We Keep Coding

Using Saxon to process XPath in a JIRA module

I want to use saxon to process xpath in a jira module.
Unit tests covering the problematic code were running fine in eclipse, so I have deployed the module, and ...
I have encountered the dreaded
java.lang.ClassCastException: org.apache.xerces.jaxp.SAXParserFactoryImpl cannot be cast to javax.xml.parsers.SAXParserFactory (see Dealing with "Xerces hell" in Java/Maven?)
I tried to exclude xml-apis from saxon dependencies, as it is suggested in https://answers.atlassian.com/questions/104121/i-m-blocked-help-cannot-be-cast-to-javax-xml-parsers-saxparserfactory
Now I got w3c.dom missing, which is strange, because I would bet my hat that it is existing somewhere in jira.
I added dom4j to pom dependencies nevertheless, and got
java.lang.NoClassDefFoundError: Could not initialize class net.sf.saxon.Configuration
With no indication of which class is missing.
Here is the code with the initial problem:
https://github.com/magwas/andreymarkelov-atlas-plugins-requestedfields/tree/feature/xsltfixes
the patch leading to current state is at http://pastebin.com/vwR43hHt
What would be the solution?

Okay, figured it out. I am not sure why, so an analysis would be welcome.
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
<version>9.4</version>
<exclusions>
<exclusion>
<artifactId>xom</artifactId>
<groupId>xom</groupId>
</exclusion>
<exclusion>
<artifactId>dom4j</artifactId>
<groupId>dom4j</groupId>
</exclusion>
</exclusions>
</dependency>

IntelliJ IDEA: How can I make sources of dependent libraries to be available in classpath on compilation?

How can I make sources of dependent libraries to be available in classpath on compilation ?
I'm using IntelliJ IDEA 11.
When I add Global Library to module and artifact IDE never copies sources and javadocs. That makes sense because they are not needed in runtime. But I need them in compile time.
Interestingly though IDEA makes sources available if I add dependency as folder. I guess in this case it doesn't differentiate what sits in that folder. Odd.
Thoughts ?

i solved this issue in maven config by specifying another dependency to hibernate-validator one with sources and one without.
the one with sources i defined:
classifier: sources
scope: provided
EX:
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>4.1.0.Final</version>
<exclusions>
<exclusion>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>4.1.0.Final</version>
<classifier>sources</classifier>
<scope>provided</scope>
</dependency>

It's a bug that sources attached to a library are not used on GWT compilation. This bug is fixed in IDEA 11.1 EAP.

java.lang.IllegalAccessError: tried to access field org.slf4j.impl.StaticLoggerBinder.SINGLETON from class org.slf4j.LoggerFactory

I am facing this error while running my GWT application.
I have these jar files in my classpath: slf4j-api & slf4j-log4j12
Any idea what could be the reason?

This problem is due to a change in slf4j-log4j12 jar. From version 1.5.6 it doesn't allow to access the field org.slf4j.impl.StaticLoggerBinder.SINGLETON.
To resolve it, use the newest jars (or at least version 1.5.6 onward) for both slf4j-api & slf4j-log4j12.
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.5.6</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.5.6</version>
</dependency>

Finally resolved this problem in my SpringBoot application. If updating version is not helping this might help. Sometimes other libraries might bring different versions of this dependencies. These are the steps:
By error stack trace figure out which dependency is giving this issue
Get maven dependency plugin tree. Using this tree details find out if this library is coming as part of the some other dependency. In my case, the logback-classic and log4j-over-slf4j were giving this problem. They came together under spring-boot-starter-web
Use <exclusions><exclusion></exclusion></exclusions> in your pom.xml in that dependency for the libraries that giving this issue. In my case it looks like this:
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<exclusions>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>log4j-over-slf4j</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
</exclusions>
</dependency>
References:
http://www.slf4j.org/faq.html#IllegalAccessError
http://www.slf4j.org/codes.html#multiple_bindings

How to exclude cyclic deprecated dependencies in maven without killing the dependencies completely?

