java.lang.ClassNotFoundException: com.mysql.jdbc.Driver for Maven runnable jar - java

I'm trying to create .jar file in my server(CentOS) using Maven. It is successfully compiling and generates the .jar file. But when I execute it, it shows the following error. This questions may look like "previously asked" but, I tried all the suggestions from here. What I believe is in my POM.xml have some issue, but I'm not able to find. If someone can verify the POM.xml it would be helpful.
Command:
$ java -jar target/ListDescCrawler-1.1-SNAPSHOT.jar
Error:
java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
My POM.xml
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.crawler4j</groupId>
<artifactId>ListDescCrawler</artifactId>
<packaging>jar</packaging>
<version>1.1-SNAPSHOT</version>
<name>SanListDescCrawlerHandu</name>
<url>http://maven.apache.org</url>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>edu.uci.ics.crawler4j.example.MainController</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.james</groupId>
<artifactId>apache-mime4j-core</artifactId>
<version>0.7</version>
</dependency>
<dependency>
<groupId>org.apache.james</groupId>
<artifactId>apache-mime4j-dom</artifactId>
<version>0.7</version>
</dependency>
<dependency>
<groupId>asm</groupId>
<artifactId>asm</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>de.l3s.boilerpipe</groupId>
<artifactId>boilerpipe</artifactId>
<version>1.1.0</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.3</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>fluent-hc</artifactId>
<version>4.3.6</version>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-stax-api_1.0_spec</artifactId>
<version>1.0.1</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.3.6</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>4.3.3</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
<version>4.3.6</version>
</dependency>
<dependency>
<groupId>com.sleepycat</groupId>
<artifactId>je</artifactId>
<version>4.0.92</version>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.8.1</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<dependency>
<groupId>com.drewnoakes</groupId>
<artifactId>metadata-extractor</artifactId>
<version>2.4.0-beta-1</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.34</version>
</dependency>
<dependency>
<groupId>org.ccil.cowan.tagsoup</groupId>
<artifactId>tagsoup</artifactId>
<version>1.2.1</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-app</artifactId>
<version>1.6</version>
</dependency>
</dependencies>
</project>
The MANIFEST.MF file in the generated .jar file:
Manifest-Version: 1.0
Archiver-Version: Plexus Archiver
Created-By: Apache Maven
Built-By: root
Build-Jdk: 1.7.0_91
Main-Class: edu.uci.ics.crawler4j.example.MainController
Class-Path: apache-mime4j-core-0.7.jar apache-mime4j-dom-0.7.jar asm-3
.1.jar boilerpipe-1.1.0.jar commons-codec-1.6.jar commons-compress-1.
3.jar commons-logging-1.1.3.jar fluent-hc-4.3.6.jar geronimo-stax-api
_1.0_spec-1.0.1.jar httpclient-4.3.6.jar httpcore-4.3.3.jar httpmime-
4.3.6.jar je-4.0.92.jar jsoup-1.8.1.jar log4j-1.2.17.jar metadata-ext
ractor-2.4.0-beta-1.jar tagsoup-1.2.1.jar tika-app-1.6.jar tika-parse
rs-1.6.jar tika-core-1.6.jar vorbis-java-tika-0.6.jar netcdf-4.2.20.j
ar unidataCommon-4.2.20.jar jcip-annotations-1.0.jar commons-httpclie
nt-3.1.jar jmatio-1.0.jar xz-1.5.jar pdfbox-1.8.6.jar fontbox-1.8.6.j
ar jempbox-1.8.6.jar bcmail-jdk15-1.45.jar bcprov-jdk15-1.45.jar poi-
3.11-beta2.jar poi-scratchpad-3.11-beta2.jar poi-ooxml-3.11-beta2.jar
poi-ooxml-schemas-3.11-beta2.jar xmlbeans-2.6.0.jar asm-debug-all-4.
1.jar isoparser-1.0.2.jar aspectjrt-1.8.0.jar rome-1.0.jar jdom-1.0.j
ar vorbis-java-core-0.6.jar juniversalchardet-1.0.3.jar jhighlight-1.
0.jar java-libpst-0.8.1.jar tika-serialization-1.6.jar tika-xmp-1.6.j
ar xmpcore-5.1.2.jar slf4j-log4j12-1.5.6.jar slf4j-api-1.5.6.jar gson
-1.7.1.jar
Commands executed:
mvn clean compile
mvn clean package
java -jar target/ListDescCrawler-1.1-SNAPSHOT.jar
There are many library files are added to the project including mysql-connector-java-5.1.34.jar. But still the error is showing. I checked in SOF for a solution and tried many suggestions from here, but nothing fixed my issue.
