khundman/marve

For extracting measurements and related entities from text

marve's Issues

JSONDecodeError

I am getting a JSONDecodeError : Expecting value: line 1 column 1 (char 0) . CoreNLP and Grobid are running fine .
The code i have written is

import Measurements as m
import json

test = "The patient returned to Europe at 28 weeks of gestation."

coreNLP = "http://localhost:9000"
grobid = "http://localhost:8070/service"
patterns = "dependency_patterns.json"
write_to = "smaple_output.txt"

out = m.extract(test, coreNLP, grobid, patterns, write_to, show_graph=False, pretty=True)

Please help me out!

Paper Data

Hello,

Reading your paper, I realized you used a dataset of 489 sentences. Did you also publish the preprocessing and the dataset themselves so that others be able to reproduce your results?

Exception in thread "pool-1-thread-3" java.lang.OutOfMemoryError: Java heap space

Hi all,

When I run the sample.py, the short program just stuck there (I run it in a python iteractive shell). I found in the stanford corenlp server, prints the following.

It seems like a memory issue? but it is just one sentence: "The patient returned to Europe at 28 weeks of gestation." Any idea on how to solve this?

[pool-1-thread-3] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator coref
Exception in thread "pool-1-thread-3" java.lang.OutOfMemoryError: Java heap space
at java.io.ObjectInputStream$HandleTable.grow(ObjectInputStream.java:3493)
at java.io.ObjectInputStream$HandleTable.assign(ObjectInputStream.java:3300)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1799)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
at java.util.HashMap.readObject(HashMap.java:1396)
at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1909)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2018)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1942)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
at edu.stanford.nlp.io.IOUtils.readObjectFromURLOrClasspathOrFileSystem(IOUtils.java:310)
at edu.stanford.nlp.coref.statistical.FeatureExtractor.loadVocabulary(FeatureExtractor.java:90)
at edu.stanford.nlp.coref.statistical.FeatureExtractor.(FeatureExtractor.java:75)
at edu.stanford.nlp.coref.statistical.StatisticalCorefAlgorithm.(StatisticalCorefAlgorithm.java:63)
at edu.stanford.nlp.coref.statistical.StatisticalCorefAlgorithm.(StatisticalCorefAlgorithm.java:44)
at edu.stanford.nlp.coref.CorefAlgorithm.fromProps(CorefAlgorithm.java:28)
at edu.stanford.nlp.coref.CorefSystem.(CorefSystem.java:34)
at edu.stanford.nlp.pipeline.CorefAnnotator.(CorefAnnotator.java:50)
at edu.stanford.nlp.pipeline.AnnotatorImplementations.coref(AnnotatorImplementations.java:243)
at edu.stanford.nlp.pipeline.AnnotatorFactories$13.create(AnnotatorFactories.java:402)
at edu.stanford.nlp.pipeline.AnnotatorPool.get(AnnotatorPool.java:152)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.construct(StanfordCoreNLP.java:451)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.(StanfordCoreNLP.java:154)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.(StanfordCoreNLP.java:145)

Is it possible to share the evalutaion data used in paper

Really intrested in your work and would like to follow it. Is it possbile to share the labeled evaluation data in the paper? So I could further test my methods. Thanks! Wrote you an e-mail few days ago.

Issues while running marve

I’ve got some problem with python and matplotlib with OSX, but I’ve managed to work around it.

I’ve noticed that coreNLP doesn’t work on my mac book with 4Gb of memory. I had to give him more (~6g) to have it running. After that I’ve run marve but I’ve got another error:

(inria-virtualenv-p2) Johan:marve lfoppiano$ frameworkpython marve/sample.py 
Traceback (most recent call last):
  File "marve/sample.py", line 28, in <module>
    m.extract(test, coreNLP, grobid, patterns, write_to, show_graph=False, pretty=True, simplify=False)
  File "/Users/lfoppiano/development/inria/inria-virtualenv-p2/lib/python2.7/site-packages/marve/Measurements.py", line 488, in extract
    A = Annotations(output["sentences"][i]["tokens"], output["sentences"][i][dep_key])
KeyError: 'enhanced-plus-plus-dependencies’

I’m using CoreNLP version stanford-corenlp-full-2016-10-31, the same as in the installation documentation.

Cheers
Luca