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Created May 23, 2015 12:55
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trace log of Sherlok before and after commit 06eb9fbb19749c197277da0dd1dc1fa3ec11515b (workaround for multiple trove4j versions conflicting with each others)
Raw
trace.new.log
,---.| | |
`---.|---.,---.,---.| ,---.|__/
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`---'` '`---'` `---'`---'` `
Sherlok Server v. 224af9bc74
INFO Done loading from local File store (local_repo): 11 bundles, 29 engines, 16 pipelines [o.s.Controller 14:50:22]
== Spark has ignited ...
>> Listening on 0.0.0.0:9600
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_commons/1.0.2-SNAPSHOT/bluima_commons-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:35]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_module/1.0.2-SNAPSHOT/bluima_module-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:36]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_parent/1.0.2-SNAPSHOT/bluima_parent-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:38]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_utils/1.0.2-SNAPSHOT/bluima_utils-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:42]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_typesystem/1.0.2-SNAPSHOT/bluima_typesystem-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:52]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/blue_commons/1.0.2-SNAPSHOT/blue_commons-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:56]
TRACE org.sherlok:bluima.regions_jsre:pom:1.0.1 () [o.s.u.AetherResolver 14:50:56]
TRACE +- net.sf.trove4j:trove4j:jar:2.0.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE +- ch.epfl.bbp.nlp:bluima_opennlp:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- de.jules:jules-utilities:jar:2.1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- ch.epfl.bbp.nlp:bluima_typesystem:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- ch.epfl.bbp.nlp:blue_commons:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- com.google.guava:guava:jar:18.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.apache.commons:commons-math3:jar:3.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.apache.uima:ruta-core:jar:2.1.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.apache.uima:uimaj-core:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.antlr:antlr-runtime:jar:3.5 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.antlr:stringtemplate:jar:3.2.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- antlr:antlr:jar:2.7.7 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.htmlparser:htmlparser:jar:1.6 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- commons-collections:commons-collections:jar:3.2.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.apache.uima:uimaj-tools:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.apache.uima:uimaj-cpe:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.apache.uima:uimaj-adapter-vinci:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.apache.uima:jVinci:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.apache.commons:commons-lang3:jar:3.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.apache.uima:uimafit-core:jar:2.0.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- commons-lang:commons-lang:jar:2.6 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- commons-logging:commons-logging-api:jar:1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.springframework:spring-core:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.springframework:spring-asm:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.springframework:spring-context:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.springframework:spring-expression:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.springframework:spring-beans:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- commons-io:commons-io:jar:2.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.apache.uima:RegularExpressionAnnotator:jar:2.3.2-BBP (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.apache.uima:SnowballAnnotator:jar:2.3.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.apache.uima:ConceptMapper:jar:2.3.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.slf4j:jcl-over-slf4j:jar:1.6.5 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- ch.qos.logback:logback-classic:jar:1.0.6 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- ch.qos.logback:logback-core:jar:1.0.6 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.slf4j:slf4j-api:jar:1.6.5 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE +- ch.epfl.bbp.nlp:bluima_regions:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- ch.epfl.bbp.nlp:mallet_utils:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- cc.mallet:mallet:jar:2.0.7 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- junit:junit:jar:4.10 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.hamcrest:hamcrest-core:jar:1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.beanshell:bsh:jar:2.0b4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- jgrapht:jgrapht:jar:0.6.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- net.sf.jwordnet:jwnl:jar:1.4_rc3 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- com.googlecode.matrix-toolkits-java:mtj:jar:0.9.14 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- com.googlecode.netlib-java:netlib-java:jar:0.9.3 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | | +- net.sourceforge.f2j:arpack_combined_all:jar:0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.jdom:jdom:jar:1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- ch.epfl.bbp.nlp:bluima_topic_models:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.scala-lang:scala-library:jar:2.10.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- com.github.scopt:scopt_2.10:jar:3.2.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- ch.epfl.bbp.nlp:bluima_lexica:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- ch.epfl.bbp.nlp:bluima_xml:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.codehaus.woodstox:woodstox-core-asl:jar:4.0.6 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.codehaus.woodstox:stax2-api:jar:3.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.apache.commons:commons-vfs2:jar:2.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.apache.maven.scm:maven-scm-api:jar:1.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | | +- org.codehaus.plexus:plexus-utils:jar:1.5.6 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | +- org.apache.maven.scm:maven-scm-provider-svnexe:jar:1.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | | +- org.apache.maven.scm:maven-scm-provider-svn-commons:jar:1.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | | | +- regexp:regexp:jar:1.3 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- org.jdom:jdom2:jar:2.0.5 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | | +- jaxen:jaxen:jar:1.1.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE +- ch.epfl.bbp.nlp:bluima_utils:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.apache.xmlbeans:xmlbeans:jar:2.5.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- stax:stax-api:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- com.googlecode.combinatoricslib:combinatoricslib:jar:2.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE +- ch.epfl.bbp.nlp:bluima_units:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE +- ch.epfl.bbp.nlp:bluima_jsre:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- commons-digester:commons-digester:jar:2.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- commons-beanutils:commons-beanutils:jar:1.8.3 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- commons-logging:commons-logging:jar:1.1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- tw.edu.ntu.csie:libsvm:jar:3.17 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- commons-cli:commons-cli:jar:1.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE +- ch.epfl.bbp.nlp:bluima_commons:jar:1.0.2-SNAPSHOT (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- bioadi:bioadi:jar:0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- bioadi:sptoolkit:jar:0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- bioadi:j-seqalign:jar:0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- mallet:mallet:jar:0.4 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- hu.u_szeged.rgai.bio.uima:linnaeus:jar:2.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- edu.ucdenver.ccp:biolemmatizer-core:jar:1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- args4j:args4j:jar:2.0.12 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- org.wiki.harvester.dependency:morphadorner:jar:1.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- edu.ucdenver.ccp:biolemmatizer-uima:jar:1.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- org.uimafit:uimafit:jar:1.2.0 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- edu.ucdenver.ccp:ccp-uima-shims:jar:0.1 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- edu.mit:jwi:jar:2.2.3 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | +- com.cybozu.labs:langdetect:jar:1.2.2 (compile) [o.s.u.AetherResolver 14:50:56]
TRACE | | +- net.arnx.jsonic:jsonic:jar:1.2.0 (compile) [o.s.u.AetherResolver 14:50:56]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_opennlp/1.0.1/bluima_opennlp-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:56]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_typesystem/1.0.1/bluima_typesystem-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:56]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/blue_commons/1.0.1/blue_commons-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:56]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_regions/1.0.1/bluima_regions-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:57]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/mallet_utils/1.0.1/mallet_utils-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:57]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_topic_models/1.0.1/bluima_topic_models-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:57]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_lexica/1.0.1/bluima_lexica-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:57]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_xml/1.0.1/bluima_xml-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:58]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_utils/1.0.1/bluima_utils-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:58]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_units/1.0.1/bluima_units-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:58]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_jsre/1.0.1/bluima_jsre-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:58]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_commons/1.0.2-SNAPSHOT/bluima_commons-1.0.2-SNAPSHOT.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:50:58]
INFO Using resource path BLUE_UIMA_ROOT=/Users/m/Prog/Projects/MasterProject/bluima/ (resolves to /Users/m/Prog/Projects/MasterProject/bluima) [c.e.b.u.BlueUima 14:51:11]
INFO DEBUG Running in infer mode [c.e.b.u.a.BrainRegionAnnotator 14:51:13]
DEBUG unzip model files [o.i.i.t.s.u.UnZipModel 14:51:15]
DEBUG extracting: train [o.i.i.t.s.u.UnZipModel 14:51:15]
DEBUG extracting: dic0 [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG extracting: dic1 [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG extracting: dic2 [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG extracting: dic3 [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG extracting: dic4 [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG extracting: model [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG extracting: param [o.i.i.t.s.u.UnZipModel 14:51:16]
DEBUG MappingFactory uses the default config file: jsre-config.xml [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG mapping-list size: 10 [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG DIST, org.itc.irst.tcc.sre.kernel.expl.DistanceContextMapping, {} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG ET, org.itc.irst.tcc.sre.kernel.expl.EntityMapping, {} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG GC, org.itc.irst.tcc.sre.kernel.expl.GlobalContextMapping, {n-gram=3} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG LC, org.itc.irst.tcc.sre.kernel.expl.LocalContextMapping, {window-size=1} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG BOW, org.itc.irst.tcc.sre.kernel.expl.BagOfWordsMapping, {n-gram=3} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG WN, org.itc.irst.tcc.sre.kernel.expl.WordNetMapping, {wordnet-file=bk/content-container.map.old} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG SL, org.itc.irst.tcc.sre.kernel.expl.ComboMapping, {arg2=LC, arg1=GC} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG COMBO1, org.itc.irst.tcc.sre.kernel.expl.ComboMapping, {arg3=DIST, arg2=LC, arg1=GC} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG COMBO2, org.itc.irst.tcc.sre.kernel.expl.ComboMapping, {arg4=ET, arg3=DIST, arg2=LC, arg1=GC} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG LSA, org.itc.irst.tcc.sre.kernel.expl.LSAMapping, {lsa-matrix-file=dir/file} [o.i.i.t.s.k.e.MappingFactory 14:51:16]
INFO mappingFactory.getInstance: SL [o.i.i.t.s.k.e.MappingFactory 14:51:16]
INFO SL (org.itc.irst.tcc.sre.kernel.expl.ComboMapping) mapping found [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG instance the mapping [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG ComboMapping.ComboMapping [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG ContextMappingFactory uses the default config file: jsre-config.xml [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG mapping-list size: 10 [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG DIST, org.itc.irst.tcc.sre.kernel.expl.DistanceContextMapping, {} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG ET, org.itc.irst.tcc.sre.kernel.expl.EntityMapping, {} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG GC, org.itc.irst.tcc.sre.kernel.expl.GlobalContextMapping, {n-gram=3} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG LC, org.itc.irst.tcc.sre.kernel.expl.LocalContextMapping, {window-size=1} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG BOW, org.itc.irst.tcc.sre.kernel.expl.BagOfWordsMapping, {n-gram=3} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG WN, org.itc.irst.tcc.sre.kernel.expl.WordNetMapping, {wordnet-file=bk/content-container.map.old} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG SL, org.itc.irst.tcc.sre.kernel.expl.ComboMapping, {arg2=LC, arg1=GC} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG COMBO1, org.itc.irst.tcc.sre.kernel.expl.ComboMapping, {arg3=DIST, arg2=LC, arg1=GC} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG COMBO2, org.itc.irst.tcc.sre.kernel.expl.ComboMapping, {arg4=ET, arg3=DIST, arg2=LC, arg1=GC} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG LSA, org.itc.irst.tcc.sre.kernel.expl.LSAMapping, {lsa-matrix-file=dir/file} [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG set the default parameters [o.i.i.t.s.k.e.MappingFactory 14:51:16]
DEBUG ComboMapping.setParameters [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG ComboMapping.number of basic kernels: 2 [o.i.i.t.s.k.e.ComboMapping 14:51:16]
INFO mappingFactory.getInstance: LC [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
INFO LC (org.itc.irst.tcc.sre.kernel.expl.LocalContextMapping) mapping found [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG instance the mapping [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG LocalContextMapping [o.i.i.t.s.k.e.LocalContextMapping 14:51:16]
DEBUG set the default parameters [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG LocalContextMapping.setParameters [o.i.i.t.s.k.e.LocalContextMapping 14:51:16]
DEBUG windowSize: 1 [o.i.i.t.s.k.e.LocalContextMapping 14:51:16]
DEBUG LC:LocalContextMapping [o.i.i.t.s.k.e.ComboMapping 14:51:16]
INFO mappingFactory.getInstance: GC [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
INFO GC (org.itc.irst.tcc.sre.kernel.expl.GlobalContextMapping) mapping found [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG instance the mapping [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG GlobalContextMapping [o.i.i.t.s.k.e.GlobalContextMapping 14:51:16]
DEBUG set the default parameters [o.i.i.t.s.k.e.ContextMappingFactory 14:51:16]
DEBUG GlobalContextMapping.setParameters [o.i.i.t.s.k.e.GlobalContextMapping 14:51:16]
DEBUG n-gram: 3 [o.i.i.t.s.k.e.GlobalContextMapping 14:51:16]
DEBUG GC:GlobalContextMapping [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG 0:LocalContextMapping:2 [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG 1:GlobalContextMapping:3 [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG subspaceCount: 5 [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG ComboMapping.setParameters [o.i.i.t.s.k.e.ComboMapping 14:51:16]
DEBUG reading feature index... [o.i.i.t.s.u.FeatureIndex 14:51:16]
DEBUG featureIndex: dic0, /var/folders/2w/r3qm7hw96z1807mg5hc95t8c0000gn/T/dic05174994661885912166.tmp, 11376 [c.e.b.u.j.JsreFilterAnnotator 14:51:16]
DEBUG reading feature index... [o.i.i.t.s.u.FeatureIndex 14:51:16]
DEBUG featureIndex: dic1, /var/folders/2w/r3qm7hw96z1807mg5hc95t8c0000gn/T/dic13760439841890988734.tmp, 11916 [c.e.b.u.j.JsreFilterAnnotator 14:51:16]
DEBUG reading feature index... [o.i.i.t.s.u.FeatureIndex 14:51:16]
DEBUG featureIndex: dic2, /var/folders/2w/r3qm7hw96z1807mg5hc95t8c0000gn/T/dic25376621626734005867.tmp, 68884 [c.e.b.u.j.JsreFilterAnnotator 14:51:16]
DEBUG reading feature index... [o.i.i.t.s.u.FeatureIndex 14:51:16]
DEBUG featureIndex: dic3, /var/folders/2w/r3qm7hw96z1807mg5hc95t8c0000gn/T/dic37304913664708654117.tmp, 51249 [c.e.b.u.j.JsreFilterAnnotator 14:51:16]
DEBUG reading feature index... [o.i.i.t.s.u.FeatureIndex 14:51:16]
DEBUG featureIndex: dic4, /var/folders/2w/r3qm7hw96z1807mg5hc95t8c0000gn/T/dic46402017587603194666.tmp, 66468 [c.e.b.u.j.JsreFilterAnnotator 14:51:16]
[o.s.UimaPipeline 14:51:18]
Raw
trace.old.log
,---.| | |
`---.|---.,---.,---.| ,---.|__/
|| ||---'| | | || \
`---'` '`---'` `---'`---'` `
Sherlok Server v. 224af9bc74
INFO Done loading from local File store (local_repo): 11 bundles, 29 engines, 16 pipelines [o.s.Controller 14:52:25]
== Spark has ignited ...
>> Listening on 0.0.0.0:9600
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_commons/1.0.2-SNAPSHOT/bluima_commons-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:52:56]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_module/1.0.2-SNAPSHOT/bluima_module-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:52:57]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_parent/1.0.2-SNAPSHOT/bluima_parent-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:52:59]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_utils/1.0.2-SNAPSHOT/bluima_utils-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:02]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_typesystem/1.0.2-SNAPSHOT/bluima_typesystem-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:07]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/blue_commons/1.0.2-SNAPSHOT/blue_commons-1.0.2-SNAPSHOT.pom: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:09]
TRACE org.sherlok:bluima.regions_jsre:pom:1.0.1 () [o.s.u.AetherResolver 14:53:09]
TRACE +- ch.epfl.bbp.nlp:bluima_regions:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- ch.epfl.bbp.nlp:mallet_utils:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- cc.mallet:mallet:jar:2.0.7 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- junit:junit:jar:4.10 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.hamcrest:hamcrest-core:jar:1.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.beanshell:bsh:jar:2.0b4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- jgrapht:jgrapht:jar:0.6.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- net.sf.jwordnet:jwnl:jar:1.4_rc3 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- com.googlecode.matrix-toolkits-java:mtj:jar:0.9.14 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- com.googlecode.netlib-java:netlib-java:jar:0.9.3 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | | +- net.sourceforge.f2j:arpack_combined_all:jar:0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.jdom:jdom:jar:1.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- ch.epfl.bbp.nlp:bluima_topic_models:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.scala-lang:scala-library:jar:2.10.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- com.github.scopt:scopt_2.10:jar:3.2.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- ch.epfl.bbp.nlp:bluima_lexica:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- ch.epfl.bbp.nlp:bluima_xml:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.codehaus.woodstox:woodstox-core-asl:jar:4.0.6 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.codehaus.woodstox:stax2-api:jar:3.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.apache.commons:commons-vfs2:jar:2.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.apache.maven.scm:maven-scm-api:jar:1.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | | +- org.codehaus.plexus:plexus-utils:jar:1.5.6 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.apache.maven.scm:maven-scm-provider-svnexe:jar:1.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | | +- org.apache.maven.scm:maven-scm-provider-svn-commons:jar:1.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | | +- regexp:regexp:jar:1.3 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.jdom:jdom2:jar:2.0.5 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- jaxen:jaxen:jar:1.1.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- ch.epfl.bbp.nlp:bluima_typesystem:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- ch.epfl.bbp.nlp:blue_commons:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- com.google.guava:guava:jar:18.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.apache.commons:commons-math3:jar:3.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.apache.uima:ruta-core:jar:2.1.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.apache.uima:uimaj-core:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.antlr:antlr-runtime:jar:3.5 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.antlr:stringtemplate:jar:3.2.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- antlr:antlr:jar:2.7.7 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.htmlparser:htmlparser:jar:1.6 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- commons-collections:commons-collections:jar:3.2.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.apache.uima:uimaj-tools:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.apache.uima:uimaj-cpe:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.apache.uima:uimaj-adapter-vinci:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.apache.uima:jVinci:jar:2.4.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.apache.commons:commons-lang3:jar:3.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.apache.uima:uimafit-core:jar:2.0.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- commons-lang:commons-lang:jar:2.6 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- commons-logging:commons-logging-api:jar:1.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.springframework:spring-core:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.springframework:spring-asm:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.springframework:spring-context:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | | +- org.springframework:spring-expression:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | | +- org.springframework:spring-beans:jar:3.1.2.RELEASE (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- commons-io:commons-io:jar:2.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.apache.uima:RegularExpressionAnnotator:jar:2.3.2-BBP (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.apache.uima:SnowballAnnotator:jar:2.3.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.apache.uima:ConceptMapper:jar:2.3.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.slf4j:jcl-over-slf4j:jar:1.6.5 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- ch.qos.logback:logback-classic:jar:1.0.6 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- ch.qos.logback:logback-core:jar:1.0.6 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.slf4j:slf4j-api:jar:1.6.5 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE +- ch.epfl.bbp.nlp:bluima_utils:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.apache.xmlbeans:xmlbeans:jar:2.5.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- stax:stax-api:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- com.googlecode.combinatoricslib:combinatoricslib:jar:2.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE +- ch.epfl.bbp.nlp:bluima_units:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE +- ch.epfl.bbp.nlp:bluima_jsre:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- commons-digester:commons-digester:jar:2.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- commons-beanutils:commons-beanutils:jar:1.8.3 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- commons-logging:commons-logging:jar:1.1.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- tw.edu.ntu.csie:libsvm:jar:3.17 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- commons-cli:commons-cli:jar:1.