Dear all,
The following dataset is failing to register with GBIF, on publish:
http://ipt.gbif.pt/ipt/resource?r=stph
The publisher is
https://www.gbif.org/publisher/4c5bf646-457d-431d-b055-6c27f468ff0a,
which is already associated to our IPT. I checked the DwC-A, and
everything seems normal
The publication log is the following:
Archive generation started for version #1.4
Start writing data file for Darwin Core Occurrence
No lines were skipped due to errors for mapping Darwin Core Occurrence
in source stph_gbif
No lines were skipped due to errors for mapping Darwin Core Occurrence
in source stph_gbif
No lines with fewer columns than mapped for mapping Darwin Core
Occurrence in source stph_gbif
All lines match the filter criteria for mapping Darwin Core Occurrence
in source stph_gbif
Data file written for Darwin Core Occurrence with 404 records and 34 columns
All data files completed
EML file added
meta.xml archive descriptor written
Validating the core file: occurrence.txt. Depending on the number of
records, this can take a while.
? Validating the core basisOfRecord is always present and its value
matches the Darwin Core Type Vocabulary.
? Validating the core ID field occurrenceID is always present and unique.
No lines are missing occurrenceID
No lines have duplicate occurrenceID
✓ Validated each line has a occurrenceID, and each occurrenceID is unique
No lines are missing a basisOfRecord
All lines have basisOfRecord that matches the Darwin Core Type Vocabulary
No lines have ambiguous basisOfRecord 'occurrence'.
✓ Validated each line has a basisOfRecord, and each basisOfRecord
matches the Darwin Core Type Vocabulary
Archive validated
Archive has been compressed
Archive version #1.4 generated successfully!
Do you have any ideas how to check why the dataset is failing to
register with GBIF.org?
Thanks,
Rui Figueira
Hello, I am trying to deploy IPT 2.5.4 to a newly configured server (Amazon
Linux 2, equivalent to Centos 7 with the stock Tomcat 7 package). I see the
errors below at WAR deployment time, any idea how to investigate? Is there
a recommended Java/Tomcat version that's guaranteed to run?
Thanks a lot,
INFO: Deploying web application archive /var/lib/tomcat/webapps/ROOT.war
Dec 16, 2021 10:13:28 AM org.apache.catalina.loader.WebappLoader
buildClassPath
INFO: Unknown loader
jdk.internal.loader.ClassLoaders$AppClassLoader@30946e09 class
jdk.internal.loader.ClassLoaders$AppClassLoader
Dec 16, 2021 10:13:32 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable
debug logging for this logger for a complete list of JARs that were scanned
but no TLDs were found in them. Skipping unneeded JARs during scanning can
improve startup time and JSP compilation time.
Dec 16, 2021 10:13:33 AM com.google.inject.internal.MessageProcessor visit
INFO: An exception was caught and reported. Message:
java.lang.reflect.InaccessibleObjectException: Unable to make protected
final java.lang.Class
java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
throws java.lang.ClassFormatError accessible: module java.base does not
"opens java.lang" to unnamed module @24d1e8c4
java.lang.IllegalStateException: Unable to load cache item
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.createEntry(LoadingCache.java:79)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.get(LoadingCache.java:34)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData.get(AbstractClassGenerator.java:116)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator.create(AbstractClassGenerator.java:291)
at
com.google.inject.internal.cglib.reflect.$FastClass$Generator.create(FastClass.java:65)
at
com.google.inject.internal.BytecodeGen.newFastClassForMember(BytecodeGen.java:258)
at
com.google.inject.internal.BytecodeGen.newFastClassForMember(BytecodeGen.java:207)
at com.google.inject.internal.ProviderMethod.create(ProviderMethod.java:69)
at
com.google.inject.internal.ProviderMethodsModule.createProviderMethod(ProviderMethodsModule.java:272)
at
com.google.inject.internal.ProviderMethodsModule.getProviderMethods(ProviderMethodsModule.java:116)
at
com.google.inject.internal.ProviderMethodsModule.configure(ProviderMethodsModule.java:100)
at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:344)
at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:353)
at com.google.inject.spi.Elements.getElements(Elements.java:103)
at
com.google.inject.internal.InjectorShell$Builder.build(InjectorShell.java:137)
at
com.google.inject.internal.InternalInjectorCreator.build(InternalInjectorCreator.java:103)
