Updates study model to better match Protocol Builder. Deletes all migrations and starts over, since Alembic has problems migrating changes to existing column constraints.

Pipfile.lock

@@ -91,10 +91,10 @@
         },
         "billiard": {
             "hashes": [
-                "sha256:26fd494dc3251f8ce1f5559744f18aeed427fdaf29a75d7baae26752a5d3816f",
+                "sha256:bff575450859a6e0fbc2f9877d9b715b0bbc07c3565bb7ed2280526a0cdf5ede",
-                "sha256:f4e09366653aa3cb3ae8ed16423f9ba1665ff426f087bcdbbed86bf3664fe02c"
+                "sha256:d91725ce6425f33a97dfa72fb6bfef0e47d4652acd98a032bd1a7fbf06d5fa6a"
             ],
-            "version": "==3.6.2.0"
+            "version": "==3.6.3.0"
         },
         "blinker": {
             "hashes": [

crc/api/study.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional, Union, Tuple, Dict
 
 from connexion import NoContent
 from flask import g
@@ -8,19 +8,14 @@ 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 crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
+from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel, WorkflowApi
 from crc.services.workflow_processor import WorkflowProcessor
 from crc.services.protocol_builder import ProtocolBuilderService
 
 
 @auth.login_required
 def all_studies():
-    user = g.user
+    return update_from_protocol_builder()
-    """:type: crc.models.user.UserModel"""
-
-    update_from_protocol_builder()
-    db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
-    return StudyModelSchema(many=True).dump(db_studies)
 
 
 @auth.login_required
@@ -47,10 +42,11 @@ def update_study(study_id, body):
         error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
         return ApiErrorSchema.dump(error), 404
 
-    study = StudyModelSchema().load(body, session=session, instance=study)
+    schema = StudyModelSchema()
+    study = schema.load(body, session=session, instance=study, partial=True)
     session.add(study)
     session.commit()
-    return StudyModelSchema().dump(study)
+    return schema.dump(study)
 
 
 @auth.login_required
@@ -71,39 +67,49 @@ def update_from_protocol_builder():
     """:type: crc.models.user.UserModel"""
 
     # Get studies matching this user from Protocol Builder
-    pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
+    pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies()
 
+    # Get studies from the database
     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))
+    pb_study_ids = list(map(lambda s: s['STUDYID'], pb_studies))
+
+    for pb_study in pb_studies:
+
+        # Update studies with latest data from Protocol Builder
+        if pb_study['STUDYID'] in db_study_ids:
+            update_study(pb_study['STUDYID'], map_pb_study_to_study(pb_study))
 
         # Add studies from Protocol Builder that aren't in the database yet
-    for pb_study in pb_studies:
+        else:
-        if pb_study['HSRNUMBER'] not in db_study_ids:
+            new_study = map_pb_study_to_study(pb_study)
-            status = ProtocolBuilderStatus.complete._value_ if pb_study[
+            add_study(new_study)
-                'Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
-            add_study({
-                'id': pb_study['HSRNUMBER'],
-                'title': pb_study['TITLE'],
-                'protocol_builder_status': status,
-                'user_uid': pb_study['NETBADGEID'],
-                '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})
 
+    # Return updated studies
+    updated_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
+    results = StudyModelSchema(many=True).dump(updated_studies)
+    return results
 
+
+@auth.login_required
 def post_update_study_from_protocol_builder(study_id):
     """Update a single study based on data received from
     the protocol builder."""
 
-    # todo: Actually get data from an external service here
+    pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies()
+    for pb_study in pb_studies:
+        if pb_study['STUDYID'] == study_id:
+            return update_study(study_id, map_pb_study_to_study(pb_study))
+
     return NoContent, 304
 
 
+@auth.login_required
 def get_study_workflows(study_id):
     workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all()
     api_models = []
@@ -115,6 +121,7 @@ def get_study_workflows(study_id):
     return schema.dump(api_models)
 
