Merge pull request #32 from sartography/feature/new_study_states

Updated the study status to use a different enumeration.  Migration c…

crc/api.yml

@@ -828,7 +828,7 @@ components:
           example: dhf8r
         protocol_builder_status:
           type: string
-          enum: [DRAFT, IN_PROCESS, IN_REVIEW, REVIEW_COMPLETE, INACTIVE]
+          enum: [INCOMPLETE, ACTIVE, HOLD, OPEN, ABANDONED]
           example: done
         sponsor:
           type: string

crc/api/study.py

@@ -82,7 +82,7 @@ def post_update_study_from_protocol_builder(study_id):
         db_study.update_from_protocol_builder(pb_study)
     else:
         db_study.inactive = True
-        db_study.protocol_builder_status = ProtocolBuilderStatus.INACTIVE
+        db_study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
 
     return NoContent, 304
 

crc/models/protocol_builder.py

@@ -18,11 +18,23 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
 
 
 class ProtocolBuilderStatus(enum.Enum):
-    DRAFT = 'draft',                      # !Q_COMPLETE
+    # • Active: found in PB and no HSR number and not hold
-    IN_PROCESS = 'in_process',            # Q_COMPLETE && !UPLOAD_COMPLETE && !HSRNUMBER
+    # • Hold: store boolean value in CR Connect (add to Study Model)
-    IN_REVIEW = 'in_review',              # Q_COMPLETE && (!UPLOAD_COMPLETE || !HSRNUMBER)
+    # • Open To Enrollment: has start date and HSR number?
-    REVIEW_COMPLETE = 'review_complete',  # Q_COMPLETE && UPLOAD_COMPLETE && HSRNUMBER
+    # • Abandoned: deleted in PB
-    INACTIVE = 'inactive',                # Not found 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
+
+
+    #DRAFT = 'draft',                      # !Q_COMPLETE
+    #IN_PROCESS = 'in_process',            # Q_COMPLETE && !UPLOAD_COMPLETE && !HSRNUMBER
+    #IN_REVIEW = 'in_review',              # Q_COMPLETE && (!UPLOAD_COMPLETE || !HSRNUMBER)
+    #REVIEW_COMPLETE = 'review_complete',  # Q_COMPLETE && UPLOAD_COMPLETE && HSRNUMBER
+    #INACTIVE = 'inactive',                # Not found in PB
+
 
 
 class ProtocolBuilderStudy(object):

crc/models/study.py

@@ -22,24 +22,22 @@ class StudyModel(db.Model):
     ind_number = db.Column(db.String, nullable=True)
     user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=False)
     investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
-    inactive = db.Column(db.Boolean, default=False)
     requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
+    on_hold = db.Column(db.Boolean, default=False)
 
     def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
         self.hsr_number = pbs.HSRNUMBER
         self.title = pbs.TITLE
         self.user_uid = pbs.NETBADGEID
         self.last_updated = pbs.DATE_MODIFIED
-        self.protocol_builder_status = ProtocolBuilderStatus.DRAFT
+        self.protocol_builder_status = ProtocolBuilderStatus.INCOMPLETE
-        self.inactive = False
-
-        if pbs.HSRNUMBER:  # And Up load complete?
-            self.protocol_builder_status = ProtocolBuilderStatus.REVIEW_COMPLETE
-        elif pbs.Q_COMPLETE:
-            self.protocol_builder_status = ProtocolBuilderStatus.IN_PROCESS
-
-
 
+        if pbs.Q_COMPLETE:
+            self.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
+        if pbs.HSRNUMBER:
+            self.protocol_builder_status = ProtocolBuilderStatus.OPEN
+        if self.on_hold:
+            self.protocol_builder_status = ProtocolBuilderStatus.HOLD
 
 
 class WorkflowMetadata(object):
@@ -106,7 +104,7 @@ class Study(object):
 
     def __init__(self, id, title, last_updated, primary_investigator_id, user_uid,
                  protocol_builder_status=None,
-                 sponsor="", hsr_number="", ind_number="", inactive=False, categories=[], **argsv):
+                 sponsor="", hsr_number="", ind_number="", categories=[], **argsv):
         self.id = id
         self.user_uid = user_uid
         self.title = title
@@ -116,7 +114,6 @@ class Study(object):
         self.sponsor = sponsor
         self.hsr_number = hsr_number
         self.ind_number = ind_number
-        self.inactive = inactive
         self.categories = categories
         self.warnings = []
 
@@ -149,7 +146,7 @@ class StudySchema(ma.Schema):
     class Meta:
         model = Study
         additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
-                      "sponsor", "ind_number", "inactive"]
+                      "sponsor", "ind_number"]
         unknown = INCLUDE
 
     @marshmallow.post_load

crc/services/study_service.py

@@ -88,8 +88,7 @@ class StudyService(object):
         for study in db_studies:
             pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
             if not pb_study:
-                study.inactive = True
+                study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
-                study.protocol_builder_status = ProtocolBuilderStatus.INACTIVE
 
         db.session.commit()
 

