Make all the tests pass

beat/cmdline/algorithms.py

@@ -310,8 +310,7 @@ def execute(prefix, cache, instructions_file):
     database_cache = {}
     algorithm_cache = {}
 
-    host = Host()
-    host.setup(raise_on_errors=False)
+    host = Host(raise_on_errors=False)
 
     executor = DockerExecutor(host, prefix, configuration, cache, dataformat_cache,
                               database_cache, algorithm_cache)

beat/cmdline/databases.py

@@ -299,6 +299,9 @@ def load_db_view(db_name, protocol_name, set_name, database, excluded_outputs=No
             logger.error('  %s', e)
         return (None, None)
 
+    if excluded_outputs is None:
+        excluded_outputs = []
+
     # Setup the inputs
     input_group = view.input_group(exclude_outputs=excluded_outputs)
 
@@ -373,7 +376,8 @@ def index_outputs(configuration, names, uid=None, db_root=None, docker=False):
 
     retcode = 0
 
-    host = dock.Host(raise_on_errors=False)
+    if docker:
+      host = dock.Host(raise_on_errors=False)
 
     for database_name in names:
       logger.info("Indexing database %s...", database_name)
@@ -388,7 +392,8 @@ def index_outputs(configuration, names, uid=None, db_root=None, docker=False):
             (view, input_group) = load_db_view(db_name, protocol_name, set_name, database)
 
             if view is None:
-                return 1
+                retcode += 1
+                continue
         else:
             (databases_container, db_socket, zmq_context, input_list) = \
                 start_db_container(
@@ -455,12 +460,13 @@ def index_outputs(configuration, names, uid=None, db_root=None, docker=False):
           retcode += 1
           continue
 
-        host.kill(databases_container)
-        host.wait(databases_container)
+        if docker:
+          host.kill(databases_container)
+          host.wait(databases_container)
 
-        db_socket.setsockopt(zmq.LINGER, 0)
-        db_socket.close()
-        zmq_context.term()
+          db_socket.setsockopt(zmq.LINGER, 0)
+          db_socket.close()
+          zmq_context.term()
 
     return retcode
 
@@ -577,7 +583,6 @@ def view_outputs(configuration, dataset_name, excluded_outputs=None, uid=None,
 
         return ('\n' + ' ' * indent).join(value.split('\n'))
 
-
     # Load the infos about the database set
     (db_name, database, sets) = load_database_sets(configuration, dataset_name)
     if (database is None) or (len(sets) != 1):

beat/cmdline/test/instructions/algo_using_cached_files.json

@@ -16,6 +16,6 @@
     },
     "environment": {
         "name": "Python 2.7",
-        "version": "1.1.0"
+        "version": "1.2.0"
     }
 }

beat/cmdline/test/instructions/algo_using_database.json

@@ -19,6 +19,6 @@
     },
     "environment": {
         "name": "Python 2.7",
-        "version": "1.1.0"
+        "version": "1.2.0"
     }
 }

beat/cmdline/test/instructions/algo_using_database_and_cached_files.json

@@ -23,6 +23,6 @@
     },
     "environment": {
         "name": "Python 2.7",
-        "version": "1.1.0"
+        "version": "1.2.0"
     }
 }

beat/cmdline/test/instructions/analyzer.json

@@ -11,6 +11,6 @@
     },
     "environment": {
         "name": "Python 2.7",
-        "version": "1.1.0"
+        "version": "1.2.0"
     }
 }

beat/cmdline/test/test_databases.py

@@ -119,7 +119,7 @@ def test_view_unknown_set():
 
 
 def test_view_bad():
-  nose.tools.eq_(call('view', 'integers_db/1/double'), 1)
+  nose.tools.eq_(call('view', 'integers_db/1/two_sets'), 1)
 
 
 def test_view_invalid():