I checked MANIFEST.MF in the generated .jar file and it looks fine.
Other points to note is, its working fine from Eclipse(without Maven)
is there any mistake in my POM.xml?
The suggestions I tried:
dependency/scope I tried all the possible values
Copied mysql-connector-java-5.1.34.jar in the lib folder and changed the POM.xml accordingly
and may other suggestions but nothing helped.
At last the things started to work with the following POM.xml
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.uci.ics.crawler4j</groupId>
<artifactId>ListDescCrawler</artifactId>
<packaging>jar</packaging>
<version>1.0-SNAPSHOT</version>
<name>SanListDescCrawlerHandu</name>
<url>http://maven.apache.org</url>
<properties>
<jdk.version>1.7</jdk.version>
<junit.version>4.11</junit.version>
<apache-mime4j-core.version>0.7</apache-mime4j-core.version>
<apache-mime4j-dom.version>0.7</apache-mime4j-dom.version>
<asm.version>3.1</asm.version>
<boilerpipe.version>1.1.0</boilerpipe.version>
<commons-codec.version>1.6</commons-codec.version>
<commons-compress.version>1.3</commons-compress.version>
<commons-logging.version>1.1.3</commons-logging.version>
<fluent-hc.version>4.3.6</fluent-hc.version>
<geronimo-stax-api_1.0_spec.version>1.0.1</geronimo-stax-api_1.0_spec.version>
<httpclient.version>4.3.6</httpclient.version>
<httpcore.version>4.3.3</httpcore.version>
<httpmime.version>4.3.6</httpmime.version>
<je.version>4.0.92</je.version>
<jsoup.version>1.8.1</jsoup.version>
<log4j.version>1.2.17</log4j.version>
<metadata-extractor.version>2.4.0-beta-1</metadata-extractor.version>
<mysql-connector-java.version>5.1.34</mysql-connector-java.version>
<tagsoup.version>1.2.1</tagsoup.version>
<tika-app.version>1.6</tika-app.version>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.james</groupId>
<artifactId>apache-mime4j-core</artifactId>
<version>${apache-mime4j-core.version}</version>
</dependency>
<dependency>
<groupId>org.apache.james</groupId>
<artifactId>apache-mime4j-dom</artifactId>
<version>${apache-mime4j-dom.version}</version>
</dependency>
<dependency>
<groupId>asm</groupId>
<artifactId>asm</artifactId>
<version>${asm.version}</version>
</dependency>
<dependency>
<groupId>de.l3s.boilerpipe</groupId>
<artifactId>boilerpipe</artifactId>
<version>${boilerpipe.version}</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>${commons-compress.version}</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>${commons-logging.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>fluent-hc</artifactId>
<version>${fluent-hc.version}</version>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-stax-api_1.0_spec</artifactId>
<version>${geronimo-stax-api_1.0_spec.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${httpclient.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>${httpcore.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
<version>${httpmime.version}</version>
</dependency>
<dependency>
<groupId>com.sleepycat</groupId>
<artifactId>je</artifactId>
<version>${je.version}</version>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>${jsoup.version}</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>${log4j.version}</version>
</dependency>
<dependency>
<groupId>com.drewnoakes</groupId>
<artifactId>metadata-extractor</artifactId>
<version>${metadata-extractor.version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql-connector-java.version}</version>
</dependency>
<dependency>
<groupId>org.ccil.cowan.tagsoup</groupId>
<artifactId>tagsoup</artifactId>
<version>${tagsoup.version}</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-app</artifactId>
<version>${tika-app.version}</version>
</dependency>
</dependencies>
<build>
<finalName>ListDescCrawler</finalName>
<plugins>
<!-- download source code in Eclipse, best practice -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>false</downloadJavadocs>
</configuration>
</plugin>
<!-- Set a compiler level -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
</configuration>
</plugin>
<!-- Maven Assembly Plugin -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>edu.uci.ics.crawler4j.example.MainController</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>


