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PavlidisLab / Gemma

Genomics data re-analysis
Apache License 2.0
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hibernate error when deleting batch factor #713

Closed ppavlidis closed 1 year ago

ppavlidis commented 1 year ago

fillBatchInfo -e GSE2018 -force

/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/bin/java -Xmx4g -Dgemma.log.dir=/Users/pzoot/gemma-tmp/logs -Dehcache.disk.store.dir=/Users/pzoot/gemma-tmp/gemmaAppData/caches -Dlog4j.configuration=file:gemma-cli/src/main/config/log4j.properties -Dontology.index.dir=/Users/pzoot/gemma-tmp/searchIndices/ontology -javaagent:/Applications/IntelliJ IDEA.app/Contents/lib/idea_rt.jar=53876:/Applications/IntelliJ IDEA.app/Contents/bin -Dfile.encoding=UTF-8 -classpath /Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/charsets.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/cldrdata.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/dnsns.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/jaccess.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/jfxrt.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/localedata.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/nashorn.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/sunec.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/sunjce_provider.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/sunpkcs11.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/ext/zipfs.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/jce.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/jfr.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/jfxswt.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/jsse.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/management-agent.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/resources.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/jre/lib/rt.jar:/Users/pzoot/Dev/eclipseworkspace/Gemma/gemma-cli/target/classes:/Users/pzoot/Dev/eclipseworkspace/Gemma/gemma-core/target/classes:/Users/pzoot/maven.repository/org/springframework/retry/spring-retry/1.0.3.RELEASE/spring-retry-1.0.3.RELEASE.jar:/Users/pzoot/maven.repository/com/sun/mail/javax.mail/1.6.2/javax.mail-1.6.2.jar:/Users/pzoot/maven.repository/javax/activation/activation/1.1/activation-1.1.jar:/Users/pzoot/maven.repository/org/apache/velocity/velocity-engine-core/2.3/velocity-engine-core-2.3.jar:/Users/pzoot/maven.repository/org/apache/lucene/lucene-core/3.6.2/lucene-core-3.6.2.jar:/Users/pzoot/maven.repository/org/apache/lucene/lucene-analyzers/3.6.2/lucene-analyzers-3.6.2.jar:/Users/pzoot/maven.repository/ubc/chibi/compass-fork/compass-fork/1.2.0/compass-fork-1.2.0.jar:/Users/pzoot/maven.repository/org/apache/lucene/lucene-queries/3.6.2/lucene-queries-3.6.2.jar:/Users/pzoot/maven.repository/jakarta-regexp/jakarta-regexp/1.4/jakarta-regexp-1.4.jar:/Users/pzoot/maven.repository/org/apache/lucene/lucene-queryparser/3.6.2/lucene-queryparser-3.6.2.jar:/Users/pzoot/maven.repository/org/apache/lucene/lucene-highlighter/3.6.2/lucene-highlighter-3.6.2.jar:/Users/pzoot/maven.repository/org/apache/lucene/lucene-memory/3.6.2/lucene-memory-3.6.2.jar:/Users/pzoot/maven.repository/javax/transaction/jta/1.1/jta-1.1.jar:/Users/pzoot/maven.repository/xpp3/xpp3/1.1.4c/xpp3-1.1.4c.jar:/Users