Replaces migration and fixes broken tests

crc/api.yml

@@ -733,7 +733,7 @@ components:
           example: "2019-12-25T09:12:33.001Z"
         protocol_builder_status:
           type: string
-          enum: [out_of_date, in_process, complete, updating]
+          enum: [DRAFT, IN_PROCESS, IN_REVIEW, REVIEW_COMPLETE, INACTIVE]
           example: done
         user_uid:
           type: string

crc/api/study.py

@@ -165,9 +165,9 @@ def map_pb_study_to_study(pb_study):
 
     # Translate Protocol Builder states to enum values
     status = ProtocolBuilderStatus.DRAFT
-    if pb_study['Q_COMPLETE']:
-        if pb_study['UPLOAD_COMPLETE']:
-            if pb_study['HSRNUMBER']:
+    if 'Q_COMPLETE' in pb_study['Q_COMPLETE'] and pb_study['Q_COMPLETE']:
+        if 'UPLOAD_COMPLETE' in pb_study and pb_study['UPLOAD_COMPLETE']:
+            if 'HSRNUMBER' in pb_study and pb_study['HSRNUMBER']:
                 status = ProtocolBuilderStatus.REVIEW_COMPLETE
             else:
                 status = ProtocolBuilderStatus.IN_REVIEW

example_data.py

@@ -9,6 +9,7 @@ from crc.models.study import StudyModel
 from crc.models.user import UserModel
 from crc.models.workflow import WorkflowSpecModel
 from crc.services.workflow_processor import WorkflowProcessor
+from models.protocol_builder import ProtocolBuilderStatus
 
 
 class ExampleDataLoader:
@@ -31,7 +32,7 @@ class ExampleDataLoader:
                 id=1,
                 title='The impact of fried pickles on beer consumption in bipedal software developers.',
                 last_updated=datetime.datetime.now(),
-                protocol_builder_status='in_process',
+                protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS.name,
                 primary_investigator_id='dhf8r',
                 sponsor='Sartography Pharmaceuticals',
                 ind_number='1234',
@@ -41,7 +42,7 @@ class ExampleDataLoader:
                 id=2,
                 title='Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
                 last_updated=datetime.datetime.now(),
-                protocol_builder_status='in_process',
+                protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS.name,
                 primary_investigator_id='dhf8r',
                 sponsor='Makerspace & Co.',
                 ind_number='5678',

migrations/versions/1c6e4e179f8e_.py

@@ -1,8 +1,8 @@
 """empty message
 
-Revision ID: cb3a03c10a0e
+Revision ID: 1c6e4e179f8e
 Revises: 
-Create Date: 2020-02-28 11:12:56.150837
+Create Date: 2020-03-03 15:51:45.550681
 
 """
 from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.
-revision = 'cb3a03c10a0e'
+revision = '1c6e4e179f8e'
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -43,7 +43,7 @@ def upgrade():
     sa.Column('id', sa.Integer(), nullable=False),
     sa.Column('title', sa.String(), nullable=True),
     sa.Column('last_updated', sa.DateTime(timezone=True), nullable=True),
-    sa.Column('protocol_builder_status', sa.Enum('out_of_date', 'in_process', 'complete', 'updating', name='protocolbuilderstatus'), nullable=True),
+    sa.Column('protocol_builder_status', sa.Enum('DRAFT', 'IN_PROCESS', 'IN_REVIEW', 'REVIEW_COMPLETE', 'INACTIVE', name='protocolbuilderstatus'), nullable=True),
     sa.Column('primary_investigator_id', sa.String(), nullable=True),
     sa.Column('sponsor', sa.String(), nullable=True),
     sa.Column('hsr_number', sa.String(), nullable=True),

tests/test_study_api.py

@@ -24,7 +24,7 @@ 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.in_process,
+            "protocol_builder_status": ProtocolBuilderStatus.IN_PROCESS,
             "primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
             "sponsor": "Sirius Cybernetics Corporation",
             "ind_number": "567890",
@@ -49,7 +49,7 @@ 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.complete
+        study.protocol_builder_status = ProtocolBuilderStatus.REVIEW_COMPLETE
         rv = self.app.put('/v1.0/study/%i' % study.id,
                           content_type="application/json",
                           headers=self.logged_in_headers(),