Make failed mongo observer dump configurable (#462)

* Fix some typos

In comments and forbidden collections

* Make mongo observer dump dir configurable

* Fix py27 and flake8 warnings

* Fix some py27 errors and move mock to own file

* Make Python 2 compatible

sacred/observers/mongo.py

@@ -2,12 +2,13 @@
 # coding=utf-8
 from __future__ import division, print_function, unicode_literals
 
+import mimetypes
+import os.path
 import pickle
 import re
-import os.path
 import sys
 import time
-import mimetypes
+from tempfile import NamedTemporaryFile
 
 import sacred.optional as opt
 from sacred.commandline_options import CommandLineOption
@@ -59,7 +60,23 @@ class MongoObserver(RunObserver):
     @staticmethod
     def create(url=None, db_name='sacred', collection='runs',
                overwrite=None, priority=DEFAULT_MONGO_PRIORITY,
-               client=None, **kwargs):
+               client=None, failure_dir=None, **kwargs):
+        """Factory method for MongoObserver.
+
+        Parameters
+        ----------
+        url: Mongo URI to connect to.
+        db_name: Database to connect to.
+        collection: Collection to write the runs to. (default: "runs").
+        overwrite: _id of a run that should be overwritten.
+        priority: (default 30)
+        client: Client to connect to. Do not use client and URL together.
+        failure_dir: Directory to save the run of a failed observer to.
+
+        Returns
+        -------
+        An instantiated MongoObserver.
+        """
         import pymongo
         import gridfs
 
@@ -81,10 +98,12 @@ def create(url=None, db_name='sacred', collection='runs',
         return MongoObserver(runs_collection,
                              fs, overwrite=overwrite,
                              metrics_collection=metrics_collection,
+                             failure_dir=failure_dir,
                              priority=priority)
 
     def __init__(self, runs_collection,
                  fs, overwrite=None, metrics_collection=None,
+                 failure_dir=None,
                  priority=DEFAULT_MONGO_PRIORITY):
         self.runs = runs_collection
         self.metrics = metrics_collection
@@ -100,6 +119,7 @@ def __init__(self, runs_collection,
         self.overwrite = overwrite
         self.run_entry = None
         self.priority = priority
+        self.failure_dir = failure_dir
 
     def queued_event(self, ex_info, command, host_info, queue_time, config,
                      meta_info, _id):
@@ -288,6 +308,8 @@ def final_save(self, attempts):
             except pymongo.errors.AutoReconnect:
                 if i < attempts - 1:
                     time.sleep(1)
+            except pymongo.errors.ConnectionFailure:
+                pass
             except pymongo.errors.InvalidDocument:
                 self.run_entry = force_bson_encodeable(self.run_entry)
                 print("Warning: Some of the entries of the run were not "
@@ -296,9 +318,13 @@ def final_save(self, attempts):
                       "Most likely it is either the 'info' or the 'result'.",
                       file=sys.stderr)
 
-        from tempfile import NamedTemporaryFile
+        if not os.path.exists(self.failure_dir):
+            os.makedirs(self.failure_dir)
         with NamedTemporaryFile(suffix='.pickle', delete=False,
-                                prefix='sacred_mongo_fail_') as f:
+                                prefix='sacred_mongo_fail_{}_'.format(
+                                    self.run_entry["_id"]
+                                ),
+                                dir=self.failure_dir) as f:
             pickle.dump(self.run_entry, f)
             print("Warning: saving to MongoDB failed! "
                   "Stored experiment entry in '{}'".format(f.name),

sacred/run.py

@@ -278,7 +278,7 @@ def _stop_heartbeat(self):
         # only stop if heartbeat was started
         if self._heartbeat is not None:
             self._stop_heartbeat_event.set()
-            self._heartbeat.join(2)
+            self._heartbeat.join(timeout=2)
 
     def _emit_queued(self):
         self.status = 'QUEUED'

sacred/utils.py

@@ -712,6 +712,7 @@ def create(cls, func, interval=10):
         return stop_event, timer_thread
 
     def __init__(self, event, func, interval=10.):
+        # TODO use super here.
         threading.Thread.__init__(self)
         self.stopped = event
         self.func = func

tests/test_observers/failing_mongo_mock.py

@@ -0,0 +1,64 @@
+
+import mongomock
+import pymongo
+import pymongo.errors
+
+
+
+class FailingMongoClient(mongomock.MongoClient):
+    def __init__(self, max_calls_before_failure=2,
+                 exception_to_raise=pymongo.errors.AutoReconnect, **kwargs):
+        super(FailingMongoClient, self).__init__(**kwargs)
+        self._max_calls_before_failure = max_calls_before_failure
+        self.exception_to_raise = exception_to_raise
+
+    def get_database(self, name, codec_options=None, read_preference=None,
+                     write_concern=None):
+        db = self._databases.get(name)
+        if db is None:
+            db = self._databases[name] = FailingDatabase(
+                max_calls_before_failure=self._max_calls_before_failure,
+                exception_to_raise=self.exception_to_raise, client=self,
+                name=name, )
+        return db
+
+
+class FailingDatabase(mongomock.Database):
+    def __init__(self, max_calls_before_failure, exception_to_raise=None,
+                 **kwargs):
+        super(FailingDatabase, self).__init__(**kwargs)
+        self._max_calls_before_failure = max_calls_before_failure
+        self.exception_to_raise = exception_to_raise
+
+    def get_collection(self, name, codec_options=None, read_preference=None,
+                       write_concern=None):
+        collection = self._collections.get(name)
+        if collection is None:
+            collection = self._collections[name] = FailingCollection(
+                max_calls_before_failure=self._max_calls_before_failure,
+                exception_to_raise=self.exception_to_raise, db=self,
+                name=name, )
+        return collection
+
+
+class FailingCollection(mongomock.Collection):
+    def __init__(self, max_calls_before_failure, exception_to_raise, **kwargs):
+        super(FailingCollection, self).__init__(**kwargs)
+        self._max_calls_before_failure = max_calls_before_failure
+        self.exception_to_raise = exception_to_raise
+        self._calls = 0
+
+    def insert_one(self, document):
+        self._calls += 1
+        if self._calls > self._max_calls_before_failure:
+            raise pymongo.errors.ConnectionFailure
+        else:
+            return super(FailingCollection, self).insert_one(document)
+
+    def update_one(self, filter, update, upsert=False):
+        self._calls += 1
+        if self._calls > self._max_calls_before_failure:
+            raise pymongo.errors.ConnectionFailure
+        else:
+            return super(FailingCollection, self).update_one(filter, update,
+                                                             upsert)