See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/100/changes>
Changes: [rodche] Created biopax-api bundle, which includes Paxtools (no need to bnd wrapping anymore!; todo: add javadoc) - extracted from biopax-impl; re-factored cpath2-impl, biopax-impl accordingly; modified several (apache commons) dependencies to uses bundles from a public repo (Springsource EBR) instead cytoscape-temp; finally, updated Karaf features for the above to work. ------------------------------------------ [...truncated 578 lines...] [INFO] Copying bundle: org.apache.karaf.assemblies.features:standard:xml:features:2.2.3 [INFO] Copying bundle: org.cytoscape.distribution:features:xml:features:3.0.0-M4-SNAPSHOT [INFO] Base repo: file:///opt/tomcat-home/.m2/repository/ [INFO] Copying bundle: org.apache.karaf.assemblies.features:standard:xml:features:2.2.3 [INFO] Copying bundle: org.cytoscape.distribution:features:xml:features:3.0.0-M4-SNAPSHOT [INFO] Copying bundle: org.apache.karaf.assemblies.features:enterprise:xml:features:2.2.3 [INFO] [INFO] --- maven-assembly-plugin:2.2:single (directory) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-dev.xml [INFO] framework/ already added, skipping [INFO] framework/system/org already added, skipping [INFO] framework/system/org/apache already added, skipping [INFO] framework/system/org/apache/karaf already added, skipping [INFO] framework/system/org/apache/karaf/assemblies already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3/enterprise-2.2.3-features.xml already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3/standard-2.2.3-features.xml already added, skipping [INFO] Copying files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/ws/trunk/assembly/target/cytoscape> [INFO] framework/ already added, skipping [INFO] framework/system/org already added, skipping [INFO] framework/system/org/apache already added, skipping [INFO] framework/system/org/apache/karaf already added, skipping [INFO] framework/system/org/apache/karaf/assemblies already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3/enterprise-2.2.3-features.xml already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3/standard-2.2.3-features.xml already added, skipping [WARNING] Assembly file: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/ws/trunk/assembly/target/cytoscape> is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] Replacement run on 1 file. [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-unix) @ cytoscape --- [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- xml-maven-plugin:1.0:transform (generate-descriptors) @ cytoscape --- [INFO] [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 4 resources [INFO] --- maven-resources-plugin:2.5:resources (filter) @ cytoscape --- [INFO] [INFO] Configured Artifact: org.cytoscape.distribution:branding:3.0.0-M4-SNAPSHOT:jar [INFO] Configured Artifact: org.cytoscape.distribution:karaf-launcher:3.0.0-M4-SNAPSHOT:jar [INFO] Copying branding-3.0.0-M4-SNAPSHOT.jar to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/ws/trunk/assembly/target/dependencies/branding/branding-3.0.0-M4-SNAPSHOT.jar> [INFO] Copying karaf-launcher-3.0.0-M4-SNAPSHOT.jar to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/ws/trunk/assembly/target/dependencies/launcher/karaf-launcher-3.0.0-M4-SNAPSHOT.jar> [INFO] --- maven-dependency-plugin:2.2:copy (copy-dependencies) @ cytoscape --- [INFO] [INFO] standard-2.2.3-features.xml already exists in destination. [INFO] apache-karaf-2.2.3.zip already exists in destination. [INFO] apache-karaf-2.2.3.tar.gz already exists in destination. [INFO] --- maven-dependency-plugin:2.2:copy-dependencies (copy-dependencies) @ cytoscape --- [INFO] [INFO] Configured Artifact: org.cytoscape.gui-distribution:splash-launcher:3.0.0-M4-SNAPSHOT:jar [INFO] splash-launcher-3.0.0-M4-SNAPSHOT.jar already unpacked. [INFO] --- maven-dependency-plugin:2.2:unpack (unpack-splash-launcher) @ cytoscape --- [INFO] [INFO] --- maven-dependency-plugin:2.2:unpack (unpack-unix) @ cytoscape --- [INFO] Configured Artifact: org.apache.karaf:apache-karaf:?:tar.gz [INFO] apache-karaf-2.2.3.tar.gz already unpacked. [INFO] [INFO] Configured Artifact: org.apache.karaf:apache-karaf:?:zip [INFO] apache-karaf-2.2.3.zip already unpacked. [INFO] --- maven-dependency-plugin:2.2:unpack (unpack-windows) @ cytoscape --- [INFO] [INFO] --- maven-assembly-plugin:2.2:single (directory) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-dev.xml [INFO] framework/ already added, skipping [INFO] framework/system/org already added, skipping [INFO] framework/system/org/apache already added, skipping [INFO] framework/system/org/apache/karaf already added, skipping [INFO] framework/system/org/apache/karaf/assemblies already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3/enterprise-2.2.3-features.xml already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3/standard-2.2.3-features.xml