Develop Reference

How to fix org.eclipse.jgit.api.errors.JGitInternalException:Entry not found by path Exception while doing commit using Egit

I am trying to integrate Git in my existing RCP application,
For that i have imported egit.core and egit.io plugin as source project into my application and when i tried to commit the file using egit's commit() from CommitOperation Class i am getting the below exception:
Caused by: org.eclipse.jgit.api.errors.JGitInternalException: Entry not found by path: D:\Test\file.txt
at org.eclipse.jgit.api.CommitCommand.createTemporaryIndex(CommitCommand.java:414)
at org.eclipse.jgit.api.CommitCommand.call(CommitCommand.java:194)
at org.eclipse.egit.core.op.CommitOperation.commit(CommitOperation.java:255)
... 39 more
And when i debugged through the code to find out where the exception is happening, it is on CommitCommand.class at the following point
// there must be no unprocessed paths left at this point; otherwise an
// untracked or unknown path has been specified
for (int i = 0; i < onlyProcessed.length; i++)
if (!onlyProcessed[i])
throw new JGitInternalException(MessageFormat.format(
JGitText.get().entryNotFoundByPath, only.get(i)));
I have no idea what the unprocessed path here is meant by?
I am able to access the path. can anyone help me how to proceed further

neo4j-admin import : Import error: Unable to open store file: ../data/databases/graph.db/neostore.propertystore.db.index

I tried to execute the following command:
$ ../bin/neo4j-admin import --mode csv -- database graph.db --nodes head.csv,file1.csv
But I got this error:
Import error: Unable to open store file: ../data/databases/graph.db/neostore.propertystore.db.index
Caused by:Unable to open store file: ../data/databases/graph.db/neostore.propertystore.db.index
org.neo4j.kernel.impl.store.UnderlyingStorageException: Unable to open store file: ../data/databases/graph.db/neostore.propertystore.db.index
at org.neo4j.kernel.impl.store.CommonAbstractStore.checkAndLoadStorage(CommonAbstractStore.java:209)
at org.neo4j.kernel.impl.store.CommonAbstractStore.initialise(CommonAbstractStore.java:133)
at org.neo4j.kernel.impl.store.NeoStores.initialize(NeoStores.java:262)
at org.neo4j.kernel.impl.store.NeoStores.createPropertyKeyTokenStore(NeoStores.java:553)
at org.neo4j.kernel.impl.store.StoreType$4.open(StoreType.java:65)
at org.neo4j.kernel.impl.store.StoreType$4.open(StoreType.java:60)
at org.neo4j.kernel.impl.store.NeoStores.openStore(NeoStores.java:255)
at org.neo4j.kernel.impl.store.NeoStores.getOrCreateStore(NeoStores.java:300)
at org.neo4j.kernel.impl.store.NeoStores.<init>(NeoStores.java:144)
at org.neo4j.kernel.impl.store.StoreFactory.openNeoStores(StoreFactory.java:169)
at org.neo4j.kernel.impl.store.StoreFactory.openAllNeoStores(StoreFactory.java:133)
at org.neo4j.unsafe.impl.batchimport.store.BatchingNeoStores.<init>(BatchingNeoStores.java:118)
at org.neo4j.unsafe.impl.batchimport.store.BatchingNeoStores.batchingNeoStores(BatchingNeoStores.java:189)
at org.neo4j.unsafe.impl.batchimport.ParallelBatchImporter.getBatchingNeoStores(ParallelBatchImporter.java:272)
at org.neo4j.unsafe.impl.batchimport.ParallelBatchImporter.doImport(ParallelBatchImporter.java:167)
at org.neo4j.tooling.ImportTool.doImport(ImportTool.java:510)
at org.neo4j.tooling.ImportTool.main(ImportTool.java:443)
at org.neo4j.tooling.ImportTool.main(ImportTool.java:354)
Caused by: java.io.FileNotFoundException: /mnt/data3/kaushik2/data/databases/graph.db/neostore.propertystore.db.index (Too many open files)
at java.io.RandomAccessFile.open(RandomAccessFile.java:333)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:257)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:68)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:53)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapper.<init>(SingleFilePageSwapper.java:152)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapperFactory.createPageSwapper(SingleFilePageSwapperFactory.java:71)
at org.neo4j.io.pagecache.impl.muninn.MuninnPagedFile.<init>(MuninnPagedFile.java:135)
at org.neo4j.io.pagecache.impl.muninn.MuninnPageCache.map(MuninnPageCache.java:362)
at org.neo4j.kernel.impl.store.CommonAbstractStore.checkAndLoadStorage(CommonAbstractStore.java:182)
... 17 more
The parameter and configurations used for this command are here. What could be the reason?

