Merge pull request #83 from kbase/dev-mongo7_upgrade

Mongo7 upgrade

.github/workflows/test.yml

@@ -24,6 +24,8 @@ jobs:
         include:
           - python: '3.7.13'
             mongo: 'mongodb-linux-x86_64-3.6.2'
+          - python: '3.7.13'
+            mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
 
     steps:
       - name: Check out GitHub repo

feeds/storage/mongodb/timeline_storage.py

@@ -69,7 +69,7 @@ def get_unseen_count(self) -> int:
             "unseen": self._user_doc(),
             "expires": {"$gt": now}
         }
-        return coll.find(query).count()
+        return coll.count_documents(query)
 
     def _user_doc(self) -> Dict[str, str]:
         return {

requirements.txt

@@ -4,6 +4,6 @@ requests==2.20.0
 gunicorn==19.9.0
 gevent==1.3.7
 cachetools==2.1.0
-pymongo==3.7.2
+pymongo==4.7.2
 redis==2.10.6
 flask-cors==3.0.6

test/mongo_controller.py

@@ -12,6 +12,9 @@
 import semver
 import test.util as test_util
 
+# semver parser
+sver = semver.VersionInfo.parse
+
 
 class MongoController:
     """
@@ -50,27 +53,50 @@ def __init__(self, mongoexe: Path, root_temp_dir: Path, use_wired_tiger: bool=Fa
         os.makedirs(data_dir)
 
         self.port = test_util.find_free_port()
+        mongodb_ver = self.get_mongodb_version(mongoexe)
+
+        command = [str(mongoexe), '--port', str(self.port), '--dbpath', str(data_dir)]
+
+        if sver(mongodb_ver) < sver('6.1.0'):
+            command.extend(['--nojournal'])
 
-        command = [str(mongoexe), '--port', str(self.port), '--dbpath', str(data_dir),
-                   '--nojournal']
         if use_wired_tiger:
             command.extend(['--storageEngine', 'wiredTiger'])
 
         self._outfile = open(self.temp_dir.joinpath('mongo.log'), 'w')
 
         self._proc = subprocess.Popen(command, stdout=self._outfile, stderr=subprocess.STDOUT)
         time.sleep(1)  # wait for server to start up
-        self.client = MongoClient('localhost', self.port)
-        # check that the server is up. See
-        # https://api.mongodb.com/python/3.7.0/api/pymongo/mongo_client.html
-        #    #pymongo.mongo_client.MongoClient
-        self.client.admin.command('ismaster')
+
+        try:
+            self.client: MongoClient = MongoClient('localhost', self.port)
+            # This line will raise an exception if the server is down
+            server_info = self.client.server_info()
+        except Exception as e:
+            raise ValueError("MongoDB server is down") from e
 
         # get some info about the db
-        self.db_version = self.client.server_info()['version']
+        self.db_version = server_info['version']
         self.index_version = 2 if (semver.compare(self.db_version, '3.4.0') >= 0) else 1
-        self.includes_system_indexes = (semver.compare(self.db_version, '3.2.0') < 0
-                                        and not use_wired_tiger)
+        self.includes_system_indexes = (
+            semver.compare(self.db_version, '3.2.0') < 0 and not use_wired_tiger
+        )
+
+    def get_mongodb_version(self, mongoexe: Path) -> str:
+        try:
+            process = subprocess.Popen(
+                [str(mongoexe), '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+            )
+            stdout, stderr = process.communicate()
+
+            if process.returncode == 0:
+                version_line = stdout.decode().split('\n')[0]
+                mongodb_version = version_line.split()[2][1:]
+                return mongodb_version.strip()
+            else:
+                raise ValueError(f"Error: {stderr.decode()}")
+        except Exception as e:
+            raise ValueError("Failed to get MongoDB version") from e
 
     def destroy(self, delete_temp_files: bool) -> None:
         """