From eeac2c2797f9e03b191a0947fbec5900fe6793d4 Mon Sep 17 00:00:00 2001
From: Samuel Gaist <samuel.gaist@idiap.ch>
Date: Fri, 12 Apr 2019 17:44:04 +0200
Subject: [PATCH] [scripts] Implement helper script to translate a v1 database
to v2
This scripts creates the needed protocol templates unless a protocol
template with the same name already exists.
---
beat/core/scripts/migrate_db_to_v2.py | 158 ++++++++++++++++++++++++++
1 file changed, 158 insertions(+)
create mode 100644 beat/core/scripts/migrate_db_to_v2.py
diff --git a/beat/core/scripts/migrate_db_to_v2.py b/beat/core/scripts/migrate_db_to_v2.py
new file mode 100644
index 00000000..707eb5d9
--- /dev/null
+++ b/beat/core/scripts/migrate_db_to_v2.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+###################################################################################
+# #
+# Copyright (c) 2019 Idiap Research Institute, http://www.idiap.ch/ #
+# Contact: beat.support@idiap.ch #
+# #
+# Redistribution and use in source and binary forms, with or without #
+# modification, are permitted provided that the following conditions are met: #
+# #
+# 1. Redistributions of source code must retain the above copyright notice, this #
+# list of conditions and the following disclaimer. #
+# #
+# 2. Redistributions in binary form must reproduce the above copyright notice, #
+# this list of conditions and the following disclaimer in the documentation #
+# and/or other materials provided with the distribution. #
+# #
+# 3. Neither the name of the copyright holder nor the names of its contributors #
+# may be used to endorse or promote products derived from this software without #
+# specific prior written permission. #
+# #
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND #
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED #
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE #
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE #
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL #
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR #
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER #
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, #
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE #
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. #
+# #
+###################################################################################
+
+"""Migrate a v1 database to v2
+
+Usage:
+ %(prog)s [-v ... | --verbose ...] [--prefix=<path>][-f|--force]
+ <database_identifier>
+ %(prog)s (--help | -h)
+ %(prog)s (--version | -V)
+
+
+Options:
+ -h, --help Show this screen
+ -V, --version Show version
+ -v, --verbose Increases the output verbosity level
+ -p, --prefix=<path> Path where the prefix is contained [default: .]
+"""
+
+import os
+import sys
+import copy
+
+from docopt import docopt
+
+from ..version import __version__
+
+from ..database import Database, Storage as DBStorage
+from ..protocoltemplate import ProtocolTemplate, Storage as PTStorage
+from ..utils import setup_logging
+
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv[1:]
+
+ prog = os.path.basename(sys.argv[0])
+ completions = dict(prog=prog, version=__version__)
+ args = docopt(
+ __doc__ % completions,
+ argv=argv,
+ options_first=True,
+ version="v%s" % __version__,
+ )
+
+ logger = setup_logging(args["--verbose"], __name__, __name__)
+
+ prefix = args["--prefix"] if args["--prefix"] is not None else "."
+ if not os.path.exists(prefix):
+ logger.error("Prefix not found at: '%s'", prefix)
+ return 1
+
+ database_identifier = args["<database_identifier>"]
+
+ database = Database(prefix, database_identifier)
+
+ if not database.valid:
+ logger.error("Invalid database: '%s'", "\n".join(database.errors))
+ return 1
+
+ if database.schema_version != 1:
+ logger.error("Can't migrate database is not v1")
+ return 1
+
+ db_name, db_version = database_identifier.split("/")
+ new_db_name = f"{db_name}/{int(db_version) + 1}"
+
+ db_storage = DBStorage(prefix, new_db_name)
+ if db_storage.exists():
+ logger.error(f"Database already exists: {new_db_name}")
+ return 1
+
+ database_json = copy.deepcopy(database.data)
+ database_json["schema_version"] = 2
+ database_json["protocols"] = []
+
+ for protocol in database.protocols:
+ sets = database.sets(protocol)
+ set_list = []
+ views = {}
+ for _, set_ in sets.items():
+ views[set_["name"]] = {
+ "view": set_["view"],
+ "parameters": set_.get("parameters", {}),
+ }
+
+ for key in ["template", "view", "parameters"]:
+ if key in set_:
+ set_.pop(key)
+ set_list.append(set_)
+
+ template = {"schema_version": 1, "sets": set_list}
+
+ pt_name = f"{protocol}/1"
+ pt_storage = PTStorage(prefix, pt_name)
+
+ if pt_storage.exists():
+ logger.info(f"Protocol template already exists: {pt_name}")
+ else:
+ protocol_template = ProtocolTemplate(prefix, template)
+ if not protocol_template.valid:
+ logger.error(
+ "Invalid protocol created:", "\n".join(protocol_template.errors)
+ )
+ return 1
+ else:
+ protocol_template.write(pt_storage)
+
+ protocol_entry = {"name": protocol, "template": pt_name, "views": views}
+
+ database_json["protocols"].append(protocol_entry)
+
+ new_database = Database(prefix, database_json)
+ if not new_database.valid:
+ logger.error("Invalid database created:", "\n".join(new_database.errors))
+ return 1
+ else:
+ new_database.code = database.code
+ new_database.description = (
+ database.description if database.description is not None else ""
+ )
+ new_database.write(db_storage)
+
+
+if __name__ == "__main__":
+ main()
--
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