at com.google.inject.Guice.createInjector(Guice.java:87)
at com.google.inject.Guice.createInjector(Guice.java:69)
at com.google.inject.Guice.createInjector(Guice.java:59)
at
org.gbif.ipt.config.IPTContextListener.getInjector(IPTContextListener.java:78)
at
com.google.inject.servlet.GuiceServletContextListener.contextInitialized(GuiceServletContextListener.java:45)
at
org.gbif.ipt.config.IPTContextListener.contextInitialized(IPTContextListener.java:46)
at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5127)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5643)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at
org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at
java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError
at
com.google.inject.internal.cglib.core.$DuplicatesPredicate.evaluate(DuplicatesPredicate.java:25)
at
com.google.inject.internal.cglib.core.$CollectionUtils.filter(CollectionUtils.java:52)
at
com.google.inject.internal.cglib.reflect.$FastClassEmitter.<init>(FastClassEmitter.java:69)
at
com.google.inject.internal.cglib.reflect.$FastClass$Generator.generateClass(FastClass.java:77)
at
com.google.inject.internal.cglib.core.$DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:25)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator.generate(AbstractClassGenerator.java:329)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData$3.apply(AbstractClassGenerator.java:93)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData$3.apply(AbstractClassGenerator.java:91)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache$2.call(LoadingCache.java:54)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.createEntry(LoadingCache.java:61)
... 34 more
Caused by: com.google.inject.internal.cglib.core.$CodeGenerationException:
java.lang.reflect.InaccessibleObjectException-->Unable to make protected
final java.lang.Class
java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
throws java.lang.ClassFormatError accessible: module java.base does not
"opens java.lang" to unnamed module @24d1e8c4
at
com.google.inject.internal.cglib.core.$ReflectUtils.defineClass(ReflectUtils.java:464)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator.generate(AbstractClassGenerator.java:336)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData$3.apply(AbstractClassGenerator.java:93)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData$3.apply(AbstractClassGenerator.java:91)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache$2.call(LoadingCache.java:54)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.createEntry(LoadingCache.java:61)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.get(LoadingCache.java:34)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData.get(AbstractClassGenerator.java:116)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator.create(AbstractClassGenerator.java:291)
at
com.google.inject.internal.cglib.core.$KeyFactory$Generator.create(KeyFactory.java:221)
at
com.google.inject.internal.cglib.core.$KeyFactory.create(KeyFactory.java:174)
at
com.google.inject.internal.cglib.core.$KeyFactory.create(KeyFactory.java:157)
at
com.google.inject.internal.cglib.core.$KeyFactory.create(KeyFactory.java:149)
at
com.google.inject.internal.cglib.core.$KeyFactory.create(KeyFactory.java:145)
at
com.google.inject.internal.cglib.core.$MethodWrapper.<clinit>(MethodWrapper.java:23)
... 45 more
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make
protected final java.lang.Class
java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
throws java.lang.ClassFormatError accessible: module java.base does not
"opens java.lang" to unnamed module @24d1e8c4
at
java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at
java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199)
at java.base/java.lang.reflect.Method.setAccessible(Method.java:193)
at
com.google.inject.internal.cglib.core.$ReflectUtils$1.run(ReflectUtils.java:61)
at
java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
at
com.google.inject.internal.cglib.core.$ReflectUtils.<clinit>(ReflectUtils.java:52)
at
com.google.inject.internal.cglib.reflect.$FastClassEmitter.<init>(FastClassEmitter.java:67)
... 42 more
Dec 16, 2021 10:13:33 AM com.google.inject.internal.MessageProcessor visit
INFO: An exception was caught and reported. Message:
java.lang.NoClassDefFoundError: Could not initialize class
com.google.inject.internal.cglib.core.$MethodWrapper
java.lang.IllegalStateException: Unable to load cache item
