EDITED
Thanks to Alvas' answer. I just learned that the following problem is caused by the 'not-so-up-to-date' NLTK since the latest 15-12-09 StanfordNLP requires more dependencies than previous versions. The exact solution to this problem is within this link https://github.com/nltk/nltk/issues/1239 as Alvas suggested.
StackOverflow identify my problem similar to this post Stanford Parser and NLTK. I still believe the two problems are different since the original one addresses more discussions on the overall proper setup of Standfordnlp while my question is focusing on the error itself. And after all, that doesn't solve my problem.
Follows is my post before I added these comments.
I've read almost all relative topics and possible solutions posted on Stackoverflow and tried them all on my computer. However, no positive result has been achieved. It is becoming frustrating everyday for an amature learning nlp and rookie in java because this problem prevents me from getting to know nltk at the very start. I would like to share the problem again and thanks again for all who tried to solve in advance.
Basically, I intend to parse Chinese characters but start from the English language. Here is the code I used (You probably have seen it because I copied it elsewhere to test):
import os
from nltk.parse import stanford
ini_path = 'C:/Users/qubo/jars/stanford-parser/'
os.environ['STANFORD_PARSER'] = ini_path + 'stanford-parser.jar'
os.environ['STANFORD_MODELS'] = ini_path + 'stanford-parser-3.6.0-models.jar'
os.environ['JAVAHOME'] = 'C:/Program Files/Java/jdk1.8.0_73/'
parser = stanford.StanfordParser(ini_path + 'stanford-parser.jar', ini_path + 'stanford-parser-3.6.0-models.jar')
sentences = parser.raw_parse_sents(("Python is fun. We should all date Python in this case."))
print (sentences)
for line in sentences:
for sentence in line:
sentence.draw()
And now I got this error msg when running parser.raw_parse_sents:
java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
at edu.stanford.nlp.parser.common.ParserGrammar.<clinit>(ParserGrammar.java:46)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 1 more
Exception in thread "main"
Traceback (most recent call last):
File "C:\Users\qubo\Desktop\nltkexample.py", line 33, in <module>
sentences = parser.raw_parse_sents(("Python is fun. We should all date Python in this case."))
File "C:\Users\qubo\Miniconda2\lib\site-packages\nltk\parse\stanford.py", line 146, in raw_parse_sents
return self._parse_trees_output(self._execute(cmd, '\n'.join(sentences), verbose))
File "C:\Users\qubo\Miniconda2\lib\site-packages\nltk\parse\stanford.py", line 212, in _execute
stdout=PIPE, stderr=PIPE)
File "C:\Users\qubo\Miniconda2\lib\site-packages\nltk\internals.py", line 134, in java
raise OSError('Java command failed : ' + str(cmd))
OSError: Java command failed : ['C:/Program Files/Java/jdk1.8.0_73/bin\\java.exe', u'-mx1000m', '-cp', 'C:/Users/qubo/jars/stanford-parser/stanford-parser.jar;C:/Users/qubo/jars/stanford-parser/stanford-parser-3.6.0-models.jar', u'edu.stanford.nlp.parser.lexparser.LexicalizedParser', u'-model', u'edu/stanford/nlp/models/lexparser/englishPCFG.ser.gz', u'-sentences', u'newline', u'-outputFormat', u'penn', u'-encoding', u'utf8', 'c:\\users\\qubo\\appdata\\local\\temp\\tmppz8u6r']
[Finished in 0.7s]
I'm using windows 64, Python 2.7.11 and all modules supporting nltk and stanford parser are updated. I've installed the jdk and jre as well. In fact, I've tried different versions and jdk (old or latest, 86 or 64), none was working.
I've tried to set java path directly in internals.py or commenting raise error lines in standford.py, still not working.
I've tried to add JAVAHOME environment variable, no use. In fact, it serves the exact same purpose as this line (as some may claim to be slightly different):
os.environ['JAVAHOME'] = 'C:/Program Files/Java/jdk1.8.0_73/'
Any thoughts? Thanks again!!!
After spending too long on this problem, I finally found the answer buried in one of the comments of this question. I think it's worth posting as a proper answer since other people might look for it here and not find it (I know I missed it at first).
The answer is in this gist, which also contains instructions on how to solve this problem for all Stanford NLTK interfaces (i.e. NER tagger, POS tagger, and all Stanford parsers).
