mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Eric Rasche
4f3052fd2b
It was really awful to have that file maintained with the rest of the source code, now it is separate.
114 lines
3.8 KiB
Mako
114 lines
3.8 KiB
Mako
<%
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import os
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import sys
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import time
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import yaml
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import shlex
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import random
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import shutil
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import tempfile
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import subprocess
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import ConfigParser
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galaxy_root_dir = os.path.abspath(trans.app.config.root)
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history_id = trans.security.encode_id( trans.history.id )
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dataset_id = trans.security.encode_id( hda.id )
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config = ConfigParser.SafeConfigParser({'port': '8080'})
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config.read( os.path.join( galaxy_root_dir, 'universe_wsgi.ini' ) )
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galaxy_paster_port = config.getint('server:main', 'port')
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# Find out where we are
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viz_plugin_dir = config.get('app:main', 'visualization_plugins_directory')
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if not os.path.isabs(viz_plugin_dir):
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# If it is NOT absolute, i.e. relative, append to galaxy root
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viz_plugin_dir = os.path.join(galaxy_root_dir, viz_plugin_dir)
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# Get this plugin's directory
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viz_plugin_dir = os.path.join(viz_plugin_dir, "ipython")
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# Store our template and configuration path
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our_config_dir = os.path.join(viz_plugin_dir, "config")
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our_template_dir = os.path.join(viz_plugin_dir, "templates")
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ipy_viz_config = ConfigParser.SafeConfigParser({'apache_urls': False, 'command': 'docker', 'image':
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'bgruening/docker-ipython-notebook'})
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ipy_viz_config.read( os.path.join( our_config_dir, "ipython.conf" ) )
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# Ensure generation of notebook id is deterministic for the dataset. Replace with history id
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# whenever we figure out how to access that.
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random.seed( history_id )
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notebook_id = ''.join(random.choice('0123456789abcdef') for _ in range(64))
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with open( os.path.join( our_template_dir, 'notebook.ipynb' ), 'r') as nb_handle:
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empty_nb = nb_handle.read()
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empty_nb = empty_nb % notebook_id
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# Find all ports that are already occupied
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cmd_netstat = shlex.split("netstat -tuln")
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p1 = subprocess.Popen(cmd_netstat, stdout=subprocess.PIPE)
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occupied_ports = set()
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for line in p1.stdout.read().split('\n'):
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if line.startswith('tcp') or line.startswith('tcp6'):
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col = line.split()
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local_address = col[3]
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local_port = local_address.split(':')[-1]
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occupied_ports.add( int(local_port) )
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# Generate random free port number for our docker container
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while True:
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PORT = random.randrange(10000,15000)
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if PORT not in occupied_ports:
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break
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HOST = request.host
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# Strip out port, we just want the URL this galaxy server was accessed at.
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if ':' in HOST:
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HOST = HOST[0:HOST.index(':')]
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temp_dir = os.path.abspath( tempfile.mkdtemp() )
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conf_file = {
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'history_id': history_id,
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'galaxy_url': request.application_url.rstrip('/'),
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'api_key': trans.user.api_keys[0].key,
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'remote_host': request.remote_addr,
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'galaxy_paster_port': galaxy_paster_port,
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'docker_port': PORT,
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}
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with open( os.path.join( temp_dir, 'conf.yaml' ), 'wb' ) as handle:
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handle.write( yaml.dump(conf_file, default_flow_style=False) )
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empty_nb_path = os.path.join(temp_dir, 'ipython_galaxy_notebook.ipynb')
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if hda.datatype.__class__.__name__ != "Ipynb":
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with open( empty_nb_path, 'w+' ) as handle:
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handle.write( empty_nb )
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else:
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shutil.copy( hda.file_name, empty_nb_path )
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docker_cmd = '%s run -d --sig-proxy=true -p %s:6789 -v "%s:/import/" %s' % \
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(ipy_viz_config.get("docker", "command"), PORT, temp_dir, ipy_viz_config.get("docker", "image"))
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if ipy_viz_config.getboolean("main", "apache_urls"):
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notebook_access_url = "http://%s/ipython/%s/notebooks/ipython_galaxy_notebook.ipynb" % ( HOST, PORT )
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else:
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notebook_access_url = "http://%s:%s/ipython/%s/notebooks/ipython_galaxy_notebook.ipynb" % ( HOST, PORT, PORT )
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subprocess.call(docker_cmd, shell=True)
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# We need to wait until the Image and IPython in loaded
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# TODO: This can be enhanced later, with some JS spinning if needed.
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time.sleep(1)
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%>
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<html>
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<body>
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<object data="${notebook_access_url}" height="100%" width="100%">
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<embed src="${notebook_access_url}" height="100%" width="100%">
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</embed>
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</object>
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</body>
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</html>
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