/pzoot/maven.repository/pull-parser/pull-parser/2.1.10/pull-parser-2.1.10.jar:/Users/pzoot/maven.repository/jaxen/jaxen/1.2.0/jaxen-1.2.0.jar:/Users/pzoot/maven.repository/net/java/dev/javacc/javacc/5.0/javacc-5.0.jar:/Users/pzoot/maven.repository/mx4j/mx4j/3.0.2/mx4j-3.0.2.jar:/Users/pzoot/maven.repository/asm/asm/3.3.1/asm-3.3.1.jar:/Users/pzoot/maven.repository/asm/asm-commons/3.3.1/asm-commons-3.3.1.jar:/Users/pzoot/maven.repository/asm/asm-tree/3.3.1/asm-tree-3.3.1.jar:/Users/pzoot/maven.repository/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar:/Users/pzoot/maven.repository/org/apache/commons/commons-math3/3.6.1/commons-math3-3.6.1.jar:/Users/pzoot/maven.repository/commons-net/commons-net/3.9.0/commons-net-3.9.0.jar:/Users/pzoot/maven.repository/javax/xml/bind/jaxb-api/2.3.1/jaxb-api-2.3.1.jar:/Users/pzoot/maven.repository/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar:/Users/pzoot/maven.repository/obo/org.geneontology/1.002/org.geneontology-1.002.jar:/Users/pzoot/maven.repository/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar:/Users/pzoot/maven.repository/jboss/jboss-ejb3x/4.2.2.GA/jboss-ejb3x-4.2.2.GA.jar:/Users/pzoot/maven.repository/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar:/Users/pzoot/maven.repository/org/apache/logging/log4j/log4j-api/2.20.0/log4j-api-2.20.0.jar:/Users/pzoot/maven.repository/baseCode/baseCode/1.1.16/baseCode-1.1.16.jar:/Users/pzoot/maven.repository/org/apache/poi/poi/5.2.3/poi-5.2.3.jar:/Users/pzoot/maven.repository/commons-codec/commons-codec/1.15/commons-codec-1.15.jar:/Users/pzoot/maven.repository/com/zaxxer/SparseBitSet/1.2/SparseBitSet-1.2.jar:/Users/pzoot/maven.repository/org/apache/httpcomponents/httpcore/4.4.16/httpcore-4.4.16.jar:/Users/pzoot/maven.repository/org/apache/httpcomponents/httpclient/4.5.14/httpclient-4.5.14.jar:/Users/pzoot/maven.repository/org/rosuda/REngine/REngine/2.1.0/REngine-2.1.0.jar:/Users/pzoot/maven.repository/RoSuDA/JRI/0.5-0/JRI-0.5-0.jar:/Users/pzoot/maven.repository/RoSuDA/JRIEngine/0.5-0/JRIEngine-0.5-0.jar:/Users/pzoot/maven.repository/com/googlecode/matrix-toolkits-java/mtj/1.0.4/mtj-1.0.4.jar:/Users/pzoot/maven.repository/net/sourceforge/f2j/arpack_combined_all/0.1/arpack_combined_all-0.1.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/core/1.1.2/core-1.1.2.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_ref-osx-x86_64/1.1/netlib-native_ref-osx-x86_64-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/native_ref-java/1.1/native_ref-java-1.1.jar:/Users/pzoot/maven.repository/com/github/fommil/jniloader/1.1/jniloader-1.1.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_ref-linux-x86_64/1.1/netlib-native_ref-linux-x86_64-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_ref-linux-i686/1.1/netlib-native_ref-linux-i686-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_ref-win-x86_64/1.1/netlib-native_ref-win-x86_64-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_ref-win-i686/1.1/netlib-native_ref-win-i686-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_ref-linux-armhf/1.1/netlib-native_ref-linux-armhf-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_system-osx-x86_64/1.1/netlib-native_system-osx-x86_64-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/native_system-java/1.1/native_system-java-1.1.