mlist’s gists

mlist / RESTful_KeyPathwayMiner.r

Created November 24, 2015 14:15

This R script contains exemplary methods for accessing the KeyPathwayMinerWeb RESTful API defined at http://tomcat.compbio.sdu.dk/keypathwayminer/documentation/rest/

	### R functions to consume the KeyPathwayMinerWeb RESTful API ###
	### Authors: Markus List and Martin Dissing-Hansen ###

	# Package dependencies. Make sure those are installed
	library(RCurl)
	library(rjson)
	library(foreach)

	# Helper method for base64 encoding. Needed to transfer network and dataset files #
	base64EncFile <- function(fileName){

mlist / copy_to_docker.sh

Created February 24, 2015 15:01

copy file to docker container

	cd /tmp/somefiles
	tar -cv * \| docker exec -i elated_hodgkin tar x -C /var/www

mlist / createdb.sh

Last active August 29, 2015 14:16

bash script to create a database + user in mysql.

	#!/bin/bash

	EXPECTED_ARGS=3
	E_BADARGS=65
	MYSQL=`which mysql`

	Q1="CREATE DATABASE IF NOT EXISTS $1;"
	Q2="GRANT USAGE ON . TO $2@localhost IDENTIFIED BY '$3';"
	Q3="GRANT ALL PRIVILEGES ON $1.* TO $2@localhost;"
	Q4="FLUSH PRIVILEGES;"

mlist / awk.csv.filter.bash

Created May 1, 2014 07:29

How to filter out lines from a CSV file that begin with either CDS or UTR3 using awk, allowing you to process a 2GB file in mere seconds

awk -F, '$1 !~ /(^CDS|^UTR3)/' microT_CDS_data.csv > microT_CDS_data.filtered.csv

mlist / miracle.groovy

Created April 8, 2014 12:15

MIRACLE example configuration

	dataSource {
	driverClassName = 'com.mysql.jdbc.Driver'
	url = 'jdbc:mysql://localhost/miracle'
	username = 'miracle'
	password = 'rppa4ever'
	dbCreate = 'update'
	pooled = true
	properties {
	maxActive = -1
	minEvictableIdleTimeMillis=1800000

mlist / Rcurl_grails.r

Created December 13, 2013 12:45

how to use RCurl to access a grails controller

	authenticate <- function(baseUrl="http://localhost:8080/GrailsApp/", user, password, verbose=F){
	require(RCurl)
	loginUrl = paste(baseUrl, "login/auth", sep="")
	authenticateUrl = paste(baseUrl, "j_spring_security_check", sep="")

	cat(paste("trying to authenticate user", user))
	agent="Mozilla/5.0"

	#Set RCurl pars
	curl = getCurlHandle()

mlist / TokenUsingController.groovy

Created December 13, 2013 12:43

how to apply security token service in a controller

	private def accessAllowed = { securityToken, uuid ->
	//check if user is authenticated
	if(!springSecurityService.isLoggedIn()){
	//alternatively check if a security token is provided
	if(!securityToken \|\| securityToken != uuid){
	return(false)
	}

	}
	return(true)

mlist / SecurityTokenService.groovy

Created December 13, 2013 12:40

SecurityTokenService in grails

	class SecurityTokenService {

	def getSecurityToken(SomeDomainClass sdc) {
	if(!sdc?.uuid){
	sdc.uuid = UUID.randomUUID().toString()
	sdc.save(flush:true)
	}

	return sdc.uuid
	}

mlist / jackson.groovy

Created December 13, 2013 12:34

grails with jackson

	def criteria = SomeDomainClass.createCriteria()
	def result = criteria.list {
	...
	}
	ObjectMapper mapper = new ObjectMapper()
	def jsonResult = mapper.writeValueAsString(result)

	response.contentType = "text/json"
	render jsonResult

mlist / projections.groovy

Created December 13, 2013 12:32

grails projections with alias and left outer join

	def criteria = Spot.createCriteria()
	def result = criteria.list {
	eq("slide.id", params.long("id"))
	createAlias('layoutSpot', 'lSpot', CriteriaSpecification.LEFT_JOIN)
	createAlias('lSpot.sample', 'smpl', CriteriaSpecification.LEFT_JOIN)
	projections {
	property "id"
	property "signal"
	property "block"
	property "row"

Markus List mlist