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.createEntry(LoadingCache.java:79)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.get(LoadingCache.java:34)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData.get(AbstractClassGenerator.java:116)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator.create(AbstractClassGenerator.java:291)
at
com.google.inject.internal.cglib.reflect.$FastClass$Generator.create(FastClass.java:65)
at
com.google.inject.internal.BytecodeGen.newFastClassForMember(BytecodeGen.java:258)
at
com.google.inject.internal.BytecodeGen.newFastClassForMember(BytecodeGen.java:207)
at com.google.inject.internal.ProviderMethod.create(ProviderMethod.java:69)
at
com.google.inject.internal.ProviderMethodsModule.createProviderMethod(ProviderMethodsModule.java:272)
at
com.google.inject.internal.ProviderMethodsModule.getProviderMethods(ProviderMethodsModule.java:116)
at
com.google.inject.internal.ProviderMethodsModule.configure(ProviderMethodsModule.java:100)
at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:344)
at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:353)
at com.google.inject.AbstractModule.install(AbstractModule.java:103)
at com.google.inject.servlet.ServletModule.configure(ServletModule.java:49)
at com.google.inject.AbstractModule.configure(AbstractModule.java:61)
at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:344)
at com.google.inject.spi.Elements.getElements(Elements.java:103)
at
com.google.inject.internal.InjectorShell$Builder.build(InjectorShell.java:137)
at
com.google.inject.internal.InternalInjectorCreator.build(InternalInjectorCreator.java:103)
at com.google.inject.Guice.createInjector(Guice.java:87)
at com.google.inject.Guice.createInjector(Guice.java:69)
at com.google.inject.Guice.createInjector(Guice.java:59)
at
org.gbif.ipt.config.IPTContextListener.getInjector(IPTContextListener.java:78)
at
com.google.inject.servlet.GuiceServletContextListener.contextInitialized(GuiceServletContextListener.java:45)
at
org.gbif.ipt.config.IPTContextListener.contextInitialized(IPTContextListener.java:46)
at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5127)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5643)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at
org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at
java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NoClassDefFoundError: Could not initialize class
com.google.inject.internal.cglib.core.$MethodWrapper
at
com.google.inject.internal.cglib.core.$DuplicatesPredicate.evaluate(DuplicatesPredicate.java:25)
at
com.google.inject.internal.cglib.core.$CollectionUtils.filter(CollectionUtils.java:52)
at
com.google.inject.internal.cglib.reflect.$FastClassEmitter.<init>(FastClassEmitter.java:69)
at
com.google.inject.internal.cglib.reflect.$FastClass$Generator.generateClass(FastClass.java:77)
at
com.google.inject.internal.cglib.core.$DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:25)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator.generate(AbstractClassGenerator.java:329)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData$3.apply(AbstractClassGenerator.java:93)
at
com.google.inject.internal.cglib.core.$AbstractClassGenerator$ClassLoaderData$3.apply(AbstractClassGenerator.java:91)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache$2.call(LoadingCache.java:54)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
com.google.inject.internal.cglib.core.internal.$LoadingCache.createEntry(LoadingCache.java:61)
... 38 more
Dec 16, 2021 10:13:33 AM org.apache.catalina.core.StandardContext
startInternal
SEVERE: One or more listeners failed to start. Full details will be found
in the appropriate container log file
Dec 16, 2021 10:13:33 AM org.apache.catalina.core.StandardContext
startInternal
SEVERE: Context [] startup failed due to previous errors
Dec 16, 2021 10:13:33 AM org.apache.catalina.loader.WebappClassLoaderBase
checkThreadLocalsForLeaks
WARNING: When running on Java 9 you need to add
"--add-opens=java.base/java.lang=ALL-UNNAMED" to the JVM command line
arguments to enable ThreadLocal memory leak detection. Alternatively, you
can suppress this warning by disabling ThreadLocal memory leak detection.
Dec 16, 2021 10:13:33 AM org.apache.catalina.loader.WebappClassLoaderBase
clearReferencesRmiTargets
WARNING: When running on Java 9 you need to add
"--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED" to the JVM command
line arguments to enable RMI Target memory leak detection. Alternatively,
you can suppress this warning by disabling RMI Target memory leak detection.
