- IPT - lists.gbif.org

IPT release 2.7.6
by Mikhail Podolskiy 26 Sep '23

26 Sep '23

Dear IPT users, We have released a new version of the IPT, version 2.7.6 [1]. This version mostly brings bug fixes and small improvements. A full list of addressed issues can be found here [2] All users are encouraged to upgrade to this version. 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/latest/releases#2-7-6-september-2023 [2] https://github.com/gbif/ipt/milestone/49?closed=1 Best regards, Mikhail ---- Mikhail Podolskiy Developer GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK e-mail: mpodolskiy(a)gbif.org<mailto:mpodolskiy@gbif.org> www.gbif.org<http://www.gbif.org>

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IPT v3 Release Candidate
by Mikhail Podolskiy 04 Sep '23

04 Sep '23

Dear IPT users, I’m happy to announce the availability of a preview release for the Integrated Publishing Toolkit Version 3.0-RC1. We’ve opted to name this version 3 as it brings in a new capability that goes beyond the Darwin Core Archive format. IPT version 3 will still provide all the functions of previous versions, but will additionally allow a user to map datasets to supported Frictionless Data [1] schemas. The first of these are the Camera Trap Data Package (Camtrap DP) [2, 3] and Catalogue of Life Data Package (CoL DP) [4]. This version also introduces a new core for Darwin Core Archives, for MaterialEntity [5], which is in preparation for the outputs of the Darwin Core Material task group. In addition, the installation requirements have been updated. Java 11 or 17 is now recommended, and Tomcat 9 or later. A Docker package for the release candidate version has been created, as well as CentOS Stream 8 and 9 test packages. Please note that this is a release candidate and is intended for testing and preview purposes only. It's NOT for production use — the IPT should be set up in test mode to register published datasets to the test system, gbif-uat.org. Documentation in the user manual for the new features is not yet available. Feedback is appreciated through issues on the GitHub issue tracker [6], or by email. If you have any questions or suggestions feel free to contact us. Best regards, Mikhail Podolskiy ---- Mikhail Podolskiy Developer GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK e-mail: mpodolskiy(a)gbif.org<mailto:mpodolskiy@gbif.org> www.gbif.org<http://www.gbif.org> [1] https://frictionlessdata.io/ [2] https://tdwg.github.io/camtrap-dp/ [3] https://github.com/tdwg/camtrap-dp [4] https://github.com/CatalogueOfLife/coldp#name [5] https://rs.gbif.org/sandbox/core/dwc_material_2023-04-29.xml [6] https://github.com/gbif/ipt/issues

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Update docker tomcat?
by Roger W. J. Alterskjær 23 Dec '22

23 Dec '22

Our university IT-security guys have noticed that our docker container for gbif/ipt is running a vulnerable version of Tomcat: Apache Tomcat 8.5.x < 8.5.83 which is vulnerable to "Request Smuggling Vulnerability" (CVE-2022-42252). They say that Tomcat 8.5.84 is the latest version of 8.5. I see that we’re using maven:3.8-jdk-8 with hasn’t been updated for five months… -Roger A

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missing organization in the ECA-IPT
by Andreas Allspach 01 Jun '22

01 Jun '22

Dear Admins, I want to insert the Basic Metadata for a resource in the ECA-IPT, but cannot select an organization. Where can I add my organization or has this to be done by you? I want to select "Senckenberg", the provider with following URL: (https://www.gbif.org/publisher/c76cf030-2a95-11da-9cc1-b8a03c50a862) Many thanks for your help and kind regards Andreas ☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀☀ Andreas Allspach Collections Manager Senckenberg Forschungsinstitut und Naturmuseum Frankfurt Senckenberganlage 25 60325 Frankfurt am Main Tel. +49-69-7542-1369 Fax: +49-69-1437 Email: andreas.allspach(a)senckenberg.de Senckenberg Gesellschaft für Naturforschung (Rechtsfähiger Verein gemäß § 22 BGB) Senckenberganlage 25 60325 Frankfurt www.senckenberg.de Direktorium: Prof. Dr. Klement Tockner, Prof. Dr. Angelika Brandt, Dr. Martin Mittelbach, Prof. Dr. Andreas Mulch, Prof. Dr. Karsten Wesche; Präsidentin: Dr. h.c. Beate Heraeus; Aufsichtsbehörde: Magistrat der Stadt Frankfurt am Main (Ordnungsamt) Mitglied der Leibniz-Gemeinschaft Senckenberg forscht für Ihr Leben gern! www.senckenberg.de ***************************************************** P Drucken Sie bitte nur, wenn es wirklich notwendig ist: Sparen Sie pro Seite ca. 200 ml Wasser, 2 g CO2 und 2 g Holz.

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Proxy disabled due to 404 response
by Yasuhiko Fujita 04 Apr '22

04 Apr '22

Dear IPT admins, I am getting the following error in my IPT 2.5.5 (Test mode). - IPT startup warnings. For additional help diagnosing the problem(s), please see logs. After fixing the problem(s), please restart your web server. - admin.config.error.connectionRefused From the logs, it seems that the proxy settings are disabled because [https://gbrds.gbif-uat.org] is getting a 404 error. ==== INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Configuring http proxy ... INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Testing new proxy by fetching https://gbrds.gbif-uat.org with 4 second timeout DEBUG [org.gbif.utils.PreemptiveAuthenticationInterceptor] - GET / HTTP/1.1 INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Proxy response is HTTP/1.1 404 Not Found INFO [org.gbif.ipt.service.admin.impl.ConfigManagerImpl] - Proxy could not be validated (tried to retrieve https://gbrds.gbif-uat.org) , reverting to previous proxy setting on HTTP client: <...masked...> WARN [org.gbif.ipt.config.ConfigWarnings] - org.gbif.ipt.service.InvalidConfigException: admin.config.error.connectionRefused ==== Could anyone help to sort out how to resolve this problem? Does anyone know what is happening to gbrds.gbif-uat.org site? Best regards, Yasuhiko Fujita

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IPT 2.5.6
by Mikhail Podolskiy 11 Feb '22

11 Feb '22

Dear IPT users, We have released a new version of the IPT, version 2.5.6 [1]. This version brings new Darwin Core functionality [2], [3], [4]. It also changes the way user password are stored to improve security. A full list of addressed issues can be found here [5] All users are encouraged to upgrade to this version. 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#2-5-6-february-2022 [2] https://github.com/gbif/ipt/issues/1532 [3] https://github.com/gbif/ipt/issues/1664 [4] https://github.com/gbif/ipt/issues/1653 [5] https://github.com/gbif/ipt/milestone/33?closed=1 Best regards, Mikhail

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resourse not registering
by Rui Figueira 27 Jan '22

27 Jan '22

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

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IPT 2.5.5
by Mikhail Podolskiy 20 Dec '21

20 Dec '21

Dear IPT users, We have released a new version of the IPT, version 2.5.5 [1]. This version contains further updates to security issues with the Log4J[2] library. This also contains a fix to the issue [3] with identifiedByID/recordedByID Darwin Core terms. All users are encouraged to upgrade to this version, especially those who use the terms above. 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#2-5-5-december-2021 [2] https://nvd.nist.gov/vuln/detail/https://nvd.nist.gov/vuln/detail/CVE-2021-… [3] https://github.com/gbif/ipt/issues/1703 Best regards, Mikhail

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Deployment issue
by Nicolas Noé 16 Dec '21

16 Dec '21

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 /var/lib/tomcat/webapps/manager has finished in 178 ms 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

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IPT security update (Log4J / Log4Shell exploit)
by Matthew Blissett 15 Dec '21

15 Dec '21

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

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