Merge pull request #3980 from jmchilton/ie_for_mac_os_x_fixes

Rework Jupyter IE for additional_ids handling.

config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample

@@ -45,6 +45,10 @@
 # inside your container to which Galaxy should connect the UI.
 #docker_connect_port = None
 
+# Set the following value to false if Docker volumes between Galaxy server and Docker
+# container cannot or should not be used.
+#use_volumes = True
+
 # To run containers in Docker Swarm mode on (an existing swarm), set the
 # following option to True *and*:
 # - set docker_connect_port above. For Jupyter the # port should most likely be

config/plugins/interactive_environments/jupyter/templates/jupyter.mako

@@ -17,19 +17,26 @@ if ie_request.attr.PASSWORD_AUTH:
 else:
     PASSWORD = "none"
 
+additional_ids = trans.request.params.get('additional_dataset_ids', None)
+
 ## Jupyter Notbook Specific
 if hda.datatype.__class__.__name__ == "Ipynb":
     DATASET_HID = hda.hid
 else:
     DATASET_HID = None
+    if not additional_ids:
+        additional_ids = str(trans.security.encode_id( hda.id ) )
+    else:
+        additional_ids += "," + trans.security.encode_id( hda.id )
 
 # Add all environment variables collected from Galaxy's IE infrastructure
 ie_request.launch(
     image=trans.request.params.get('image_tag', None),
-    additional_ids=trans.request.params.get('additional_dataset_ids', None),
+    additional_ids=additional_ids if ie_request.use_volumes else None,
     env_override={
         'notebook_password': PASSWORD,
         'dataset_hid': DATASET_HID,
+        'additional_ids': additional_ids if not ie_request.use_volumes else None,
     }
 )
 

config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample

@@ -47,6 +47,10 @@ password_auth = True
 # inside your container to which Galaxy should connect the UI.
 #docker_connect_port = None
 
+# Set the following value to false if Docker volumes between Galaxy server and Docker
+# container cannot or should not be used.
+#use_volumes = True
+
 # To run containers in Docker Swarm mode on (an existing swarm), set the
 # following option to True *and*:
 # - set docker_connect_port above. For erasche/docker-rstudio-notebook the port

config/plugins/interactive_environments/rstudio/templates/rstudio.mako

@@ -13,16 +13,23 @@ USERNAME = "rstudio"
 # Then override it again
 ie_request.notebook_pw = "rstudio"
 
+additional_ids = trans.request.params.get('additional_dataset_ids', None)
+if not additional_ids:
+    additional_ids = str(trans.security.encode_id( hda.id ) )
+else:
+    additional_ids += "," + trans.security.encode_id( hda.id )
+
 DATASET_HID = hda.hid
 
 # Add all environment variables collected from Galaxy's IE infrastructure
 ie_request.launch(
     image=trans.request.params.get('image_tag', None),
-    additional_ids=trans.request.params.get('additional_dataset_ids', None),
+    additional_ids=additional_ids if ie_request.use_volumes else None,
     env_override={
         'notebook_username': USERNAME,
         'notebook_password': PASSWORD,
         'dataset_hid': DATASET_HID,
+        'additional_ids': additional_ids if not ie_request.use_volumes else None,
     }
 )
 

lib/galaxy/web/base/interactive_environments.py

@@ -256,7 +256,7 @@ def _get_env_for_run(self, env_override=None):
         return dict([(key.upper(), item) for key, item in conf.items()])
 
     def _get_import_volume_for_run(self):
-        if self.attr.import_volume:
+        if self.use_volumes and self.attr.import_volume:
             return '{temp_dir}:/import/'.format(temp_dir=self.temp_dir)
         return ''
 
@@ -272,7 +272,7 @@ def docker_cmd(self, image, env_override=None, volumes=None):
         env = self._get_env_for_run(env_override)
         import_volume_def = self._get_import_volume_for_run()
         env_str = ' '.join(['-e "%s=%s"' % (key, item) for key, item in env.items()])
-        volume_str = ' '.join(['-v "%s"' % volume for volume in volumes])
+        volume_str = ' '.join(['-v "%s"' % volume for volume in volumes]) if self.use_volumes else ''
         import_volume_str = '-v "{import_volume}"'.format(import_volume=import_volume_def) if import_volume_def else ''
         name = None
         # This is the basic docker command such as "sudo -u docker docker {docker_args}"
@@ -298,6 +298,13 @@ def docker_cmd(self, image, env_override=None, volumes=None):
         )
         return command
 
+    @property
+    def use_volumes(self):
+        if self.attr.viz_config.has_option("docker", "use_volumes"):
+            return string_as_bool_or_none(self.attr.viz_config.get("docker", "use_volumes"))
+        else:
+            return True
+
     def container_run_args(self, image, env_override=None, volumes=None):
         if volumes is None:
             volumes = []
@@ -434,6 +441,8 @@ def launch(self, image=None, additional_ids=None, env_override=None, volumes=Non
         :param volumes: dictionary of docker volume mounts
 
         """
+        if volumes is None:
+            volumes = []
         if image is None:
             image = self.default_image