Merge pull request #170 from sartography/feature/update_study_status_latest

Update study status

crc/api.yml

@@ -1086,9 +1086,9 @@ components:
         user_uid:
           type: string
           example: dhf8r
-        protocol_builder_status:
+        status:
           type: string
-          enum: ['incomplete', 'active', 'hold', 'open', 'abandoned']
+          enum: ['in_progress', 'hold', 'open_for_enrollment', 'abandoned']
           example: done
         sponsor:
           type: string

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 Study, StudyModel, StudySchema, StudyStatus
 from crc.services.study_service import StudyService
 from crc.services.user_service import UserService
 
@@ -22,7 +22,7 @@ def add_study(body):
                              title=body['title'],
                              primary_investigator_id=body['primary_investigator_id'],
                              last_updated=datetime.now(),
-                             protocol_builder_status=ProtocolBuilderStatus.active)
+                             status=StudyStatus.in_progress)
 
     session.add(study_model)
     errors = StudyService._add_all_workflow_specs_to_study(study_model)

crc/models/protocol_builder.py

@@ -17,6 +17,7 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
     SCI = "Scientific Contact"
 
 
+# Deprecated: Marked for removal
 class ProtocolBuilderStatus(enum.Enum):
     # • Active: found in PB and no HSR number and not hold
     # • Hold: store boolean value in CR Connect (add to Study Model)

crc/models/study.py

@@ -1,3 +1,7 @@
+import datetime
+import enum
+import json
+
 import marshmallow
 from marshmallow import INCLUDE, fields
 from marshmallow_enum import EnumField
@@ -11,12 +15,26 @@ from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, Workfl
     WorkflowModel
 
 
+class StudyStatus(enum.Enum):
+    in_progress = 'in_progress'
+    hold = 'hold'
+    open_for_enrollment = 'open_for_enrollment'
+    abandoned = 'abandoned'
+
+
+class IrbStatus(enum.Enum):
+    incomplete_in_protocol_builder = 'incomplete in protocol builder'
+    completed_in_protocol_builder = 'completed in protocol builder'
+    hsr_assigned = 'hsr number assigned'
+
+
 class StudyModel(db.Model):
     __tablename__ = 'study'
     id = db.Column(db.Integer, primary_key=True)
     title = db.Column(db.String)
     last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
-    protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
+    status = db.Column(db.Enum(StudyStatus))
+    irb_status = db.Column(db.Enum(IrbStatus))
     primary_investigator_id = db.Column(db.String, nullable=True)
     sponsor = db.Column(db.String, nullable=True)
     hsr_number = db.Column(db.String, nullable=True)
@@ -33,11 +51,13 @@ class StudyModel(db.Model):
         self.user_uid = pbs.NETBADGEID
         self.last_updated = pbs.DATE_MODIFIED
 
-        self.protocol_builder_status = ProtocolBuilderStatus.active
+        self.irb_status = IrbStatus.incomplete_in_protocol_builder
+        self.status = StudyStatus.in_progress
         if pbs.HSRNUMBER:
-            self.protocol_builder_status = ProtocolBuilderStatus.open
+            self.irb_status = IrbStatus.hsr_assigned
+            self.status = StudyStatus.open_for_enrollment
         if self.on_hold:
-            self.protocol_builder_status = ProtocolBuilderStatus.hold
+            self.status = StudyStatus.hold
 
 
 class WorkflowMetadata(object):
@@ -108,15 +128,15 @@ class CategorySchema(ma.Schema):
 class Study(object):
 
     def __init__(self, title, last_updated, primary_investigator_id, user_uid,
-                 id=None,
+                 id=None, status=None, irb_status=None,
-                 protocol_builder_status=None,
                  sponsor="", hsr_number="", ind_number="", categories=[],
                  files=[], approvals=[], enrollment_date=None, **argsv):
         self.id = id
         self.user_uid = user_uid
         self.title = title
         self.last_updated = last_updated
-        self.protocol_builder_status = protocol_builder_status
+        self.status = status
+        self.irb_status = irb_status
         self.primary_investigator_id = primary_investigator_id
         self.sponsor = sponsor
         self.hsr_number = hsr_number
@@ -135,9 +155,29 @@ class Study(object):
         return instance
 
     def update_model(self, study_model: StudyModel):
-        for k,v in  self.__dict__.items():
+        """As the case for update was very reduced, it's mostly and specifically
-            if not k.startswith('_'):
+        updating only the study status and generating a history record
-                study_model.__dict__[k] = v
+        """
+        status = StudyStatus(self.status)
+        study_model.last_updated = datetime.datetime.now()
+        study_model.status = status
+
+        if status == StudyStatus.open_for_enrollment:
+            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."""
@@ -147,12 +187,33 @@ class Study(object):
         return self_dict
 
