Merge pull request #1076 from natefoo/ie-conditional-import-volume

[15.10] Fix a bug in IEs when proxying the proxy

config/plugins/interactive_environments/ipython/config/ipython.ini.sample

@@ -17,7 +17,7 @@
 #command = docker {docker_args}
 
 # The docker image name that should be started.
-image = bgruening/docker-ipython-notebook:15.10
+image = bgruening/docker-ipython-notebook:15.10.1
 
 # Additional arguments that are passed to the `docker run` command.
 #command_inject = --sig-proxy=true -e DEBUG=false

config/plugins/interactive_environments/ipython/templates/ipython.mako

@@ -8,8 +8,7 @@ import hashlib
 # Sets ID and sets up a lot of other variables
 ie_request.load_deploy_config()
 ie_request.attr.docker_port = 6789
-# Create tempdir in galaxy
-temp_dir = ie_request.temp_dir
+ie_request.attr.import_volume = False
 
 if ie_request.attr.PASSWORD_AUTH:
     m = hashlib.sha1()
@@ -19,23 +18,15 @@ else:
     PASSWORD = "none"
 
 ## IPython Specific
-# Prepare an empty notebook
-notebook_id = ie_request.generate_hex(64)
-with open( os.path.join( ie_request.attr.our_template_dir, 'notebook.ipynb' ), 'r') as nb_handle:
-    empty_nb = nb_handle.read()
-empty_nb = empty_nb % notebook_id
-# Copy over default notebook, unless the dataset this viz is running on is a notebook
-empty_nb_path = os.path.join(temp_dir, 'ipython_galaxy_notebook.ipynb')
-
-if hda.datatype.__class__.__name__ != "Ipynb":
-    with open( empty_nb_path, 'w+' ) as handle:
-        handle.write( empty_nb )
+if hda.datatype.__class__.__name__ == "Ipynb":
+    DATASET_HID = hda.hid
 else:
-    shutil.copy( hda.file_name, empty_nb_path )
+    DATASET_HID = None
 
 # Add all environment variables collected from Galaxy's IE infrastructure
 ie_request.launch(env_override={
     'notebook_password': PASSWORD,
+    'dataset_hid': DATASET_HID,
 })
 
 ## General IE specific

lib/galaxy/web/base/interactive_environments.py

@@ -31,6 +31,7 @@ class InteractiveEnviornmentRequest(object):
         self.attr.galaxy_root_dir = os.path.abspath(self.attr.galaxy_config.root)
         self.attr.root = web.url_for("/")
         self.attr.app_root = self.attr.root + "plugins/interactive_environments/" + self.attr.viz_id + "/static/"
+        self.attr.import_volume = True
 
         plugin_path = os.path.abspath( plugin.path )
 
@@ -60,8 +61,12 @@ class InteractiveEnviornmentRequest(object):
 
         # This duplicates the logic in the proxy manager
         if self.attr.galaxy_config.dynamic_proxy_external_proxy:
-            self.attr.proxy_prefix = '%s/%s' % (
+            slash = '/'
+            if self.attr.galaxy_config.cookie_path.endswith('/'):
+                slash = ''
+            self.attr.proxy_prefix = '%s%s%s' % (
                 self.attr.galaxy_config.cookie_path,
+                slash,
                 self.attr.galaxy_config.dynamic_proxy_prefix)
         else:
             self.attr.proxy_prefix = ''
@@ -184,18 +189,19 @@ class InteractiveEnviornmentRequest(object):
         conf.update(env_override)
         env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()])
         volume_str = ' '.join(['-v "%s"' % volume for volume in volumes])
+        import_volume_str = '-v "{temp_dir}:/import/"'.format(temp_dir=temp_dir) if self.attr.import_volume else ''
         # This is the basic docker command such as "sudo -u docker docker {docker_args}"
         # or just "docker {docker_args}"
         command = self.attr.viz_config.get("docker", "command")
         # Then we format in the entire docker command in place of
         # {docker_args}, so as to let the admin not worry about which args are
         # getting passed
-        command = command.format(docker_args='run {command_inject} {environment} -d -P -v "{temp_dir}:/import/" {volume_str} {image}')
+        command = command.format(docker_args='run {command_inject} {environment} -d -P {import_volume_str} {volume_str} {image}')
         # Once that's available, we format again with all of our arguments
         command = command.format(
             command_inject=self.attr.viz_config.get("docker", "command_inject"),
             environment=env_str,
-            temp_dir=temp_dir,
+            import_volume_str=import_volume_str,
             volume_str=volume_str,
             image=self.attr.viz_config.get("docker", "image")
         )