Merge branch 'dev' into rrt/dev

Dockerfile

@@ -17,7 +17,6 @@ RUN pip install pipenv && \
 COPY . /app/
 
 ENV FLASK_APP=/app/crc/__init__.py
-CMD ["pipenv", "run", "flask", "db", "upgrade"]
 CMD ["pipenv", "run", "python", "/app/run.py"]
 
 # expose ports

crc/api/user.py

@@ -32,7 +32,7 @@ def verify_token(token):
 def get_current_user():
     return UserModelSchema().dump(g.user)
 
-@app.route('/login')
+@app.route('/v1.0/login')
 def sso_login():
     # This what I see coming back:
     # X-Remote-Cn: Daniel Harold Funk (dhf8r)

crc/models/approval.py

@@ -18,7 +18,7 @@ class ApprovalModel(db.Model):
     __tablename__ = 'approval'
     id = db.Column(db.Integer, primary_key=True)
     study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
-    study = db.relationship(StudyModel, backref='approval')
+    study = db.relationship(StudyModel, backref='approval', cascade='all,delete')
     workflow_id = db.Column(db.Integer, db.ForeignKey(WorkflowModel.id), nullable=False)
     workflow_version = db.Column(db.String)
     approver_uid = db.Column(db.String)  # Not linked to user model, as they may not have logged in yet.

docker_run.sh

@@ -3,17 +3,15 @@
 # run migrations
 export FLASK_APP=./crc/__init__.py
 
-for entry in ./instance/* ; do
-  echo "$entry"
-  cat $entry
-done
-
 if [ "$DOWNGRADE_DB" = "true" ]; then
-  echo 'Downgrading...'
+  echo 'Downgrading database...'
   pipenv run flask db downgrade
 fi
 
-pipenv run flask db upgrade
+if [ "$UPGRADE_DB" = "true" ]; then
+  echo 'Upgrading database...'
+  pipenv run flask db upgrade
+fi
 
 if [ "$RESET_DB" = "true" ]; then
   echo 'Resetting database...'

example_data.py

@@ -14,7 +14,8 @@ class ExampleDataLoader:
         session.flush()  # Clear out any transactions before deleting it all to avoid spurious errors.
         for table in reversed(db.metadata.sorted_tables):
             session.execute(table.delete())
-            session.flush()
+        session.commit()
+        session.flush()
 
     def load_all(self):
 

migrations/versions/55c6cd407d89_.py

@@ -0,0 +1,39 @@
+"""empty message
+
+Revision ID: 55c6cd407d89
+Revises: cc4bccc5e5a8
+Create Date: 2020-05-22 22:02:46.650170
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '55c6cd407d89'
+down_revision = 'cc4bccc5e5a8'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('approval',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('study_id', sa.Integer(), nullable=False),
+    sa.Column('workflow_id', sa.Integer(), nullable=False),
+    sa.Column('workflow_version', sa.String(), nullable=True),
+    sa.Column('approver_uid', sa.String(), nullable=True),
+    sa.Column('status', sa.String(), nullable=True),
+    sa.Column('message', sa.String(), nullable=True),
+    sa.ForeignKeyConstraint(['study_id'], ['study.id'], ),
+    sa.ForeignKeyConstraint(['workflow_id'], ['workflow.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('approval')
+    # ### end Alembic commands ###

tests/test_authentication.py

@@ -44,7 +44,7 @@ class TestAuthentication(BaseTest):
         self.assertIsNone(user)
         redirect_url = 'http://worlds.best.website/admin'
         headers = dict(Uid=new_uid)
-        rv = self.app.get('login', follow_redirects=False, headers=headers)
+        rv = self.app.get('v1.0/login', follow_redirects=False, headers=headers)
         self.assert_success(rv)
         user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
         self.assertIsNotNone(user)