Merge pull request #577 from scitran/upgrade-robust

Log & discard malformed gears during v18 upgrade

api/jobs/rules.py

@@ -79,7 +79,7 @@ def eval_match(match_type, match_param, file_, container):
     # Match the container having any file (including this one) with this type
     elif match_type == 'container.has-type':
         for c_file in container['files']:
-            if match_param == c_file['type']:
+            if match_param == c_file.get('type'):
                 return True
 
         return False

bin/database.py

@@ -494,7 +494,15 @@ def upgrade_to_18():
     if gear_doc is not None:
         gear_list = gear_doc.get('gear_list', [])
         for gear in gear_list:
-            gears.upsert_gear(gear)
+            try:
+                gears.upsert_gear(gear)
+            except Exception as e:
+                logging.error("")
+                logging.error("Error upgrading gear:")
+                logging.error(type(e))
+                logging.error("Gear will not be retained. Document follows:")
+                logging.error(gear)
+                logging.error("")
 
         config.db.singletons.remove({"_id": "gears"})
 

test/unit_tests/python/test_rules.py

@@ -95,8 +95,8 @@ def test_eval_match_container_measurement():
 
 def test_eval_match_container_has_type():
     part = rulePart(match_type='container.has-type', container={'files': [
-            {'measurements': ['a', 'diffusion', 'b']},
-            {'measurements': ['c', 'other', 'b']},
+            {'type': 'diffusion'},
+            {'type': 'other'},
         ]})
 
     args = part.gen(match_param='other')