Merge pull request #357 from sartography/426-remove-hsr-number

remove hsr number #426

crc/api.yml

@@ -1627,10 +1627,6 @@ components:
           type: string
           x-nullable: true
           example: "27b-6-42"
-        hsr_number:
-          type: string
-          x-nullable: true
-          example: "27b-6-1212"
     StudyAssociate:
       properties:
         uid:

crc/models/protocol_builder.py

@@ -19,32 +19,31 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
 
 # Deprecated: Marked for removal
 class ProtocolBuilderStatus(enum.Enum):
-    # • Active: found in PB and no HSR number and not hold
+    # • Active: found in PB and not hold
     # • Hold: store boolean value in CR Connect (add to Study Model)
-    # • Open To Enrollment: has start date and HSR number?
+    # • Open To Enrollment: has start date?
     # • 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
+    active = 'active'  # found in PB, marked as "q_complete" 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?
+    open = 'open'  # Open To Enrollment: has start date?
     abandoned = 'abandoned'  # Not found in PB
 
 
     #DRAFT = 'draft',                      # !Q_COMPLETE
-    #IN_PROCESS = 'in_process',            # Q_COMPLETE && !UPLOAD_COMPLETE && !HSRNUMBER
+    #IN_PROCESS = 'in_process',            # Q_COMPLETE && !UPLOAD_COMPLETE
-    #IN_REVIEW = 'in_review',              # Q_COMPLETE && (!UPLOAD_COMPLETE || !HSRNUMBER)
+    #IN_REVIEW = 'in_review',              # Q_COMPLETE && (!UPLOAD_COMPLETE)
-    #REVIEW_COMPLETE = 'review_complete',  # Q_COMPLETE && UPLOAD_COMPLETE && HSRNUMBER
+    #REVIEW_COMPLETE = 'review_complete',  # Q_COMPLETE && UPLOAD_COMPLETE
     #INACTIVE = 'inactive',                # Not found in PB
 
 
 
 class ProtocolBuilderStudy(object):
     def __init__(
-            self, STUDYID: int, HSRNUMBER: str, TITLE: str, NETBADGEID: str,
+            self, STUDYID: int, TITLE: str, NETBADGEID: str,
             DATE_MODIFIED: str
     ):
         self.STUDYID = STUDYID
-        self.HSRNUMBER = HSRNUMBER
         self.TITLE = TITLE
         self.NETBADGEID = NETBADGEID
         self.DATE_MODIFIED = DATE_MODIFIED
@@ -54,7 +53,7 @@ class ProtocolBuilderStudySchema(ma.Schema):
     class Meta:
         model = ProtocolBuilderStudy
         unknown = INCLUDE
-        fields = ["STUDYID", "HSRNUMBER", "TITLE", "NETBADGEID",
+        fields = ["STUDYID", "TITLE", "NETBADGEID",
                   "DATE_MODIFIED"]
 
     @post_load

crc/models/study.py

@@ -27,7 +27,6 @@ class StudyStatus(enum.Enum):
 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 StudyEventType(enum.Enum):
@@ -46,7 +45,6 @@ class StudyModel(db.Model):
     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)
     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)
@@ -57,7 +55,6 @@ class StudyModel(db.Model):
     events_history = db.relationship("StudyEvent", cascade="all, delete, delete-orphan")
 
     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
@@ -172,7 +169,7 @@ class Study(object):
 
     def __init__(self, title, short_title, last_updated, primary_investigator_id, user_uid,
                  id=None, status=None, irb_status=None, comment="",
-                 sponsor="", hsr_number="", ind_number="", categories=[],
+                 sponsor="", ind_number="", categories=[],
                  files=[], approvals=[], enrollment_date=None, events_history=[],
                  last_activity_user="",last_activity_date =None,create_user_display="", **argsv):
         self.id = id
@@ -188,7 +185,6 @@ class Study(object):
         self.comment = comment
         self.primary_investigator_id = primary_investigator_id
         self.sponsor = sponsor
-        self.hsr_number = hsr_number
         self.ind_number = ind_number
         self.categories = categories
         self.approvals = approvals
@@ -220,7 +216,6 @@ 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)
@@ -252,7 +247,6 @@ class StudySchema(ma.Schema):
     warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
     protocol_builder_status = EnumField(StudyStatus, by_value=True)
     status = EnumField(StudyStatus, by_value=True)
-    hsr_number = fields.String(allow_none=True)
     short_title = fields.String(allow_none=True)
     sponsor = fields.String(allow_none=True)
     ind_number = fields.String(allow_none=True)

crc/services/study_service.py

@@ -398,11 +398,6 @@ class StudyService(object):
                     session.add(db_study)
                     db_studies.append(db_study)
 