Basically, you need to change the Parser object's classpath property with this function:
from nltk.internals import find_jars_within_path
from nltk.parse.stanford import StanfordParser
parser = StanfordParser(model_path="path/to/englishPCFG.ser.gz")
parser._classpath = tuple(find_jars_within_path(stanford_dir))
All credit for the solution goes to alvas, I'm just reposting it here so it's easier to find.
You need to download slf4j jar from here and add that on the path as well.
Related
I´m using Krextor to convert XML to RDF. It runs fine from the command line.
I try to run it from Java (Eclipse) using this code.
private static void XMLToRDF() throws KrextorException, ValidityException, ParsingException, IOException, XSLException{
Element root = new Element("person");
Attribute friend = new Attribute("friends", "http://van-houten.name/milhouse");
root.addAttribute(friend);
Element name = new Element("name");
name.appendChild("Bart Simpson");
root.appendChild(name);
nu.xom.Document inputDocument = new nu.xom.Document(root);
System.out.println(inputDocument.toXML());
Element root1 = inputDocument.getRootElement();
System.out.println(root1);
Krextor k = new Krextor();
nu.xom.Document outputDocument = k.extract("socialnetwork","turtle",inputDocument);
System.out.println(outputDocument.toString());
}
I have the following problem problem
Exception in thread "main" java.lang.NoClassDefFoundError: net/sf/saxon/CollectionURIResolver
Caused by: java.lang.ClassNotFoundException: net.sf.saxon.CollectionURIResolver
I have included Saxon9he in the classpath, and I have also added manually as a library in the project but the error is the same.
I am the main developer of Krextor. And, #Michael Kay, actually a colleague of Grangel, so I will resolve the concrete problem with him locally.
So indeed the last Saxon version with which I did serious testing was 9.1; after that I haven't used Krextor integrated into Java but mainly used Krextor from the command line.
#Grangel, could you please file an issue for Krextor, and then we can work on fixing it together.
Indeed, #Michael Kay, for a while I had been including more recent Saxon versions with Krextor and updated the command line wrapper to use them (such as to add different JARs to the classpath), but I have not necessarily updated the Java wrapper code.
I found when all values are the same, the lm function throws errors. But it worked on GNU R. I am using the latest renjin-script-engine-0.8.1593.jar.
Any exception is thrown:
Caused by: org.renjin.eval.EvalException: contrasts can be applied only to factors with 2 or more levels
at org.renjin.primitives.Conditions.stop(Conditions.java:193)
at org.renjin.primitives.R$primitive$stop.doApply(R$primitive$stop.java:72)"
when I called RenjinScriptEngine.eval(..) with this script:
fit<-lm("formula"=vals~index,"data"=data)
The data of input is
"2015-36",9
"2015-37",9
"2015-41",9.
Renjin's goal is to be compatible with the latest version of GNU R. If you find a difference or encounter error like that above, please file a bug report at https://github.com/bedatadriven/renjin/issues. We're happy to have the test cases!
I am planing to install head pluging for elasticsearch.
in both these two official documentation, http://mobz.github.io/elasticsearch-head/ and http://docs.couchbase.com/admin/elastic/install-plugin.html they said to use this:
bin/plugin -install mobz/elasticsearch-head
I did, but i got the following error:
PS C:\elasticsearch-1.3.9\elasticsearch-1.3.9> bin/plugin -install mobz/elasticsearch-head
Exception in thread "main" org.elasticsearch.common.settings.SettingsException: Failed to load settings from [file:/C:/
lasticsearch-1.3.9/elasticsearch-1.3.9/config/elasticsearch.yml]