migrations/versions/0f38d7a36f21_.py

@@ -0,0 +1,38 @@
+"""empty message
+
+Revision ID: 0f38d7a36f21
+Revises: 476f8a4933ba
+Create Date: 2020-04-21 15:42:46.430272
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '0f38d7a36f21'
+down_revision = '476f8a4933ba'
+branch_labels = None
+depends_on = None
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('on_hold', sa.Boolean(), nullable=True))
+    op.drop_column('study', 'inactive')
+    # ### end Alembic commands ###
+
+    op.execute('ALTER TYPE protocolbuilderstatus RENAME TO pbs_old;')
+    op.execute("CREATE TYPE protocolbuilderstatus AS ENUM('INCOMPLETE', 'ACTIVE', 'HOLD', 'OPEN', 'ABANDONED')")
+    op.execute("ALTER TABLE study ALTER COLUMN protocol_builder_status TYPE protocolbuilderstatus USING protocol_builder_status::text::protocolbuilderstatus;")
+    op.execute('DROP TYPE pbs_old;')
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('inactive', sa.BOOLEAN(), autoincrement=False, nullable=True))
+    op.drop_column('study', 'on_hold')
+    # ### end Alembic commands ###
+
+    op.execute('ALTER TYPE protocolbuilderstatus RENAME TO pbs_old;')
+    op.execute("CREATE TYPE protocolbuilderstatus AS ENUM('DRAFT', 'IN_PROCESS', 'IN_REVIEW', 'REVIEW_COMPLETE', 'INACTIVE')")
+    op.execute("ALTER TABLE study ALTER COLUMN protocol_builder_status TYPE protocolbuilderstatus USING protocol_builder_status::text::protocolbuilderstatus;")
+    op.execute('DROP TYPE pbs_old;')

tests/base_test.py

@@ -53,7 +53,7 @@ class BaseTest(unittest.TestCase):
             'id':0,
             'title':'The impact of fried pickles on beer consumption in bipedal software developers.',
             'last_updated':datetime.datetime.now(),
-            'protocol_builder_status':ProtocolBuilderStatus.IN_PROCESS,
+            'protocol_builder_status':ProtocolBuilderStatus.ACTIVE,
             'primary_investigator_id':'dhf8r',
             'sponsor':'Sartography Pharmaceuticals',
             'ind_number':'1234',
@@ -63,7 +63,7 @@ class BaseTest(unittest.TestCase):
             'id':1,
             'title':'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
             'last_updated':datetime.datetime.now(),
-            'protocol_builder_status':ProtocolBuilderStatus.IN_PROCESS,
+            'protocol_builder_status':ProtocolBuilderStatus.ACTIVE,
             'primary_investigator_id':'dhf8r',
             'sponsor':'Makerspace & Co.',
             'ind_number':'5678',

tests/data/pb_responses/user_studies.json

@@ -9,7 +9,7 @@
   },
   {
     "DATE_MODIFIED": "2020-02-19T14:24:55.101695",
-    "HSRNUMBER": "56753",
+    "HSRNUMBER": "",
     "NETBADGEID": "dhf8r",
     "Q_COMPLETE": true,
     "STUDYID": 65432,
@@ -17,9 +17,9 @@
   },
   {
     "DATE_MODIFIED": "2020-02-19T14:24:55.101695",
-    "HSRNUMBER": "45678",
+    "HSRNUMBER": "",
     "NETBADGEID": "dhf8r",
-    "Q_COMPLETE": true,
+    "Q_COMPLETE": false,
     "STUDYID": 1,
     "TITLE": "Efficacy of xenomorph bio-augmented circuits on dexterity of cybernetic prostheses"
   }

tests/test_study_api.py

@@ -21,7 +21,7 @@ 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.ACTIVE,
         "primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
         "sponsor": "Sirius Cybernetics Corporation",
         "ind_number": "567890",
@@ -104,7 +104,7 @@ 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.REVIEW_COMPLETE
+        study.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
         rv = self.app.put('/v1.0/study/%i' % study.id,
                           content_type="application/json",
                           headers=self.logged_in_headers(),
@@ -142,26 +142,31 @@ class TestStudyApi(BaseTest):
         self.assert_success(api_response)
         json_data = json.loads(api_response.get_data(as_text=True))
 
-        num_inactive = 0
+        num_incomplete = 0
+        num_abandoned = 0
         num_active = 0
+        num_open = 0
 
         for study in json_data:
-            if study['inactive']:
+            if study['protocol_builder_status'] == 'INCOMPLETE':  # One study in user_studies.json is not q_complete
-                num_inactive += 1
+                num_incomplete += 1
-            else:
+            if study['protocol_builder_status'] == 'ABANDONED': # One study does not exist in user_studies.json
+                num_abandoned += 1
+            if study['protocol_builder_status'] == 'ACTIVE': # One study is marked complete without HSR Number
                 num_active += 1
+            if study['protocol_builder_status'] == 'OPEN':  # One study is marked complete and has an HSR Number
+                num_open += 1
 
         db_studies_after = session.query(StudyModel).all()
         num_db_studies_after = len(db_studies_after)
         self.assertGreater(num_db_studies_after, num_db_studies_before)
-        self.assertGreater(num_inactive, 0)
+        self.assertEquals(num_abandoned, 1)
-        self.assertGreater(num_active, 0)
+        self.assertEquals(num_open, 1)
+        self.assertEquals(num_active, 1)
+        self.assertEquals(num_incomplete, 1)
         self.assertEqual(len(json_data), num_db_studies_after)
-        self.assertEqual(num_active + num_inactive, num_db_studies_after)
+        self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)
 
-        # Assure that the existing study is properly updated.
-        test_study = session.query(StudyModel).filter_by(id=54321).first()
-        self.assertFalse(test_study.inactive)
 
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')  # mock_docs
     def test_get_single_study(self, mock_docs):

tests/test_study_service.py

@@ -29,7 +29,7 @@ class TestStudyService(BaseTest):
         user = UserModel(uid="dhf8r", email_address="whatever@stuff.com", display_name="Stayathome Smellalots")
         db.session.add(user)
         db.session.commit()
-        study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS, user_uid=user.uid)
+        study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.ACTIVE, user_uid=user.uid)
         cat = WorkflowSpecCategoryModel(name="cat", display_name="cat", display_order=0)
         db.session.add_all([study, cat])
         db.session.commit()