Commit dc4600f5 authored by André Anjos's avatar André Anjos 💬

Merge branch 'fix_db_migration_helper' into 'master'

Fix protocole template creation when migrating a database

See merge request !134
parents 8ee5c54e 224b8000
Pipeline #47492 passed with stages
in 25 minutes and 25 seconds
......@@ -47,11 +47,15 @@ Options:
-V, --version Show version
-v, --verbose Increases the output verbosity level
-p, --prefix=<path> Path where the prefix is contained [default: .]
-f, --force Force overwrite
import copy
import os
import sys
from collections import OrderedDict
import simplejson as json
from docopt import docopt
from ..database import Database
......@@ -62,6 +66,24 @@ from ..utils import setup_logging
from ..version import __version__
def yes_or_no(question):
"""Helper method to get a yes or no answer
Inspired from:
while "the answer is invalid":
reply = str(input(question + " (y/n): ")).lower().strip() # nosec
except EOFError:
return False
if reply[:1] == "y":
return True
if reply[:1] == "n":
return False
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
......@@ -98,7 +120,7 @@ def main(argv=None):
new_db_name = f"{db_name}/{int(db_version) + 1}"
db_storage = DBStorage(prefix, new_db_name)
if db_storage.exists():
if db_storage.exists() and not args["--force"]:
logger.error(f"Database already exists: {new_db_name}")
return 1
......@@ -107,6 +129,7 @@ def main(argv=None):
database_json["protocols"] = []
for protocol in database.protocols:
sets = database.sets(protocol)
set_list = []
views = {}
......@@ -121,22 +144,35 @@ def main(argv=None):
template = {"schema_version": 1, "sets": set_list}
template = OrderedDict(schema_version=1, sets=set_list)
pt_name = f"{protocol}/1"
pt_name = f"{database.protocols[protocol]['template']}/1"
pt_storage = PTStorage(prefix, pt_name)
protocol_template = ProtocolTemplate(prefix, template)
if not protocol_template.valid:
"Invalid protocol created:", "\n".join(protocol_template.errors)
return 1
if pt_storage.exists():"Protocol template already exists: {pt_name}")
protocol_template = ProtocolTemplate(prefix, template)
if not protocol_template.valid:"Protocol template for {db_name} already exists: {pt_name}")
original_pt = ProtocolTemplate(prefix, pt_name)
# This will simplify the comparison as the data are loaded using
# OrderedDict
original_data = json.loads(json.dumps(
new_data = json.loads(json.dumps(
if new_data != original_data:
"Invalid protocol created:", "\n".join(protocol_template.errors)
f"{pt_name} current content for {db_name} does not match original"
return 1
if not yes_or_no("Do you want to continue ?"):
return 1
protocol_entry = {"name": protocol, "template": pt_name, "views": views}
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