Eventhough your class path in MANIFEST.MF contains jar that you are dependent it does not mean that they actually on your class path when you run your project. You have two option here either put all the dependent jar in the same directory of your runnable jar, or create a shaded jar.
A shaded (fat) jar contains all of your dependencies. You can create shaded jar using maven. Here is an example.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>${project.build.finalName}-with-dependencies</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass> edu.uci.ics.crawler4j.example.MainController </mainClass>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

Related

NoClassDefFoundError for org/apache/poi/xssf/usermodel/XSSFWorkbook

I've searched along foruns and even though there's a lot of issues regarding this same error, none of them actually helped me with solving this error.
I'm getting this error:
org.apache.cxf.interceptor.Fault: org/apache/poi/xssf/usermodel/XSSFWorkbook
at org.apache.cxf.service.invoker.AbstractInvoker.createFault(AbstractInvoker.java:162)
at [internal classes]
Caused by: java.lang.NoClassDefFoundError: org/apache/poi/xssf/usermodel/XSSFWorkbook
at com.test.GetFromExcel.readXLSX(GetFromExcel.java:25)
... 1 more
[ERROR ] SRVE0315E: Ocorreu uma exceção: java.lang.Throwable: org.apache.cxf.interceptor.Fault: org/apache/poi/xssf/usermodel/XSSFWorkbook
at com.ibm.ws.webcontainer.webapp.WebApp.handleRequest(WebApp.java:4998)
I've tried removing .m2 folder and downloading dependencies again, still not a successfull atempt.
I've added the .jar files, as you can see in the image.
And I can see that same class the error is complaining about listed right where the path indicates in org/apache/poi/xssf/usermodel/XSSFWorkbook .
Not clear to me why the error is frequent if I can see the class in my project.
Project's pom.xml as requested.
Thing is I have 2 other projects where I use this library and they both never gave me any headache like this to make POI library works. I used the same configuration I used previously in those projects.
<?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>
<parent>
<groupId>net.wasdev.maven.parent</groupId>
<artifactId>java8-parent</artifactId>
<version>1.4</version>
<relativePath></relativePath>
</parent>
<groupId>net.wasdev.wlp.sample</groupId>
<artifactId>my-project</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<name>MYPROJECT</name>
<url>http://google.com</url>
<licenses>
<license>
<name>The Apache Software License, Version 2.0</name>
<url>https://raw.github.com/WASdev/sample.servlet/master/LICENSE</url>
<distribution>repo</distribution>
</license>
</licenses>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
<version>1.0</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<!-- https://mvnrepository.com/artifact/net.wasdev.maven.tools.targets/liberty-apis -->
<dependency>
<groupId>net.wasdev.maven.tools.targets</groupId>
<artifactId>liberty-apis</artifactId>
<version>17.0.0.2</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.5.1</version>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>javax.ws.rs-api</artifactId>
<version>2.0</version>
</dependency>
<dependency>
<groupId>com.cloudant</groupId>
<artifactId>cloudant-client</artifactId>
<version>2.12.0</version>
</dependency>
<!-- lib local -->
<dependency>
<groupId>com.ibm.db2.jcc</groupId>
<artifactId>db2jcc</artifactId>
<version>3.1</version>
<scope>system</scope>
<systemPath>${basedir}/libs/db2jcc.jar</systemPath>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.8.11.2</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.4</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<version>2.22.2</version>
<scope>test</scope>
</dependency>
<!-- PropertyUtils -->
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.8.3</version>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<version>2.0.0</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.9.2</version>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-s3</artifactId>
<version>1.11.425</version>
</dependency>
<dependency>
<groupId>com.ibm.cos</groupId>
<artifactId>ibm-cos-java-sdk</artifactId>
<version>2.4.2</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>3.13</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>1.1</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
<warName>bms-code-management</warName>
<webXml>src/main/web.xml</webXml>
<warSourceDirectory>front/dist</warSourceDirectory>
</configuration>
</plugin>
<plugin>
<groupId>net.wasdev.wlp.maven.plugins</groupId>
<artifactId>liberty-maven-plugin</artifactId>
<version>1.2.1</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>net.wasdev.wlp.maven.plugins</groupId>
<artifactId>liberty-maven-plugin</artifactId>
<configuration>
<configFile>src/main/wlp/server.xml</configFile>
<bootstrapProperties>
<appLocation>../../../../../${project.build.finalName}</appLocation>
</bootstrapProperties>
</configuration>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<executions>
<execution>
<id>copy-resources</id>
<phase>package</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/server</outputDirectory>
<resources>
<resource>
<directory>server</directory>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.7</version>
<configuration>
<dependencyLocationsEnabled>false</dependencyLocationsEnabled>
</configuration>
</plugin>
</plugins>
</reporting>
</project>

In my case I had to add the following dependencies in my pom.xml
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>5.2.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>5.2.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax.xml.stream</groupId>
<artifactId>stax-api</artifactId>
<version>1.0-2</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.11.0</version>
</dependency>
All those 4 libs with exact versions, including stax-api. It should be noted that I use Maven.
Hope it'll help someone (I literally spent hours to fix this problem).