at org.elasticsearch.common.settings.ImmutableSettings$Builder.loadFromStream(ImmutableSettings.java:947)
at org.elasticsearch.common.settings.ImmutableSettings$Builder.loadFromUrl(ImmutableSettings.java:931)
at org.elasticsearch.node.internal.InternalSettingsPreparer.prepareSettings(InternalSettingsPreparer.java:77)
at org.elasticsearch.plugins.PluginManager.main(PluginManager.java:382)
Caused by: unacceptable character ' ' (0x0) special characters are not allowed
in "'reader'", position 13489
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.reader.StreamReader.checkPrintable(StreamReader.j
va:93)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.reader.StreamReader.update(StreamReader.java:192)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.reader.StreamReader.peek(StreamReader.java:146)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.scanner.ScannerImpl.scanToNextToken(ScannerImpl.j
va:1199)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.scanner.ScannerImpl.fetchMoreTokens(ScannerImpl.j
va:289)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.scanner.ScannerImpl.checkToken(ScannerImpl.java:2
6)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.parser.ParserImpl$ParseImplicitDocumentStart.prod
ce(ParserImpl.java:195)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.parser.ParserImpl.peekEvent(ParserImpl.java:158)
at org.elasticsearch.common.jackson.dataformat.yaml.snakeyaml.parser.ParserImpl.getEvent(ParserImpl.java:168)
at org.elasticsearch.common.jackson.dataformat.yaml.YAMLParser.nextToken(YAMLParser.java:331)
at org.elasticsearch.common.xcontent.json.JsonXContentParser.nextToken(JsonXContentParser.java:50)
at org.elasticsearch.common.settings.loader.XContentSettingsLoader.load(XContentSettingsLoader.java:60)
at org.elasticsearch.common.settings.loader.XContentSettingsLoader.load(XContentSettingsLoader.java:45)
at org.elasticsearch.common.settings.loader.YamlSettingsLoader.load(YamlSettingsLoader.java:46)
at org.elasticsearch.common.settings.ImmutableSettings$Builder.loadFromStream(ImmutableSettings.java:944)
... 3 more
as I was trying to diagnosis the error, I found that there might b something wrong in elasticsearch.yml file. I went to that file, and opened it using notpadd++, and it was all commented except the last three-four lines, they were letters not understandable. this is a print screen of them:
could you help please
In that file you shouldn't have those chars. Remove them and start over. Or take a clean instance of ES, take the config file from that and use it.
I am doing final year project on "web video categorization", in which one part is to find the similar (synonyms) words for a particular word and I want to remove similar terms from it.
I know Java language, so I chosen "Word Similarity For Java" ws4j
For that I have only used WS4J1.0.1 jar file , even I have not downloaded any extra files like WordNet lexical database or sqlite database to store it. Because in that website they have mentioned that all are contained as precompiled in this jar file.
When I executed Demo program SimilarityCalculationDemo.java, I got the following errors:
java.sql.BatchUpdateException: batch entry 0: [SQLITE_CORRUPT] The database disk image is malformed (database disk image is malformed)
at org.sqlite.Stmt.executeBatch(Stmt.java:226)
at org.sqlite.Stmt.executeBatch(Stmt.java:226)
at edu.cmu.lti.jawjaw.db.SQL.createIndexIfNotExists(SQL.java:118)
at edu.cmu.lti.jawjaw.db.SQL.createSQLConnection(SQL.java:98)
at edu.cmu.lti.jawjaw.db.SQL.<init>(SQL.java:55)
at edu.cmu.lti.jawjaw.db.SQL.<clinit>(SQL.java:45)
at edu.cmu.lti.jawjaw.db.WordDAO.findWordsByLemmaAndPos(WordDAO.java:124)
at edu.cmu.lti.jawjaw.util.WordNetUtil.wordToSynsets(WordNetUtil.java:38)
