Adds study inactive flag. Sets study to inactive if not found in Protocol Builder.

crc/api/study.py

@@ -1,18 +1,16 @@
 from typing import List
 
-from dateutil.parser import parse
 from connexion import NoContent
 from flask import g
 
 from crc import session, auth
 from crc.api.common import ApiError, ApiErrorSchema
 from crc.api.workflow import __get_workflow_api_model
+from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
 from crc.models.study import StudyModelSchema, StudyModel
-from models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
 from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
-from crc.services import protocol_builder
 from crc.services.workflow_processor import WorkflowProcessor
-from services.protocol_builder import ProtocolBuilderService
+from crc.services.protocol_builder import ProtocolBuilderService
 
 
 @auth.login_required
@@ -77,10 +75,13 @@ def update_from_protocol_builder():
 
     db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
     db_study_ids = list(map(lambda s: s.id, db_studies))
+    pb_study_ids = list(map(lambda s: s.id, pb_studies))
 
+    # Add studies from Protocol Builder that aren't in the database yet
     for pb_study in pb_studies:
         if pb_study['HSRNUMBER'] not in db_study_ids:
-            status = ProtocolBuilderStatus.complete._value_ if pb_study['Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
+            status = ProtocolBuilderStatus.complete._value_ if pb_study[
+                'Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
             add_study({
                 'id': pb_study['HSRNUMBER'],
                 'title': pb_study['TITLE'],
@@ -89,6 +90,11 @@ def update_from_protocol_builder():
                 'last_updated': pb_study['DATE_MODIFIED']
             })
 
+    # Mark studies as inactive that are no longer in Protocol Builder
+    for study_id in db_study_ids:
+        if study_id not in pb_study_ids:
+            update_study(study_id=study_id, body={'inactive': True})
+
 
 def post_update_study_from_protocol_builder(study_id):
     """Update a single study based on data received from

crc/models/study.py

@@ -3,7 +3,7 @@ from marshmallow_sqlalchemy import ModelSchema
 from sqlalchemy import func
 
 from crc import db
-from models.protocol_builder import ProtocolBuilderStatus
+from crc.models.protocol_builder import ProtocolBuilderStatus
 
 
 class StudyModel(db.Model):
@@ -17,6 +17,7 @@ class StudyModel(db.Model):
     ind_number = db.Column(db.String)
     user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=True)
     investigator_uids = db.Column(db.ARRAY(db.String))
+    inactive = db.Column(db.Boolean, default=False)
 
 
 class StudyModelSchema(ModelSchema):

crc/services/protocol_builder.py

@@ -4,7 +4,7 @@ from typing import List, Optional
 import requests
 
 from crc import app
-from models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
+from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
     ProtocolBuilderRequiredDocument, ProtocolBuilderStudyDetails, ProtocolBuilderInvestigatorSchema, \
     ProtocolBuilderRequiredDocumentSchema, ProtocolBuilderStudyDetailsSchema
 

migrations/versions/2c88e49d0ffc_.py

@@ -0,0 +1,28 @@
+"""empty message
+
+Revision ID: 2c88e49d0ffc
+Revises: 726d09a4fa0c
+Create Date: 2020-02-27 11:17:01.768161
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '2c88e49d0ffc'
+down_revision = '726d09a4fa0c'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('inactive', sa.Boolean(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('study', 'inactive')
+    # ### end Alembic commands ###

tests/test_study_api.py

@@ -3,7 +3,7 @@ from datetime import datetime, timezone
 
 from crc import session
 from crc.models.study import StudyModel, StudyModelSchema
-from models.protocol_builder import ProtocolBuilderStatus
+from crc.models.protocol_builder import ProtocolBuilderStatus
 from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
     WorkflowApiSchema
 from tests.base_test import BaseTest