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE +- ch.epfl.bbp.nlp:bluima_commons:jar:1.0.2-SNAPSHOT (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- bioadi:bioadi:jar:0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- bioadi:sptoolkit:jar:0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- bioadi:j-seqalign:jar:0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- mallet:mallet:jar:0.4 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- hu.u_szeged.rgai.bio.uima:linnaeus:jar:2.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- edu.ucdenver.ccp:biolemmatizer-core:jar:1.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- args4j:args4j:jar:2.0.12 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- org.wiki.harvester.dependency:morphadorner:jar:1.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- edu.ucdenver.ccp:biolemmatizer-uima:jar:1.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- org.uimafit:uimafit:jar:1.2.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- edu.ucdenver.ccp:ccp-uima-shims:jar:0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- edu.mit:jwi:jar:2.2.3 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- com.cybozu.labs:langdetect:jar:1.2.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | | +- net.arnx.jsonic:jsonic:jar:1.2.0 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE +- ch.epfl.bbp.nlp:bluima_opennlp:jar:1.0.1 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- net.sf.trove4j:trove4j:jar:2.0.2 (compile) [o.s.u.AetherResolver 14:53:09]
TRACE | +- de.jules:jules-utilities:jar:2.1.1 (compile) [o.s.u.AetherResolver 14:53:09]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_regions/1.0.1/bluima_regions-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:09]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/mallet_utils/1.0.1/mallet_utils-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:09]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_topic_models/1.0.1/bluima_topic_models-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:10]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_lexica/1.0.1/bluima_lexica-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:10]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_xml/1.0.1/bluima_xml-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:10]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_typesystem/1.0.1/bluima_typesystem-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:10]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/blue_commons/1.0.1/blue_commons-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:10]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_utils/1.0.1/bluima_utils-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:11]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_units/1.0.1/bluima_units-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:11]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_jsre/1.0.1/bluima_jsre-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:11]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_commons/1.0.2-SNAPSHOT/bluima_commons-1.0.2-SNAPSHOT.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:12]
WARN Could not validate integrity of download from file:/Users/m/.m2/repository/ch/epfl/bbp/nlp/bluima_opennlp/1.0.1/bluima_opennlp-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 14:53:13]
INFO Using resource path BLUE_UIMA_ROOT=/Users/m/Prog/Projects/MasterProject/bluima/ (resolves to /Users/m/Prog/Projects/MasterProject/bluima) [c.e.b.u.BlueUima 14:53:23]
INFO DEBUG Running in infer mode [c.e.b.u.a.BrainRegionAnnotator 14:53:26]
[o.s.UimaPipeline 14:53:26]
INFO could not TEST pipeline '{"name":"bluima.regions_jsre","version":"1.0.1","description":"annotate brain regions","domain":"bluima","script":["ENGINE SentenceAnnotator:1.0.1;","ENGINE TokenAnnotator:1.0.1;","ENGINE PosTagAnnotator:1.0.1;","ENGINE BlueBioLemmatizer:1.0.1;","ENGINE MeasureRegexAnnotator:1.0.1;","ENGINE PruneMeasuresAnnotator:1.0.1;","ENGINE LinnaeusAnnotator:1.0.1;","ENGINE BrainRegionAnnotator:1.0.1;","ENGINE KeepLargestBrainRegionAnnotator:1.0.1;","ENGINE ExtractSameBrainRegionCoocurrences:1.0.1;","ENGINE JsreBrainRegionFilterAnnotator:1.0.1;","ENGINE KeepLargestCooccurrenceAnnotator:1.0.1;"],"output":{},"tests":[{"input":"Sex differences in the gross size of the rat neocortex.","expected":{"BrainRegion":[{"begin":45,"end":54}]},"visible":false,"actual":{"BrainRegion":[{"begin":45,"end":54}]}}]}' could not initialize UIMA pipeline: Initialization of annotator class "org.apache.uima.ruta.engine.RutaEngine" failed. (Descriptor: <unknown>) [o.s.SherlokServer 14:53:26]
org.sherlok.utils.ValidationException: could not initialize UIMA pipeline: Initialization of annotator class "org.apache.uima.ruta.engine.RutaEngine" failed. (Descriptor: <unknown>)
at org.sherlok.PipelineLoader.load(PipelineLoader.java:185) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at org.sherlok.SherlokServer$3.handle(SherlokServer.java:162) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_75]
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.uima.ruta.engine.RutaEngine" failed. (Descriptor: <unknown>)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:264) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:169) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:205) ~[uimafit-core-2.1.0.jar:2.1.0]