Error:osgi:Exception in parsing jar file for extract from jar

while trying to run app from intellij,i am getting below error:
Error:osgi: [owlapi-distribution] Exception in parsing jar file for extract from jar: C:/Users/User/Desktop/taheriDSS/pom.xml java.util.zip.ZipException: The JAR/ZIP file (C:\Users\User\Desktop\taheriDSS\pom.xml) seems corrupted, error: error in opening zip file
if i delete osgi from facets, then i encounter with a new error :
Exception in thread "main" org.semanticweb.owlapi.model.OWLOntologyFactoryNotFoundException: Could not find an appropriate factory to load ontology from ontology document:
BTW deleting .m2 repository and redownloading had no result.
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/maven-v4_0_0.xsd">
<parent>
<artifactId>owlapi-parent</artifactId>
<groupId>net.sourceforge.owlapi</groupId>
<version>5.1.11</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>owlapi-distribution</artifactId>
<packaging>bundle</packaging>
<name>OWLAPI :: Distribution</name>
<build>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>3.2.0</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Implementation-Title>${project.name}</Implementation-Title>
<Implementation-Vendor>${project.organization.name}</Implementation-Vendor>
<Implementation-Version>${project.version}.${maven.build.timestamp}</Implementation-Version>
<Bundle-SymbolicName>org.semanticweb.owl.owlapi</Bundle-SymbolicName>
<Bundle-Version>${project.version}</Bundle-Version>
<Embed-Dependency>groupId=${project.groupId};inline=true;scope=compile|runtime|provided</Embed-Dependency>
<Embed-Directory>lib</Embed-Directory>
<Embed-Transitive>true</Embed-Transitive>
<_exportcontents>!org.semanticweb.owlapi.test.*,
com.clarkparsia.*,
de.uulm.*,
org.semanticweb.owlapi.*;-split-package:=merge-first,
org.semanticweb.owlapitools.*;-split-package:=merge-first,
org.coode.*,
uk.ac.manchester.*;-split-package:=merge-first,
org.obolibrary.*;-split-package:=merge-first</_exportcontents>
<Import-Package>!sun.misc,
org.eclipse.rdf4j.*;version="[2.0,3.0)",
!javax.annotation,
!com.google.inject.internal.*;resolution:=optional,
org.apache.commons.io.*;version=2.5,
org.apache.commons.logging.*;version=1.2,
*</Import-Package>
</instructions>
</configuration>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<artifactSet>
<includes>
<include>net.sourceforge.owlapi:owlapi-api</include>
<include>net.sourceforge.owlapi:owlapi-apibinding</include>
<include>net.sourceforge.owlapi:owlapi-impl</include>
<include>net.sourceforge.owlapi:owlapi-oboformat</include>
<include>net.sourceforge.owlapi:owlapi-parsers</include>
<include>net.sourceforge.owlapi:owlapi-rio</include>
<include>net.sourceforge.owlapi:owlapi-tools</include>
</includes>
<excludes>
<exclude>org.apache.felix:org.osgi.core</exclude>
<exclude>org.eclipse.rdf4j:*</exclude>
<exclude>com.fasterxml.jackson.core:*</exclude>
<exclude>com.github.jsonld-java:*</exclude>
<exclude>com.fasterxml.jackson.core:*</exclude>
<exclude>org.apache.httpcomponents:*</exclude>
<exclude>commons-codec:commons-codec:*</exclude>
<exclude>org.slf4j:*</exclude>
<exclude>org.semarglproject:*</exclude>
<exclude>com.github.ben-manes.caffeine:*</exclude>
<exclude>com.google.guava:*</exclude>
<exclude>com.google.inject:*</exclude>
<exclude>javax.inject:*</exclude>
<exclude>aopalliance:*</exclude>
<exclude>com.google.inject.extensions:*</exclude>
<exclude>com.google.code.findbugs:*</exclude>
<exclude>org.slf4j:slf4j-api</exclude>
<exclude>commons-io:*</exclude>
<exclude>org.tukaani:*</exclude>
<exclude>com.carrotsearch:*</exclude>
</excludes>
</artifactSet>
<transformers>
<transformer />
</transformers>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.4</version>
<executions>
<execution>
<id>attach-javadoc</id>
<phase>package</phase>
<goals>
<goal>jar</goal>
</goals>
<configuration>
<skip>${no-javadoc}</skip>
<show>public</show>