at edu.cmu.lti.lexical_db.NictWordNet.getAllConcepts(NictWordNet.java:38)
atedu.cmu.lti.ws4j.util.WordSimilarityCalculator.calcRelatednessOfWords(WordSimilarityCalculator.java:79)
at edu.cmu.lti.ws4j.RelatednessCalculator.calcRelatednessOfWords(RelatednessCalculator.java:61)
at web_cat.SimilarityCalculationDemo.run(SimilarityCalculationDemo.java:37)
at web_cat.SimilarityCalculationDemo.main(SimilarityCalculationDemo.java:43)
java.sql.SQLException: [SQLITE_CORRUPT] The database disk image is malformed (database disk image is malformed)
at org.sqlite.DB.newSQLException(DB.java:383)
at org.sqlite.DB.newSQLException(DB.java:387)
at org.sqlite.DB.throwex(DB.java:374)
at org.sqlite.NativeDB.prepare(Native Method)
at org.sqlite.DB.prepare(DB.java:123)
at org.sqlite.Stmt.execute(Stmt.java:113)
at edu.cmu.lti.jawjaw.db.SQL.setPragmaCacheSize(SQL.java:137)
at edu.cmu.lti.jawjaw.db.SQL.createSQLConnection(SQL.java:99)
at edu.cmu.lti.jawjaw.db.SQL.<init>(SQL.java:55)
at edu.cmu.lti.jawjaw.db.SQL.<clinit>(SQL.java:45)
at edu.cmu.lti.jawjaw.db.WordDAO.findWordsByLemmaAndPos(WordDAO.java:124)
at edu.cmu.lti.jawjaw.util.WordNetUtil.wordToSynsets(WordNetUtil.java:38)
at edu.cmu.lti.lexical_db.NictWordNet.getAllConcepts(NictWordNet.java:38)
at edu.cmu.lti.ws4j.util.WordSimilarityCalculator.calcRelatednessOfWords(WordSimilarityCalculator.java:79)
at edu.cmu.lti.ws4j.RelatednessCalculator.calcRelatednessOfWords(RelatednessCalculator.java:61)
at web_cat.SimilarityCalculationDemo.run(SimilarityCalculationDemo.java:37)
at web_cat.SimilarityCalculationDemo.main(SimilarityCalculationDemo.java:43)
java.sql.SQLException: [SQLITE_CORRUPT] The database disk image is malformed (database disk image is malformed)
at org.sqlite.DB.newSQLException(DB.java:383)
at org.sqlite.DB.newSQLException(DB.java:387)
at org.sqlite.DB.throwex(DB.java:374)
at org.sqlite.NativeDB.prepare(Native Method)
at org.sqlite.DB.prepare(DB.java:123)
at org.sqlite.PrepStmt.<init>(PrepStmt.java:42)
at org.sqlite.Conn.prepareStatement(Conn.java:404)
at org.sqlite.Conn.prepareStatement(Conn.java:399)
at org.sqlite.Conn.prepareStatement(Conn.java:383)
at edu.cmu.lti.jawjaw.db.SQL.prepareStatements(SQL.java:151)
at edu.cmu.lti.jawjaw.db.SQL.<init>(SQL.java:56)
at edu.cmu.lti.jawjaw.db.SQL.<clinit>(SQL.java:45)
at edu.cmu.lti.jawjaw.db.WordDAO.findWordsByLemmaAndPos(WordDAO.java:124)
at edu.cmu.lti.jawjaw.util.WordNetUtil.wordToSynsets(WordNetUtil.java:38)
at edu.cmu.lti.lexical_db.NictWordNet.getAllConcepts(NictWordNet.java:38)
at edu.cmu.lti.ws4j.util.WordSimilarityCalculator.calcRelatednessOfWords(WordSimilarityCalculator.java:79)
at edu.cmu.lti.ws4j.RelatednessCalculator.calcRelatednessOfWords(RelatednessCalculator.java:61)
at web_cat.SimilarityCalculationDemo.run(SimilarityCalculationDemo.java:37)
at web_cat.SimilarityCalculationDemo.main(SimilarityCalculationDemo.java:43)
Exception in thread "main" java.lang.NullPointerException
at edu.cmu.lti.jawjaw.db.WordDAO.findWordsByLemmaAndPos(WordDAO.java:125)
at edu.cmu.lti.jawjaw.util.WordNetUtil.wordToSynsets(WordNetUtil.java:38)
at edu.cmu.lti.lexical_db.NictWordNet.getAllConcepts(NictWordNet.java:38)
at edu.cmu.lti.ws4j.util.WordSimilarityCalculator.calcRelatednessOfWords(WordSimilarityCalculator.java:79)
at edu.cmu.lti.ws4j.RelatednessCalculator.calcRelatednessOfWords(RelatednessCalculator.java:61)
at web_cat.SimilarityCalculationDemo.run(SimilarityCalculationDemo.java:37)
at web_cat.SimilarityCalculationDemo.main(SimilarityCalculationDemo.java:43)
Java Result: 1
I am Using Netbeans IDE 7.4 with JDK 6.
Could any please assist me, how to overcome from this problem, because there is a less documentation available in the internet about ws4j.
