granvold
commented
8 years ago Hi Peter and Tom,
First, an NPE. How embarrassing!
From the log provided, the problem appears to be that content is not properly being loaded into the database. I would expect to see a variety of lines like:
Loading Concepts … 2000 complete 4000 complete 6000 complete .. Loading Descriptions .. Loading Relationships …
And so forth. Specifically, at the point of failure, the metadata handler is expecting the concept representing the IsA relationship to exist and is failing to retrieve it.
The most likely cause of failure will lie with the sorted RF2 files that are automatically generated by the loader. Looking back at our code, I’m realizing that we have a pretty bad check for whether or not to sort files based on modification dates … I’ll make a Jira MAP ticket for this. Basically the loader is incorrectly assuming that pre-sorted files exist and can be used, when they don’t and can’t.
In the meantime, the problem should be solved by the following: (1) Check for the existence of folder /home/tom/Data/snomedct-20140731-snapshot/RF2-sorted-temp. It may or may not contain files, doesn't matter. (2) Delete this folder (3) Re-run the loader. (4) The files should be re-sorted and the load should continue normally. (5) On any subsequent cancellations or re-loads, repeat that deletion …. Just to be safe.
If that folder doesn't exist, let us know, because that would be extremely weird.
Cheers, Patrick
P.S. Edited for some styling and as much clarity as I can get before coffee kicks in.
From: Peter G. Williams [mailto:notifications@github.com] Sent: Friday, May 27, 2016 1:43 AM To: IHTSDO/OTF-Mapping-Service OTF-Mapping-Service@noreply.github.com Subject: [IHTSDO/OTF-Mapping-Service] Null pointer on loading data (#43)
Tom wrote to IHTSDO with the following issue which has been partially discussed via our internal issue tracking system. Full stack trace included at the end:
TOM: On loading SCT into the mapping tool (according to step 7 on https://confluence.ihtsdotools.org/display/MT/Building+and+Deploying+in+Eclipse) the following error occurs: [ERROR] Failed to execute goal org.ihtsdo.otf.mapping:mapping-admin-mojo:1.0.10-SNAPSHOT:load-rf2-snapshot (load-rf2-snapshot) on project mapping-admin-loader: Unexpected exception: NullPointerException -> [Help 1] The full error is added it this email. Can you help me fix this?
KAI: Is this the first time you are attempting the load the data? It could be worth trying running truncate_all.sql and trying again. From the documentation: "NOTE: if re-running this, you first have to run the sql in "truncate_all.sql" to clear your database of tables."
TOM: I tried that already, same error occurs at the same time in the dev-windows build as well as in the prod build.
`------------------------------------------------
Starting ...Thu May 26 01:14:47 PDT 2016
MAPPING_CODE = /home/tom/Code MAPPING_DATA = /home/tom/Code MAPPING_CONFIG = /home/tom/Code Run updatedb with hibernate.hbm2ddl.auto = create ...Thu May 26 01:14:47 PDT 2016 Clear indexes ...Thu May 26 01:15:01 PDT 2016 Load SNOMEDCT ...Thu May 26 01:15:12 PDT 2016 ERROR loading SNOMEDCT [INFO] Scanning for projects... [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building OTF RF2 Admin RF2 Loader 1.0.10-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- mapping-admin-mojo:1.0.10-SNAPSHOT:load-rf2-snapshot (load-rf2-snapshot) @ mapping-admin-loader --- [INFO] Starting loading RF2 data [INFO] inputDir = /home/tom/Data/snomedct-20140731-snapshot [INFO] terminology = SNOMEDCT [INFO] sendNotification = false 2016-05-26_01:15:17.108 INFO - run.config = /home/tom/Config/config.properties 2016-05-26_01:15:17.114 INFO - properties = {workflow.path.handler.NON_LEGACY_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowNonLegacyPathHandler, loader.defaultPreferredNames.typeId=900000000000003001, mail.smtp.starttls.enable=true, index.viewer.subSubSearchEndLevel=2, mail.smtp.auth=true, mail.smtp.to.feedback.user=delnoy@gmail.com mailto:delnoy@gmail.com , hibernate.jdbc.default_batch_fetch_size=16, mail.smtp.password=tdrg2ewm, workflow.path.handler=NON_LEGACY_PATH,LEGACY_PATH,REVIEW_PROJECT_PATH,FIX_ERROR_PATH,QA_PATH,SIMPLE_PATH, javax.persistence.jdbc.user=root, send.notification.recipients=delnoy@gmail.com mailto:delnoy@gmail.com , metadata.service.handler.GMDN.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, base.url.webapp=http://localhost:8080/mapping-webapp, deploy.footer.link=http://www.ihtsdo.org/, loader.defaultPreferredNames.refSetId=900000000000509007, javax.per sistence .jdbc.password=tdrg2ewm, hibernate.search.default.indexBase=/home/tom/Data, metadata.service.handler.ICPC.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, metadata.service.handler.ICD10.