I have a case that I have the following cyclic dependencies in maven:
JAR A version 1.1 depends on JAR B version 1.0
JAR B version 1.1 depends on JAR A version 1.0
For some reason that I don't know, Maven brings all the 4 JARs: A 1.0, A 1.1, B 1.0 and B 1.1, which results in a classpath conflict.
This really sucks. I already ask the developers of both JARs to fix this, however I can't simply sit and wait for the day that they decide to fix this.
I tried this:
<dependency>
<groupId>groupA</groupId>
<artifactId>artifactA</artifactId>
<version>1.1</version>
<type>pom</type>
<scope>compile</scope>
<exclusions>
<exclusion>
<groupId>groupB</groupId>
<artifactId>artifactB</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>groupB</groupId>
<artifactId>artifactB</artifactId>
<version>1.1</version>
<type>pom</type>
<scope>compile</scope>
<exclusions>
<exclusion>
<groupId>groupA</groupId>
<artifactId>artifactA</artifactId>
</exclusion>
</exclusions>
</dependency>
The result is that maven excludes all of the JARs as if none dependency were added, and the project does not compiles because there are missing classes.
So, other than just asking both JARs developers to solve this, what can I do? How can I import both the new dependencies while leaving out both the old ones?

Pragmatic solution would be to redeclare the unwanted dependencies as provided, for example:
<dependency>
<groupId>groupA</groupId>
<artifactId>artifactA</artifactId>
<version>1.0</version>
<scope>provided</scope>
</dependency>
I'm not particularly fond of using provided in such manner, since it leaves the dependency in the compile time and could lead to unwanted compile dependencies, but I see no other way in your case ;(.

ClassCastException while parsing XML with WebLogic

I'm getting the following error message:
java.lang.ClassCastException: weblogic.xml.jaxp.RegistryDocumentBuilderFactory cannot be cast to javax.xml.parsers.DocumentBuilderFactory
I've gone through some forums researching this. They said to remove xml-apis.jar or that JAR files were conflicting. But even though I did all the suggested steps, I'm getting the same error.

It's always the xml-apis.jar. Remove them from your classpath (e.g. remove them from WEB-INF/lib of your webapp).

Remove xml-beans-1.xb2 to the lib directory. Modified the POM so it does not include that jar file with the following:
<dependency>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
<version>1.0.b2</version>
<scope>provided</scope>
</dependency>

I think Banang is right. Forum http://forum.springsource.org/showthread.php?t=22597 describes solution for similar problem.
Typically such problems happen when there are several versions of the same class in class path while those versions are loaded by different class loaders. One version of DocumentBuilderFactory was loaded by system class loader, other by class loader of your enterprise application. When you are calling the XML parser the parent's version of the class is used. When you are casting yours private version is utilized. These versions are incompatible that causes ClassCastException.

The reason for this issue is you are having multiple jars with same class name in library.
Go to WEB-INF/lib and remove xml-apis-1.0.b2.jar and stax-api-1.0.1.jar or remove them from you pom.xml itself and you would be good to go.

I wanted make a slight addition to the previous answers to this question, in the event that anyone else is in the same situation I was. I had the same problem on our WebLogic 9.2 server due to my use of CXF 2.2.3. In addition to the removal of the xml-apis.jar mentioned previously, I also had to remove a xmlParserAPIs library.
As I am using Maven2 it was just a simple matter of adding another inclusion.
<!-- CXF -->
<dependency>
<groupId>org.apache.cxf</groupId>
<artifactId>cxf-bundle</artifactId>
<version>${dependency.version.cxf}</version>
<scope>compile</scope>
<exclusions>
<exclusion>
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
<exclusion>
<artifactId>xercesImpl</artifactId>
<groupId>xerces</groupId>
</exclusion>
<exclusion>
<artifactId>xmlbeans</artifactId>
<groupId>org.apache.xmlbeans</groupId>
</exclusion>
<exclusion>
<artifactId>xmlParserAPIs</artifactId>
<groupId>xerces</groupId>
</exclusion>
</exclusions>
</dependency>
Hope this helps someone!

We also has such trouble. The reason of error was in gwt library. Receipe: exlude all gwt client libraries from distr.

As for my case, I managed to solve this issue by removing xml-apis library and also upgrading an XML processing library:
From
org.apache.xmlbeans/xmlbeans/2.4.0
Into
org.apache.xmlbeans/xmlbeans/2.6.0
FYI, I'm using Weblogic 10.3.6.0.