Updating properly study status & fixing tests

crc/models/study.py

@@ -1,3 +1,6 @@
+import datetime
+import json
+
 import marshmallow
 from marshmallow import INCLUDE, fields
 from marshmallow_enum import EnumField
@@ -26,6 +29,7 @@ class StudyModel(db.Model):
     requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
     on_hold = db.Column(db.Boolean, default=False)
     enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
+    changes_history = db.Column(db.JSON, nullable=True)
 
     def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
         self.hsr_number = pbs.HSRNUMBER
@@ -135,9 +139,29 @@ 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
+        """As the case for update was very reduced, it's mostly and specifically
+        updating only the study status and generating a history record
+        """
+        pb_status = ProtocolBuilderStatus(self.protocol_builder_status)
+        study_model.last_updated = datetime.datetime.now()
+        study_model.protocol_builder_status = pb_status
+
+        if pb_status == ProtocolBuilderStatus.OPEN:
+            study_model.enrollment_date = self.enrollment_date
+
+        change = {
+            'status': ProtocolBuilderStatus(self.protocol_builder_status).value,
+            'comment': '' if not hasattr(self, 'comment') else self.comment,
+            'date': str(datetime.datetime.now())
+        }
+
+        if study_model.changes_history:
+            changes_history = json.loads(study_model.changes_history)
+            changes_history.append(change)
+        else:
+            changes_history = [change]
+        study_model.changes_history = json.dumps(changes_history)
+
 
     def model_args(self):
         """Arguments that can be passed into the Study Model to update it."""
@@ -147,6 +171,26 @@ 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.DateTime(allow_none=True)
+    comment = fields.String(allow_none=True)
+
+    class Meta:
+        model = Study
+        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)

migrations/versions/369d65dcb269_.py

@@ -0,0 +1,28 @@
+"""empty message
+
+Revision ID: 369d65dcb269
+Revises: c4ddb69e7ef4
+Create Date: 2020-07-27 20:05:29.524553
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '369d65dcb269'
+down_revision = 'c4ddb69e7ef4'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('changes_history', sa.JSON(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('study', 'changes_history')
+    # ### end Alembic commands ###

tests/study/test_study_api.py

@@ -24,16 +24,17 @@ class TestStudyApi(BaseTest):
         "title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
                  "for Interstellar Spacecraft",
         "last_updated": datetime.now(tz=timezone.utc),
-        "protocol_builder_status": ProtocolBuilderStatus.active,
         "primary_investigator_id": "tmm2x",
         "user_uid": "dhf8r",
     }
 
     def add_test_study(self):
+        study_schema = StudySchema().dump(self.TEST_STUDY)
+        study_schema['protocol_builder_status'] = ProtocolBuilderStatus.ACTIVE.value
         rv = self.app.post('/v1.0/study',
                            content_type="application/json",
                            headers=self.logged_in_headers(),
-                           data=json.dumps(StudySchema().dump(self.TEST_STUDY)))
+                           data=json.dumps(study_schema))
         self.assert_success(rv)
         return json.loads(rv.get_data(as_text=True))
 
@@ -135,11 +136,12 @@ class TestStudyApi(BaseTest):
         self.load_example_data()
         study: StudyModel = session.query(StudyModel).first()
         study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
-        study.protocol_builder_status = ProtocolBuilderStatus.active
+        study_schema = StudySchema().dump(study)
+        study_schema['protocol_builder_status'] = ProtocolBuilderStatus.ACTIVE.value
         rv = self.app.put('/v1.0/study/%i' % study.id,
                           content_type="application/json",
                           headers=self.logged_in_headers(),
-                          data=json.dumps(StudySchema().dump(study)))
+                          data=json.dumps(study_schema))
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
         self.assertEqual(study.title, json_data['title'])