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_system-linux-x86_64/1.1/netlib-native_system-linux-x86_64-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_system-linux-i686/1.1/netlib-native_system-linux-i686-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_system-linux-armhf/1.1/netlib-native_system-linux-armhf-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_system-win-x86_64/1.1/netlib-native_system-win-x86_64-1.1-natives.jar:/Users/pzoot/maven.repository/com/github/fommil/netlib/netlib-native_system-win-i686/1.1/netlib-native_system-win-i686-1.1-natives.jar:/Users/pzoot/maven.repository/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar:/Users/pzoot/maven.repository/org/apache/jena/jena-core/2.7.4/jena-core-2.7.4.jar:/Users/pzoot/maven.repository/org/apache/jena/jena-iri/0.9.4/jena-iri-0.9.4.jar:/Users/pzoot/maven.repository/org/apache/jena/jena-larq/1.0.0-incubating/jena-larq-1.0.0-incubating.jar:/Users/pzoot/maven.repository/org/apache/jena/jena-arq/2.9.4/jena-arq-2.9.4.jar:/Users/pzoot/maven.repository/org/slf4j/jcl-over-slf4j/1.7.36/jcl-over-slf4j-1.7.36.jar:/Users/pzoot/maven.repository/com/opencsv/opencsv/5.7.1/opencsv-5.7.1.jar:/Users/pzoot/maven.repository/pavlab/gemma-gsec/0.0.12-SNAPSHOT/gemma-gsec-0.0.12-20230518.173052-8.jar:/Users/pzoot/maven.repository/org/springframework/security/spring-security-web/3.2.10.RELEASE/spring-security-web-3.2.10.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-web/3.2.18.RELEASE/spring-web-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar:/Users/pzoot/maven.repository/org/json/json/20230227/json-20230227.jar:/Users/pzoot/maven.repository/org/springframework/spring-core/3.2.18.RELEASE/spring-core-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-beans/3.2.18.RELEASE/spring-beans-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-expression/3.2.18.RELEASE/spring-expression-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-context/3.2.18.RELEASE/spring-context-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-context-support/3.2.18.RELEASE/spring-context-support-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-aspects/3.2.18.RELEASE/spring-aspects-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/aspectj/aspectjweaver/1.9.19/aspectjweaver-1.9.19.jar:/Users/pzoot/maven.repository/org/springframework/spring-aop/3.2.18.RELEASE/spring-aop-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-tx/3.2.18.RELEASE/spring-tx-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/security/spring-security-core/3.2.10.RELEASE/spring-security-core-3.2.10.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/security/spring-security-acl/3.2.10.RELEASE/spring-security-acl-3.2.10.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/security/spring-security-config/3.2.10.RELEASE/spring-security-config-3.2.10.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-jdbc/3.2.18.RELEASE/spring-jdbc-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/springframework/spring-orm/3.2.18.RELEASE/spring-orm-3.2.18.RELEASE.jar:/Users/pzoot/maven.repository/org/hibernate/hibernate-core/4.2.21.Final/hibernate-core-4.2.21.Final.jar:/Users/pzoot/maven.repository/antlr/antlr/2.7.7/antlr-2.7.7.jar:/Users/pzoot/maven.repository/org/jboss/logging/jboss-logging/3.1.0.GA/jboss-logging-3.1.0.GA.jar:/Users/pzoot/maven.repository/org