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, index.viewer.data=/home/tom/Data/ihtsdo-mapping-tool-data/indexViewerData, index.viewer.linkSubstitutions=s/Complications/Complication/;, index.viewer.searchStartLevel=0, mail.smtp.user=delnoy@gmail.com mailto:delnoy@gmail.com , workflow.path.handler.SIMPLE_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowSimplePathHandler, metadata.service.handler.SNOMEDCT.class=org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper, index.viewer.subSubSearchStartLevel=2, javax.persistence.jdbc.url=jdbc:mysql://127.0.0.1:3306/mappingservicedb, index.viewer.artifactId=index-viewer-data-empty, metadata.service.handler=SNOMEDCT,SNOMEDCT_US,ICD10,ICD10CM,ICD9CM,ICPC,GMDN, javax.persis tence.jd bc.driver=com.mysql.jdbc.Driver, ihtsdo.security.activated=false, mail.smtp.port=587, workflow.path.handler.REVIEW_PROJECT_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowReviewProjectPathHandler, loader.defaultPreferredNames.acceptabilityId=900000000000548007, deploy.title=IHTSDO Mapping Tool - DEV, hibernate.format_sql=true, deploy.footer.copyright=Copyright @2015 https://github.com/2015 IHTSDO, base.url=http://localhost:8080/mapping-rest, index.viewer.searchEndLevel=0, index.viewer.maxHits=10000, hibernate.use_sql_comments=true, hibernate.show_sql=false, workflow.path.handler.FIX_ERROR_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowFixErrorPathHandler, map.principle.source.document.dir=/home/tom/Data/doc, hibernate.dialect=org.hibernate.dialect.MySQLDialect, index.viewer.phonet=./config/dict/phonet.en, index.viewer.version=1.3.0-SNAPSHOT, index.viewer.groupId=org.ihtsdo.otf.mapping, workflow.path.handler.QA_PATH.class=org. ihtsdo.o tf.mapping.jpa.handlers.WorkflowQaPathHandler, metadata.service.handler.ICD10CM.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, workflow.path.handler.LEGACY_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowLegacyPathHandler, hibernate.jdbc.batch_size=30, index.viewer.subSearchStartLevel=1, hibernate.search.lucene_version=LUCENE_36, index.viewer.subSearchEndLevel=1, mail.smtp.host=smtp.gmail.com, metadata.service.handler.SNOMEDCT_US.class=org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper, metadata.service.handler.ICD9CM.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, hibernate.search.default.directory_provider=filesystem, mail.smtp.to=delnoy@gmail.com mailto:delnoy@gmail.com } [INFO] No notifications will be sent as a result of workflow computation. [INFO] Request to send notification email for any errors to recipients: delnoy@gmail.com mailto:delnoy@gmail.com
[INFO] terminology = SNOMEDCT [INFO] version = latest [INFO] Default preferred name settings: [INFO] typeId = 900000000000003001 [INFO] refsetId = 900000000000509007 [INFO] acceptabilityId = 900000000000548007 [INFO] Objects committed in blocks of 1000 [INFO] MEMORY USAGE: [INFO] Total: 48693248 [INFO] Free: 29550368 [INFO] Max: 758251520 [INFO] Sorting input files... [INFO] Sorted files exist and are up to date. No sorting required [INFO] complete in 0s 2016-05-26_01:15:17.117 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:17.122 INFO - Setting root service entity manager factory. 2016-05-26_01:15:21.795 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:21.796 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:21.796 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:21.796 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.797 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.798 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.798 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.798 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper java.lang.NullPointerException at org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper.getHierarchicalRelationshipTypes(SnomedMetadataServiceJpaHelper.java:319) at org.ihtsdo.otf.mapping.jpa.services.MetadataServiceJpa.getHierarchicalRelationshipTypes(MetadataServiceJpa.java:345) at org.ihtsdo.otf.mapping.mojo.TerminologyRf2SnapshotLoaderMojo.execute(TerminologyRf2SnapshotLoaderMojo.java:331) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207) 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:116) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106) at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863) at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288) at org.apache.maven.cli.MavenCli.main(MavenCli.java:199) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415) at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356) java.lang.NullPointerException at org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper.getHierarchicalRelationshipTypes(SnomedMetadataServiceJpaHelper.java:319) at org.ihtsdo.otf.mapping.jpa.services.MetadataServiceJpa.getHierarchicalRelationshipTypes(MetadataServiceJpa.java:345) at org.ihtsdo.otf.mapping.mojo.TerminologyRf2SnapshotLoaderMojo.execute(TerminologyRf2SnapshotLoaderMojo.java:331) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207) 