Merge branch 'fix_db_migration_helper' into 'master'

Fix protocole template creation when migrating a database

See merge request !134

beat/core/scripts/migrate_db_to_v2.py

@@ -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:
+        https://gist.github.com/garrettdreyfus/8153571
+    """
+
+    while "the answer is invalid":
+        try:
+            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):
                     set_.pop(key)
             set_list.append(set_)
 
-        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:
+            logger.error(
+                "Invalid protocol created:", "\n".join(protocol_template.errors)
+            )
+            return 1
+
         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.info(f"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(original_pt.data))
+            new_data = json.loads(json.dumps(protocol_template.data))
+
+            if new_data != original_data:
                 logger.error(
-                    "Invalid protocol created:", "\n".join(protocol_template.errors)
+                    f"{pt_name} current content for {db_name} does not match original"
                 )
-                return 1
-            else:
-                protocol_template.write(pt_storage)
+                if not yes_or_no("Do you want to continue ?"):
+                    return 1
+        else:
+            protocol_template.write(pt_storage)
 
         protocol_entry = {"name": protocol, "template": pt_name, "views": views}