You're facing a Too many open files problem.
ulimit -a
will show the current limit and either a particular process is taking up too many (check that with lsof for example) and you'll have to kick that process or you'll have to raise the limit (the how depends on your os but there's many many many procedures floating around, you should have no trouble finding one).
Hope this helps,
Tom

H2 - General error: "java.lang.NullPointerException" [50000-182]

I have a quite big (>2.5 GB) h2 database file. Driver version is 1.4.182. Everything worked fine but recently the DB stop to work with exception:
Błąd ogólny: "java.lang.NullPointerException"
General error: "java.lang.NullPointerException" [50000-182] HY000/50000 (Help)
org.h2.jdbc.JdbcSQLException: Błąd ogólny: "java.lang.NullPointerException"
General error: "java.lang.NullPointerException" [50000-182]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:345)
at org.h2.message.DbException.get(DbException.java:168)
at org.h2.message.DbException.convert(DbException.java:295)
at org.h2.engine.Database.openDatabase(Database.java:297)
at org.h2.engine.Database.<init>(Database.java:260)
at org.h2.engine.Engine.openSession(Engine.java:60)
at org.h2.engine.Engine.openSession(Engine.java:167)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:145)
at org.h2.engine.Engine.createSession(Engine.java:128)
at org.h2.engine.Engine.createSession(Engine.java:26)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:347)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:108)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:92)
at org.h2.Driver.connect(Driver.java:72)
at org.h2.server.web.WebServer.getConnection(WebServer.java:750)
at org.h2.server.web.WebApp.test(WebApp.java:895)
at org.h2.server.web.WebApp.process(WebApp.java:221)
at org.h2.server.web.WebApp.processRequest(WebApp.java:170)
at org.h2.server.web.WebThread.process(WebThread.java:137)
at org.h2.server.web.WebThread.run(WebThread.java:93)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.NullPointerException
at org.h2.mvstore.db.ValueDataType.compare(ValueDataType.java:102)
at org.h2.mvstore.MVMap.compare(MVMap.java:741)
at org.h2.mvstore.Page.binarySearch(Page.java:388)
at org.h2.mvstore.MVMap.put(MVMap.java:179)
at org.h2.mvstore.MVMap.put(MVMap.java:133)
at org.h2.mvstore.db.TransactionStore.rollbackTo(TransactionStore.java:491)
at org.h2.mvstore.db.TransactionStore$Transaction.rollback(TransactionStore.java:785)
at org.h2.mvstore.db.MVTableEngine$Store.initTransactions(MVTableEngine.java:223)
at org.h2.engine.Database.open(Database.java:736)
at org.h2.engine.Database.openDatabase(Database.java:266)
... 17 more
The problem occurs in my application and using H2 web frontend.
I have tried solution from similar question but I cannot downgrade H2 to 1.3.x as it cannot read 1.4.x DB files.
My questions are:
How to handle it? Is it to possible to make it work again? I have tried downgrade H2 to 1.4.177 but it didn't help.
Is there any way to at least recover data to other format? I could use other DB (Sqlite, etc.) however I would need a way to get to these data.
EDIT: updated stacktrace
EDIT 2: Result of using Recovery tool:
$ java -cp h2-1.4.182.jar org.h2.tools.Recover
Exception in thread "main" java.lang.IllegalStateException: Unknown tag 50 [1.4.182/6]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:762)
at org.h2.mvstore.type.ObjectDataType.read(ObjectDataType.java:222)
at org.h2.mvstore.db.TransactionStore$ArrayType.read(TransactionStore.java:1792)
at org.h2.mvstore.db.TransactionStore$ArrayType.read(TransactionStore.java:1759)
at org.h2.mvstore.Page.read(Page.java:843)
at org.h2.mvstore.Page.read(Page.java:230)
at org.h2.mvstore.MVStore.readPage(MVStore.java:1813)
at org.h2.mvstore.MVMap.readPage(MVMap.java:769)
at org.h2.mvstore.Page.getChildPage(Page.java:252)
at org.h2.mvstore.MVMap.getFirstLast(MVMap.java:351)
at org.h2.mvstore.MVMap.firstKey(MVMap.java:218)
at org.h2.mvstore.db.TransactionStore.init(TransactionStore.java:169)
at org.h2.mvstore.db.TransactionStore.<init>(TransactionStore.java:117)
at org.h2.mvstore.db.TransactionStore.<init>(TransactionStore.java:81)
at org.h2.tools.Recover.dumpMVStoreFile(Recover.java:593)
at org.h2.tools.Recover.process(Recover.java:331)
at org.h2.tools.Recover.runTool(Recover.java:192)
at org.h2.tools.Recover.main(Recover.java:155)
I also noticed that two another files (.txt and .sql) has been created but they don't seem to contain a data.