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:116) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106) at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863) at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288) at org.apache.maven.cli.MavenCli.main(MavenCli.java:199) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415) at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356) [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 6.924 s [INFO] Finished at: 2016-05-26T01:15:22-07:00 [INFO] Final Memory: 18M/46M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.ihtsdo.otf.mapping:mapping-admin-mojo:1.0.10-SNAPSHOT:load-rf2-snapshot (load-rf2-snapshot) on project mapping-admin-loader: Unexpected exception: NullPointerException -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException` http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException%60
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Delnoy
bcarlsenca
rorydavidson
Tom wrote to IHTSDO with the following issue which has been partially discussed via our internal issue tracking system. Full stack trace included at the end:
TOM: On loading SCT into the mapping tool (according to step 7 on https://confluence.ihtsdotools.org/display/MT/Building+and+Deploying+in+Eclipse) the following error occurs: [ERROR] Failed to execute goal org.ihtsdo.otf.mapping:mapping-admin-mojo:1.0.10-SNAPSHOT:load-rf2-snapshot (load-rf2-snapshot) on project mapping-admin-loader: Unexpected exception: NullPointerException -> [Help 1] The full error is added it this email. Can you help me fix this?
KAI: Is this the first time you are attempting the load the data? It could be worth trying running truncate_all.sql and trying again. From the documentation: "NOTE: if re-running this, you first have to run the sql in "truncate_all.sql" to clear your database of tables."
TOM: I tried that already, same error occurs at the same time in the dev-windows build as well as in the prod build.
`------------------------------------------------
Starting ...Thu May 26 01:14:47 PDT 2016
MAPPING_CODE = /home/tom/Code MAPPING_DATA = /home/tom/Code MAPPING_CONFIG = /home/tom/Code Run updatedb with hibernate.hbm2ddl.auto = create ...Thu May 26 01:14:47 PDT 2016 Clear indexes ...Thu May 26 01:15:01 PDT 2016 Load SNOMEDCT ...Thu May 26 01:15:12 PDT 2016 ERROR loading SNOMEDCT [INFO] Scanning for projects... [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building OTF RF2 Admin RF2 Loader 1.0.10-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- mapping-admin-mojo:1.0.10-SNAPSHOT:load-rf2-snapshot (load-rf2-snapshot) @ mapping-admin-loader --- [INFO] Starting loading RF2 data [INFO] inputDir = /home/tom/Data/snomedct-20140731-snapshot [INFO] terminology = SNOMEDCT [INFO] sendNotification = false 2016-05-26_01:15:17.108 INFO - run.config = /home/tom/Config/config.properties 2016-05-26_01:15:17.114 INFO - properties = {workflow.path.handler.NON_LEGACYPATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowNonLegacyPathHandler, loader.defaultPreferredNames.typeId=900000000000003001, mail.smtp.starttls.enable=true, index.viewer.subSubSearchEndLevel=2, mail.smtp.auth=true, mail.smtp.to.feedback.user=____*, hibernate.jdbc.default_batch_fetchsize=16, mail.smtp.password=____*, workflow.path.handler=NON_LEGACY_PATH,LEGACY_PATH,REVIEW_PROJECT_PATH,FIX_ERROR_PATH,QA_PATH,SIMPLEPATH, javax.persistence.jdbc.user=root, send.notification.recipients=____* , metadata.service.handler.GMDN.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, base.url.webapp=http://localhost:8080/mapping-webapp, deploy.footer.link=http://www.ihtsdo.org/, loader.defaultPreferredNames.refSetId=900000000000509007, javax.persistence.jdbc.password=_, hibernate.search.default.indexBase=/home/tom/Data, metadata.service.handler.ICPC.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, metadata.service.handler.ICD10.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, index.viewer.data=/home/tom/Data/ihtsdo-mapping-tool-data/indexViewerData, index.viewer.linkSubstitutions=s/Complications/Complication/;, index.viewer.searchStartLevel=0, mail.smtp.user=_____ , workflow.path.handler.SIMPLE_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowSimplePathHandler, metadata.service.handler.SNOMEDCT.class=org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper, index.viewer.subSubSearchStartLevel=2, javax.persistence.jdbc.url=jdbc:mysql://127.0.0.1:3306/mappingservicedb, index.viewer.artifactId=index-viewer-data-empty, metadata.service.handler=SNOMEDCT,SNOMEDCT_US,ICD10,ICD10CM,ICD9CM,ICPC,GMDN, javax.persistence.jdbc.driver=com.mysql.jdbc.Driver, ihtsdo.security.activated=false, mail.smtp.port=587, workflow.path.handler.REVIEW_PROJECT_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowReviewProjectPathHandler, loader.defaultPreferredNames.acceptabilityId=900000000000548007, deploy.title=IHTSDO