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Errors while running the DB Loader Script #51

Closed dsull1 closed 4 years ago

dsull1 commented 4 years ago

Hi, I am following the deployment guide to setup the SNOMED Mapping tool, and am experiencing some errors when running the DB loader script (config/bin/load.bat) for the Dev Windows build. It will connect and succeed with the first step (updatedb) and create the tables in the database , but all other steps fail with a similar error to below. The database tables appear to remain empty due to the errors. Note I have also tried this in eclipse using the ResetDemoDatabase junit test as suggested here step 7 with the same errors:

Environment details: Windows 10 Enterprise 64bit Tomcat 7 Maven 3.6.3 MySQL 5.6 JDK 1.8.0_241

Error Log from MVN.log whilst running the reindex step from Load.bat:

[INFO] Scanning for projects... [INFO] [INFO] ------------< org.ihtsdo.otf.mapping:mapping-admin-lucene >------------- [INFO] Building OTF RF2 Admin RF2 Lucene 1.6.6 [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- mapping-admin-mojo:1.6.6:reindex (reindex) @ mapping-admin-lucene --- [INFO] Lucene reindexing called via mojo. [INFO] Indexed objects = null [INFO] Expect server up = false 2020-03-09_15:18:38.082 INFO - server is:false 2020-03-09_15:18:38.094 INFO - run.config = C:\Projects\Config\config.properties 2020-03-09_15:18:38.097 INFO - properties = {metadata.service.handler.ICD9CM.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, metadata.service.handler.ICD10CM.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, security.handler.IMS.url.logout=https://ims.ihtsdotools.org/#/logout, hibernate.search.default.indexBase=C:ProjectsDataindexes, security.handler.IMS.url=https://ims.ihtsdotools.org, map.principle.source.document.dir=C:/Projects/Data/doc, aws.access.key.id=EDIT_THIS, deploy.footer.copyright=Copyright @2019 SNOMED International, authoring.authHeader=Basic REMOVED, deploy.snomed.dailybuild.url.other=index.html?perspective=full&&acceptLicense=true, mail.smtp.port=587, mail.smtp.password=xxx, javax.persistence.jdbc.user=root, deploy.title=Mapping Tool - DEV, hibernate.c3p0.acquireIncrement=1, index.viewer.searchEndLevel=0, gmdnsftp.port=4432, admin.user=admin, loader.defaultPreferredNames.refSetId=900000000000509007, security.handler.DEFAULT.class=org.ihtsdo.otf.mapping.jpa.handlers.DefaultSecurityServiceHandler, index.viewer.searchStartLevel=0, hibernate.c3p0.preferredTestQuery=select 1;, security.timeout=7200000, mail.smtp.user=mapping@ihtsdotools.org, metadata.service.handler.ICPC.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, index.viewer.linkSubstitutions=s/Complications/Complication/;, workflow.path.handler=NON_LEGACY_PATH,LEGACY_PATH,REVIEW_PROJECT_PATH,FIX_ERROR_PATH,QA_PATH,SIMPLE_PATH, mail.smtp.auth=true, workflow.path.handler.REVIEW_PROJECT_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowReviewProjectPathHandler, workflow.path.handler.QA_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowQaPathHandler, admin.password=xxx, hibernate.format_sql=true, gmdnsftp.user=cassiel, deploy.snomed.dailybuild.url.base=https://dailybuild.ihtsdotools.org/, jira.authHeader=Basic REMOVED, loader.defaultPreferredNames.typeId=900000000000003001, hibernate.c3p0.idleConnectionTestPeriod=1800, workflow.path.handler.SIMPLE_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowSimplePathHandler, deploy.terminology.browser.label=, index.viewer.subSubSearchEndLevel=2, metadata.service.handler.GMDN.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, authoring.defaultUrl=https://authoring.ihtsdotools.org, javax.persistence.jdbc.url=jdbc:mysql://127.0.0.1:3306/mappingservicedb, index.viewer.subSearchEndLevel=1, hibernate.jdbc.batch_size=30, mail.smtp.to.feedback.user=EDIT_THIS, mail.smtp.starttls.enable=true, deploy.mapproject.showdelta.button.enabled=false, index.viewer.subSearchStartLevel=1, security.guest.disabled=false, metadata.service.handler.SNOMEDCT.class=org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper, index.viewer.subSubSearchStartLevel=2, metadata.service.handler=SNOMEDCT,SNOMEDCT_US,ICD10,ICD10CM,ICD9CM,ICPC,GMDN,MEDDRA, security.handler.IMS.class=org.ihtsdo.otf.mapping.jpa.handlers.ImsSecurityServiceHandler, hibernate.c3p0.maxIdleTime=3600, data.dir=C:/Projects/Data, hibernate.dialect=org.hibernate.dialect.MySQLDialect, mail.smtp.to=xxx, security.handler=DEFAULT, hibernate.search.lucene_version=LUCENE_36, workflow.path.handler.NON_LEGACY_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowNonLegacyPathHandler, gmdnsftp.password=xxx, deploy.footer.link=http://www.snomed.org/, metadata.service.handler.ICD10.class=org.ihtsdo.otf.mapping.jpa.services.ClamlMetadataServiceJpaHelper, javax.persistence.jdbc.driver=com.mysql.jdbc.Driver, hibernate.connection.provider_class=org.hibernate.connection.C3P0ConnectionProvider, deploy.snomed.browser.force=true, deploy.reset.password.link=http://localhost:8080/mapping-rest, workflow.path.handler.FIX_ERROR_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowFixErrorPathHandler, base.url=http://localhost:8080/mapping-rest, deploy.terminology.browser.url=, mail.smtp.host=auth.smtp.1and1.co.uk, loader.defaultPreferredNames.acceptabilityId=900000000000548007, jira.defaultUrl=https://jira.ihtsdotools.org/rest/api/2, security.handler.DEFAULT.users.admin=admin, metadata.service.handler.SNOMEDCT_US.class=org.ihtsdo.otf.mapping.jpa.services.SnomedMetadataServiceJpaHelper, hibernate.search.default.directory_provider=filesystem, hibernate.use_sql_comments=true, javax.persistence.jdbc.password=xxx, sqlreport.send.notification.recipients.meddra=nmarques@westcoastinformatics.com, hibernate.c3p0.maxConnectionAge=3600, send.notification.recipients.devops=EDIT_THIS, send.notification.recipients=EDIT_THIS, index.viewer.phonet=./config/dict/phonet.en, jira.project=MTFP, index.viewer.maxHits=10000, hibernate.c3p0.testConnectionOnCheckin=true, gmdnsftp.host=ftp.gmdnagency.org, workflow.path.handler.LEGACY_PATH.class=org.ihtsdo.otf.mapping.jpa.handlers.WorkflowLegacyPathHandler, hibernate.c3p0.acquire_increment=1, security.handler.DEFAULT.users.viewer=guest,guest1,specialist1,lead1,guest2,specialist2,lead2,guest3,specialist3,lead3,admin1,admin2,admin3,demo_lead,kgi,nin,dmo,kli, deploy.show.authoring.history.button=true, aws.secret.access.key=EDIT_THIS, hibernate.jdbc.default_batch_fetch_size=16, deploy.snomed.dailybuild.url.us=us.html?perspective=full&&acceptLicense=true, index.viewer.version=1.4.1, gmdnsftp.dir=/home/ihtsdo/data/GMDN, deploy.snomed.browser.url=http://browser.ihtsdotools.org/index.html?perspective=full&acceptLicense=true&release=v20190131, metadata.service.handler.MEDDRA.class=org.ihtsdo.otf.mapping.jpa.services.MeddraMetadataServiceJpaHelper, hibernate.show_sql=false} [INFO] Server status detected: DOWN [INFO] Running directly 2020-03-09_15:18:39.914 INFO - Setting root service entity manager factory. 2020-03-09_15:18:41.306 WARN - HHH000208: org.hibernate.connection.C3P0ConnectionProvider has been deprecated in favor of org.hibernate.service.jdbc.connections.internal.C3P0ConnectionProvider; that provider will be used instead. 2020-03-09_15:18:41.339 WARN - HHH010001: Both hibernate-style property 'hibernate.c3p0.acquire_increment' and c3p0-style property 'hibernate.c3p0.acquireIncrement' have been set in hibernate.properties. Hibernate-style property 'hibernate.c3p0.acquire_increment' will be used and c3p0-style property 'hibernate.c3p0.acquireIncrement' will be ignored! 2020-03-09_15:18:45.142 INFO - Instantiate org.ihtsdo.otf.mapping.jpa.handlers.DefaultSecurityServiceHandler 2020-03-09_15:18:45.143 INFO - property class = org.ihtsdo.otf.mapping.jpa.handlers.DefaultSecurityServiceHandler 2020-03-09_15:18:45.143 INFO - property users.admin = admin 2020-03-09_15:18:45.143 INFO - property users.viewer = guest,guest1,specialist1,lead1,guest2,specialist2,lead2,guest3,specialist3,lead3,admin1,admin2,admin3,demo_lead,kgi,nin,dmo,kli [INFO] elapsed time = 7s / 0m / 0h [INFO] done ... [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 11.075 s [INFO] Finished at: 2020-03-09T15:18:45+11:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.ihtsdo.otf.mapping:mapping-admin-mojo:1.6.6:reindex (reindex) on project mapping-admin-lucene: 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

Any guidance on how to solve this would be appreciated!

RichardAWood commented 4 years ago

There was an update made to one of the loaders which affected the ResetDemoDatabase. A code-update has been pushed, and the instructions and mapping-demo.zip file at https://confluence.ihtsdotools.org/display/MT/Building+and+Deploying+in+Eclipse have been updated accordingly.

Daniel and I then did a video call, and confirmed that he was able to get his system up and running successfully.