<includeDependencySources>true</includeDependencySources>
<dependencySourceIncludes>
<dependencySourceInclude>net.sourceforge.owlapi:owlapi-api</dependencySourceInclude>
<dependencySourceInclude>net.sourceforge.owlapi:owlapi-apibinding</dependencySourceInclude>
<dependencySourceInclude>net.sourceforge.owlapi:owlapi-parsers</dependencySourceInclude>
<dependencySourceInclude>net.sourceforge.owlapi:owlapi-tools</dependencySourceInclude>
<dependencySourceInclude>net.sourceforge.owlapi:owlapi-impl</dependencySourceInclude>
<dependencySourceInclude>net.sourceforge.owlapi:owlapi-oboformat</dependencySourceInclude>
</dependencySourceIncludes>
</configuration>
</execution>
</executions>
<configuration>
<show>public</show>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<attach>true</attach>
<descriptors>
<descriptor>src/assembly/sources.xml</descriptor>
</descriptors>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-compatibility</artifactId>
<version>5.1.11</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>2.9.9</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.9.9</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.9.9</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-rdf-api</artifactId>
<version>0.5.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.tukaani</groupId>
<artifactId>xz</artifactId>
<version>1.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.22</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>1.7.22</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-model</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-api</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-languages</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-datatypes</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-binary</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-n3</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-nquads</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-ntriples</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-rdfjson</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-jsonld</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-rdfxml</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-trix</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-turtle</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-trig</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-util</artifactId>
<version>2.3.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.github.jsonld-java</groupId>
<artifactId>jsonld-java</artifactId>
<version>0.12.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.github.vsonnier</groupId>
<artifactId>hppcrt</artifactId>
<version>0.7.5</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>2.20.0</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>byte-buddy</artifactId>
<groupId>net.bytebuddy</groupId>
</exclusion>
<exclusion>
<artifactId>byte-buddy-agent</artifactId>
<groupId>net.bytebuddy</groupId>
</exclusion>
<exclusion>
<artifactId>objenesis</artifactId>
<groupId>org.objenesis</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
<version>2.6.1</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>[18.0,22.0]</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>[2.0.0,4)</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>[1.7.0,1.7.26)</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.5</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.github.galigator.openllet</groupId>
<artifactId>openllet-owlapi</artifactId>
<version>2.6.4</version>
</dependency>
<dependency>
<groupId>com.github.galigator.openllet</groupId>
<artifactId>openllet-jena</artifactId>
<version>2.6.4</version>
</dependency>
</dependencies>
<properties>
<inherited.rdf4j.version>${rdf4j.version}</inherited.rdf4j.version>
</properties>
</project>
EDIT:Issue solved after deleting pom.xml,recreating it and restarting intellij several times!
It seems there was something wrong with intellij

