Add create/migrate scripts for tool shed

create_toolshed_db.sh

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+#!/bin/sh
+
+#######
+# Use this script to verify the state of the Tool Shed database.
+# If the database does not exist or is empty, it will be created
+# and initialized.
+# (For Galaxy and Tool Shed Install databases, use create_db.sh).
+#######
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+setup_python
+
+python ./scripts/create_toolshed_db.py "$@" tool_shed

migrate_toolshed_db.sh

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+#!/bin/sh
+
+#######
+# Use this script to manage Tool Shed migrations.
+# (Use migrate_db.sh to manage Galaxy and Tool Shed Install migrations.)
+#
+# To downgrade to a specific version, use something like:
+# sh manage_toolshed_db.sh downgrade --version=3 tool_shed
+#######
+
+cd `dirname $0`
+
+. ./scripts/common_startup_functions.sh
+
+setup_python
+
+find lib/galaxy/model/migrate/versions -name '*.pyc' -delete
+python ./scripts/migrate_toolshed_db.py $@

scripts/create_toolshed_db.py

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+"""
+Creates the initial tool shed database schema using the settings defined in config/tool_shed.yml.
+
+Note: pass '-c /location/to/your_config.yml' for non-standard ini file locations.
+
+Note: if no database_connection is set in tool_shed.yml, the default, sqlite database will be constructed.
+
+This script is also wrapped by create_ts_db.sh.
+"""
+import logging
+import os.path
+import sys
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+
+from galaxy.model.orm.scripts import get_config
+from tool_shed.webapp.model.migrate.check import create_or_verify_database as create_tool_shed_db
+
+logging.basicConfig(level=logging.DEBUG)
+log = logging.getLogger(__name__)
+
+
+def invoke_create():
+    config = get_config(sys.argv)
+    create_tool_shed_db(config['db_url'])
+
+
+if __name__ == "__main__":
+    invoke_create()

scripts/migrate_toolshed_db.py

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+"""
+This script parses the Tool Shed config file for database connection
+and then delegates to sqlalchemy_migrate shell main function in
+migrate.versioning.shell.
+It is wrapped by migrate_toolshed_db.sh (see that file for usage).
+"""
+import logging
+import os.path
+import sys
+
+from migrate.versioning.shell import main
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+
+from galaxy.model.orm.scripts import get_config
+
+logging.basicConfig(level=logging.DEBUG)
+log = logging.getLogger(__name__)
+
+
+def invoke_migrate_main():
+    # Migrate has its own args, so cannot use argparse
+    config = get_config(sys.argv, use_argparse=False, cwd=os.getcwd())
+    db_url = config['db_url']
+    repo = config['repo']
+
+    main(repository=repo, url=db_url)
+
+
+if __name__ == "__main__":
+    invoke_migrate_main()