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/*
A KBase Atlas to liquid chromatography–mass spectrometry (LCMS) data
*/

module MetaboliteAtlas2 {

    /* Metabolite Compound object
     *
     *  name - common name of the compound

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stevensilvester: ~
$ xonsh
/usr/local/etc/bash_completion.d/abook: line 3: have: command not found
/usr/local/etc/bash_completion.d/ant: line 45: syntax error in conditional expression: unexpected token `('
/usr/local/etc/bash_completion.d/ant: line 45: syntax error near `-@(?'
/usr/local/etc/bash_completion.d/ant: line 45: `            if [[ "${COMP_WORDS[i]}" == -@(?(build)file|f) ]]; then'
/usr/local/etc/bash_completion.d/apache2ctl: line 3: have: command not found
/usr/local/etc/bash_completion.d/apt: line 12: syntax error in conditional expression: unexpected token `('
/usr/local/etc/bash_completion.d/apt: line 12: syntax error near `@(i'
/usr/local/etc/bash_completion.d/apt: line 12: `        if [[ ${COMP_WORDS[i]} == @(install|remove|autoremove|purge|source|build-dep) ]]; then'

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import zmq
from multiprocessing import Process
import time


def node(router_port, dealer_port1, dealer_port2):
    context = zmq.Context.instance()
    router = context.socket(zmq.ROUTER)
    router.bind("tcp://*:%s" % router_port)
    print("Running server on port: ", router_port)

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import os
import sys
import socket
import netifaces
import platform
import struct
import atexit
import logging
import base64
import time

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Log in to https://ipython.nersc.gov/. Run the following in a notebook cell to get set up (note this only has to be done once for a given user):

%%file ~/.ipython/profile_default/startup/ipython_config.py
import sys
sys.path.insert(0, '/project/projectdirs/metatlas/python_pkgs/')
import os
os.environ['R_LIBS_USER'] = '/project/projectdirs/metatlas/r_pkgs/'

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from pygments.lexers import get_lexer_for_filename
from pygments.token import Token


def get_matches(code, filename):
    """Get token-based matches for the current context in a file.
    """
    lexer = get_lexer_for_filename(filename)

    tokens = [i for i in lexer.get_tokens(code)]

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