I got the same situation last week with JIRA database, it took me few hours to do google regarding to this problem however, there are no answers which can resolve the situation.
I decided to take a look at H2 source code and I can recover the whole database with very simple code. I may not understand whole picture about the situation e.g. root cause, in which condition it happened, etc.
However, the cause is: when you connect to h2 file then H2 engine will look into auditLog and rollback the in-progress transactions, there are some data which have unknown type (id is 17) and H2 fails to rollback due to exception during recognize the type (id 17).
My code is simple, add h2 lib into your build path then just manual connect to file and clear auditLog because I think it is just the log and will not have big impact (someone may correct me).
Hopefully, you can resolve your problem as well.
public static void main(final String[] args) {
// open the store (in-memory if fileName is null)
final MVStore store = MVStore.open("C:\\temp\\h2db.mv.db");
final MVMap<Object, Object> openMap = store.openMap("undoLog");
openMap.clear();
// close the store (this will persist changes)
store.close();
}

Another solution for this problem:
Go to your home folder (~ in linux).
Move all files named [*.mv.db] to a backup with a different name. For example: mv xyz.mv.db xyz.mv.db.backup
Restart your database.
This seems to clear out MVStore meta-data used for H2 undo features, and resolves the NPE from the MV Store compare.

I had a similar problem:
[HY000][50000] Allgemeiner Fehler: "java.lang.NullPointerException"
General error: "java.lang.NullPointerException" [50000-176]
java.lang.NullPointerException
I tried to connect with IntelliJ to H2 file DB. H2 driver version was 1.3.176 but the DB file version had 1.3.161. So downgraded the driver to 1.3.161 in IntelliJ solved the problem completely.

Groovy project won't build in GGTS

I have some Groovy code which will from fine from the command line, but when I try to use Springsource's GGTS fails:
Caught: java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException
java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException
at empyrean.Empyrean.run(Empyrean.groovy:20)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.cli.ParseException
... 1 more
I know this is because I have not got paths or something similar set correctly in GGTS but I cannot work out how to fix this (I used to use STS without a problem, this is the first time I have tried GGTS)
The non-compiling code is this (first line here is line 20 in the file):
def empyreanCli = new CliBuilder(usage:'empyrean [-d] <empyrean script>')
empyreanCli.d(longOpt:'debug',
'output debug data as we go')
empyreanCli.f(longOpt:'file',
'Empyrean script to run')
empyreanCli.u(longOpt:'usage',
'show this usage message')
def empyreanParse = empyreanCli.parse(args)
if (empyreanParse.u || args.size() == 0)
empyreanCli.usage()
else {
def engine = new EmpyreanEngine()
if (empyreanParse.d)
engine.debug = true
if (empyreanParse.f)
engine.process(binsicParse.f)
else
engine.process(args[args.size() - 1])
}
Which, as I say, runs fine from the command line...

To get the project to build I have to explictly add the necessary .jar files to the build path:
project -> properties -> java build path -> libraries -> add JARs

How to train the Stanford Parser with Genia Corpus?

I have some problems to create a new model for Stanford Parser.
I have also downloaded the last version from Stanford:
http://nlp.stanford.edu/software/lex-parser.shtml
And here, Genia Corpus in 2 formats, xml and ptb (Penn Treebank).
Standford Parser can train with ptd files ; then I downloaded Genia Corpus, because I want to work with biomedical text:
http://categorizer.tmit.bme.hu/~illes/genia_ptb/ (link no longer available) (genia_ptb.tar.gz)
Then, I have a short Main class to get dependency representation of one biomedical sentence:
String treebankPath = "/stanford-parser-2012-05-22/genia_ptb/GENIA_treebank_v1/ptb";
Treebank tr = op.tlpParams.diskTreebank();
tr.loadPath(treebankPath);
LexicalizedParser lpc=LexicalizedParser.trainFromTreebank(tr,op);
I have tried different ways, but always get the same result.
I have an error in the last line. This is my output:
Currently Fri Jun 01 15:02:57 CEST 2012
Options parameters:
useUnknownWordSignatures 2
smoothInUnknownsThreshold 100
smartMutation false
useUnicodeType false
unknownSuffixSize 1
unknownPrefixSize 1
flexiTag true
useSignatureForKnownSmoothing false
parserParams edu.stanford.nlp.parser.lexparser.EnglishTreebankParserParams
forceCNF false
doPCFG true
doDep false
freeDependencies false
directional true
genStop true
distance true
coarseDistance false
dcTags false
nPrune false
Train parameters: smooth=false PA=true GPA=false selSplit=true (400.0; deleting [VP^SQ, VP^VP, VP^SINV, VP^NP]) mUnary=1 mUnaryTags=false sPPT=false tagPA=true tagSelSplit=false (0.0) rightRec=true leftRec=false collinsPunc=false markov=true mOrd=2 hSelSplit=true (10) compactGrammar=3 postPA=false postGPA=false selPSplit=false (0.0) tagSelPSplit=false (0.0) postSplitWithBase=false fractionBeforeUnseenCounting=0.5 openClassTypesThreshold=50 preTransformer=null taggedFiles=null
Using EnglishTreebankParserParams splitIN=4 sPercent=true sNNP=0 sQuotes=false sSFP=false rbGPA=false j#=false jJJ=false jNounTags=false sPPJJ=false sTRJJ=false sJJCOMP=false sMoreLess=false unaryDT=true unaryRB=true unaryPRP=false reflPRP=false unaryIN=false sCC=1 sNT=false sRB=false sAux=2 vpSubCat=false mDTV=2 sVP=3 sVPNPAgr=false sSTag=0 mVP=false sNP%=0 sNPPRP=false dominatesV=1 dominatesI=false dominatesC=false mCC=0 sSGapped=4 numNP=false sPoss=1 baseNP=1 sNPNNP=0 sTMP=1 sNPADV=1 cTags=true rightPhrasal=false gpaRootVP=false splitSbar=0 mPPTOiIN=0
Binarizing trees...done. Time elapsed: 141 ms
Extracting PCFG...done. Time elapsed: 56 ms
Compiling grammar...done Time elapsed: 1 ms
Extracting Lexicon...Exception in thread "main" edu.stanford.nlp.util.ReflectionLoading$ReflectionLoadingException: edu.stanford.nlp.util.MetaClass$ClassCreationException: java.lang.ClassNotFoundException: edu.stanford.nlp.parser.lexparser.EnglishUnknownWordModelTrainer
at edu.stanford.nlp.util.ReflectionLoading.loadByReflection(ReflectionLoading.java:39)
at edu.stanford.nlp.parser.lexparser.BaseLexicon.initializeTraining(BaseLexicon.java:335)
at edu.stanford.nlp.parser.lexparser.LexicalizedParser.getParserFromTreebank(LexicalizedParser.java:800)
at edu.stanford.nlp.parser.lexparser.LexicalizedParser.trainFromTreebank(LexicalizedParser.java:226)
at edu.stanford.nlp.parser.lexparser.LexicalizedParser.trainFromTreebank(LexicalizedParser.java:237)
at ABravoDemo.main(ABravoDemo.java:35)
Caused by: edu.stanford.nlp.util.MetaClass$ClassCreationException: java.lang.ClassNotFoundException: edu.stanford.nlp.parser.lexparser.EnglishUnknownWordModelTrainer
at edu.stanford.nlp.util.MetaClass.createFactory(MetaClass.java:353)
at edu.stanford.nlp.util.MetaClass.createInstance(MetaClass.java:370)
at edu.stanford.nlp.util.ReflectionLoading.loadByReflection(ReflectionLoading.java:37)
... 5 more
Caused by: java.lang.ClassNotFoundException: edu.stanford.nlp.parser.lexparser.EnglishUnknownWordModelTrainer
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:303)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:316)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at edu.stanford.nlp.util.MetaClass$ClassFactory.construct(MetaClass.java:119)
at edu.stanford.nlp.util.MetaClass$ClassFactory.<init>(MetaClass.java:192)
at edu.stanford.nlp.util.MetaClass$ClassFactory.<init>(MetaClass.java:53)
at edu.stanford.nlp.util.MetaClass.createFactory(MetaClass.java:349)
... 7 more
How could I create a new model with this corpus ?

As andrucz stated in his comment, the real cause of your problem seems to stem from a missing class.
Try checking whether you correctly imported your library ( and make sure that it contains the class EnglishUnknownWordModelTra‌​iner in edu.stanford.nlp.parser.lexparser.
(If you're using Maven, verify that you correctly added the dependency - a quick google brougt this up : Stanford Parser Maven Repo )

Did the NLP library install correctly?
Check in the logs to verify there are no errors. Most of the times this issue comes when there the stanford nltk library does not install correctly.
A quick way to check is by running the GUI to try out the parser if that runs successfully then the library installed correctly otherwise if that throws errors then you know your installation was poor.
The Stanford website also mentions this take a look:
If you're new to parsing, you can start by running the GUI to try out the parser. Scripts are included for linux (lexparser-gui.sh) and Windows (lexparser-gui.bat).
Take a look at the Javadoc lexparser package documentation and LexicalizedParser class documentation. (Point your web browser at the index.html file in the included javadoc directory and navigate to those items.)
Look at the parser FAQ for answers to common questions.
If none of that helps, please see our email guidelines for instructions on how to reach us for further assistance.

Check whether you have correctly imported library and make sure that it is containing the class {EnglishUnknownWordModelTra‌​iner} and also make sure that version you downloaded properly works with Genia Corps.