Asset folder not found when running jar - scala

I'm trying to run a jar which accesses a save file from a predefined directory. It runs properly when running with IntelliJ, but When I run it with "java -jar", I get a NullPointerException pointing to the third line in the following snippet:
val dir = new File("./statFiles")
dir.listFiles
.filter(_.getName.takeRight(3) == "cmf")
.map(_.getName)
I get the same exception from IntelliJ if I remove the directory, so it's probably caused by the directory not being found. I'm assuming IntelliJ does something automatically that I should do manually, but I can't tell what the issue is.
edit: I've tried running the jar both from a folder that also houses the 'statFiles' folder as well as from the path in which IntelliJ creates the jar ({project root}/classes/artifacts/{name}_jar).
Stacktrace:
Exception in thread "main" java.lang.ExceptionInInitializerError
at cmsoft.ui.GUI.main(GUI.scala)
Caused by: java.lang.NullPointerException
at scala.collection.ArrayOps$.filter$extension(ArrayOps.scala:191)
at cmsoft.io.FileHandler$.findSavedStats(FileHandler.scala:24)
at cmsoft.io.FileHandler$.findSavedStat(FileHandler.scala:32)
at cmsoft.Control$.startup(Control.scala:30)
at cmsoft.ui.GUI$.<clinit>(GUI.scala:340)
... 1 more

Related

Spark Scala Unit test getting failed

I am getting this below error while running the test for maven. I have HADOOP_HOME, hadoop.dll file , everything is set up in my local machine and path , environmental variables for my machine. Previously it was running fine. While I had to clone a different repository I started getting this error. Can anyone help me with this.
org.apache.spark.sql.AnalysisException: java.lang.UnsatisfiedLinkError: org.apache.hadoop.io.nativeio.NativeIO$Windows.createDirectoryWithMode0(Ljava/lang/String;I)V;
at org.apache.spark.sql.hive.HiveExternalCatalog.withClient(HiveExternalCatalog.scala:108)
at org.apache.spark.sql.hive.HiveExternalCatalog.databaseExists(HiveExternalCatalog.scala:196)
at org.apache.spark.sql.internal.SharedState.externalCatalog$lzycompute(SharedState.scala:114)
at org.apache.spark.sql.internal.SharedState.externalCatalog(SharedState.scala:102)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.externalCatalog(HiveSessionStateBuilder.scala:39)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog$lzycompute(HiveSessionStateBuilder.scala:54)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog(HiveSessionStateBuilder.scala:52)
at org.apache.spark.sql.hive.HiveSessionStateBuilder$$anon$1.<init>(HiveSessionStateBuilder.scala:69)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.analyzer(HiveSessionStateBuilder.scala:69)
at org.apache.spark.sql.internal.BaseSessionStateBuilder$$anonfun$build$2.apply(BaseSessionStateBuilder.scala:293)
...
Cause: java.lang.UnsatisfiedLinkError: org.apache.hadoop.io.nativeio.NativeIO$Windows.createDirectoryWithMode0(Ljava/lang/String;I)V
at org.apache.hadoop.io.nativeio.NativeIO$Windows.createDirectoryWithMode0(Native Method)
at org.apache.hadoop.io.nativeio.NativeIO$Windows.createDirectoryWithMode(NativeIO.java:524)
at org.apache.hadoop.fs.RawLocalFileSystem.mkOneDirWithMode(RawLocalFileSystem.java:465)
at org.apache.hadoop.fs.RawLocalFileSystem.mkdirsWithOptionalPermission(RawLocalFileSystem.java:518)
at org.apache.hadoop.fs.RawLocalFileSystem.mkdirs(RawLocalFileSystem.java:496)
at org.apache.hadoop.fs.FilterFileSystem.mkdirs(FilterFileSystem.java:316)
at org.apache.hadoop.hive.ql.session.SessionState.createPath(SessionState.java:694)
at org.apache.hadoop.hive.ql.session.SessionState.createSessionDirs(SessionState.java:613)
at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:547)
at org.apache.spark.sql.hive.client.HiveClientImpl.newState(HiveClientImpl.scala:180)
The problem is that you havenĀ“t set the library path. Try to set the java.library.path java property with the folder where the hadoop.dll is located. If you execute your tests with maven you can set the property of the forked jvm that executes the tests with the argLine option:
mvn -DargLine="-Djava.library.path=[hadoop_dll_dir_path]"