 
+class StudyForUpdateSchema(ma.Schema):
+
+    id = fields.Integer(required=False, allow_none=True)
+    status = EnumField(StudyStatus, 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)
     categories = fields.List(fields.Nested(CategorySchema), dump_only=True)
     warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
-    protocol_builder_status = EnumField(ProtocolBuilderStatus)
+    protocol_builder_status = EnumField(StudyStatus, by_value=True)
+    status = EnumField(StudyStatus, by_value=True)
     hsr_number = fields.String(allow_none=True)
     sponsor = fields.String(allow_none=True)
     ind_number = fields.String(allow_none=True)

crc/services/study_service.py

@@ -12,7 +12,7 @@ from crc.api.common import ApiError
 from crc.models.file import FileModel, FileModelSchema, File
 from crc.models.ldap import LdapSchema
 from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
-from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
+from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata
 from crc.models.task_event import TaskEventModel, TaskEvent
 from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
     WorkflowStatus
@@ -64,7 +64,7 @@ class StudyService(object):
         # Calling this line repeatedly is very very slow.  It creates the
         # master spec and runs it.  Don't execute this for Abandoned studies, as
         # we don't have the information to process them.
-        if study.protocol_builder_status != ProtocolBuilderStatus.abandoned:
+        if study.status != StudyStatus.abandoned:
             status = StudyService.__get_study_status(study_model)
             study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
 
@@ -265,7 +265,7 @@ 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.protocol_builder_status = ProtocolBuilderStatus.abandoned
+                    study.status = StudyStatus.abandoned
 
             db.session.commit()
 

migrations/versions/1c3f88dbccc3_.py

@@ -0,0 +1,36 @@
+"""empty message
+
+Revision ID: 1c3f88dbccc3
+Revises: 2e7b377cbc7b
+Create Date: 2020-07-30 18:51:01.816284
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '1c3f88dbccc3'
+down_revision = 'ab06a94e5d4c'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned')")
+    op.execute("CREATE TYPE studystatus AS ENUM('in_progress', 'hold', 'open_for_enrollment', 'abandoned')")
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('irb_status', sa.Enum('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned', name='irbstatus'), nullable=True))
+    op.add_column('study', sa.Column('status', sa.Enum('in_progress', 'hold', 'open_for_enrollment', 'abandoned', name='studystatus'), nullable=True))
+    op.drop_column('study', 'protocol_builder_status')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('protocol_builder_status', postgresql.ENUM('incomplete', 'active', 'hold', 'open', 'abandoned', name='protocolbuilderstatus'), autoincrement=False, nullable=True))
+    op.drop_column('study', 'status')
+    op.drop_column('study', 'irb_status')
+    # ### end Alembic commands ###
+    op.execute('DROP TYPE studystatus')
+    op.execute('DROP TYPE irbstatus')

tests/base_test.py

@@ -15,9 +15,8 @@ from crc import app, db, session
 from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
 from crc.models.approval import ApprovalModel, ApprovalStatus
 from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
-from crc.models.protocol_builder import ProtocolBuilderStatus
-from crc.models.study import StudyModel
 from crc.models.task_event import TaskEventModel
+from crc.models.study import StudyModel, StudyStatus
 from crc.models.user import UserModel
 from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel
 from crc.services.file_service import FileService
@@ -69,24 +68,24 @@ class BaseTest(unittest.TestCase):
 
     studies = [
         {
-            'id': 0,
+            'id':0,
-            'title': 'The impact of fried pickles on beer consumption in bipedal software developers.',
+            'title':'The impact of fried pickles on beer consumption in bipedal software developers.',
-            'last_updated': datetime.datetime.now(),
+            'last_updated':datetime.datetime.now(),
-            'protocol_builder_status': ProtocolBuilderStatus.active,
+            'status':StudyStatus.in_progress,
-            'primary_investigator_id': 'dhf8r',
+            'primary_investigator_id':'dhf8r',
-            'sponsor': 'Sartography Pharmaceuticals',
+            'sponsor':'Sartography Pharmaceuticals',
-            'ind_number': '1234',
+            'ind_number':'1234',
-            'user_uid': 'dhf8r'
+            'user_uid':'dhf8r'
         },
         {
-            'id': 1,
+            'id':1,
-            'title': 'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
+            'title':'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
-            'last_updated': datetime.datetime.now(),
+            'last_updated':datetime.datetime.now(),
-            'protocol_builder_status': ProtocolBuilderStatus.active,
+            'status':StudyStatus.in_progress,
-            'primary_investigator_id': 'dhf8r',
+            'primary_investigator_id':'dhf8r',
-            'sponsor': 'Makerspace & Co.',
+            'sponsor':'Makerspace & Co.',
-            'ind_number': '5678',
+            'ind_number':'5678',
-            'user_uid': 'dhf8r'
+            'user_uid':'dhf8r'
         }
     ]
 