 
+@auth.login_required
 def add_workflow_to_study(study_id, body):
     workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
     if workflow_spec_model is None:
@@ -122,3 +129,38 @@ def add_workflow_to_study(study_id, body):
         return ApiErrorSchema.dump(error), 404
     processor = WorkflowProcessor.create(study_id, workflow_spec_model.id)
     return WorkflowApiSchema().dump(__get_workflow_api_model(processor))
+
+
+@auth.login_required
+def get_user_pb_studies() -> List[ProtocolBuilderStudy]:
+    """Get studies from Protocol Builder matching the given user"""
+
+    user = g.user
+    """:type: crc.models.user.UserModel"""
+
+    return ProtocolBuilderService.get_studies(user.uid)
+
+
+def map_pb_study_to_study(pb_study):
+    """Translates the given dict of ProtocolBuilderStudy properties to dict of StudyModel attributes"""
+    prop_map = {
+        'STUDYID': 'id',
+        'HSRNUMBER': 'hsr_number',
+        'TITLE': 'title',
+        'NETBADGEID': 'user_uid',
+        'DATE_MODIFIED': 'last_updated',
+    }
+    study_info = {}
+
+    # Translate Protocol Builder property names to Study attributes
+    for k, v in pb_study.items():
+        if k in prop_map:
+            study_info[prop_map[k]] = v
+
+    if pb_study['Q_COMPLETE']:
+        study_info['protocol_builder_status'] = ProtocolBuilderStatus.complete._value_
+    else:
+        study_info['protocol_builder_status'] = ProtocolBuilderStatus.in_process._value_
+
+    return study_info
+

crc/models/study.py

@@ -12,12 +12,14 @@ class StudyModel(db.Model):
     title = db.Column(db.String)
     last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
     protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
-    primary_investigator_id = db.Column(db.String)
+    primary_investigator_id = db.Column(db.String, nullable=True)
-    sponsor = db.Column(db.String)
+    sponsor = db.Column(db.String, nullable=True)
-    ind_number = db.Column(db.String)
+    hsr_number = db.Column(db.String, nullable=True)
-    user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=True)
+    ind_number = db.Column(db.String, nullable=True)
-    investigator_uids = db.Column(db.ARRAY(db.String))
+    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)
 
 
 class StudyModelSchema(ModelSchema):

migrations/versions/0a6e0b829398_.py

@@ -1,36 +0,0 @@
-"""empty message
-
-Revision ID: 0a6e0b829398
-Revises: ad5483cb7f3b
-Create Date: 2020-02-20 15:42:16.473470
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '0a6e0b829398'
-down_revision = 'ad5483cb7f3b'
-branch_labels = None
-depends_on = None
-
-
-def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column('user', sa.Column('affiliation', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('eppn', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('first_name', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('last_name', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('title', sa.String(), nullable=True))
-    # ### end Alembic commands ###
-
-
-def downgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column('user', 'title')
-    op.drop_column('user', 'last_name')
-    op.drop_column('user', 'first_name')
-    op.drop_column('user', 'eppn')
-    op.drop_column('user', 'affiliation')
-    # ### end Alembic commands ###

migrations/versions/2c88e49d0ffc_.py

@@ -1,28 +0,0 @@
-"""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 ###

migrations/versions/726d09a4fa0c_.py

@@ -1,32 +0,0 @@
-"""empty message
-
-Revision ID: 726d09a4fa0c
-Revises: 0a6e0b829398
-Create Date: 2020-02-26 16:35:05.854328
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '726d09a4fa0c'
-down_revision = '0a6e0b829398'
-branch_labels = None
-depends_on = None
-
-
-def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column('study', sa.Column('investigator_uids', sa.ARRAY(sa.String()), nullable=True))
-    op.add_column('study', sa.Column('user_uid', sa.String(), nullable=True))
-    op.create_foreign_key(None, 'study', 'user', ['user_uid'], ['uid'])
-    # ### end Alembic commands ###
-
-
-def downgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_constraint(None, 'study', type_='foreignkey')
-    op.drop_column('study', 'user_uid')
-    op.drop_column('study', 'investigator_uids')
-    # ### end Alembic commands ###

migrations/versions/ad5483cb7f3b_.py

@@ -1,35 +0,0 @@
-"""empty message
-
-Revision ID: ad5483cb7f3b
-Revises: 02fcf09d9085
-Create Date: 2020-02-19 11:59:09.948767
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = 'ad5483cb7f3b'
-down_revision = '02fcf09d9085'
-branch_labels = None
-depends_on = None
-
-
-def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('user',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('uid', sa.String(), nullable=True),
-    sa.Column('email_address', sa.String(), nullable=True),
-    sa.Column('display_name', sa.String(), nullable=True),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('uid')
-    )
-    # ### end Alembic commands ###
-
-
-def downgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_table('user')
-    # ### end Alembic commands ###

migrations/versions/cb3a03c10a0e_.py

@@ -1,8 +1,8 @@
 """empty message
 
-Revision ID: 02fcf09d9085
+Revision ID: cb3a03c10a0e
 Revises: 
-Create Date: 2020-02-05 17:18:35.324675
+Create Date: 2020-02-28 11:12:56.150837
 
