MrCreosote

import datetime, time, functools, operator, types

default_fudge = datetime.timedelta(seconds=0, microseconds=0, days=0)

def deep_eq(_v1, _v2, datetime_fudge=default_fudge, _assert=False):
  """
  Tests for deep equality between two python data structures recursing 
  into sub-structures if necessary. Works with all python types including
  iterators and generators. This function was dreampt up to test API responses
  but could be used for anything. Be careful. With deeply nested structures

MrCreosote

'''
Makes the specified workspaces non-public.
Parameters:
wsclient - an initialized workspace client. The user logged into the client
    must be a workspace administrator.
wslist - a list of workspace IDs and / or names.
'''

MrCreosote

import org.junit.Test;

import nl.jqno.equalsverifier.EqualsVerifier;

public class EqualsVerifierTesting {

	private static class Foo {
		
		private final String s;

MrCreosote

import os
import sys

from pymongo.mongo_client import MongoClient

WS_MONGO_PWD = 'WS_MONGO_PWD'

MONGO_COL_WSOBJS = 'workspaceObjVersions'

def get_ws_obj_collection():

MrCreosote

import os
import sys

from pymongo.mongo_client import MongoClient

WS_MONGO_PWD = 'WS_MONGO_PWD'

MONGO_COL_WSOBJS = 'workspaceObjVersions'

def get_ws_obj_collection(argv):

MrCreosote

import random


def stochastic_sortedness(list_, num_samples):
    ''' Based on https://stackoverflow.com/a/16994740/643675 '''
    if len(list_) < 2:
        return 0
    # a 2 item list works, but is a pretty dumb thing to pass to this function *shrug*
    maxindex = len(list_) - 1 
    score = 0

MrCreosote

import os
import random
import requests
import sys
import tempfile
import time

"""
Issues:

MrCreosote

"""
Totally gross Q&D implementation of mapping microtrait traits to gene / hmm names.
"""

_RULE2_TRAIT = "./microtrait/data-raw/microtrait_rule2trait.txt"
_SUBSTRATE2_RULE = "./microtrait/data-raw/microtrait_substrate2rule.txt"
_RULE_UNWRAPPED = "./microtrait/data-raw/microtrait_ruleunwrapped.txt"

_OUT = "./traits2genes.tsv"

MrCreosote

• Note: this is not a reasonable general solution for images in narratives because:
  • Even if all the steps below were automated for the user, it suffers from the so called "copy of a copy" problem. Namely, if the narrative is copied by a different user and the user loses access to the source narrative, the narrative will no longer be able to access the report object embedded in the HtmlFileSetService URL.
  • The HTMLFileSetService dynamic url is hardcoded into the narrative markdown text and it's, well, dynamic. It can change at any time at which point the images will 404.

Procedure:

• Add all your images to a zip file
• Using your kbase token, upload the zip file to Shock

MrCreosote

24/07/17 21:30:49 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
24/07/17 21:30:49 INFO DefaultNoHARMFailoverProxyProvider: Connecting to ResourceManager at yarn-resourcemanager/172.26.0.3:8032
24/07/17 21:30:49 INFO Configuration: resource-types.xml not found
24/07/17 21:30:49 INFO ResourceUtils: Unable to find 'resource-types.xml'.
24/07/17 21:30:49 INFO Client: Verifying our application has not requested more than the maximum memory capability of the cluster (8192 MB per container)
24/07/17 21:30:49 INFO Client: Will allocate AM container, with 1408 MB memory including 384 MB overhead
24/07/17 21:30:49 INFO Client: Setting up container launch context for our AM
24/07/17 21:30:49 INFO Client: Setting up the launch environment for our AM container
24/07/17 21:30:49 INFO Client: Preparing resources for our AM container
24/07/17 21:30:49 WARN Client: Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading lib