- Preserves usage of legacy script while not hiding the Alembic script.
(see manage_db.sh and run_alembic.sh)
- Adds documentation (see top of script files)
- Includes misc. relevant refactorings
- Includes unit tests for testing legacy script handling
Also add exec permissions to create/migrate python scripts.
(not sure this is required, adding for consistency with previous
version)
+ A few fixes for TS scripts, tests
Squashed:
- pick b62443245e Add create/migrate scripts for Alembic dbs
- squash 06f0a923ca Fix integration test (test only relevant for TS)
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
Do this by calling common_startup.sh prior to manage_db.sh in
run_test_wrapper.sh. Will require a rebuild of the testing-base image.
Also, have scripts in Galaxy root activate .venv if it exists.
