renaud

    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;

renaud

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

'''
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

#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

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

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

/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

// 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

{
  "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" : {

renaud

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():");