ClassNotFoundException for Spark job on Yarn-cluster mode

So I am trying to run a Spark job on Yarn-cluster mode kicked off via Oozie workflow, but have been encountering the following error (relevant stacktrace below)
java.sql.SQLException: ERROR 103 (08004): Unable to establish connection.
at org.apache.phoenix.exception.SQLExceptionCode$Factory$1.newException(SQLExceptionCode.java:388)
at org.apache.phoenix.exception.SQLExceptionInfo.buildException(SQLExceptionInfo.java:145)
at org.apache.phoenix.query.ConnectionQueryServicesImpl.openConnection(ConnectionQueryServicesImpl.java:296)
at org.apache.phoenix.query.ConnectionQueryServicesImpl.access$300(ConnectionQueryServicesImpl.java:179)
at org.apache.phoenix.query.ConnectionQueryServicesImpl$12.call(ConnectionQueryServicesImpl.java:1917)
at org.apache.phoenix.query.ConnectionQueryServicesImpl$12.call(ConnectionQueryServicesImpl.java:1896)
at org.apache.phoenix.util.PhoenixContextExecutor.call(PhoenixContextExecutor.java:77)
at org.apache.phoenix.query.ConnectionQueryServicesImpl.init(ConnectionQueryServicesImpl.java:1896)
at org.apache.phoenix.jdbc.PhoenixDriver.getConnectionQueryServices(PhoenixDriver.java:180)
at org.apache.phoenix.jdbc.PhoenixEmbeddedDriver.connect(PhoenixEmbeddedDriver.java:132)
at org.apache.phoenix.jdbc.PhoenixDriver.connect(PhoenixDriver.java:151)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:208)
...
Caused by: java.io.IOException: java.lang.reflect.InvocationTargetException
at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:240)
at org.apache.hadoop.hbase.client.ConnectionManager.createConnection(ConnectionManager.java:414)
at org.apache.hadoop.hbase.client.ConnectionManager.createConnectionInternal(ConnectionManager.java:323)
at org.apache.hadoop.hbase.client.HConnectionManager.createConnection(HConnectionManager.java:144)
at org.apache.phoenix.query.HConnectionFactory$HConnectionFactoryImpl.createConnection(HConnectionFactory.java:47)
at org.apache.phoenix.query.ConnectionQueryServicesImpl.openConnection(ConnectionQueryServicesImpl.java:294)
... 28 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:238)
... 33 more
Caused by: java.lang.UnsupportedOperationException: Unable to find org.apache.hadoop.hbase.ipc.controller.ClientRpcControllerFactory
at org.apache.hadoop.hbase.util.ReflectionUtils.instantiateWithCustomCtor(ReflectionUtils.java:36)
at org.apache.hadoop.hbase.ipc.RpcControllerFactory.instantiate(RpcControllerFactory.java:58)
at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.createAsyncProcess(ConnectionManager.java:2317)
at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.<init>(ConnectionManager.java:688)
at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.<init>(ConnectionManager.java:630)
... 38 more
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hbase.ipc.controller.ClientRpcControllerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.apache.hadoop.hbase.util.ReflectionUtils.instantiateWithCustomCtor(ReflectionUtils.java:32)
... 42 more
Some background information:
The job runs on spark 1.4.1 (specified correct spark.yarn.jar field in the spark.conf file).
oozie.libpath is set to the hdfs directory in which the jar of my program resides.
org.apache.hadoop.hbase.ipc.controller.ClientRpcControllerFactory, the class not found, exists in phoenix-4.5.1-HBase-1.0-client.jar. I've specified this jar in spark.driver.extraClassPath and spark.executor.extraClassPath in my spark.conf file. I've also added the phoenix-core dependency in my pom file, so that the class exists in my shaded project jar as well.
Observations so far:
adding an extra field in my spark.conf file spark.driver.userClassPathFirst and setting it to true gets rid of the classnotfound exception. However, it also prevents me from initializing a spark context (null pointer exception). From googling around it seems that including this field messes up classpaths, so may not be the way to go about it since I cannot even initialize a spark context this way.
I noticed that in the oozie stdout log, I do not see the classpath of the phoenix jar. So maybe for some reason spark.driver.extraClassPath and spark.executor.extraClassPath aren't actually picking up the jar as an extraClassPath? I do know that I'm specifying the correct jar file path, as other jobs have spark.conf files with the same parameters.