Dec 16, 2021 10:13:33 AM org.apache.catalina.core.ContainerBase
addChildInternal
SEVERE: ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component
[StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:162)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at
org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at
java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: org.apache.catalina.LifecycleException: Failed to stop component
[StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:233)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:149)
... 10 more
Caused by: org.apache.catalina.LifecycleException: Failed to stop component
[WebappLoader[]]
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:233)
at
org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5881)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:221)
... 11 more
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make
field private static final java.util.concurrent.ConcurrentMap
java.util.ResourceBundle.cacheList accessible: module java.base does not
"opens java.util" to unnamed module @7eda2dbb
at
java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at
java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at
org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesResourceBundles(WebappClassLoaderBase.java:3028)
at
org.apache.catalina.loader.WebappClassLoaderBase.clearReferences(WebappClassLoaderBase.java:2255)
at
org.apache.catalina.loader.WebappClassLoaderBase.stop(WebappClassLoaderBase.java:2123)
at
org.apache.catalina.loader.WebappLoader.stopInternal(WebappLoader.java:663)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:221)
... 13 more
Dec 16, 2021 10:13:33 AM org.apache.catalina.startup.HostConfig deployWAR
SEVERE: Error deploying web application archive
/var/lib/tomcat/webapps/ROOT.war
java.lang.IllegalStateException: ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component
[StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:903)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at
org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at
java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Dec 16, 2021 10:13:33 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive
/var/lib/tomcat/webapps/ROOT.war has finished in 6,559 ms
Dec 16, 2021 10:13:33 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Dec 16, 2021 10:13:33 AM org.apache.catalina.loader.WebappLoader
buildClassPath
INFO: Unknown loader
jdk.internal.loader.ClassLoaders$AppClassLoader@30946e09 class
jdk.internal.loader.ClassLoaders$AppClassLoader
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already
defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI:
http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already
defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI:
http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable
debug logging for this logger for a complete list of JARs that were scanned
but no TLDs were found in them. Skipping unneeded JARs during scanning can
improve startup time and JSP compilation time.
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deployment of web application directory
/var/lib/tomcat/webapps/examples has finished in 462 ms
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Dec 16, 2021 10:13:34 AM org.apache.catalina.loader.WebappLoader
buildClassPath
INFO: Unknown loader
jdk.internal.loader.ClassLoaders$AppClassLoader@30946e09 class
jdk.internal.loader.ClassLoaders$AppClassLoader
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable
debug logging for this logger for a complete list of JARs that were scanned
but no TLDs were found in them. Skipping unneeded JARs during scanning can
improve startup time and JSP compilation time.
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deployment of web application directory
/var/lib/tomcat/webapps/sample has finished in 224 ms
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deploying web application directory
/var/lib/tomcat/webapps/host-manager
Dec 16, 2021 10:13:34 AM org.apache.catalina.loader.WebappLoader
buildClassPath
INFO: Unknown loader
jdk.internal.loader.ClassLoaders$AppClassLoader@30946e09 class
jdk.internal.loader.ClassLoaders$AppClassLoader
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable
debug logging for this logger for a complete list of JARs that were scanned
but no TLDs were found in them. Skipping unneeded JARs during scanning can
improve startup time and JSP compilation time.
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deployment of web application directory
/var/lib/tomcat/webapps/host-manager has finished in 231 ms
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Dec 16, 2021 10:13:34 AM org.apache.catalina.loader.WebappLoader
buildClassPath
INFO: Unknown loader
jdk.internal.loader.ClassLoaders$AppClassLoader@30946e09 class
jdk.internal.loader.ClassLoaders$AppClassLoader
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable
debug logging for this logger for a complete list of JARs that were scanned
but no TLDs were found in them. Skipping unneeded JARs during scanning can
improve startup time and JSP compilation time.
Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deployment of web application directory
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Dec 16, 2021 10:13:34 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Dec 16, 2021 10:13:35 AM org.apache.catalina.loader.WebappLoader
buildClassPath
INFO: Unknown loader
jdk.internal.loader.ClassLoaders$AppClassLoader@30946e09 class
jdk.internal.loader.ClassLoaders$AppClassLoader
Dec 16, 2021 10:13:35 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable
debug logging for this logger for a complete list of JARs that were scanned
but no TLDs were found in them. Skipping unneeded JARs during scanning can
improve startup time and JSP compilation time.
Dec 16, 2021 10:13:35 AM org.apache.catalina.startup.HostConfig
deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs
has finished in 179 ms
Dec 16, 2021 10:13:35 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2021 10:13:35 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 7928 ms
Dear IPT users,
We have released a new version of the IPT, version 2.5.4 [1]. This
version contains fixes to critical security issues with the Struts and
Log4J[2] libraries.
According to the press [3], the problem with the Log4J library
vulnerability is being exploited by malicious users — and I can already
see queries containing "jndi" in the web server logs for the IPTs GBIF
hosts at cloud.gbif.org, although they are random attempts and would not
succeed.
All users are highly encouraged to upgrade to this version as soon as
possible.
As usual, upgrade and installation instructions are in the manual [1].
Please remember to check your data directory backup is working before
starting the upgrade.
[1] https://ipt.gbif.org/manual/en/ipt/2.5/releases#2-5-4-december-2021
[2] https://www.lunasec.io/docs/blog/log4j-zero-day/
[3]
https://www.theguardian.com/technology/2021/dec/10/software-flaw-most-criti…
Best regards,
Matthew
Dear IPT users,
I have released a new version of the IPT, version 2.5.3. There are only
two changes since the previous version:
- The Spanish translation has been completed, for both the user
interface and the user manual. This is the reason for this release.
- A minor bug when viewing vocabularies in the administration section
has been fixed. This is probably only of interest for people running
IPTs in test mode, working on this year's changes to the Darwin Core
standard.
It's not necessary to upgrade unless you need these changes.
Instructions are in the manual as usual, and you should check your data
directory backups are still working before starting the process.
Best regards,
Matthew Blissett
Further information in English:
https://ipt.gbif.org/manual/en/ipt/2.5/releases
Further information in Spanish:
https://ipt.gbif.org/manual/es/ipt/2.5/releases
Dear all,
We are using IPT 2.5.1, on a server with Java(TM) SE Runtime Environment
(build 1.8.0_131-b11) and tomcat7.
In managing a newly created resource, if we navigate to Metadata,
section citation, we get the following error:
=====
FreeMarker template error (HTML_DEBUG mode; use RETHROW in production!)
Java method
"org.gbif.ipt.model.Resource.generateResourceCitation(String, String)"
threw an exception when invoked on org.gbif.ipt.model.Resource object
"Resource ibi_mantodea_01"; see cause exception in the Java stack trace.
----
FTL stack trace ("~" means nesting-related):
- Failed at: ${action.resource.generateResourceCit... [in template
"WEB-INF/pages/manage/eml/citations.ftl" at line 14, column 41]
----
Java stack trace (for programmers):
----
freemarker.core._TemplateModelException: [... Exception message was
already printed; see it above ...]
at
freemarker.ext.beans._MethodUtil.newInvocationTemplateModelException(_MethodUtil.java:289)
at
freemarker.ext.beans._MethodUtil.newInvocationTemplateModelException(_MethodUtil.java:261)
at
freemarker.ext.beans.OverloadedMethodsModel.exec(OverloadedMethodsModel.java:65)
at freemarker.core.MethodCall._eval(MethodCall.java:65)
at freemarker.core.Expression.eval(Expression.java:81)
...
Caused by: java.lang.NullPointerException
at java.util.Calendar.setTime(Calendar.java:1770)
at org.gbif.ipt.model.Resource.getPublicationYear(Resource.java:1240)
at
org.gbif.ipt.model.Resource.generateResourceCitation(Resource.java:1153)
at
org.gbif.ipt.model.Resource.generateResourceCitation(Resource.java:1113)
at sun.reflect.GeneratedMethodAccessor967.invoke(Unknown Source)
=====
Could anyone help to sort out how to resolve this problem? Let me know
if you need any more information.
best,
Rui
--
------------------
Rui Figueira
Coordenador do Nó Português do GBIF
ruifigueira(a)isa.ulisboa.pt
Instituto Superior de Agronomia
Herbário
Tapada da Ajuda, 1349-017 Lisboa, Portugal
Tel. +351 213653165 | Fax. +351 213653195
http://www.gbif.pthttp://www.isa.ulisboa.pt