The problem is not in the POM file, but in the fact IntelliJ is trying to open it as if it was a zip file. A similar issue could be reproduced with Ant, when the classpath includes a text file. Seems likely that the IDE is not going to be fixed, given that the issue linked in the comment above by #CrazyCoder is six years old.
Try and restrict the libraries in the classpath to only actual Jar files. That's the root problem.
On the other hand, you say "while trying to run app" - but owlapi-distribution is not an app, it's a library. There is no main class to run; therefore, the app you're trying to run is not shown here. We won't be able to advise further without seeing the pom for your application; the OWLAPI pom is not important here.

mvn install generate jar file with only META-INF in the output jar

With the following maven pom.xml
<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>com.wewherego</groupId>
<artifactId>api-core</artifactId>
<version>1.0.0</version>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>3.10-FINAL</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>19.0-rc2</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.1</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
<dependency>
<groupId>com.oracle</groupId>
<artifactId>ojdbc6</artifactId>
<version>10.2.0.4.0</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>3.0-alpha-1</version>
</dependency>
<dependency>
<groupId>com.thetransactioncompany</groupId>
<artifactId>cors-filter</artifactId>
<version>1.3.2</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>4.1.0.RELEASE</version>
</dependency>
<dependency>
<groupId>javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.12.1.GA</version>
</dependency>
<dependency>
<groupId>javax.transaction</groupId>
<artifactId>jta</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>3.3.2.GA</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-annotations</artifactId>
<version>3.3.1.GA</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.6</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>false</downloadJavadocs>
</configuration>
</plugin>
</plugins>
</build>
</project>
When I run:
mvn install
The output is:
So if I unzip the jar file, it contains only the meta-inf folder without any .class file inside.
The maven project structure looks like this:
What did I miss?

why I am unable to run this jar file of a maven project?

Why I am unable to run this jar file? I clean and build the project successfully. but when I try to run the jar file in command prompt I get the error like
java -jar FSP-1.3.0 rc 1.jar
Error: Unable to access jarfile FSP-1.3.0
This is maven project done in netbeans IDE 7.2.1. Below is my pom.xml
<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>com.powerelectronics.freesun</groupId>
<artifactId>FSP</artifactId>
<version>1.3.0 rc 1</version>
<packaging>jar</packaging>
<name>FSPApp</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>javax.persistence</artifactId>
<version>2.0.4.v201112161009</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.1</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>au.com.alderaan</groupId>
<artifactId>eclipselink-staticweave-maven-plugin</artifactId>
<version>1.0.3</version>
</dependency>
<dependency>
<artifactId>maven-settings</artifactId>
<groupId>org.apache.maven</groupId>
<version>2.0.9</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>1.7.1</version>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>eclipselink</artifactId>
<version>2.4.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>6.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>9.3-1100-jdbc4</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.1.0</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>com.application.SIA</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<artifactId>eclipselink-staticweave-maven-plugin</artifactId>
<groupId>au.com.alderaan</groupId>
<version>1.0.3</version>
<executions>
<execution>
<goals>
<goal>weave</goal>
</goals>
<phase>process-classes</phase>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>eclipselink</artifactId>
<version>2.4.0</version>
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>EclipseLink</id>
<url>http://download.eclipse.org/rt/eclipselink/maven.repo</url>
</repository>
</repositories>
</project>
Please reply me soon. Please tell me what I am doing wrong here?

Java is tripping about the spaces in your filename. Either rename your version from "1.3.0 rc 1" to something like "1.3.0-rc-1" or put the filename in quotes when calling java from the command-line:
java -jar "FSP-1.3.0 rc 1.jar"

Couple of options
1) As Joachim suggested put quotes around the jar file
java -jar "FSP-1.3.0 rc 1.jar"
2) Escape the spaces that exist in the jar name
java -jar FSP-1.3.0\ rc\ 1.jar
Both should work.

How can I create an executable jar with dependencies in sub folder in jar using Maven?

How can I create an executable jar with dependencies in sub folder in jar using Maven?
The following pom.xml will make a executable jar with the dependencies in the root but what if I wanted all the dependencies in a sub-folder in the jar so its easy if someone else would want to look in the jar. How can I change the following pom.xml file:
<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>org.xxxx</groupId>
<artifactId>DRBP</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>DRBP</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java-version>1.7</java-version>
<springframework-version>3.2.1.RELEASE</springframework-version>
</properties>
<dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${springframework-version}</version>
</dependency>
<!--
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${springframework-version}</version>
</dependency>
-->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>${springframework-version}</version>
</dependency>
<dependency>
<groupId>javax.transaction</groupId>
<artifactId>jta</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>1.4.5</version>
</dependency>
<dependency>
<groupId>cglib</groupId>
<artifactId>cglib</artifactId>
<version>2.2.2</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.21</version>
</dependency>
<dependency>
<groupId>net.sf.jt400</groupId>
<artifactId>jt400-full</artifactId>
<version>4.7.0</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.7</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<finalName>DRBP</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>attached</goal>
</goals>
<phase>package</phase>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.xxxx.batch.MainBatch</mainClass>
</manifest>
</archive>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

You want to look at the Maven Shade plugin.
If you want a full web app in a single jar there are a couple of options:
Do what DropWizard does which is an example maven shade + jetty.
The Tomcat version +2 Maven plugin
Winstone

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