@@ -258,7 +257,7 @@ class BaseTest(unittest.TestCase):
         study = session.query(StudyModel).filter_by(user_uid=uid).filter_by(title=title).first()
         if study is None:
             user = self.create_user(uid=uid)
-            study = StudyModel(title=title, protocol_builder_status=ProtocolBuilderStatus.active,
+            study = StudyModel(title=title, status=StudyStatus.in_progress,
                                user_uid=user.uid, primary_investigator_id=primary_investigator_id)
             session.add(study)
             session.commit()

tests/study/test_study_api.py

@@ -11,7 +11,7 @@ from crc.models.protocol_builder import ProtocolBuilderStatus, \
     ProtocolBuilderStudySchema
 from crc.models.approval import ApprovalStatus
 from crc.models.task_event import TaskEventModel
-from crc.models.study import StudyModel, StudySchema
+from crc.models.study import StudyModel, StudySchema, StudyStatus
 from crc.models.workflow import WorkflowSpecModel, WorkflowModel
 from crc.services.file_service import FileService
 from crc.services.workflow_processor import WorkflowProcessor
@@ -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['status'] = StudyStatus.in_progress.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))
 
@@ -135,15 +136,16 @@ 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['status'] = StudyStatus.in_progress.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'])
-        self.assertEqual(study.protocol_builder_status.name, json_data['protocol_builder_status'])
+        self.assertEqual(study.status.value, json_data['status'])
 
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')  # mock_studies
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')  # mock_docs
@@ -181,15 +183,15 @@ class TestStudyApi(BaseTest):
 
         num_incomplete = 0
         num_abandoned = 0
-        num_active = 0
+        num_in_progress = 0
         num_open = 0
 
         for study in json_data:
-            if study['protocol_builder_status'] == 'abandoned': # One study does not exist in user_studies.json
+            if study['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
+            if study['status'] == 'in_progress': # One study is marked complete without HSR Number
-                num_active += 1
+                num_in_progress += 1
-            if study['protocol_builder_status'] == 'open':  # One study is marked complete and has an HSR Number
+            if study['status'] == 'open_for_enrollment':  # One study is marked complete and has an HSR Number
                 num_open += 1
 
         db_studies_after = session.query(StudyModel).all()
@@ -197,10 +199,10 @@ class TestStudyApi(BaseTest):
         self.assertGreater(num_db_studies_after, num_db_studies_before)
         self.assertEqual(num_abandoned, 1)
         self.assertEqual(num_open, 1)
-        self.assertEqual(num_active, 2)
+        self.assertEqual(num_in_progress, 2)
         self.assertEqual(num_incomplete, 0)
         self.assertEqual(len(json_data), num_db_studies_after)
-        self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)
+        self.assertEqual(num_open + num_in_progress + num_incomplete + num_abandoned, num_db_studies_after)
 
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')  # mock_studies
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')  # mock_docs
@@ -228,7 +230,7 @@ class TestStudyApi(BaseTest):
         json_data = json.loads(rv.get_data(as_text=True))
         self.assertEqual(study.id, json_data['id'])
         self.assertEqual(study.title, json_data['title'])
-        self.assertEqual(study.protocol_builder_status.name, json_data['protocol_builder_status'])
+        self.assertEqual(study.status.value, json_data['status'])
         self.assertEqual(study.primary_investigator_id, json_data['primary_investigator_id'])
         self.assertEqual(study.sponsor, json_data['sponsor'])
         self.assertEqual(study.ind_number, json_data['ind_number'])

tests/study/test_study_service.py

@@ -6,7 +6,7 @@ from tests.base_test import BaseTest
 
 from crc import db, app
 from crc.models.protocol_builder import ProtocolBuilderStatus
-from crc.models.study import StudyModel
+from crc.models.study import StudyModel, StudyStatus
 from crc.models.user import UserModel
 from crc.models.workflow import WorkflowModel, WorkflowStatus, \
     WorkflowSpecCategoryModel
@@ -40,7 +40,7 @@ class TestStudyService(BaseTest):
             for study in db.session.query(StudyModel).all():
                 StudyService().delete_study(study.id)
 
-        study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.active, user_uid=user.uid)
+        study = StudyModel(title="My title", status=StudyStatus.in_progress, user_uid=user.uid)
         db.session.add(study)
 
         self.load_test_spec("random_fact", category_id=cat.id)

tests/test_authentication.py

@@ -8,7 +8,7 @@ from tests.base_test import BaseTest
 from crc import app, session
 from crc.api.common import ApiError
 from crc.models.protocol_builder import ProtocolBuilderStatus
-from crc.models.study import StudySchema, StudyModel
+from crc.models.study import StudySchema, StudyModel, StudyStatus
 from crc.models.user import UserModel
 
 
@@ -274,7 +274,7 @@ class TestAuthentication(BaseTest):
         return {
             "title": "blah",
             "last_updated": datetime.now(tz=timezone.utc),
-            "protocol_builder_status": ProtocolBuilderStatus.active,
+            "status": StudyStatus.in_progress,
             "primary_investigator_id": uid,
             "user_uid": uid,
         }