I found a hacky way to make the phoenix jar show up in the classpath (in the oozie stdout log) by copying the jar to the same directory as where my program jar resides. This works whether or not spark.executor.extraClassPath is changed to point to the new jar location. However, the classnotfound exception persists, even though I clearly see the ClientRpcControllerFactory jar when I unzip the jar)
Other things I've tried:
I tried using the sparkConf.setJars() and sparkContext.addJar() methods, but still encountered the same error
added the jar in the spark.driver.extraClassPath field in my job properties file, but it hasn't seemed to help (Spark docs indicated that this field is necessary when running in client mode, so may not be relevant for my case)
Any help/ideas/suggestions would be greatly appreciated.
I use CDH 5.5.1 + Phoenix 4.5.2 (both installed with parcels) and faced the same problem. I think the problem disappeared after I switched to client mode. I can't verify this because I am getting other error with cluster mode now.
I tried to trace Phoenix source code and found some interesting things. Hope Java / Scala expert identify the root cause.
The PhoenixDriver class was loaded.
This showed the jar was found initially. After layers of Class Loader /
context switch (?), the jar lost from the classpath.
If I Class.forName() a non-existing class in my program, there is no need to call sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331). The stack is like:
java.lang.ClassNotFoundException: NONEXISTINGCLASS
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
I copied Phoenix code into my program for testing. I still get the ClassNotFoundExcpetion if I call ConnectionQueryServicesImpl.init (ConnectionQueryServicesImpl.java:1896). However, a call to ConnectionQueryServicesImpl.openConnection (ConnectionQueryServicesImpl.java:296) returned usable HBase connection. So it seems PhoenixContextExecutor was causing the loss of the jar, but I don't know how.
Source code of Cloudera Phoenix 4.5.2 : https://github.com/cloudera-labs/phoenix/blob/phoenix1-4.5.2_1.2.0/phoenix-core/src/main/java/org/apache/
(Not sure whether I should post a comment... but I have no reputation anyway)
So I managed to fix my issue and get my job to run. My solution is very hacky, but will post it here in case it may help others in the future.
Basically, the problem as I understand it was that the org.apache.hadoop.hbase.util.ReflectionUtils class, which is responsible for finding the ClientRpcControllerFactory class, was being loaded from some cloudera directory in the cluster instead of from my own jar. When I set spark.driver.userClassPathFirst to true, it prioritized loading the ReflectionUtils class from my jar, and so was able to location the ClientRpcControllerFactory class. But that messed up some other classpaths and kept giving me a NullPointerException when I tried to initialize a SparkContext, so I looked for another solution.
I tried to figure out if it was possible to exclude all default cdh jars from being included in my classpath, but found that the value in spark.yarn.jar was pulling in all these cdh jars, and I definitely needed to specify that jar.
So the solution was to include all classes under org.apache.hadoop.hbase from the Phoenix jar into spark-assembly jar (the jar that spark.yarn.jar pointed to), which got rid of the original exception and did not give me a NPE when trying to initialize a SparkContext. I found that now the ReflectionUtils class was being loaded from the spark-assembly jar, and since the ClientRpcControllerFactorywas also included in that jar, it was able to find it. After this, I encountered a few more classNotFoundExceptions for Phoenix classes, so I put those classes into the spark-assembly jar as well.
Finally, I had a java.lang.RuntimeException: hbase-default.xml File Seems to be for and old Version of HBase problem. I found that my application jar contained such a file, but changing hbase.defaults.for.version.skip to true didn't do anything. So I included another hbase-default.xml file in the spark-assembly jar with the skip flag to true, and it finally worked.
Some observations:
I noticed that my spark-assembly jar was completely missing an org.apache.hadoop.hbase directory. A coworker told me that usually I should expect to find an hbase directory in my spark-assembly jar, so maybe I was working with a bad spark-assembly jar. Edit: I checked a spark-assembly jar that I newly downloaded (v1.5.2) and it doesn't have it, so maybe the apache.hadoop.hbase package is not included in it.
ClassNotFoundExceptions and classloader problems are hard to debug.

