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Renaud Richardet renaud

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  • Lausanne, Switzerland
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@renaud
renaud / diff
Created March 13, 2015 14:42
log level
diff --git a/src/main/java/org/sherlok/PipelineLoader.java b/src/main/java/org/sherlok/PipelineLoader.java
index 74a42cf..c057421 100644
--- a/src/main/java/org/sherlok/PipelineLoader.java
+++ b/src/main/java/org/sherlok/PipelineLoader.java
@@ -263,6 +263,14 @@ public class PipelineLoader {
resolvedArtifact);
}
}
+ if (LOG.isTraceEnabled()) {
+ LOG.trace("CLASSPATH at end of solveDependencies():");
@renaud
renaud / gist:a025fb10d66575412355
Created March 13, 2015 14:02
http://localhost:9600/annotate/bluima.token?text=Text
{
"cause" : {
"arguments" : [ "org.apache.uima.ruta.engine.RutaEngine", "<unknown>" ],
"cause" : {
"arguments" : [ "file:/Volumes/HDD2/ren_data/dev_hdd/uima/sherlok/sherlok_core/config/resources/.engines/TokenAnnotator___0_1.xml" ],
"cause" : {
"arguments" : [ "file:/Volumes/HDD2/ren_data/dev_hdd/uima/sherlok/sherlok_core/config/resources/.engines/TokenAnnotator___0_1.xml" ],
"cause" : {
"arguments" : [ "file:/Volumes/HDD2/ren_data/dev_hdd/uima/sherlok/sherlok_core/config/resources/.engines/TokenAnnotator___0_1.xml" ],
"cause" : {
// Modifies $httpProvider for correct server communication (POST variable format)
angular.module('http-post-fix', [], function($httpProvider) {
// This code is taken from http://victorblog.com/2012/12/20/make-angularjs-http-service-behave-like-jquery-ajax/
// Use x-www-form-urlencoded Content-Type
$httpProvider.defaults.headers.post['Content-Type'] = 'application/x-www-form-urlencoded;charset=utf-8';
// Override $http service's default transformRequest
$httpProvider.defaults.transformRequest = [function(data) {
/**
@renaud
renaud / lucas.diff
Created August 11, 2014 21:10
Fixing UIMA Lucas
/uima-addons-2.3.1/Lucas$ st
M src/main/java/org/apache/uima/lucas/indexer/analysis/SplitterFilter.java
M pom.xml
/uima-addons-2.3.1/Lucas$ svn diff
Index: src/main/java/org/apache/uima/lucas/indexer/analysis/SplitterFilter.java
===================================================================
--- src/main/java/org/apache/uima/lucas/indexer/analysis/SplitterFilter.java (revision 1347596)
+++ src/main/java/org/apache/uima/lucas/indexer/analysis/SplitterFilter.java (working copy)
@@ -20,6 +20,7 @@
package org.apache.uima.lucas.indexer.analysis;
@renaud
renaud / psi.m
Created May 21, 2014 21:29
Digamma (psi) function, since Octave does not implement it yet
function y = psi(x)
%DIGAMMA Digamma function.
% DIGAMMA(X) returns digamma(x) = d log(gamma(x)) / dx
% If X is a matrix, returns the digamma function evaluated at each element.
% Reference:
%
% J Bernardo,
% Psi ( Digamma ) Function,
% Algorithm AS 103,
@renaud
renaud / LenientMultiSegmentationEvaluator.java
Created May 15, 2014 22:19
Lenient (overlap) evaluation for Mallet
package cc.mallet.fst;
import java.text.DecimalFormat;
import java.util.LinkedList;
import java.util.List;
import cc.mallet.types.FeatureVector;
import cc.mallet.types.Instance;
import cc.mallet.types.InstanceList;
import cc.mallet.types.Sequence;
@renaud
renaud / parse_obo.py
Created April 29, 2014 22:15
Parse OBO
#http://techoverflow.net/blog/2013/11/18/a-geneontology-obo-v1.2-parser-in-python/
import go_obo_parser
for p in go_obo_parser.parseGOOBO('....../pro.obo'):
if 'is_a' in p and p['is_a'] == 'PR:000000001 ! protein':
print p['name']
@renaud
renaud / tornado_continuous_reload.py
Created April 10, 2014 08:35
Example of Tornado that autoreloads/watches all files in folder 'static'
'''
Example of Tornado that autoreloads/watches all files in folder 'static'
'''
import tornado.ioloop
import tornado.web
import tornado.autoreload
import os
''' serves index.html'''
@renaud
renaud / add_pandas.py
Created March 11, 2014 08:52
adding two Pandas dataframes
import numpy as np
import pandas as pd
df1 = pd.DataFrame([(1,2),(2,4),(5,6)], columns=['a','b'])
df1
df2 = pd.DataFrame([(100,200),(300,400),(500,600)], columns=['a','b'])
df2
df_add = df1.add(df2, fill_value=0)
df_add
@renaud
renaud / Ruta101.java
Created March 4, 2014 08:26
Hello Ruta from whithin UIMAfit
package org.apache.uima.ruta.engine;
import static org.junit.Assert.assertEquals;
import java.util.Collection;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.junit.Test;