Merge remote-tracking branch 'origin/release_18.05' into dev

galaxyproject · May 2, 2018 · 6006d9b · 6006d9b
2 parents 7af3b32 + cacbcdf
commit 6006d9b
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Showing 3 changed files with 14 additions and 11 deletions.
diff --git a/lib/galaxy/containers/__init__.py b/lib/galaxy/containers/__init__.py
@@ -150,7 +150,8 @@ def map_port(self, port):
         :rtype:         :class:`ContainerPort` instance
         """
         mapping = None
-        for mapping in self.ports:
+        ports = self.ports or []
+        for mapping in ports:
             if port == mapping.port:
                 return mapping
             if port is None:

diff --git a/lib/galaxy/containers/docker_model.py b/lib/galaxy/containers/docker_model.py
@@ -176,9 +176,7 @@ def inspect(self):
 class DockerService(Container):
 
     def __init__(self, interface, id, name=None, image=None, inspect=None):
-        self._interface = interface
-        self._id = id
-        self._name = name
+        super(DockerService, self).__init__(interface, id, name=name)
         self._image = image
         self._inspect = inspect
         self._env = {}
@@ -278,11 +276,14 @@ def state(self):
     @property
     def env(self):
         if not self._env:
-            for env_str in self.inspect['Spec']['TaskTemplate']['ContainerSpec']['Env']:
-                try:
-                    self._env.update([env_str.split('=', 1)])
-                except ValueError:
-                    self._env[env_str] = None
+            try:
+                for env_str in self.inspect['Spec']['TaskTemplate']['ContainerSpec']['Env']:
+                    try:
+                        self._env.update([env_str.split('=', 1)])
+                    except ValueError:
+                        self._env[env_str] = None
+            except KeyError as exc:
+                log.debug('Cannot retrieve container environment: KeyError: %s', str(exc))
         return self._env
 
     @property

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
@@ -1683,15 +1683,16 @@ def from_json(self, value, trans, other_values={}):
         else:
             rval = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(value)
         values = util.listify(rval)
-        dataset_matcher = DatasetMatcher(trans, self, None, other_values)
+        dataset_matcher_factory = get_dataset_matcher_factory(trans)
+        dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
         for v in values:
             if v:
                 if v.deleted:
                     raise ValueError("The previously selected dataset has been deleted.")
                 elif hasattr(v, "dataset") and v.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED]:
                     raise ValueError("The previously selected dataset has entered an unusable state")
                 elif hasattr(v, "dataset"):
-                    match = dataset_matcher.hda_match(v, check_security=False)
+                    match = dataset_matcher.hda_match(v)
                     if match and match.implicit_conversion:
                         v.implicit_conversion = True
         if not self.multiple: