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# Install Spark on CentOS 7
yum install java -y
java -version
yum install wget -y
tar xvf scala-2.11.7.tgz
sudo mv scala-2.11.7 /usr/lib
sudo ln -s /usr/lib/scala-2.11.7 /usr/lib/scala
palexander / benchmark_dbs_vs_marshal.rb
Created Apr 28, 2015
Benchmark Ruby storage mechanisms
View benchmark_dbs_vs_marshal.rb
def time_code(name, &block)
t1 =
puts "#{name}: #{( - t1).to_f.round(2)}s"
def time_code_aggregate(name, &block)
unless @tc_at_exit
at_exit do
@tc_timers.each do |name, time|
palexander / expand_labels.go
Created Sep 18, 2014
Find RXNORM ingredients and brand names then expand the labels across CUI mappings to NCI and SNOMEDCT_US
View expand_labels.go
package main
import ""
import "log"
func main() {
// Filters for queries
rxnorm := toEntries("RXNORM")
rxnormTTY := toEntries("IN", "BN")
expandedTTY := toEntries("AB", "PT", "SY")
palexander / 0_reuse_code.js
Created Jun 3, 2014
Here are some things you can do with Gists in GistBox.
View 0_reuse_code.js
// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console
palexander / header_data.txt
Last active Aug 29, 2015
Example format for NCBO multipart/mixed ontology submission with file
View header_data.txt
Content-Type: multipart/mixed; boundary=OntologiesAPIMultipartPost; type=application/json; start=json
Content-Length: 328853
palexander / ruby_optional_arguments_benchmark.rb
Last active Jan 4, 2016
Benchmark to compare hash and keyword arguments in method invocations
View ruby_optional_arguments_benchmark.rb
require 'benchmark'
COUNT = 10_000_000
NAME = "Test Name"
EMAIL = ""
class Person
attr_accessor :name, :email
def set_with_hash(options = {})
palexander / ruby_data_object_comparison.rb
Created Jan 24, 2014
Benchmark to compare hash, OpenStruct, struct, and classes in Ruby
View ruby_data_object_comparison.rb
require 'ostruct'
require 'benchmark'
COUNT = 10_000_000
NAME = "Test Name"
EMAIL = ""
class Person
attr_accessor :name, :email
View virtual_to_acronym_mapping.csv
1000 MA
1005 BTO
1006 CL
1007 CHEBI
1009 DOID
1010 EMAP
1011 IEV
1012 ECO
View docker_parallel_rake_test_advanced.rb
namespace :docker do
desc "Run tasks in parallel using docker"
task :test do
forks = 4
# Start docker containers (serially, docker seems to have problems with concurrency)
ports = {}
forks.times do |i|
# Start redis and get the mapped port
`docker run -d -p 6379 -name redis#{i} yourdockeruser/redis`
View docker_parallel_rake_tests_try_catch.diff
@@ -27,6 +27,7 @@ namespace :docker do
pids = []
forks.times do |i|
pids << fork do
+ begin
# Configure your environment
# You'll want to do something here to make the environment
@@ -49,7 +50,9 @@ namespace :docker do
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