Renaud Richardet renaud

DkPro Binary Cas evaluation

Quick evaluation on 126 pdfs, with some preprocessing.

reading is very fast
writing with BinaryCasWriter and no compression is much slower than BinaryCasWriter with compression, where is the catch?!?
Maybe this is the catch "Be advised that binary serialization may have drawbacks compared to XMI serialization."
BinaryCasWriter with compression yields very decent file size

	@Test
	public void testSubscripts() throws Exception {

	final Pattern SUBSCRIPTS = Pattern.compile("^[ \\d]{10,1000}$");

	File ROOT = new File(
	"/Volumes/scratch/richarde/pdfs/201307/");
	for (File pdf : ROOT.listFiles()) {
	if (pdf.getName().endsWith(".pdf")) {
	try {

	import urllib, sys
	from xml.etree import cElementTree as ElementTree

	def get_go_name(go_id):
	sys.stdout.write("GO"+go_id+"\t"),
	#get the GO entry as XML
	xml = urllib.urlopen("http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:"+go_id+"&format=oboxml")
	#open in cElementTree, for fast XML parsing
	for event, element in ElementTree.iterparse(xml):
	#need to make sure we are getting the name contained within the 'term' entry

	package topic

	import spark.broadcast._
	import spark.SparkContext
	import spark.SparkContext._
	import spark.RDD
	import spark.storage.StorageLevel
	import scala.util.Random
	import scala.math.{ sqrt, log, pow, abs, exp, min, max }
	import scala.collection.mutable.HashMap

	'''
	Transforms topic-model input file,
	from DCA format (space separated)
	to LDA-C format (column-separated)

	@author [email protected]
	'''
	import sys

	dca_file = sys.argv[1]

	#!/bin/sh

	############################################
	# MAKE SURE TO BACKUP YOUR FILES FIRST
	############################################

	# see http://uima.apache.org/d/uimafit-2.0.0/tools.uimafit.book.html#d5e617

	#Change of package names:
	find . -name '*.java' -print \| xargs perl -p -i -e 's/org.uimafit/org.apache.uima.fit/g'

	alias gita="git status \| egrep 'modified: ' \| sed $'s/#\tmodified:/git add/g'"
	alias gitd="git status \| egrep 'deleted: ' \| sed $'s/#\tdeleted:/git rm/g'"

	package ch.epfl.bbp.uima.projects.references;

	import static cc.mallet.pipe.iterator.FileIterator.LAST_DIRECTORY;
	import static com.google.common.collect.Lists.newArrayList;
	import static java.util.regex.Pattern.compile;
	import static org.apache.commons.lang.StringUtils.join;
	import static org.slf4j.LoggerFactory.getLogger;

	import java.io.File;
	import java.io.FileFilter;

	package ch.epfl.bbp.nlp.obo;

	import java.io.BufferedReader;
	import java.io.File;
	import java.io.FileReader;
	import java.io.IOException;
	import java.util.HashMap;
	import java.util.HashSet;
	import java.util.Map;
	import java.util.Set;