Adding the migration - very destructive, but required for running the app.

minor fixes - there is still some weird problems with study id and user id being null that I need to track down, but the issue is sporadic, and hard to track down.

crc/api/common.py

@@ -29,9 +29,9 @@ class ApiError(Exception):
         self.offset = offset
         self.error_type = error_type
         self.error_line = error_line
-        if hasattr(g, 'user'):
+        try:
             user = g.user.uid
-        else:
+        except Exception as e:
             user = 'Unknown'
         self.task_user = user
         # This is for sentry logging into Slack

crc/services/study_service.py

@@ -468,7 +468,7 @@ class StudyService(object):
     @staticmethod
     def add_all_workflow_specs_to_study(study_model: StudyModel, specs: List[WorkflowSpecInfo]):
         existing_models = session.query(WorkflowModel).filter(WorkflowModel.study == study_model).all()
-        existing_spec_ids = map(lambda x: x.workflow_spec_id, existing_models)
+        existing_spec_ids = list(map(lambda x: x.workflow_spec_id, existing_models))
         errors = []
         for workflow_spec in specs:
             if workflow_spec.id in existing_spec_ids:

migrations/versions/29bad12c9945_.py

@@ -0,0 +1,65 @@
+"""empty message
+
+Revision ID: 29bad12c9945
+Revises: c51ea6590f5d
+Create Date: 2022-02-10 10:24:27.796228
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '29bad12c9945'
+down_revision = 'c51ea6590f5d'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint('task_event_workflow_spec_id_fkey', 'task_event', type_='foreignkey')
+    op.drop_constraint('workflow_workflow_spec_id_fkey', 'workflow', type_='foreignkey')
+    op.drop_constraint('workflow_library_workflow_spec_id_fkey', 'workflow_library', type_='foreignkey')
+    op.drop_table('workflow_library')
+    op.drop_table('workflow_spec')
+    op.drop_table('workflow_spec_category')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_foreign_key('workflow_workflow_spec_id_fkey', 'workflow', 'workflow_spec', ['workflow_spec_id'], ['id'])
+    op.create_foreign_key('task_event_workflow_spec_id_fkey', 'task_event', 'workflow_spec', ['workflow_spec_id'], ['id'])
+    op.create_table('workflow_spec',
+    sa.Column('id', sa.VARCHAR(), autoincrement=False, nullable=False),
+    sa.Column('display_name', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True),
+    sa.Column('is_master_spec', sa.BOOLEAN(), autoincrement=False, nullable=True),
+    sa.Column('category_id', sa.INTEGER(), autoincrement=False, nullable=True),
+    sa.Column('display_order', sa.INTEGER(), autoincrement=False, nullable=True),
+    sa.Column('standalone', sa.BOOLEAN(), autoincrement=False, nullable=True),
+    sa.Column('library', sa.BOOLEAN(), autoincrement=False, nullable=True),
+    sa.Column('primary_file_name', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('primary_process_id', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('is_review', sa.BOOLEAN(), autoincrement=False, nullable=True),
+    sa.ForeignKeyConstraint(['category_id'], ['workflow_spec_category.id'], name='workflow_spec_category_id_fkey'),
+    sa.PrimaryKeyConstraint('id', name='workflow_spec_pkey'),
+    postgresql_ignore_search_path=False
+    )
+    op.create_table('workflow_library',
+    sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False),
+    sa.Column('workflow_spec_id', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('library_spec_id', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.ForeignKeyConstraint(['library_spec_id'], ['workflow_spec.id'], name='workflow_library_library_spec_id_fkey'),
+    sa.ForeignKeyConstraint(['workflow_spec_id'], ['workflow_spec.id'], name='workflow_library_workflow_spec_id_fkey'),
+    sa.PrimaryKeyConstraint('id', name='workflow_library_pkey')
+    )
+    op.create_table('workflow_spec_category',
+    sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False),
+    sa.Column('display_name', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('display_order', sa.INTEGER(), autoincrement=False, nullable=True),
+    sa.Column('admin', sa.BOOLEAN(), autoincrement=False, nullable=True),
+    sa.PrimaryKeyConstraint('id', name='workflow_spec_category_pkey')
+    )
+    # ### end Alembic commands ###