Merge pull request #782 from erasche/gie-docker-cmd

Unify the docker command, command_inject, and command_wrapper
2026-09-24 16:30:27 +08:00 · 2015-09-24 14:31:09 +01:00
parent cc1d7a509c 03ee295e7b
commit f0ea4be884
3 changed files with 84 additions and 42 deletions
@@ -1,5 +1,4 @@
 [main]
-
 # Following options are ignored if using the Galaxy dynamic proxy but
 # are useful if mapping a range of ports for environment consumption.
 #apache_urls = False
@@ -7,32 +6,39 @@
 #ssl = False

 [docker]
-
-# Command to execute docker. For example `sudo docker` or `docker-lxc`.
-command = docker
+# 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}'`
+#
+# 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 {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
-
-# Command to wrap around the full docker command.
-# For example, `sg 'docker' '{cmd}'` where {cmd} will be replaced by the full
-# docker command. Make sure to surround the {cmd} with single quotes(').
-# Default: empty
-#command_wrapper = 
+#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.
-#galaxy_url = 
+#galaxy_url =

 # The Docker hostname. It can be useful to run the Docker daemon on a different
 # host than Galaxy.
 #docker_hostname = localhost

 # Try to set the tempdirectory to world execute - this can fix the issue 
-# where	  'sudo docker' is not able to mount the folder otherwise.
+# where 'sudo docker' is not able to mount the folder otherwise.
 # "finalize namespace chdir to /import permission denied"
-wx_tempdir = False
+#wx_tempdir = False
+
+# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
+# located on an NFS share, which does not work well as Docker volume. In this case
+# you can have a shared sshfs share which you can use as temporary directory to
+# share data between the IE and Galaxy.
+#docker_galaxy_temp_dir = None
+
@@ -1,19 +1,44 @@
 [main]
-# This cannot be changed
+# This CANNOT be changed. Eventually will be deprecated
 password_auth = True
-# Other
-apache_urls = False
-ssl = False
+# Following options are ignored if using the Galaxy dynamic proxy but
+# are useful if mapping a range of ports for environment consumption.
+#apache_urls = False
+#ssl = False

 [docker]
-command = docker
+# 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}'`
+#
+# 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 {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. `-u`
-# settings are completely ignored.
-command_inject = --sig-proxy=true -e DEBUG=false
+# 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 spawned Docker container, if empty
+# 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.
-#galaxy_url=
+# Docker host of the spawned container if that is also not set.
+#galaxy_url =
+
+# The Docker hostname. It can be useful to run the Docker daemon on a different
+# host than Galaxy.
+#docker_hostname = localhost
+
+# Try to set the tempdirectory to world execute - this can fix the issue 
+# where 'sudo docker' is not able to mount the folder otherwise.
+# "finalize namespace chdir to /import permission denied"
+#wx_tempdir = False
+
+# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
+# located on an NFS share, which does not work well as Docker volume. In this case
+# you can have a shared sshfs share which you can use as temporary directory to
+# share data between the IE and Galaxy.
+#docker_galaxy_temp_dir = None
@@ -51,7 +51,9 @@ class InteractiveEnviornmentRequest(object):
        self.notebook_pw_salt = self.generate_password(length=12)
        self.notebook_pw = self.generate_password(length=24)

-        self.temp_dir = os.path.abspath( tempfile.mkdtemp() )
+        ie_parent_temp_dir = self.attr.viz_config.get("docker", "docker_galaxy_temp_dir") or None
+        self.temp_dir = os.path.abspath( tempfile.mkdtemp( dir=ie_parent_temp_dir ) )
+
        if self.attr.viz_config.getboolean("docker", "wx_tempdir"):
            # Ensure permissions are set
            try:
@@ -65,10 +67,13 @@ class InteractiveEnviornmentRequest(object):
        # 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'] = ''
+        default_dict = {
+            'command': 'docker {docker_args}',
+            'command_inject': '--sig-proxy=true -e DEBUG=false',
+            'docker_hostname': 'localhost',
+            'wx_tempdir': 'False',
+            'docker_galaxy_temp_dir': None
+        }
        viz_config = ConfigParser.SafeConfigParser(default_dict)
        conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" )
        if not os.path.exists( conf_path ):
@@ -182,18 +187,24 @@ 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])
-        cmd = '%s run %s -d %s -p %s:%s -v "%s:/import/" %s %s' % \
-            (self.attr.viz_config.get("docker", "command"),
-             env_str,
-             self.attr.viz_config.get("docker", "command_inject"),
-             self.attr.PORT, self.attr.docker_port,
-             temp_dir,
-             volume_str,
-             self.attr.viz_config.get("docker", "image"))
-        cmd_wrapper = self.attr.viz_config.get("docker", "command_wrapper")
-        if cmd_wrapper != '' and '{cmd}' in cmd_wrapper:
-            cmd = cmd_wrapper.format( cmd=cmd )
-        return cmd
+        # 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 {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,
+            temp_dir=temp_dir,
+            volume_str=volume_str,
+            image=self.attr.viz_config.get("docker", "image")
+        )
+        return command

    def launch(self, raw_cmd=None, env_override={}, volumes=[]):
        if raw_cmd is None: