<% import os import sys import time import yaml import shlex import random import shutil import tempfile import subprocess import ConfigParser galaxy_root_dir = os.path.abspath(trans.app.config.root) history_id = trans.security.encode_id( trans.history.id ) dataset_id = trans.security.encode_id( hda.id ) config = ConfigParser.SafeConfigParser({'port': '8080'}) config.read( os.path.join( galaxy_root_dir, 'universe_wsgi.ini' ) ) galaxy_paster_port = config.getint('server:main', 'port') # Find out where we are viz_plugin_dir = config.get('app:main', 'visualization_plugins_directory') if not os.path.isabs(viz_plugin_dir): # If it is NOT absolute, i.e. relative, append to galaxy root viz_plugin_dir = os.path.join(galaxy_root_dir, viz_plugin_dir) # Get this plugin's directory viz_plugin_dir = os.path.join(viz_plugin_dir, "ipython") # Store our template and configuration path our_config_dir = os.path.join(viz_plugin_dir, "config") our_template_dir = os.path.join(viz_plugin_dir, "templates") ipy_viz_config = ConfigParser.SafeConfigParser({'apache_urls': False, 'command': 'docker', 'image': 'bgruening/docker-ipython-notebook'}) ipy_viz_config.read( os.path.join( our_config_dir, "ipython.conf" ) ) # Ensure generation of notebook id is deterministic for the dataset. Replace with history id # whenever we figure out how to access that. random.seed( history_id ) notebook_id = ''.join(random.choice('0123456789abcdef') for _ in range(64)) with open( os.path.join( our_template_dir, 'notebook.ipynb' ), 'r') as nb_handle: empty_nb = nb_handle.read() empty_nb = empty_nb % notebook_id # Find all ports that are already occupied cmd_netstat = shlex.split("netstat -tuln") p1 = subprocess.Popen(cmd_netstat, stdout=subprocess.PIPE) occupied_ports = set() for line in p1.stdout.read().split('\n'): if line.startswith('tcp') or line.startswith('tcp6'): col = line.split() local_address = col[3] local_port = local_address.split(':')[-1] occupied_ports.add( int(local_port) ) # Generate random free port number for our docker container while True: PORT = random.randrange(10000,15000) if PORT not in occupied_ports: break HOST = request.host # Strip out port, we just want the URL this galaxy server was accessed at. if ':' in HOST: HOST = HOST[0:HOST.index(':')] temp_dir = os.path.abspath( tempfile.mkdtemp() ) conf_file = { 'history_id': history_id, 'galaxy_url': request.application_url.rstrip('/'), 'api_key': trans.user.api_keys[0].key, 'remote_host': request.remote_addr, 'galaxy_paster_port': galaxy_paster_port, 'docker_port': PORT, } with open( os.path.join( temp_dir, 'conf.yaml' ), 'wb' ) as handle: handle.write( yaml.dump(conf_file, default_flow_style=False) ) 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 ) else: shutil.copy( hda.file_name, empty_nb_path ) docker_cmd = '%s run -d --sig-proxy=true -p %s:6789 -v "%s:/import/" %s' % \ (ipy_viz_config.get("docker", "command"), PORT, temp_dir, ipy_viz_config.get("docker", "image")) if ipy_viz_config.getboolean("main", "apache_urls"): notebook_access_url = "http://%s/ipython/%s/notebooks/ipython_galaxy_notebook.ipynb" % ( HOST, PORT ) else: notebook_access_url = "http://%s:%s/ipython/%s/notebooks/ipython_galaxy_notebook.ipynb" % ( HOST, PORT, PORT ) subprocess.call(docker_cmd, shell=True) # We need to wait until the Image and IPython in loaded # TODO: This can be enhanced later, with some JS spinning if needed. time.sleep(1) %>