 """
 from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.
-revision = '02fcf09d9085'
+revision = 'cb3a03c10a0e'
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -18,15 +18,18 @@ depends_on = None
 
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('study',
+    op.create_table('user',
     sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('uid', sa.String(), nullable=True),
+    sa.Column('email_address', sa.String(), nullable=True),
+    sa.Column('display_name', sa.String(), nullable=True),
+    sa.Column('affiliation', sa.String(), nullable=True),
+    sa.Column('eppn', sa.String(), nullable=True),
+    sa.Column('first_name', sa.String(), nullable=True),
+    sa.Column('last_name', sa.String(), nullable=True),
     sa.Column('title', sa.String(), nullable=True),
-    sa.Column('last_updated', sa.DateTime(timezone=True), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
-    sa.Column('protocol_builder_status', sa.Enum('out_of_date', 'in_process', 'complete', 'updating', name='protocolbuilderstatus'), nullable=True),
+    sa.UniqueConstraint('uid')
-    sa.Column('primary_investigator_id', sa.String(), nullable=True),
-    sa.Column('sponsor', sa.String(), nullable=True),
-    sa.Column('ind_number', sa.String(), nullable=True),
-    sa.PrimaryKeyConstraint('id')
     )
     op.create_table('workflow_spec',
     sa.Column('id', sa.String(), nullable=False),
@@ -36,6 +39,22 @@ def upgrade():
     sa.Column('primary_process_id', sa.String(), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
+    op.create_table('study',
+    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('primary_investigator_id', sa.String(), nullable=True),
+    sa.Column('sponsor', sa.String(), nullable=True),
+    sa.Column('hsr_number', sa.String(), nullable=True),
+    sa.Column('ind_number', sa.String(), nullable=True),
+    sa.Column('user_uid', sa.String(), nullable=False),
+    sa.Column('investigator_uids', sa.ARRAY(sa.String()), nullable=True),
+    sa.Column('inactive', sa.Boolean(), nullable=True),
+    sa.Column('requirements', sa.ARRAY(sa.Integer()), nullable=True),
+    sa.ForeignKeyConstraint(['user_uid'], ['user.uid'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
     op.create_table('workflow',
     sa.Column('id', sa.Integer(), nullable=False),
     sa.Column('bpmn_workflow_json', sa.JSON(), nullable=True),
@@ -79,6 +98,7 @@ def downgrade():
     op.drop_table('file_data')
     op.drop_table('file')
     op.drop_table('workflow')
-    op.drop_table('workflow_spec')
     op.drop_table('study')
+    op.drop_table('workflow_spec')
+    op.drop_table('user')
     # ### end Alembic commands ###

tests/test_study_api.py

@@ -27,6 +27,7 @@ class TestStudyApi(BaseTest):
             "primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
             "sponsor": "Sirius Cybernetics Corporation",
             "ind_number": "567890",
+            "user_uid": "dhf8r",
         }
         rv = self.app.post('/v1.0/study',
                            content_type="application/json",
@@ -41,6 +42,7 @@ class TestStudyApi(BaseTest):
         self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id)
         self.assertEqual(study["sponsor"], db_study.sponsor)
         self.assertEqual(study["ind_number"], db_study.ind_number)
+        self.assertEqual(study["user_uid"], db_study.user_uid)
 
     def test_update_study(self):
         self.load_example_data()

tests/test_tasks_api.py

@@ -13,8 +13,12 @@ class TestTasksApi(BaseTest):
     def create_workflow(self, workflow_name):
         study = session.query(StudyModel).first()
         spec = session.query(WorkflowSpecModel).filter_by(id=workflow_name).first()
-        self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
+        rv = self.app.post(
+            '/v1.0/study/%i/workflows' % study.id,
+            headers=self.logged_in_headers(),
+            content_type="application/json",
             data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
+        self.assert_success(rv)
         workflow = session.query(WorkflowModel).filter_by(study_id=study.id, workflow_spec_id=workflow_name).first()
         return workflow