General info (maybe even docs) on the whole colfusion project (including all its components and refs to other repos)
colfusionserver's Introduction
colfusionserver's People
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grprashanthkumarcolfusionserver's Issues
Exception in ProcessManager
Refactor DataverseBL to prepare it for #19
Wrong column type in colfusion.colfusion_pentaho_log_step for column LOG_FIELD. Found: mediumtext, expected: longtext
org.hibernate.HibernateException: Wrong column type in colfusion.colfusion_pentaho_log_step for column LOG_FIELD. Found: mediumtext, expected: longtext
at org.hibernate.mapping.Table.validateColumns(Table.java:372) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.cfg.Configuration.validateSchema(Configuration.java:1336) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.tool.hbm2ddl.SchemaValidator.validate(SchemaValidator.java:155) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:525) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1857) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:66) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.war.infra.LoggingFilter.doFilter(LoggingFilter.java:47) [LoggingFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.18]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.18]
at org.apache.logging.log4j.core.web.Log4jServletFilter.doFilter(Log4jServletFilter.java:66) [log4j-core-2.0-rc1.jar:2.0-rc1]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.18]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) [catalina.jar:8.0.18]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) [catalina.jar:8.0.18]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) [catalina.jar:8.0.18]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) [catalina.jar:8.0.18]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:516) [catalina.jar:8.0.18]
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1086) [tomcat-coyote.jar:8.0.18]
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:659) [tomcat-coyote.jar:8.0.18]
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:223) [tomcat-coyote.jar:8.0.18]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1558) [tomcat-coyote.jar:8.0.18]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1515) [tomcat-coyote.jar:8.0.18]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_45]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_45]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:8.0.18]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
Wrong column type in colfusion.colfusion_executeinfo for column log. Found: text, expected: longtext
SEVERE: Servlet.service() for servlet [Jersey Web Application] in context with path [/ColFusionServer] threw exception [Filter execution threw an exception] with root cause
org.hibernate.HibernateException: Wrong column type in colfusion.colfusion_executeinfo for column log. Found: text, expected: longtext
at org.hibernate.mapping.Table.validateColumns(Table.java:372)
at org.hibernate.cfg.Configuration.validateSchema(Configuration.java:1336)
at org.hibernate.tool.hbm2ddl.SchemaValidator.validate(SchemaValidator.java:155)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:525)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1857)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:66)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40)
at edu.pitt.sis.exp.colfusion.war.infra.LoggingFilter.doFilter(LoggingFilter.java:47)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.logging.log4j.core.web.Log4jServletFilter.doFilter(Log4jServletFilter.java:66)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:516)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1086)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:659)
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:223)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1558)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1515)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Wrong column type in colfusion.colfusion_sourceinfo for column Description. Found: text, expected: varchar(40)
org.hibernate.HibernateException: Wrong column type in colfusion.colfusion_sourceinfo for column Description. Found: text, expected: varchar(40)
at org.hibernate.mapping.Table.validateColumns(Table.java:372) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.cfg.Configuration.validateSchema(Configuration.java:1336) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.tool.hbm2ddl.SchemaValidator.validate(SchemaValidator.java:155) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:525) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1857) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:66) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.war.infra.LoggingFilter.doFilter(LoggingFilter.java:47) [LoggingFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.18]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.18]
at org.apache.logging.log4j.core.web.Log4jServletFilter.doFilter(Log4jServletFilter.java:66) [log4j-core-2.0-rc1.jar:2.0-rc1]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.18]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) [catalina.jar:8.0.18]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) [catalina.jar:8.0.18]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) [catalina.jar:8.0.18]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) [catalina.jar:8.0.18]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) [catalina.jar:8.0.18]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:516) [catalina.jar:8.0.18]
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1086) [tomcat-coyote.jar:8.0.18]
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:659) [tomcat-coyote.jar:8.0.18]
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:223) [tomcat-coyote.jar:8.0.18]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1558) [tomcat-coyote.jar:8.0.18]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1515) [tomcat-coyote.jar:8.0.18]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_45]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_45]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:8.0.18]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
Create Container for Responses to REST API calls that would wrap any ViewModel
There is rounding problem with data matching ratios.
There is rounding problem with data matching ratios that always cause troubles in reading/writing to db data matching values. Fix it once and for good.
Look at the datamatching ratio calculation code and see the Decimal type. We don't really need super high precision at the very last digit. So replace with it something more stable code.
[Maven] Clean and organize dependencies
There might be some dependencies declared in pom files that we don't use/need anymore. Also dependencies might be updated to newer versions.
Secure rest api and add token&client base auth
[Hibernate/C3P0] Exceptions/warning after running server for long time
On my mac after I start ColfuisonServer in tomcat and then leave my computer for some time (and it probably goes to sleep), after I get back to my computer I see following in the console. Make sure if that is only related to the fact that my computer goes to sleep and maybe VMs shut down all connections or if there is anymore more serious going on here.
Sep 17, 2015 12:52:31 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector@75457092 -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
Sep 17, 2015 12:52:31 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector@75457092 -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@90f9e31
on thread: C3P0PooledConnectionPoolManager[identityToken->15ukxnc9b1oynprx8ea3q7|23d05748]-HelperThread-#1
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@ddd14e0
on thread: C3P0PooledConnectionPoolManager[identityToken->15ukxnc9b1oynprx8ea3q7|23d05748]-HelperThread-#2
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@58525bb9
on thread: C3P0PooledConnectionPoolManager[identityToken->15ukxnc9b1oynprx8ea3q7|23d05748]-HelperThread-#0
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@64d61c1
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@7346892f
Pool thread stack traces:
Thread[C3P0PooledConnectionPoolManager[identityToken->15ukxnc9b1oynprx8ea3q7|23d05748]-HelperThread-#0,5,main]
java.net.PlainSocketImpl.socketConnect(Native Method)
java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:345)
java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
java.net.Socket.connect(Socket.java:589)
java.net.Socket.connect(Socket.java:538)
java.net.Socket.<init>(Socket.java:434)
java.net.Socket.<init>(Socket.java:244)
com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:256)
com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:308)
com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2498)
com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2535)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2320)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
sun.reflect.GeneratedConstructorAccessor57.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:422)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:146)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:195)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:184)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:200)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1086)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquireAndDecrementPendingAcquiresWithinLockOnSuccess(BasicResourcePool.java:1073)
com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:44)
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask.run(BasicResourcePool.java:1810)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:648)
Thread[C3P0PooledConnectionPoolManager[identityToken->15ukxnc9b1oynprx8ea3q7|23d05748]-HelperThread-#1,5,main]
java.net.PlainSocketImpl.socketConnect(Native Method)
java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:345)
java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
java.net.Socket.connect(Socket.java:589)
java.net.Socket.connect(Socket.java:538)
java.net.Socket.<init>(Socket.java:434)
java.net.Socket.<init>(Socket.java:244)
com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:256)
com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:308)
com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2498)
com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2535)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2320)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
sun.reflect.GeneratedConstructorAccessor57.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:422)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:146)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:195)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:184)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:200)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1086)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquireAndDecrementPendingAcquiresWithinLockOnSuccess(BasicResourcePool.java:1073)
com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:44)
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask.run(BasicResourcePool.java:1810)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:648)
Thread[C3P0PooledConnectionPoolManager[identityToken->15ukxnc9b1oynprx8ea3q7|23d05748]-HelperThread-#2,5,main]
java.net.PlainSocketImpl.socketConnect(Native Method)
java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:345)
java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
java.net.Socket.connect(Socket.java:589)
java.net.Socket.connect(Socket.java:538)
java.net.Socket.<init>(Socket.java:434)
java.net.Socket.<init>(Socket.java:244)
com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:256)
com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:308)
com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2498)
com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2535)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2320)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
sun.reflect.GeneratedConstructorAccessor57.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:422)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:146)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:195)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:184)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:200)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1086)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquireAndDecrementPendingAcquiresWithinLockOnSuccess(BasicResourcePool.java:1073)
com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:44)
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask.run(BasicResourcePool.java:1810)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:648)
Sep 17, 2015 1:22:20 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner processReplacedThreads
WARNING: Task com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@58525bb9 (in deadlocked PoolThread) failed to complete in maximum time 60000ms. Trying interrupt().
Sep 17, 2015 1:22:20 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner processReplacedThreads
WARNING: Task com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@90f9e31 (in deadlocked PoolThread) failed to complete in maximum time 60000ms. Trying interrupt().
Sep 17, 2015 1:22:20 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner processReplacedThreads
WARNING: Task com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask@ddd14e0 (in deadlocked PoolThread) failed to complete in maximum time 60000ms. Trying interrupt().
[TODO] The separator should be passed from UI as parameter.
See CDVImporter.java method readLinesFromTo
[ExcelFileImport] Excel with two sheets, second sheet selected, return 3 empty variabls
Tired to import an excel file with two sheets. On the second page of the wizard, selected second sheet, 1 row and A column, on the next page of the wizard, three variables was shown (the excel sheet had more than 3 variables) and those variables didn't have names.
[Neo4j][Relationships] New nodes and edges were not added to neo4j after a relation was discovered
Submitted two files that have one common variable, a relationship was discovered, but neo4j graph was not updated, e.g. new nodes and edges were not created.
P.S.: This code might still be in the php codebase
MetadataDbHandler - FAILED to creating edit log for
Tried to click on edit link to open openrefine, but got the following stack trace with exception
com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Column 'endChangeTime' cannot be null
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_45]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[?:1.8.0_45]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:1.8.0_45]
at java.lang.reflect.Constructor.newInstance(Constructor.java:422) ~[?:1.8.0_45]
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.Util.getInstance(Util.java:386) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1041) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2828) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1842) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1764) ~[mysql-connector-java-5.1.29.jar:?]
at edu.pitt.sis.exp.colfusion.dal.databaseHandlers.MetadataDbHandler.createEditLog(MetadataDbHandler.java:364) [classes/:?]
at com.google.refine.commands.colfusion.CreateProjectFromColfusionStoryCommand.doGet(CreateProjectFromColfusionStoryCommand.java:73) [classes/:?]
at com.google.refine.RefineServlet.service(RefineServlet.java:173) [classes/:?]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820) [servlet-api-2.5.jar:2.5]
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81) [jetty-util-6.1.22.jar:6.1.22]
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:132) [jetty-util-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.Server.handle(Server.java:326) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228) [jetty-6.1.22.jar:6.1.22]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_45]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_45]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
20:12:34.709 [pool-1-thread-14] INFO edu.pitt.sis.exp.colfusion.dal.databaseHandlers.MetadataDbHandler - FAILED to creating edit log for sid 5, table Sheet1 and user 2
20:12:34.735 [ command] Exception caught (514ms)
com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Column 'endChangeTime' cannot be null
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.Util.getInstance(Util.java:386)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1041)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2828)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1842)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1764)
at edu.pitt.sis.exp.colfusion.dal.databaseHandlers.MetadataDbHandler.createEditLog(MetadataDbHandler.java:364)
at com.google.refine.commands.colfusion.CreateProjectFromColfusionStoryCommand.doGet(CreateProjectFromColfusionStoryCommand.java:73)
at com.google.refine.RefineServlet.service(RefineServlet.java:173)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:132)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923)
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Move all test classes one level up in their package hierarchy and remove "test" part of the package name
All tests in ColfusionServer project are located under edu.pitt.sis.exp.colfusion.tests.* package. Remote the tests part of the package name
Fix swagger api annotations for dataverse restservice
Add doGet overloaded function to accept parameter for "accept" header
Currently doGet by default set the content type accept header to application/json. Add the version of doGet method to let users of that util class to provide other values for accept header.
[Dataverse] Propagate specific error messages if any functionality related to dataverse failed because of the dataverse, not us
If dataverse server is down or has 500 or any other error, we should propagate a specific message to the outside of the rest api to let the clients of our service know that a third part has issues, not us.
Hibernate cannot create some tables and report 3 errors
INFO: HHH000227: Running hbm2ddl schema export
Sep 07, 2015 6:06:05 PM org.hibernate.tool.hbm2ddl.SchemaExport perform
ERROR: HHH000389: Unsuccessful: create table colfusion.`colfusion_pentaho_log_step` (`ID_BATCH` integer not null, `CHANNEL_ID` varchar(255) not null, `LOG_DATE` datetime not null, `TRANSNAME` varchar(255) not null, `STEPNAME` varchar(255) not null, `STEP_COPY` integer not null, `LINES_READ` bigint not null, `LINES_WRITTEN` bigint not null, `LINES_UPDATED` bigint not null, `LINES_INPUT` bigint not null, `LINES_OUTPUT` bigint not null, `LINES_REJECTED` bigint not null, `ERRORS` bigint not null, `LOG_FIELD` longtext not null, primary key (`ID_BATCH`, `CHANNEL_ID`, `LOG_DATE`, `TRANSNAME`, `STEPNAME`, `STEP_COPY`, `LINES_READ`, `LINES_WRITTEN`, `LINES_UPDATED`, `LINES_INPUT`, `LINES_OUTPUT`, `LINES_REJECTED`, `ERRORS`, `LOG_FIELD`))
Sep 07, 2015 6:06:05 PM org.hibernate.tool.hbm2ddl.SchemaExport perform
ERROR: BLOB/TEXT column 'LOG_FIELD' used in key specification without a key length
Sep 07, 2015 6:06:05 PM org.hibernate.tool.hbm2ddl.SchemaExport perform
ERROR: HHH000389: Unsuccessful: create table colfusion.`colfusion_pentaho_log_transformaion` (`ID_BATCH` integer not null, `CHANNEL_ID` varchar(255) not null, `TRANSNAME` varchar(255) not null, `STATUS` varchar(15) not null, `LINES_READ` bigint not null, `LINES_WRITTEN` bigint not null, `LINES_UPDATED` bigint not null, `LINES_INPUT` bigint not null, `LINES_OUTPUT` bigint not null, `LINES_REJECTED` bigint not null, `ERRORS` bigint not null, `STARTDATE` datetime not null, `ENDDATE` datetime not null, `LOGDATE` datetime not null, `DEPDATE` datetime not null, `REPLAYDATE` datetime not null, `LOG_FIELD` longtext not null, primary key (`ID_BATCH`, `CHANNEL_ID`, `TRANSNAME`, `STATUS`, `LINES_READ`, `LINES_WRITTEN`, `LINES_UPDATED`, `LINES_INPUT`, `LINES_OUTPUT`, `LINES_REJECTED`, `ERRORS`, `STARTDATE`, `ENDDATE`, `LOGDATE`, `DEPDATE`, `REPLAYDATE`, `LOG_FIELD`))
Sep 07, 2015 6:06:05 PM org.hibernate.tool.hbm2ddl.SchemaExport perform
ERROR: Too many key parts specified; max 16 parts allowed
Sep 07, 2015 6:06:06 PM org.hibernate.tool.hbm2ddl.SchemaExport execute
INFO: HHH000230: Schema export complete
[TODO] might need to move to the utils projects
See todo in the IOUtilsTest.java file in ColfusionServer project. That file should be moved to the colfusionUtils project.
