msalvadores’s gists

msalvadores / traverse_go_classes.py

Last active August 29, 2015 14:07

A simple script to traverse all GO classes

	import requests
	import time
	import pdb
	import json
	import sys
	import urllib

	FILE_NAME = "ontology_ids_and_parents.txt"
	APIKEY = 'YOUR KEY'

msalvadores / dwcterms_owl.rdf

Created June 5, 2014 19:47

dwc_terms_owl.rdf

	<?xml version="1.0"?>

	<!DOCTYPE rdf:RDF [
	<!ENTITY dcam "http://purl.org/dc/dcam/" >
	<!ENTITY dcterms "http://purl.org/dc/terms/" >
	<!ENTITY dcmitype "http://purl.org/dc/dcmitype/" >
	<!ENTITY dwc "http://rs.tdwg.org/dwc/terms/" >
	<!ENTITY dwctype "http://rs.tdwg.org/dwc/dwctype/" >
	<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
	<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >

msalvadores / play_log.py

Created June 20, 2013 23:56

	import sys
	import urllib,urllib2
	import traceback
	import pdb
	import time
	import json
	import os

	def query(q,epr,f='text/plain'):
	params = {'query': q}

msalvadores / array_append_len_known.py

Last active December 15, 2015 08:09

A benchmark of two approaches to constructing an array. Bytearray vs array+join. Limitation: one should know the length of the array. Within pypy-1.9 the bytearray approach is one order of magnitude faster. In CPython-2.7, bytearray aprox. 35% faster.

	import timeit

	DATA = 'abcdef'

	def bytearr():
	bytesn = 1024 * 1024 * 5
	s = bytearray(bytesn)
	i = 0
	while i < bytesn:
	s[i] = DATA[i%len(DATA)]

msalvadores / mini_dsl.rb

Last active December 15, 2015 00:38

A mini DSL to dynamically generate objects in Ruby.

	require 'pry'

	module Test
	module Settings
	def self.included(base)
	base.extend(ClassMethods)
	end

	module ClassMethods
	attr_accessor :settings

msalvadores / gist:2210565

Created March 26, 2012 23:20

Java function to pass the api key to BioPortal SPARQL

	public ResultSet executeQuery(String queryString) throws Exception {
	Query query = QueryFactory.create(queryString) ;

	QueryEngineHTTP qexec = QueryExecutionFactory.createServiceRequest(this.service, query)
	qexec.addParam("apikey", this.apikey)
	ResultSet results = qexec.execSelect() ;
	return results;
	}

msalvadores / gist:2210491

Created March 26, 2012 23:12

Simple Python Script to Query sparql.bioportal.org

	import json,urllib2,urllib,traceback, sys

	def query(q,apikey,epr,f='application/json'):
	try:
	params = {'query': q, 'apikey': apikey}
	params = urllib.urlencode(params)
	opener = urllib2.build_opener(urllib2.HTTPHandler)
	request = urllib2.Request(epr+'?'+params)
	request.add_header('Accept', f)
	request.get_method = lambda: 'GET'

msalvadores / gist:1473419

Created December 13, 2011 19:12

fast filtered output test

	package test;

	import java.io.PrintStream;

	public class TestOutput {

	public static void outputFiltered(String label, PrintStream out) {
	for (byte b : label.getBytes()) {
	if (Character.isLetterOrDigit((char)b)) {
	out.print((char)b);

msalvadores / test_sparql_bioportal.py

Created October 5, 2011 01:53

BioPortal SPARQL Sample Script (Python)

	import json
	import urllib2
	import urllib
	import traceback
	import sys

	def query(q,apikey,epr,f='application/json'):
	"""Function that uses urllib/urllib2 to issue a SPARQL query.
	By default it requests json as data format for the SPARQL resultset"""

msalvadores / gist:1251188

Created September 29, 2011 16:34

Bioportal Mapping Example (Turtle Syntax)

	#Ontology here http://protege.stanford.edu/ontologies/mappings/mappings.rdfs

	<http://purl.bioontology.org/mapping/21d7a8e0-004d-012e-74a1-005056bd0010>
	<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_source_ontology_version> 40400 ;
	<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_target_ontology_version> 42693 ;
	<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#date> "2010-05-17T23:24:34Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
	<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source> "Application" ;
	<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_algorithm> "Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym." ;
	<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_contact_info> "[email protected]" ;
	<http://protege.stanford.

Manuel Salvadores msalvadores