mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Eric Rasche
4b64a70906
In order to whitelist IPs allowed to connect to notebooks, we need to know who the remote target connecting is. We can blacklist on IP address only, as we have no way of authenticating them. While we do have access to other information like cookies, we have no SSL nor way to know what authentication method the galaxy server will be using.
125 lines
3.4 KiB
Mako
125 lines
3.4 KiB
Mako
<%
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import os
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import sys
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import tempfile
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import shutil
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import time
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import subprocess
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import yaml
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import random
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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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# 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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empty_nb = """{
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"metadata": {
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"name": "",
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"signature": "sha256:%s"
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},
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"nbformat": 3,
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"nbformat_minor": 0,
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"worksheets": [
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{
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"cells": [
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{
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"cell_type": "heading",
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"level": 2,
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"metadata": {},
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"source": [
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"Welcome to the interactive Galaxy IPython Notebook."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"You can access your data via the dataset number. For example: handle = open('42', 'r')"
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]
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},
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{
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"cell_type": "code",
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"collapsed": false,
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"input": [],
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"language": "python",
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"metadata": {},
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"outputs": []
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}
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],
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"metadata": {}
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}
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]
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}""" % (notebook_id, )
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# Find all ports that are already occupied
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import shlex
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cmd_netstat = shlex.split("netstat -tnaAinet")
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p1 = subprocess.Popen(cmd_netstat, stdout=subprocess.PIPE)
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cmd_awk = shlex.split("awk 'NR >= 3 { print $4 }'")
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p2 = subprocess.Popen(cmd_awk, stdin=p1.stdout, stdout=subprocess.PIPE)
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cmd_cut = shlex.split("cut -d: -f2")
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p3 = subprocess.Popen(cmd_cut, stdin=p2.stdout, stdout=subprocess.PIPE)
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cmd_sort = shlex.split("sort -un")
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p4 = subprocess.Popen(cmd_sort, stdin=p3.stdout, stdout=subprocess.PIPE)
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netstat_out = p4.stdout.read()
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occupied_ports = [port for port in netstat_out.split('\n') if port.isdigit()]
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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 PORTS 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,
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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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}
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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) )
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# TODO: Implement proper IPyNB datatype atop a proper JSON datatype
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# For now we assume all "text" datatypes are ipynbs.
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# <datatype extension="ipynb" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="True"/>
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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__ != "Text":
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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 = 'docker run -d --sig-proxy=true -p %s:6789 -v "%s:/import/" bgruening/docker-ipython-notebook' % (PORT, temp_dir)
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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="http://${HOST}:${PORT}/notebooks/ipython_galaxy_notebook.ipynb" height="100%" width="100%">
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<embed src="http://${HOST}:${PORT}/notebooks/ipython_galaxy_notebook.ipynb" 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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