/javassist/javassist/3.29.2-GA/javassist-3.29.2-GA.jar:/Users/pzoot/maven.repository/org/jboss/spec/javax/transaction/jboss-transaction-api_1.1_spec/1.0.1.Final/jboss-transaction-api_1.1_spec-1.0.1.Final.jar:/Users/pzoot/maven.repository/org/hibernate/javax/persistence/hibernate-jpa-2.0-api/1.0.1.Final/hibernate-jpa-2.0-api-1.0.1.Final.jar:/Users/pzoot/maven.repository/org/hibernate/common/hibernate-commons-annotations/4.0.2.Final/hibernate-commons-annotations-4.0.2.Final.jar:/Users/pzoot/maven.repository/org/dom4j/dom4j/2.1.4/dom4j-2.1.4.jar:/Users/pzoot/maven.repository/org/hibernate/hibernate-ehcache/4.2.21.Final/hibernate-ehcache-4.2.21.Final.jar:/Users/pzoot/maven.repository/com/mysql/mysql-connector-j/8.0.32/mysql-connector-j-8.0.32.jar:/Users/pzoot/maven.repository/com/google/protobuf/protobuf-java/3.21.9/protobuf-java-3.21.9.jar:/Users/pzoot/maven.repository/com/zaxxer/HikariCP/4.0.3/HikariCP-4.0.3.jar:/Users/pzoot/maven.repository/net/sf/ehcache/ehcache-core/2.4.3/ehcache-core-2.4.3.jar:/Users/pzoot/maven.repository/colt/colt/1.2.0/colt-1.2.0.jar:/Users/pzoot/maven.repository/concurrent/concurrent/1.3.4/concurrent-1.3.4.jar:/Users/pzoot/maven.repository/com/google/guava/guava/31.1-jre/guava-31.1-jre.jar:/Users/pzoot/maven.repository/com/google/guava/failureaccess/1.0.1/failureaccess-1.0.1.jar:/Users/pzoot/maven.repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:/Users/pzoot/maven.repository/org/checkerframework/checker-qual/3.12.0/checker-qual-3.12.0.jar:/Users/pzoot/maven.repository/com/google/errorprone/error_prone_annotations/2.11.0/error_prone_annotations-2.11.0.jar:/Users/pzoot/maven.repository/com/google/j2objc/j2objc-annotations/1.3/j2objc-annotations-1.3.jar:/Users/pzoot/maven.repository/javax/resource/javax.resource-api/1.7.1/javax.resource-api-1.7.1.jar:/Users/pzoot/maven.repository/javax/transaction/javax.transaction-api/1.3/javax.transaction-api-1.3.jar:/Users/pzoot/maven.repository/org/apache/ant/ant/1.10.13/ant-1.10.13.jar:/Users/pzoot/maven.repository/org/apache/ant/ant-launcher/1.10.13/ant-launcher-1.10.13.jar:/Users/pzoot/Library/Java/JavaVirtualMachines/corretto-1.8.0_372/Contents/Home/lib/tools.jar:/Users/pzoot/maven.repository/org/jfree/jfreechart/1.5.4/jfreechart-1.5.4.jar:/Users/pzoot/maven.repository/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar:/Users/pzoot/maven.repository/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar:/Users/pzoot/maven.repository/commons-logging/commons-logging/1.2/commons-logging-1.2.jar:/Users/pzoot/maven.repository/commons-logging/commons-logging-api/1.1/commons-logging-api-1.1.jar:/Users/pzoot/maven.repository/commons-beanutils/commons-beanutils/1.9.4/commons-beanutils-1.9.4.jar:/Users/pzoot/maven.repository/org/apache/commons/commons-collections4/4.4/commons-collections4-4.4.jar:/Users/pzoot/maven.repository/commons-collections/commons-collections/3.2.2/commons-collections-3.2.2.jar:/Users/pzoot/maven.repository/org/apache/commons/commons-configuration2/2.8.0/commons-configuration2-2.8.0.jar:/Users/pzoot/maven.repository/commons-io/commons-io/2.11.0/commons-io-2.11.0.jar:/Users/pzoot/maven.repository/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar:/Users/pzoot/maven.repository/com/fasterxml/jackson/core/jackson-core/2.14.2/jackson-core-2.14.2.jar:/Users/pzoot/maven.repository/com/fasterxml/jackson/core/jackson-annotations/2.14.2/jackson-annotations-2.14.2.jar:/Users/pzoot/maven.repository/com/fasterxml/jackson/core/jackson-databind/2.14.2/jackson-databind-2.14.2.jar:/Users/pzoot/maven.repository/xml-apis/xml-apis/1.4.01/xml-apis-1.4.01.jar:/Users/pzoot/maven.repository/xerces/xercesImpl/2.12.2/xercesImpl-2.12.2.jar:/Users/pzoot/maven.repository/org/apache/logging/log4j/log4j-core/2.20.0/log4j-core-2.20.0.jar:/Users/pzoot/maven.repository/org/apache/logging/log4j/log4j-slf4j-impl/2.20.0/log4j-slf4j-impl-2.20.0.jar:/Users/pzoot/maven.repository/org/apache/logging/log4j/log4j-1.2-api/2.20.0/log4j-1.2-api-2.20.0.jar:/Users/pzoot/maven.repository/org/apache/logging/log4j/log4j-jcl/2.20.0/log4j-jcl-2.20.0.jar:/Users/pzoot/maven.repository/org/apache/logging/log4j/log4j-jul/2.20.0/log4j-jul-2.20.0.jar:/Users/pzoot/maven.repository/io/micrometer/micrometer-core/1.10.4/micrometer-core-1.10.4.jar:/Users/pzoot/maven.repository/io/micrometer/micrometer-commons/1.10.4/micrometer-commons-1.10.4.jar:/Users/pzoot/maven.repository/io/micrometer/micrometer-observation/1.10.4/micrometer-observation-1.10.4.jar:/Users/pzoot/maven.repository/org/hdrhistogram/HdrHistogram/2.1.12/HdrHistogram-2.1.12.jar:/Users/pzoot/maven.repository/org/latencyutils/LatencyUtils/2.0.3/LatencyUtils-2.0.3.jar:/Users/pzoot/maven.repository/io/micrometer/micrometer-registry-jmx/1.10.4/micrometer-registry-jmx-1.10.4.jar:/Users/pzoot/maven.repository/io/dropwizard/metrics/metrics-jmx/4.2.16/metrics-jmx-4.2.16.jar:/Users/pzoot/maven.repository/io/dropwizard/metrics/metrics-core/4.2.16/metrics-core-4.2.16.jar:/Users/pzoot/maven.repository/org/projectlombok/lombok/1.18.26/lombok-1.18.26.jar:/Users/pzoot/maven.repository/com/google/code/findbugs/jsr305/3.0.2/jsr305-3.0.2.jar ubic.gemma.core.apps.GemmaCLI fillBatchInfo -e GSE2018 -force
2023-06-05 14:05:53,436 WARN 55054 [main] ubic.gemma.persistence.util.SpringContextUtil.prepareContext(102) | No profiles were detected, activating the 'dev' profile as a fallback. Use -Dspring.profiles.active=dev explicitly to remove this warning.
2023-06-05 14:05:53,548 INFO 55054 [main] ubic.gemma.persistence.util.SpringContextUtil.prepareContext(106) | Loading Gemma 1.30.0-SNAPSHOT built 2023-05-30T17:29:34Z (active profiles: cli, dev), hold on!
2023-06-05 14:05:55,571 WARN 55054 [main] ubic.gemma.core.ontology.providers.OntologyServiceFactory.<clinit>(25) | Auto-loading of ontologies is disabled, enable it by setting load.ontologies=true in Gemma.properties.
2023-06-05 14:06:09,019 INFO 55054 [main] ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.afterPropertiesSet(151) | Auto-loading of ontologies is disabled, GO terms will not be available.
2023-06-05 14:06:09,619 WARN 55054 [main] ubic.gemma.core.ontology.OntologyServiceImpl.afterPropertiesSet(137) | No ontologies are enabled, consider enabling them by setting 'load.{name}Ontology' options in Gemma.properties.
2023-06-05 14:06:10,603 WARN 55054 [main] ubic.gemma.core.util.DummyMailSender.afterPropertiesSet(42) | Emails will be sent to a dummy mail sender. If this is not intended, activate the 'production' profile by setting -Dspring.profiles.active=production.
2023-06-05 14:06:11,236 INFO 55054 [main] ubic.gemma.persistence.util.SpringContextUtil.getApplicationContext(68) | Got Gemma context in 17869 ms.
