amergin’s gists

amergin / client.py

Created August 4, 2012 16:23

	# -- coding: utf-8 --
	# Modified lightsocket import script, based on Lightsocket
	# example script by James Thornton (http://jamesthornton.com)

	# mundane modification stuff
	import os
	import commands
	import sys
	import datetime
	import re # regexp

amergin / importclass.py

Created August 4, 2012 16:25

	# -- coding: utf-8 --
	# Class implementation for importing stuff to Neo4j
	# based on Lightsocket examples by
	#James Thornton (http://jamesthornton.com)

	from java.lang import Long, Double, Integer, String

	from com.tinkerpop.rexster.util import ElementHelper
	from com.tinkerpop.blueprints.pgm.impls.neo4j import Neo4jGraph
	from com.tinkerpop.blueprints.pgm.impls.neo4jbatch import Neo4jBatchGraph

amergin / jythoimporter.py

Created August 6, 2012 17:33

	# -- coding: utf-8 --
	# Modified lightsocket import script, based on Lightsocket
	# example script by James Thornton (http://jamesthornton.com)

	# mundane modification stuff
	import os
	import commands
	import sys
	import datetime
	import re # regexp

amergin / gremlin-test1.groovy

Created October 10, 2012 17:59

Gremlin test script for bulbs

	def regulatory(clinicalNodeId, distanceThreshold, middleNodeType, mutatedType, targetType) {
	if( targetType == 'GNAB' )
	{
	if( mutatedType == 'aberrated' )
	{
	/*distanceThreshold = 100000;
	middleNodeType = 'GEXP';
	clinicalNodeId = 137059;
	mutatedType = 'aberrated';
	targetType = 'GNAB'; */

amergin / gist:3873399

Created October 11, 2012 16:01

cypher test

	START node1=node(1456) MATCH node1-[rel1]->node2
	WITH node1, rel1, node2 ORDER BY rel1.distance! ASC LIMIT 10
	MATCH node2-[rel2]->node3
	WHERE node3 <> node1
	WITH node2,node3, rel2, rel1 ORDER BY rel2.distance! ASC LIMIT 10
	MATCH node3-[rel3]->node4
	WHERE node4 <> node2
	RETURN DISTINCT rel1, rel2, rel3
	ORDER BY rel2.distance! ASC LIMIT 10;

amergin / cytoproblem.html

Created October 22, 2012 09:26

	<!DOCTYPE html>
	<html>
	<head>
	<title>Test</title>
	<style type="text/css">
	.options { font-family:"Times New Roman", Times, serif; text-size: 12px; text-color: #A8A8A8; margin: 0px auto; background-color: #E3E3E3;}
	.full-height { height: 800px; margin: 0 0; padding: 0 0; width: 800px; }
	</style>
	<script type='text/javascript' src="http://code.jquery.com/jquery-1.8.2.js"></script>
	<script type='text/javascript' src="lib/cytoscape.js"></script>

amergin / gist:3960966

Created October 26, 2012 19:35

Neo4j autocomplete test

	eo4j-sh (0)$ start a=node:cbm_pc_quantrev_0706_i_n_GEXP('label:TP53') return id(a);
	==> +-------+
	==> \| id(a) \|
	==> +-------+
	==> \| 48228 \|
	==> +-------+
	==> 1 row
	==> 249 ms
	==>
	neo4j-sh (0)$ start a=node:cbm_pc_quantrev_0706_i_n_GEXP('label:T*') return count(a);

amergin / gist:4262270

Created December 11, 2012 21:27

Cypher branching example

	START a = node(137059)
	MATCH a-[rel]->b
	WITH a,b,rel
	ORDER BY rel.pvalue DESC LIMIT 5
	MATCH b-[rel2]->c
	WITH a,b,c,rel,rel2
	ORDER BY rel2.pvalue DESC LIMIT 5
	RETURN a.label?, rel.pvalue, b.label?, b.source, rel2.pvalue, c.label?, c.source;

amergin / dump_after_warming_idle.txt

Created December 31, 2012 00:31

jstack after warming the cache, at idle, CPU ~33%.

	2012-12-31 02:25:57
	Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.10-b01 mixed mode):

	"Attach Listener" daemon prio=10 tid=0x00007ff318003800 nid=0x63fe waiting on condition [0x0000000000000000]
	java.lang.Thread.State: RUNNABLE

	"712944945@qtp-2058324786-3" prio=10 tid=0x00007ff2a8003800 nid=0x63d0 in Object.wait() [0x00007ff25502e000]
	java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	- waiting on <0x00000005202a9ef0> (a org.mortbay.thread.QueuedThreadPool$PoolThread)

amergin / dump_while_traversing_highCPU.txt

Created December 31, 2012 00:32

jstack dump while high-CPU traversal.

	2012-12-31 02:28:04
	Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.10-b01 mixed mode):

	"1964274118@qtp-2058324786-4" prio=10 tid=0x00007ff2a8014800 nid=0x6429 in Object.wait() [0x00007ff271190000]
	java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	- waiting on <0x00000005337d6da0> (a org.mortbay.thread.QueuedThreadPool$PoolThread)
	at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:626)
	- locked <0x00000005337d6da0> (a org.mortbay.thread.QueuedThreadPool$PoolThread)

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