at org.sherlok.UimaPipeline.createEngines(UimaPipeline.java:270) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at org.sherlok.UimaPipeline.initEngines(UimaPipeline.java:228) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at org.sherlok.UimaPipeline.<init>(UimaPipeline.java:122) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at org.sherlok.PipelineLoader.load(PipelineLoader.java:183) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
... 14 common frames omitted
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "ch.epfl.bbp.uima.ae.BrainRegionAnnotator" failed. (Descriptor: file:/Users/m/Prog/Projects/MasterProject/sherlok/config/resources/.engines/BrainRegionAnnotator___1_0_1.xml)
at org.apache.uima.ruta.engine.RutaEngine.initialize(RutaEngine.java:468) ~[ruta-core-2.2.1.jar:2.2.1]
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:262) ~[uimaj-core-2.7.0.jar:2.7.0]
... 25 common frames omitted
Caused by: org.apache.uima.analysis_engine.AnalysisEngineProcessException: Initialization of annotator class "ch.epfl.bbp.uima.ae.BrainRegionAnnotator" failed. (Descriptor: file:/Users/m/Prog/Projects/MasterProject/sherlok/config/resources/.engines/BrainRegionAnnotator___1_0_1.xml)
at org.apache.uima.ruta.engine.RutaEngine.initializeScript(RutaEngine.java:755) ~[ruta-core-2.2.1.jar:2.2.1]
at org.apache.uima.ruta.engine.RutaEngine.initialize(RutaEngine.java:466) ~[ruta-core-2.2.1.jar:2.2.1]
... 26 common frames omitted
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "ch.epfl.bbp.uima.ae.BrainRegionAnnotator" failed. (Descriptor: file:/Users/m/Prog/Projects/MasterProject/sherlok/config/resources/.engines/BrainRegionAnnotator___1_0_1.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:264) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:169) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371) ~[uimaj-core-2.7.0.jar:2.7.0]
at org.apache.uima.ruta.engine.Ruta.wrapAnalysisEngine(Ruta.java:98) ~[ruta-core-2.2.1.jar:2.2.1]
at org.apache.uima.ruta.engine.Ruta.wrapAnalysisEngine(Ruta.java:89) ~[ruta-core-2.2.1.jar:2.2.1]
at org.apache.uima.ruta.extensions.DefaultEngineLoader.loadEngineMyself(DefaultEngineLoader.java:49) ~[ruta-core-2.2.1.jar:2.2.1]
at org.apache.uima.ruta.extensions.RutaEngineLoader.loadEngine(RutaEngineLoader.java:52) ~[ruta-core-2.2.1.jar:2.2.1]
at org.apache.uima.ruta.engine.RutaEngine.initializeScript(RutaEngine.java:753) ~[ruta-core-2.2.1.jar:2.2.1]
... 27 common frames omitted
Caused by: org.apache.uima.resource.ResourceInitializationException: null
at ch.epfl.bbp.uima.ae.BrainRegionAnnotator.initialize(BrainRegionAnnotator.java:146) ~[bluima_regions-1.0.1.jar:na]
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:262) ~[uimaj-core-2.7.0.jar:2.7.0]
... 37 common frames omitted
Caused by: java.io.InvalidClassException: gnu.trove.TObjectHash; local class incompatible: stream classdesc serialVersionUID = -3461112548087185871, local class serialVersionUID = 876253628862239263
at java.io.ObjectStreamClass.initNonProxy(ObjectStreamClass.java:617) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1622) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1517) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1622) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1517) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1771) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) ~[na:1.7.0_75]
at cc.mallet.pipe.tsf.LexiconMembership.readObject(LexiconMembership.java:107) ~[mallet-2.0.7.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_75]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_75]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_75]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_75]
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) ~[na:1.7.0_75]
at java.util.ArrayList.readObject(ArrayList.java:771) ~[na:1.7.0_75]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_75]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_75]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_75]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_75]
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) ~[na:1.7.0_75]
at cc.mallet.pipe.SerialPipes.readObject(SerialPipes.java:142) ~[mallet-2.0.7.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_75]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_75]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_75]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_75]
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) ~[na:1.7.0_75]
at cc.mallet.fst.Transducer.readObject(Transducer.java:219) ~[mallet-2.0.7.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_75]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_75]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_75]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_75]
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) ~[na:1.7.0_75]
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) ~[na:1.7.0_75]
at ch.epfl.bbp.uima.ae.BrainRegionAnnotator.initialize(BrainRegionAnnotator.java:134) ~[bluima_regions-1.0.1.jar:na]
... 38 common frames omitted
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