========= Gemma CLI invocation of fillBatchInfo ============
Options: -e GSE2018 -force
Gemma version 1.30.0-SNAPSHOT built 2023-05-30T17:29:34Z
2023-06-05 14:06:11,382 INFO 55054 [main] ubic.gemma.core.util.AbstractSpringAwareCLI.authenticate(230) | Logged in as administrator
2023-06-05 14:06:12,202 INFO 55054 [main] ubic.gemma.core.apps.BatchEffectPopulationCli.doWork(65) | Processing: ExpressionExperiment Id=1 Name=Human Lung Transplant - BAL Short Name=GSE2018
2023-06-05 14:06:12,314 INFO 55054 [main] ubic.gemma.core.util.NetDatasourceUtil.connect(46) | Connecting to ftp.ncbi.nih.gov with anonymous : gemma@ubic.ca
2023-06-05 14:06:13,850 INFO 55054 [pool-28-thread-1] ubic.gemma.core.loader.util.fetcher.FtpFetcher$1.call(91) | Fetching geo/series//GSE2nnn/GSE2018/suppl/GSE2018_RAW.tar to /Users/pzoot/gemma-tmp/arraydata/GEO/GSE2018/rawDataFiles/GSE2018_RAW.tar
2023-06-05 14:06:23,854 INFO 55054 [main] ubic.gemma.core.loader.util.fetcher.AbstractFetcher.waitForDownload(282) | 62924556/119521280 bytes read (52.6%)
2023-06-05 14:06:33,859 INFO 55054 [main] ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher.doTask(87) | Unpacking /Users/pzoot/gemma-tmp/arraydata/GEO/GSE2018/rawDataFiles/GSE2018_RAW.tar
2023-06-05 14:06:43,867 INFO 55054 [main] ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher.unPack(225) | Unpacking archive ... 10.0 seconds elapsed
2023-06-05 14:06:43,885 INFO 55054 [main] ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher.fetch(107) | 68 files obtained from archive
2023-06-05 14:06:49,811 INFO 55054 [main] ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl.removeExistingBatchFactor(449) | Removing existing batch factor: ExperimentalFactor Id=8997 Name=batch
2023-06-05 14:06:51,550 ERROR 55054 [main] ubic.gemma.core.util.AbstractCLI.addErrorObject(399) | Failed to pre-process GSE2018
ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException: Failed to pre-process GSE2018
    at ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl.fillBatchInformation(BatchInfoPopulationServiceImpl.java:149) ~[classes/:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_372]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_372]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_372]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_372]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:96) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:260) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.retry.interceptor.RetryOperationsInterceptor$1.doWithRetry(RetryOperationsInterceptor.java:69) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.retry.support.RetryTemplate.doExecute(RetryTemplate.java:255) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.retry.support.RetryTemplate.execute(RetryTemplate.java:148) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.retry.interceptor.RetryOperationsInterceptor.invoke(RetryOperationsInterceptor.java:90) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:91) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at com.sun.proxy.$Proxy163.fillBatchInformation(Unknown Source) ~[?:?]
    at ubic.gemma.core.apps.BatchEffectPopulationCli.doWork(BatchEffectPopulationCli.java:69) [classes/:?]
    at ubic.gemma.core.util.AbstractCLI.executeCommand(AbstractCLI.java:133) [classes/:?]
    at ubic.gemma.core.apps.GemmaCLI.main(GemmaCLI.java:197) [classes/:?]
Caused by: org.hibernate.ObjectDeletedException: deleted object would be re-saved by cascade (remove deleted object from associations): [ubic.gemma.model.expression.experiment.ExperimentalFactor#8997]
    at org.hibernate.internal.SessionImpl.forceFlush(SessionImpl.java:1208) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:184) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:114) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:90) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.internal.SessionImpl.fireSaveOrUpdate(SessionImpl.java:654) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:646) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.spi.CascadingAction$5.cascade(CascadingAction.java:258) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeToOne(Cascade.java:396) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:339) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:207) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeCollectionElements(Cascade.java:426) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeCollection(Cascade.java:366) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:342) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:207) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.engine.internal.Cascade.cascade(Cascade.java:164) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:165) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:156) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:89) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:61) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1166) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1223) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101) ~[hibernate-core-4.2.21.Final.jar:4.2.21.Final]
    at gemma.gsec.acl.domain.AclDaoImpl.find(AclDaoImpl.java:129) ~[gemma-gsec-0.0.12-20230518.173052-8.jar:?]