Mapping Tool - DEV, hibernate.format_sql=true, deploy.footer.copyright=Copyright @2015 IHTSDO, base.url=http://localhost:8080/mapping-rest, index.viewer.searchEndLevel=0, index.viewer.maxHits=10000, hibernate.use_sql_comments=true, hibernate.show_sql=false, workflow.path.handler.FIX_ERROR_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowFixErrorPathHandler, map.principle.source.document.dir=/home/tom/Data/doc, hibernate.dialect=org.hibernate.dialect.MySQLDialect, index.viewer.phonet=./config/dict/phonet.en, index.viewer.version=1.3.0-SNAPSHOT, index.viewer.groupId=org.ihtsdo.otf.mapping, workflow.path.handler.QA_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowQaPathHandler, metadata.service.handler.ICD10CM.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, workflow.path.handler.LEGACY_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowLegacyPathHandler, hibernate.jdbc.batch_size=30, index.viewer.subSearchStartLevel=1, hibernate.search.lucene_version=LUCENE36, index.viewer.subSearchEndLevel=1, mail.smtp.host=____*, metadata.service.handler.SNOMEDCT_US.class=org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper, metadata.service.handler.ICD9CM.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, hibernate.search.default.directory_provider=filesystem, mail.smtp.to=_ } [INFO] No notifications will be sent as a result of workflow computation. [INFO] Request to send notification email for any errors to recipients: _____
[INFO] terminology = SNOMEDCT [INFO] version = latest [INFO] Default preferred name settings: [INFO] typeId = 900000000000003001 [INFO] refsetId = 900000000000509007 [INFO] acceptabilityId = 900000000000548007 [INFO] Objects committed in blocks of 1000 [INFO] MEMORY USAGE: [INFO] Total: 48693248 [INFO] Free: 29550368 [INFO] Max: 758251520 [INFO] Sorting input files... [INFO] Sorted files exist and are up to date. No sorting required [INFO] complete in 0s 2016-05-26_01:15:17.117 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:17.122 INFO - Setting root service entity manager factory. 2016-05-26_01:15:21.795 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:21.796 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:21.796 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper 2016-05-26_01:15:21.796 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.797 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.798 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.798 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.798 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper 2016-05-26_01:15:21.799 INFO - property class = org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper java.lang.NullPointerException at org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper.getHierarchicalRelationshipTypes(SnomedMetadataServiceJpaHelper.java:319) at org.ihtsdo.otf.mapping.jpa.services.MetadataServiceJpa.getHierarchicalRelationshipTypes(MetadataServiceJpa.java:345) at org.ihtsdo.otf.mapping.mojo.TerminologyRf2SnapshotLoaderMojo.execute(TerminologyRf2SnapshotLoaderMojo.java:331) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207) 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:116) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106) at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863) at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288) at org.apache.maven.cli.MavenCli.main(MavenCli.java:199) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415) at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356) java.lang.NullPointerException at org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper.getHierarchicalRelationshipTypes(SnomedMetadataServiceJpaHelper.java:319) at org.ihtsdo.otf.mapping.jpa.services.MetadataServiceJpa.getHierarchicalRelationshipTypes(MetadataServiceJpa.java:345) at org.ihtsdo.otf.mapping.mojo.TerminologyRf2SnapshotLoaderMojo.execute(TerminologyRf2SnapshotLoaderMojo.java:331) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207) 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:116) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106) at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863) at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288) at org.apache.maven.cli.MavenCli.main(MavenCli.java:199) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415) at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356) [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 6.924 s [INFO] Finished at: 2016-05-26T01:15:22-07:00 [INFO] Final Memory: 18M/46M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.ihtsdo.otf.mapping:mapping-admin-mojo:1.0.10-SNAPSHOT:load-rf2-snapshot (load-rf2-snapshot) on project mapping-admin-loader: Unexpected exception: NullPointerException -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException`