Hi Andy (et al.),
I hope this is a minimal, reproducible example - and shows that I still get
the error after compilation with maven. If I run the same code as an
independent project in Eclipse (i.e. without maven integration) then it
works as expected and the final tdbquery command returns the result, rather
than an error.
Cheers
Chris
----------
result of the `tree /F` command before compilation:
PS C:\Users\chris\jena_test> tree /F
Folder PATH listing for volume Windows
Volume serial number is 000000BF 3C06:564C
C:.
│ .classpath
│ .project
│ mvnout.txt
│ pom.xml
│
├───.settings
│ org.eclipse.jdt.core.prefs
│ org.eclipse.m2e.core.prefs
│
└───src
└───main
└───java
jena_test.java
mvn version:
PS C:\Users\chris> mvn -version
Apache Maven 3.5.0 (ff8f5e7444045639af65f6095c62210b5713f426;
2017-04-03T20:39:06+01:00)
Maven home: C:\tools\mvn\apache-maven-3.5.0\bin\..
Java version: 1.8.0_31, vendor: Oracle Corporation
Java home: C:\Program Files\Java\jdk1.8.0_31\jre
Default locale: en_GB, platform encoding: Cp1252
OS name: "windows 8.1", version: "6.3", arch: "amd64", family: "windows"
-----------
jena_test.java:
import org.apache.jena.query.Dataset;
import org.apache.jena.query.ReadWrite;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.impl.StatementImpl;
import org.apache.jena.sparql.vocabulary.FOAF;
import org.apache.jena.tdb.TDBFactory;
public class jena_test {
public static void main(String[] args) {
Dataset dataset = TDBFactory.createDataset("my_dataset");
dataset.begin(ReadWrite.WRITE);
Model bodc_model = dataset.getDefaultModel();
try {
bodc_model.add(new StatementImpl(
ModelFactory.createDefaultModel().createResource("person:1"),
FOAF.name,
ModelFactory.createDefaultModel().createResource("Chris")));
dataset.commit();
} finally {
dataset.close();
}
}
}
-----------
pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="
http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<groupId>test</groupId>
<artifactId>jena_test</artifactId>
<version>1.0.0</version>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>3.6.0</version>
<type>pom</type>
</dependency>
</dependencies>
<build>
<finalName>${project.artifactId}</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<shadedArtifactAttached>false</shadedArtifactAttached>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>org.apache.jena.fuseki.cmd.FusekiCmd</mainClass>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"
/>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer"
/>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
<addHeader>false</addHeader>
</transformer>
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.5.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/tdb_generator_resources/</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>tdb_generator_resources/</classpathPrefix>
<mainClass>jena_test</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</project>
-----------
result of the `tree /F` command after running `mvn compile package`:
PS C:\Users\chris\jena_test> tree /F
Folder PATH listing for volume Windows
Volume serial number is 000000C0 3C06:564C
C:.
│ .classpath
│ .project
│ mvnout.txt
│ pom.xml
│
├───.settings
│ org.eclipse.jdt.core.prefs
│ org.eclipse.m2e.core.prefs
│
├───src
│ └───main
│ └───java
│ jena_test.java
│
└───target
│ jena_test.jar
│
├───classes
│ jena_test.class
│
├───maven-archiver
│ pom.properties
│
└───tdb_generator_resources
apache-jena-libs-3.6.0.pom
collection-0.7.jar
commons-cli-1.4.jar
commons-codec-1.9.jar
commons-csv-1.5.jar
commons-io-2.5.jar
commons-lang3-3.4.jar
httpclient-4.5.3.jar
httpclient-cache-4.5.3.jar
httpcore-4.4.6.jar
jackson-annotations-2.9.0.jar
jackson-core-2.9.0.jar
jackson-databind-2.9.0.jar
jcl-over-slf4j-1.7.25.jar
jena-arq-3.6.0.jar
jena-base-3.6.0.jar
jena-core-3.6.0.jar
jena-dboe-base-3.6.0.jar
jena-dboe-index-3.6.0.jar
jena-dboe-trans-data-3.6.0.jar
jena-dboe-transaction-3.6.0.jar
jena-iri-3.6.0.jar
jena-rdfconnection-3.6.0.jar
jena-shaded-guava-3.6.0.jar
jena-tdb-3.6.0.jar
jena-tdb2-3.6.0.jar
jsonld-java-0.11.1.jar
libthrift-0.10.0.jar
slf4j-api-1.7.25.jar
xercesImpl-2.11.0.jar
xml-apis-1.4.01.jar
-----------
PS C:\Users\chris\jena_test> java -jar .\target\jena_test.jar
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further
details.
-----------
C:\Users\chris\jena_test>tdbquery --loc="my_dataset" "SELECT (count(*) as
?t) where {?a ?b ?c . }"
Exception
java.lang.NullPointerException
at
org.apache.jena.tdb.transaction.JournalControl.replay(JournalControl.java:280)
at
org.apache.jena.tdb.transaction.JournalControl.recoverSegment(JournalControl.java:185)
at
org.apache.jena.tdb.transaction.JournalControl.recoverFromJournal(JournalControl.java:137)
at
org.apache.jena.tdb.StoreConnection.forceRecoverFromJournal(StoreConnection.java:150)
at
org.apache.jena.tdb.StoreConnection._makeAndCache(StoreConnection.java:255)
at
org.apache.jena.tdb.StoreConnection.make(StoreConnection.java:214)
at
org.apache.jena.tdb.StoreConnection.make(StoreConnection.java:220)
at
org.apache.jena.tdb.transaction.DatasetGraphTransaction.<init>(DatasetGraphTransaction.java:70)
at org.apache.jena.tdb.sys.TDBMaker._create(TDBMaker.java:55)
at
org.apache.jena.tdb.sys.TDBMaker.createDatasetGraphTransaction(TDBMaker.java:42)
at
org.apache.jena.tdb.TDBFactory._createDatasetGraph(TDBFactory.java:89)
at
org.apache.jena.tdb.TDBFactory.createDatasetGraph(TDBFactory.java:71)
at org.apache.jena.tdb.TDBFactory.createDataset(TDBFactory.java:55)
at tdb.cmdline.ModTDBDataset.createDataset(ModTDBDataset.java:103)
at arq.cmdline.ModDataset.getDataset(ModDataset.java:36)
at arq.query.getDataset(query.java:176)
at arq.query.queryExec(query.java:213)
at arq.query.exec(query.java:153)
at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
at tdb.tdbquery.main(tdbquery.java:33)
On 1 March 2018 at 12:40, Chris Wood <[email protected]> wrote:
> Hi Andy,
>
> Yeh, that was on my debugging list! I've seemingly tracked it down to a
> maven problem. I'm working in eclipse: when I created a new project and
> copied all the files across and ran it in eclipse, it worked; as soon as I
> built and packed via maven, I got the error. I'll do some more digging...
>
> Chris
>
> On 28 February 2018 at 18:31, Andy Seaborne <[email protected]> wrote:
>
>> Chris,
>>
>> It looks like details matter - could you send a complete, minimal example
>> (i.e. standalone and runnable)?
>>
>> Thanks
>>
>> Andy
>>
>> On 28/02/18 17:26, Chris Wood wrote:
>>
>>> Yeh, I thought I was doing that! I've taken that line of code out anyway
>>> but it seems to make no difference...
>>>
>>> On 28 February 2018 at 16:55, Rob Vesse <[email protected]> wrote:
>>>
>>> Notice that Andy specifically said in his response:
>>>>
>>>> call this very early (before any TDB related activity)
>>>>
>>>> Rob
>>>>
>>>> On 28/02/2018, 16:21, "Chris Wood" <[email protected]> wrote:
>>>>
>>>> Hi Rob - sorry, that was an over-simplification of the psedocode;
>>>> I do
>>>> call
>>>>
>>>> dataset.begin(ReadWrite.WRITE);
>>>>
>>>> after initialising it.
>>>>
>>>> I had also wondered if setFileMode makes any difference - I was
>>>> using
>>>> it
>>>> because of this Andy's comment here:
>>>> http://users.jena.apache.narkive.com/zUPFzLcm/tdb-
>>>> shutdown-does-not-release-the-files
>>>>
>>>> Chris
>>>>
>>>> On 28 February 2018 at 14:54, Rob Vesse <[email protected]>
>>>> wrote:
>>>>
>>>> > Two things look odd:
>>>> >
>>>> > - You never call dataset.begin() to start the transaction yet you
>>>> later
>>>> > try to commit() it
>>>> > - Calling SystemTDB.setFileMode() after opening a dataset
>>>> probably
>>>> doesn't
>>>> > have any effect on already open datasets though I could be wrong
>>>> on
>>>> this
>>>> > point
>>>> >
>>>> > Rob
>>>> >
>>>> > On 28/02/2018, 13:08, "Chris Wood" <[email protected]> wrote:
>>>> >
>>>> > Hi Andy,
>>>> >
>>>> > It's probably a bit more complicated than I originally
>>>> suggested.
>>>> > Inside my
>>>> > try statement I do a bit of processing in a separate class (I
>>>> create a
>>>> > new
>>>> > in-memory Dataset, and return the model from it, so I can
>>>> add it
>>>> to my
>>>> > my
>>>> > main dataset); but I also use this class to initialise the
>>>> default
>>>> > model. I
>>>> > wonder if this is confusing the transaction...
>>>> >
>>>> > With a bit of pseudocode:
>>>> >
>>>> > Dataset dataset = TDBFactory.createDataset("path
>>>> /to/tdb");
>>>> > Model model = new Processing(dataset).;
>>>> > SystemTDB.setFileMode(FileMode.direct);
>>>> >
>>>> > try {
>>>> > Model m = model.dataStructure();
>>>> > model.add(m);
>>>> > dataset.commit();
>>>> > } finally {
>>>> > dataset.close();
>>>> > }
>>>> >
>>>> > Processing.java:
>>>> >
>>>> > main:
>>>> > public Processing(Dataset dataset) {
>>>> > super(dataset.getDefaultModel().getGraph());
>>>> > }
>>>> >
>>>> > dataStructure():
>>>> > Dataset d1 = TDBFactory.createDataset();
>>>> > Model m1 = d1.getDefaultModel();
>>>> >
>>>> > // add stuff to m1 from an independent datasource
>>>> >
>>>> > return m1;
>>>> >
>>>> >
>>>> > On 28 February 2018 at 11:30, Andy Seaborne <[email protected]
>>>> >
>>>> wrote:
>>>> >
>>>> > > Chris,
>>>> > >
>>>> > > Is the dataset TDB (from TDBFactory) or a dataset holding a
>>>> model,
>>>> > maybe
>>>> > > with added inference, where the base graph is backed by
>>>> TDB?
>>>> > >
>>>> > > It is better to put changes to the dataset inside a
>>>> transaction.
>>>> > Failing
>>>> > > that, it should be sync'ed -- TDB.sync().
>>>> > >
>>>> > > Andy
>>>> > >
>>>> > > http://jena.staging.apache.org/documentation/txn/
>>>> > >
>>>> > > On 27/02/18 18:33, Chris Wood wrote:
>>>> > >
>>>> > >> I've got a small application that follows the standard
>>>> recommended
>>>> > >> pattern:
>>>> > >>
>>>> > >> // initialise dataset / model
>>>> > >> ...
>>>> > >> try {
>>>> > >> // ... add statements
>>>> > >> StmtIterator r = this.my_model.listStatements();
>>>> > >> System.out.println(r.toList().size());
>>>> > >> this.dataset.commit();
>>>> > >> } catch (SQLException e) {
>>>> > >> e.printStackTrace();
>>>> > >> } finally {
>>>> > >> this.dataset.close();
>>>> > >> }
>>>> > >>
>>>> > >> I was running this with Jena 3.0.1, and all was fine. I've
>>>> just
>>>> > upgraded
>>>> > >> to
>>>> > >> 3.6.0. When I run the code and then check the tdb that is
>>>> generated
>>>> > with
>>>> > >> (on Windows):
>>>> > >>
>>>> > >> tdbquery --loc="database" "SELECT (count(*) as ?t)
>>>> where {?a
>>>> > ?b ?c
>>>> > >> . }"
>>>> > >>
>>>> > >> I get a NullPointerException:
>>>> > >>
>>>> > >> Exception
>>>> > >> java.lang.NullPointerException
>>>> > >> at
>>>> > >> org.apache.jena.tdb.transaction.JournalControl.replay(
>>>> > >> JournalControl.java:280)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.transactio
>>>> n.JournalControl.recoverSegmen
>>>> > >> t(JournalControl.java:185)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.transactio
>>>> n.JournalControl.recoverFromJo
>>>> > >> urnal(JournalControl.java:137)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.StoreConne
>>>> ction.forceRecoverFromJournal(
>>>> > >> StoreConnection.java:150)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.StoreConne
>>>> ction._makeAndCache(StoreConne
>>>> > >> ction.java:255)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.StoreConnection.make(
>>>> StoreConnection.java:214)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.StoreConnection.make(
>>>> StoreConnection.java:220)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.transaction.DatasetGraphTransaction.<
>>>> > >> init>(DatasetGraphTransaction.java:70)
>>>> > >> at org.apache.jena.tdb.sys.
>>>> TDBMaker._create(TDBMaker.
>>>> > java:55)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.sys.TDBMak
>>>> er.createDatasetGraphTransacti
>>>> > >> on(TDBMaker.java:42)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.TDBFactory._
>>>> createDatasetGraph(TDBFactory.
>>>> > java:89)
>>>> > >> at
>>>> > >> org.apache.jena.tdb.TDBFactory.createDatasetGraph(
>>>> > TDBFactory.java:71)
>>>> > >> at org.apache.jena.tdb.TDBFactory.createDataset(
>>>> > TDBFactory.
>>>> > >> java:55)
>>>> > >> at tdb.cmdline.ModTDBDataset.
>>>> createDataset(ModTDBDataset.
>>>> > java:
>>>> > >> 103)
>>>> > >> at arq.cmdline.ModDataset.
>>>> getDataset(ModDataset.java:36)
>>>> > >> at arq.query.getDataset(query.java:176)
>>>> > >> at arq.query.queryExec(query.java:213)
>>>> > >> at arq.query.exec(query.java:153)
>>>> > >> at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>> > >> at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>> > >> at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>> > >> at tdb.tdbquery.main(tdbquery.java:33)
>>>> > >>
>>>> > >> What seems really weird is that if I run the code *again*
>>>> (without
>>>> > >> deleting
>>>> > >> the dataset directory) the triplestore is populated.
>>>> > >>
>>>> > >> - If I run the code ensuring I use v3.0.1, this doesn't
>>>> happen,
>>>> > and the
>>>> > >> tdbquery command works on the first attempt.
>>>> > >> - The print statement showing the number of statements
>>>> in
>>>> the
>>>> > dataset
>>>> > >> shows the correct number in all cases.
>>>> > >>
>>>> > >> What has changed between 3.0.1 and 3.6.0 to cause this
>>>> (and
>>>> any
>>>> > hints on
>>>> > >> what I need to do to resolve it would be greatly
>>>> appreciated!)
>>>> > >>
>>>> > >> Thanks
>>>> > >> Chris
>>>> > >>
>>>> > >>
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>