-                if pb_study.HSRNUMBER:
-                    db_study.irb_status = IrbStatus.hsr_assigned
-                    if db_study.status != StudyStatus.open_for_enrollment:
-                        new_status = StudyStatus.open_for_enrollment
-
                 db_study.update_from_protocol_builder(pb_study)
                 StudyService._add_all_workflow_specs_to_study(db_study)
 

migrations/versions/3d9ae7cfc231_.py

@@ -0,0 +1,40 @@
+"""Remove HSR Number
+
+Revision ID: 3d9ae7cfc231
+Revises: 2a6f7ea00e5f
+Create Date: 2021-08-16 11:28:40.027495
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '3d9ae7cfc231'
+down_revision = '2a6f7ea00e5f'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # Remove `hsr_assigned` values from Study table
+    op.execute("UPDATE study SET irb_status = 'incomplete_in_protocol_builder' where irb_status = 'hsr_assigned'")
+
+    # Remove `hsr_assigned` from IRB Status Enum
+    op.execute("ALTER TYPE irbstatus RENAME TO irbstatus_old")
+    op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder')")
+    op.execute("ALTER TABLE study ALTER COLUMN irb_status TYPE irbstatus USING irb_status::text::irbstatus")
+    op.execute("DROP TYPE irbstatus_old")
+
+    # Remove hsr_number column from Study table
+    op.drop_column('study', 'hsr_number')
+
+
+
+def downgrade():
+    op.execute("ALTER TYPE irbstatus RENAME TO irbstatus_old")
+    op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned')")
+    op.execute("ALTER TABLE study ALTER COLUMN irb_status TYPE irbstatus USING irb_status::text::irbstatus")
+    op.execute("DROP TYPE irbstatus_old")
+
+    op.add_column('study', sa.Column('hsr_number', sa.String(), nullable=True))

tests/data/pb_responses/user_studies.json

@@ -1,21 +1,18 @@
 [
   {
     "DATE_MODIFIED": "2020-02-19T14:26:49.127756",
-    "HSRNUMBER": "12345",
     "NETBADGEID": "dhf8r",
     "STUDYID": 54321,
     "TITLE": "Another study about the effect of a naked mannequin on software productivity"
   },
   {
     "DATE_MODIFIED": "2020-02-19T14:24:55.101695",
-    "HSRNUMBER": "",
     "NETBADGEID": "dhf8r",
     "STUDYID": 65432,
     "TITLE": "Peanut butter consumption among quiet dogs"
   },
   {
     "DATE_MODIFIED": "2020-02-19T14:24:55.101695",
-    "HSRNUMBER": "",
     "NETBADGEID": "dhf8r",
     "STUDYID": 1,
     "TITLE": "Efficacy of xenomorph bio-augmented circuits on dexterity of cybernetic prostheses"

tests/study/test_study_api.py

@@ -190,17 +190,20 @@ class TestStudyApi(BaseTest):
                 num_abandoned += 1
             if study['status'] == 'in_progress': # One study is marked complete without HSR Number
                 num_in_progress += 1
-            if study['status'] == 'open_for_enrollment':  # One study is marked complete and has an HSR Number
+            if study['status'] == 'open_for_enrollment':  # Currently, we don't automatically set studies to open for enrollment
                 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.assertEqual(num_abandoned, 1)
-        self.assertEqual(num_open, 1)
+        self.assertEqual(num_open, 0)  # Currently, we don't automatically set studies to open for enrollment
         self.assertEqual(num_in_progress, 2)
         self.assertEqual(len(json_data), num_db_studies_after)
-        self.assertEqual(num_open + num_in_progress + num_abandoned, num_db_studies_after)
+        # The sum below is off, since we don't automatically set studies to Open for Enrollment
+        # Leaving the test here because we will need it again
+        # when we implement a new way to set Open for Enrollment
+        # self.assertEqual(num_open + num_in_progress + num_abandoned, num_db_studies_after)
 
         # Automatic events check
         in_progress_events = session.query(StudyEvent).filter_by(status=StudyStatus.in_progress)
@@ -209,8 +212,11 @@ class TestStudyApi(BaseTest):
         abandoned_events = session.query(StudyEvent).filter_by(status=StudyStatus.abandoned)
         self.assertEqual(abandoned_events.count(), 1)  # 1 study has been abandoned
 
-        open_for_enrollment_events = session.query(StudyEvent).filter_by(status=StudyStatus.open_for_enrollment)
+        # We don't currently set any studies to Open for Enrollment automatically
-        self.assertEqual(open_for_enrollment_events.count(), 1)  # 1 study was moved to open for enrollment
+        # Leaving the test here because we will need it again
+        # when we implement a new way to set Open for Enrollment
+        # open_for_enrollment_events = session.query(StudyEvent).filter_by(status=StudyStatus.open_for_enrollment)
+        # self.assertEqual(open_for_enrollment_events.count(), 1)  # 1 study was moved to open for enrollment
 
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')  # mock_studies
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')  # mock_docs