Well, I could not reproduce your error. For me it just worked perfectly out of the box, using eclipse, so I'll try to help you reproducing exactly what I've did
download ws4j-1.0.1.jar from https://ws4j.googlecode.com/files/ws4j-1.0.1.jar and ensure it's size after the download is 41,362,723 bytes (at least, that's what eclipse told me in my linux box)
Use java 7
Create a simple eclipse project and drop the jar there. Then add the jar to the build path
(right click -> build path -> add)
Create an appropriate package and class to accommodate the demo class
Just run the demo and you'll get something like
edu.cmu.lti.ws4j.impl.HirstStOnge 0.0
edu.cmu.lti.ws4j.impl.LeacockChodorow 1.3862943611198906
edu.cmu.lti.ws4j.impl.Lesk 0.0
edu.cmu.lti.ws4j.impl.WuPalmer 0.4
edu.cmu.lti.ws4j.impl.Resnik 2.5031573470157453
edu.cmu.lti.ws4j.impl.JiangConrath 0.11150424023847051
edu.cmu.lti.ws4j.impl.Lin 0.3582442863008455
edu.cmu.lti.ws4j.impl.Path 0.14285714285714285
Done in 1951 msec.
First of all I would like to thank in advance everyone for reading such a long post. I really appreciate your help.
The thing is that I've been doing some research on how to "connect" Matlab and Java for a project I am working on for university. I figured that the most suitable option was using Matlab Builder JA, but I'm having a lot of troubles with it.
I follow step by step the instructions described on a tutorial (the link of the video in below) but get compilation errors over and over, and I really don't know how to fix them. The tutorial is about creating a Java package (demo.jar) with MATLAB ("com.demo"), which contains a class (MLTestClass) with a function makeSqr(n) which returns an n × n square matrix. Then I go to Eclipse, I add to the project both libraries javabuilder.jar and demo.jar and then create the following class:
public class Driver {
public static void main (String[] args) {
MLTestClass x = null;
Object result [] = null;
try {
x = new MLTestClass ();
result = x.makeSqr (1, 5);
System.out.println (result [0]);
} catch (MWException e) {
e.printStackTrace();
}
}
}
Of course I import com.demo.* and com.mathworks.toolbox.javabuilder.*.
Here are the errors the console gives me:
Exception in thread "main" java.lang.ExceptionInInitializerError
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration.getProxyLibraryDir(MCRConfiguration.java:163)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$MCRRoot.get(MCRConfiguration.java:77)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$MCRRoot.<clinit>(MCRConfiguration.java:87)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration.getMCRRoot(MCRConfiguration.java:92)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$ModuleDir.<clinit>(MCRConfiguration.java:66)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration.getModuleDir(MCRConfiguration.java:71)
at com.mathworks.toolbox.javabuilder.internal.MWMCR.<clinit>(MWMCR.java:1573)
at com.demo.DemoMCRFactory.(DemoMCRFactory.java:122)
at com.demo.MLTestClass.(MLTestClass.java:63)
at Driver.main(Driver.java:12)
Caused by: java.lang.NullPointerException
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$ProxyLibraryDir.get(MCRConfiguration.java:143)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$ProxyLibraryDir.<clinit>(MCRConfiguration.java:158)
... 10 more
Just in case, link tutorial (it's the video): http://www.mathworks.nl/products/javabuilder/description2.html
Anyone has any ideas what the problem could be? It says something about NullPointerException, but I don't know how to solve it as the constructor is provided by the class created with MATLAB. I didn't have any issues installing MCR, and by the way I have MacOS, which I hope is not the source of the problem :).
Again, sorry for the long post and thank you for your time.
Béntor.
Yes, please install MCR. The installation also mentions about setting environmental variables like LD_LIBRARY_PATH etc. If you are using eclipse, i would recommend you update the environmental variables
right click->
properties ->
run/debug settings->
environmental variables
I also had to make sure that variable MCR_CACHE_ROOT pointed to different directory since my home directory was not big enough.
You have install MCR (avaliable in http://www.mathworks.com/products/compiler/mcr/index.html)
None of the above solutions helped me (I already had MCR installed and Macs use DYLD_LIBRARY_PATH instead of LD_LIBRARY_PATH), and noone else online seemed to know. Finally in desperation, I tried editing the DYLD_LIBRARY_PATH and finally got it to work by removing the last part of it: /Applications/MATLAB/MATLAB_Compiler_Runtime/v82/sys/java/jre/maci64/jre/lib
Now the demo application from the tutorial works.
Next comes trying to make my code work.
OS X Paths for Run-Time Deployment
Use these setenv commands to set your MATLAB Runtime paths.
setenv DYLD_LIBRARY_PATH \
mcr_root/version/runtime/maci64 \
mcr_root/version/bin/maci64 \
mcr_root/version/sys/os/maci64
Source: http://www.mathworks.com/help/compiler_sdk/java/mcr-path-settings-for-run-time-deployment.html