Caused by: org.dom4j.DocumentException: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory

I've a gradle project which uses hibernate > 4 . If I run my war file in Apache tomcat, I don't get any error. But when I'm deploying it in Wildfly 8.2 , I get the following exception
Caused by: org.hibernate.InvalidMappingException: Error while parsing file: /G:/wildfly-8.2.0.Final/bin/content/mywar-1.0.war/WEB-INF/classes/com/mysite/
hbm/Role.hbm.xml
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.buildHibernateConfiguration(EntityManagerFactoryBuilderImpl.java:1182) [hibernate-ent
itymanager-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:848) [hibernate-entitymanager-4.3.7.Fi
nal.jar:4.3.7.Final]
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:845) [hibernate-entitymanager-4.3.7.Fi
nal.jar:4.3.7.Final]
at org.hibernate.boot.registry.classloading.internal.ClassLoaderServiceImpl.withTccl(ClassLoaderServiceImpl.java:398) [hibernate-core-4.3.7.Final.jar:4.
3.7.Final]
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:844) [hibernate-entitymanager-4.3.7.Final.
jar:4.3.7.Final]
at org.jboss.as.jpa.hibernate4.TwoPhaseBootstrapImpl.build(TwoPhaseBootstrapImpl.java:44) [jipijapa-hibernate4-3-1.0.1.Final.jar:]
at org.jboss.as.jpa.service.PersistenceUnitServiceImpl$1$1.run(PersistenceUnitServiceImpl.java:154) [wildfly-jpa-8.2.0.Final.jar:8.2.0.Final]
... 8 more
Caused by: org.hibernate.InvalidMappingException: Unable to read XML
at org.hibernate.internal.util.xml.MappingReader.legacyReadMappingDocument(MappingReader.java:375) [hibernate-core-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.internal.util.xml.MappingReader.readMappingDocument(MappingReader.java:304) [hibernate-core-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.cfg.Configuration.add(Configuration.java:518) [hibernate-core-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.cfg.Configuration.add(Configuration.java:514) [hibernate-core-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.cfg.Configuration.add(Configuration.java:688) [hibernate-core-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.cfg.Configuration.addInputStream(Configuration.java:726) [hibernate-core-4.3.7.Final.jar:4.3.7.Final]
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.buildHibernateConfiguration(EntityManagerFactoryBuilderImpl.java:1177) [hibernate-ent
itymanager-4.3.7.Final.jar:4.3.7.Final]
... 14 more
Caused by: org.dom4j.DocumentException: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory Nested exception: org.dom4j.DocumentFactory cannot
be cast to org.dom4j.DocumentFactory
at org.dom4j.io.SAXReader.read(SAXReader.java:484) [dom4j-1.6.1.jar:1.6.1]
I just added a exclude in my Gradle file like
runtime.exclude group: "dom4j"
Now when I run gradle build, dom4j.jar is not created in the war file. Now I can run my deploy and run my project successfully on Wildfly 8.2 without any error. But the real problem starts here.
One of the feature in my project is that, it'll copy a file.xlsm to anotherfile.xlsm where I'm using jars like Apache Poi for those purposes. Here, Apache Poi is trying to access a method in dom4j.jar during file processing, it results in the following error
18:40:13,261 ERROR [io.undertow.request] (default task-29) UT005023: Exception handling request to /app/parentPath/myAction: org.springframework.web.util.NestedSe
rvletException: Handler processing failed; nested exception is java.lang.NoClassDefFoundError: org/dom4j/DocumentException
at org.springframework.web.servlet.DispatcherServlet.triggerAfterCompletionWithError(DispatcherServlet.java:1287) [spring-webmvc-4.1.4.RELEASE.jar:4.1.4
.RELEASE]
Any ideas how I can permanently use dom4j.jar inside my classpath? I've searched for many question and most of them suggested to remove dom4j from classpath. I do successfully run my program by removing it from classpath but it results in the above error during excel file processing. Wasted more than a day on this..!! IS it possible to include dom4j.jar in my classpath?
Update:
I've done a little trick in MANIFEST.MF file.
I've opened
mywar.war > META-INF > MANIFEST.MF
and added
Dependencies: org.dom4j export
at the end of the file and saved it. So if I deploy my war file, I'm successfully running it without any error.
Can someone explain where I've to add this kind of property in my src/ file so that it will be automatcially added to MANIFEST.MF after gradle build..
This exception on wildfly usually occurs when you include a hibernate lib in your war that's different from the wildfly one, since you are deploying to wildfly it already include hibernate so you can set you live as provided in gradle aka compileProvided and deploy without exporting the dependence.
If you still got the same error try declaring the hibernate dependency on manifest but keep the lib as provided it should work fine.
I had this same problem and i know how frustrating this one can be. I was able to resolve this problem. see my answer here. Hope this help

Error while trying to run the jar file in command prompt

My requirement is to run a eclipse java project in command prompt. I am using following program structure:
project name:parser
package name:xml
class name:Sample (with the main method)
I tried exporting the jar file by right clicking the project name-->export-->jar file-->gave the destination path for jar file->checked the Generate Manifest file and selected the main program(Sample.java).
Now in the command prompt i tried to run the jar file in the cmd using
java -jar myjar.jar.
And the error message I get is:
Exception in thread "main" java.lang.UnsupportedClassVersionError: XML/Sample:
Unsupported major.minor version 51.0
Could not find the main class: XML.Sample. Program will exit.
I have been searching for a solution for a long time but failed to find one. I would be very thankful if someone could help me with this problem. Kindly excuse for any mistakes in my question as I am new to java coding. Thanks in advance

FileNotFoundException after packing in executable jar

After using maven shade plugin and running the executable jar, my application failed due to FileNotFoundException. During the application development I put my files in src/main/resources and so my path was defined like this "src/main/resources/maps/map.shp". Should I change all my paths in the code and how should I do that? Why does this happen?
Exception in thread "main" java.io.FileNotFoundException: C:\Users\ilija\Desktop
\MavenizedCP\cp-map\target\src\main\resources\maps\ParcelsCountyRDMFinal5.shp (T
he system cannot find the path specified)