Revert command inject and document rationale

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

@@ -9,11 +9,19 @@
 # Command to launch docker container. For example `sudo docker` or `docker-lxc`.
 # If you need to use a command like `sg` you can do that here, just be sure to
 # wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
-command = docker run --sig-proxy=true -e DEBUG=false {docker_args}
+#
+# It is recommended that you use command_inject if you need to inject
+# additional parameters. This command string is re-used for a `docker inspect`
+# command and will likely cause errors if it is extensively modified, past the
+# usual group/sudo changes.
+command = docker run {docker_args}
 
 # The docker image name that should be started.
 image = bgruening/docker-ipython-notebook:dev
 
+# Additional arguments that are passed to the `docker run` command.
+command_inject = --sig-proxy=true -e DEBUG=false
+
 # URL to access the Galaxy API with from the spawn Docker containter, if empty
 # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
 # Docker host of the spawned container if that is also not set.

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

@@ -10,11 +10,19 @@ password_auth = True
 # Command to launch docker container. For example `sudo docker` or `docker-lxc`.
 # If you need to use a command like `sg` you can do that here, just be sure to
 # wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
-command = docker run --sig-proxy=true -e DEBUG=false {docker_args} 
+#
+# It is recommended that you use command_inject if you need to inject
+# additional parameters. This command string is re-used for a `docker inspect`
+# command and will likely cause errors if it is extensively modified, past the
+# usual group/sudo changes.
+command = docker run {docker_args}
 
 # The docker image name that should be started.
 image = erasche/docker-rstudio-notebook:dev
 
+# Additional arguments that are passed to the `docker run` command.
+command_inject = --sig-proxy=true -e DEBUG=false
+
 # URL to access the Galaxy API with from the spawn Docker containter, if empty
 # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
 # Docker host of the spawned container if that is also not set.

lib/galaxy/web/base/interactive_environments.py

@@ -65,6 +65,7 @@ def load_deploy_config(self, default_dict={}):
         # will need to be recorded here. The ConfigParser doesn't provide a
         # .get() that will ignore missing sections, so we must make use of
         # their defaults dictionary instead.
+        default_dict['command_inject'] = '--sig-proxy=true'
         default_dict['docker_hostname'] = 'localhost'
         default_dict['wx_tempdir'] = 'False'
         default_dict['command_wrapper'] = ''
@@ -187,9 +188,10 @@ def docker_cmd(self, env_override={}, volumes=[]):
         # 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='{environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}')
+        command = command.format(docker_args='{command_inject} {environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {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,
             port_ext=self.attr.PORT,
             port_int=self.attr.docker_port,