already added, skipping [INFO] Copying files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/ws/trunk/assembly/target/cytoscape> [INFO] framework/ already added, skipping [INFO] framework/system/org already added, skipping [INFO] framework/system/org/apache already added, skipping [INFO] framework/system/org/apache/karaf already added, skipping [INFO] framework/system/org/apache/karaf/assemblies already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3 already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/enterprise/2.2.3/enterprise-2.2.3-features.xml already added, skipping [INFO] framework/system/org/apache/karaf/assemblies/features/standard/2.2.3/standard-2.2.3-features.xml already added, skipping [WARNING] Assembly file: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20GUI%20Distribution/ws/trunk/assembly/target/cytoscape> is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-unix) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-windows) @ cytoscape --- [INFO] Replacement run on 1 file. ignoring exception during new ExecutedMojo null [INFO] [INFO] --- features-maven-plugin:2.2.3:add-features-to-repo (add-features-to-repo) @ cytoscape --- [INFO] Copying bundle: org.apache.karaf.assemblies.features:standard:xml:features:2.2.3 [INFO] Copying bundle: org.apache.karaf.assemblies.features:enterprise:xml:features:2.2.3 [INFO] Copying bundle: org.apache.karaf.assemblies.features:enterprise:xml:features:2.2.3 [INFO] Copying bundle: org.apache.karaf.assemblies.features:standard:xml:features:2.2.3 [INFO] Copying bundle: org.cytoscape.distribution:features:xml:features:3.0.0-M4-SNAPSHOT [INFO] Adding contents for feature: cytoscape-gui [INFO] Base repo: file:///opt/tomcat-home/.m2/repository/ [INFO] Copying bundle: org.apache.commons:com.springsource.org.apache.commons.codec:jar:1.3.0 Downloading: http://code.cytoscape.org/nexus/content/repositories/releases/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/thirdparty/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/biopax-release/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/ops4j-release/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar Downloaded: http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/org/apache/commons/com.springsource.org.apache.commons.codec/1.3.0/com.springsource.org.apache.commons.codec-1.3.0.jar (47 KB at 514.8 KB/sec) [INFO] Copying bundle: org.cytoscape:spacial:jar:3.0.0-alpha8-SNAPSHOT [INFO] Copying bundle: org.cytoscape:swing-application-api:jar:3.0.0-alpha8-SNAPSHOT [INFO] Copying bundle: cytoscape-temp:jfree-jcommon:jar:1.0.15 [INFO] Copying bundle: org.cytoscape:session-impl:jar:3.0.0-alpha8-SNAPSHOT [INFO] Copying bundle: org.apache.xmlbeans:com.springsource.org.apache.xmlbeans:jar:2.4.0 [INFO] Copying bundle: cytoscape-temp:freehep-graphicsio-svg:jar:2.1.3 [INFO] Copying bundle: cytoscape-temp:l2fprod-common-fontchooser:jar:7.3 [INFO] Copying bundle: org.cytoscape:cpath2-impl:jar:3.0.0-alpha8-SNAPSHOT [INFO] Copying bundle: org.cytoscape:psi-mi-impl:jar:3.0.0-alpha8-SNAPSHOT [INFO] Copying bundle: org.cytoscape:editor-impl:jar:3.0.0-alpha8-SNAPSHOT [INFO] Copying bundle: org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/biopax-snapshot/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar Downloading: http://maven.itextpdf.com/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-release/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-milestone/org/cytoscape/app-impl/3.0.0-alpha8-SNAPSHOT/app-impl-3.0.0-alpha8-SNAPSHOT.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Distribution ............................ SUCCESS [4.303s] [INFO] SplashScreen Launcher ............................. SUCCESS [9.352s] [INFO] Cytoscape Launcher ................................ SUCCESS [3.770s] [INFO] Cytoscape Command Line Provider Implementation .... SUCCESS [4.644s] [INFO] Cytoscape Branding ................................ SUCCESS [3.353s] [INFO] Cytoscape Feature Repository ...................... SUCCESS [1.863s] [INFO] Cytoscape Karaf Distribution ...................... FAILURE [1:10.712s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1:41.334s [INFO] Finished at: Wed Dec 07 15:05:34 GMT-05:00 2011 [INFO] Final Memory: 26M/62M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.karaf.tooling:features-maven-plugin:2.2.3:add-features-to-repo (add-features-to-repo) on project cytoscape: Can't resolve bundle org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT cause : Can't resolve bundle org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.karaf.tooling:features-maven-plugin:2.2.3:add-features-to-repo (add-features-to-repo) on project cytoscape: Can't resolve bundle org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59) at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:319) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156) at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239) at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158) at hudson.maven.Maven3Builder.call(Maven3Builder.java:112) at hudson.maven.Maven3Builder.call(Maven3Builder.java:70) at hudson.remoting.UserRequest.perform(UserRequest.java:118) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:287) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:636) Caused by: org.apache.maven.plugin.MojoFailureException: Can't resolve bundle org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT at org.apache.karaf.tooling.features.AddFeaturesToRepoMojo.resolveBundle(AddFeaturesToRepoMojo.java:245) at org.apache.karaf.tooling.features.AddFeaturesToRepoMojo.execute(AddFeaturesToRepoMojo.java:198) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Caused by: org.apache.maven.artifact.resolver.ArtifactNotFoundException: Could not find artifact org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT in cytoscape_snapshots (http://code.cytoscape.org/nexus/content/repositories/snapshots/) Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=org.cytoscape -DartifactId=app-impl -Dversion=3.0.0-alpha8-SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file Alternatively, if you host your own repository you can deploy the file there: mvn deploy:deploy-file -DgroupId=org.cytoscape -DartifactId=app-impl -Dversion=3.0.0-alpha8-SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id] org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT from the specified remote repositories: cytoscape_snapshots (http://code.cytoscape.org/nexus/content/repositories/snapshots/, releases=false, snapshots=true), cytoscape_releases (http://code.cytoscape.org/nexus/content/repositories/releases/, releases=true, snapshots=false), cytoscape_thirdparty (http://code.cytoscape.org/nexus/content/repositories/thirdparty/, releases=true, snapshots=false), cytoscape_biopax_release (http://code.cytoscape.org/nexus/content/repositories/biopax-release/, releases=true, snapshots=false), cytoscape_biopax_snapshot (http://code.cytoscape.org/nexus/content/repositories/biopax-snapshot/, releases=false, snapshots=true), ops4j-release (http://code.cytoscape.org/nexus/content/repositories/ops4j-release/, releases=true, snapshots=false), spring-osgi (http://code.cytoscape.org/nexus/content/repositories/spring-osgi/, releases=true, snapshots=true), spring-osgi-snapshots (http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/, releases=true, snapshots=true), itextpdf.com (http://maven.itextpdf.com/, releases=true, snapshots=true), zodiac-repository (http://code.cytoscape.org/nexus/content/repositories/zodiac-release/, releases=true, snapshots=true), zodiac-milestone-repository (http://code.cytoscape.org/nexus/content/repositories/zodiac-milestone/, releases=true, snapshots=true), sonatype-oss (http://code.cytoscape.org/nexus/content/repositories/sonatype-oss/, releases=true, snapshots=false), central (http://repo1.maven.org/maven2, releases=true, snapshots=false) at org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:219) at org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:157) at org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:525) at org.apache.karaf.tooling.features.AddFeaturesToRepoMojo.resolveBundle(AddFeaturesToRepoMojo.java:232) ... 30 more Caused by: org.sonatype.aether.resolution.ArtifactResolutionException: Could not find artifact org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT in cytoscape_snapshots (http://code.cytoscape.org/nexus/content/repositories/snapshots/) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:541) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:220) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:197) at org.sonatype.aether.impl.internal.DefaultRepositorySystem.resolveArtifact(DefaultRepositorySystem.java:323) at org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:213) ... 33 more Caused by: org.sonatype.aether.transfer.ArtifactNotFoundException: Could not find artifact org.cytoscape:app-impl:jar:3.0.0-alpha8-SNAPSHOT in cytoscape_snapshots (http://code.cytoscape.org/nexus/content/repositories/snapshots/) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$4.wrap(WagonRepositoryConnector.java:945) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$4.wrap(WagonRepositoryConnector.java:940) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.flush(WagonRepositoryConnector.java:695) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.flush(WagonRepositoryConnector.java:689) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector.get(WagonRepositoryConnector.java:445) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:460) ... 37 more Sending e-mails to: [email protected] channel stopped -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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