    at gemma.gsec.acl.domain.AclServiceImpl.deleteAcl(AclServiceImpl.java:80) ~[gemma-gsec-0.0.12-20230518.173052-8.jar:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_372]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_372]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_372]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_372]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:96) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:260) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at com.sun.proxy.$Proxy48.deleteAcl(Unknown Source) ~[?:?]
    at gemma.gsec.acl.BaseAclAdvice.deleteAcl(BaseAclAdvice.java:521) ~[gemma-gsec-0.0.12-20230518.173052-8.jar:?]
    at gemma.gsec.acl.BaseAclAdvice.process(BaseAclAdvice.java:712) ~[gemma-gsec-0.0.12-20230518.173052-8.jar:?]
    at gemma.gsec.acl.BaseAclAdvice.doAclAdvice(BaseAclAdvice.java:118) ~[gemma-gsec-0.0.12-20230518.173052-8.jar:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_372]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_372]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_372]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_372]
    at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethodWithGivenArgs(AbstractAspectJAdvice.java:621) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethod(AbstractAspectJAdvice.java:603) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.aspectj.AspectJAfterReturningAdvice.afterReturning(AspectJAfterReturningAdvice.java:58) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.adapter.AfterReturningAdviceInterceptor.invoke(AfterReturningAdviceInterceptor.java:52) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:91) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at com.sun.proxy.$Proxy79.remove(Unknown Source) ~[?:?]
    at ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl.delete(ExperimentalFactorServiceImpl.java:60) ~[classes/:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_372]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_372]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_372]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_372]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:166) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:166) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:96) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:260) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94) ~[spring-tx-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.retry.interceptor.RetryOperationsInterceptor$1.doWithRetry(RetryOperationsInterceptor.java:69) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.retry.support.RetryTemplate.doExecute(RetryTemplate.java:255) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.retry.support.RetryTemplate.execute(RetryTemplate.java:148) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.retry.interceptor.RetryOperationsInterceptor.invoke(RetryOperationsInterceptor.java:90) ~[spring-retry-1.0.3.RELEASE.jar:?]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:64) ~[spring-security-core-3.2.10.RELEASE.jar:?]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:91) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) ~[spring-aop-3.2.18.RELEASE.jar:3.2.18.RELEASE]
    at com.sun.proxy.$Proxy80.delete(Unknown Source) ~[?:?]
    at ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl.removeExistingBatchFactor(BatchInfoPopulationServiceImpl.java:450) ~[classes/:?]
    at ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl.getBatchDataFromRawFiles(BatchInfoPopulationServiceImpl.java:265) ~[classes/:?]
    at ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl.fillBatchInformation(BatchInfoPopulationServiceImpl.java:145) ~[classes/:?]
    ... 23 more
2023-06-05 14:06:51,561 ERROR 55054 [main] ubic.gemma.core.util.AbstractCLI.summarizeProcessing(427) | 
---------------------
Errors occurred during the processing of 1 objects:
ExpressionExperiment Id=1 Name=Human Lung Transplant - BAL Short Name=GSE2018:
    Failed to pre-process GSE2018
---------------------

2023-06-05 14:06:51,562 INFO 55054 [main] ubic.gemma.core.util.AbstractCLI.executeCommand(141) | Elapsed time: 40 seconds.

Process finished with exit code 1
arteymix commented 1 year ago

Something in the session is still referring to the EF, I'm tracking it down.

arteymix commented 1 year ago

Ok, figured it out, it was the owning ExperimentalDesign that had still a hold on its EF.

arteymix commented 1 year ago

Take 2 in 9ea0791560c7538a6338070ad61460422159b96b. I moved the fix in the DAO layer, added some tests and also simplified some of the tests since we don't need to detach the factor manually anymore (it's done by the service/dao).