Schema):
 
     id = fields.Integer(required=False, allow_none=True)