HibernateUtil.initiSessionFactory run twice during unit testing
During debugging a unit test, I noticed that initiSessionFactory was executed twice.
Introduce very lightweight way to manage database migrations
Add license info as separate file and as comment to each file
Consider adding jersey filter to handle uncaptured exceptions
If any exception was not captured, this filter would then prepare a general response
Add Readme.md file with description of the project
MySQLDataTruncation Exception when submitting a test file
Tried to submit test ABC file, but at the end of the wizard got this errors in the console log on server:
19:46:04.687 [1] ERROR edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil - commitTransaction failed
org.hibernate.exception.DataException: could not execute statement
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:69) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:190) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:62) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3281) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:3183) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3525) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.action.internal.EntityUpdateAction.execute(EntityUpdateAction.java:158) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:461) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:347) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:350) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:56) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1222) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:425) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.beforeTransactionCommit(JdbcTransaction.java:101) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:177) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:137) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dal.managers.ExecutionInfoManagerImpl.appendLog(ExecutionInfoManagerImpl.java:202) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dataLoadExecutors.DataLoadExecutorKTRImpl.changeTransformationName(DataLoadExecutorKTRImpl.java:247) [colfusionserver-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dataLoadExecutors.DataLoadExecutorKTRImpl.execute(DataLoadExecutorKTRImpl.java:95) [colfusionserver-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.process.ProcessBase.run(ProcessBase.java:174) [colfusionserver-2.0-SNAPSHOT.jar:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for column 'log' at row 1
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4235) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2834) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2441) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2366) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2350) ~[mysql-connector-java-5.1.29.jar:?]
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:147) ~[c3p0-0.9.2.1.jar:0.9.2.1]
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:187) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
... 19 more
19:46:04.691 [1] INFO edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil - commitTransaction: commited trasaction org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction@2a05ac53
19:46:04.691 [1] ERROR edu.pitt.sis.exp.colfusion.dal.managers.ExecutionInfoManagerImpl - appendLog failed HibernateException
org.hibernate.HibernateException: org.hibernate.exception.DataException: could not execute statement
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:165) ~[colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dal.managers.ExecutionInfoManagerImpl.appendLog(ExecutionInfoManagerImpl.java:202) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dataLoadExecutors.DataLoadExecutorKTRImpl.changeTransformationName(DataLoadExecutorKTRImpl.java:247) [colfusionserver-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dataLoadExecutors.DataLoadExecutorKTRImpl.execute(DataLoadExecutorKTRImpl.java:95) [colfusionserver-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.process.ProcessBase.run(ProcessBase.java:174) [colfusionserver-2.0-SNAPSHOT.jar:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
Caused by: org.hibernate.exception.DataException: could not execute statement
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:69) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:190) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:62) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3281) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:3183) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3525) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.action.internal.EntityUpdateAction.execute(EntityUpdateAction.java:158) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:461) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:347) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:350) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:56) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1222) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:425) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.beforeTransactionCommit(JdbcTransaction.java:101) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:177) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:137) ~[colfusionserverdal-2.0-SNAPSHOT.jar:?]
... 5 more
Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for column 'log' at row 1
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4235) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2834) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2441) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2366) ~[mysql-connector-java-5.1.29.jar:?]
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2350) ~[mysql-connector-java-5.1.29.jar:?]
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:147) ~[c3p0-0.9.2.1.jar:0.9.2.1]
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:187) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:62) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3281) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:3183) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3525) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.action.internal.EntityUpdateAction.execute(EntityUpdateAction.java:158) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:461) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:347) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:350) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:56) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1222) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:425) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.beforeTransactionCommit(JdbcTransaction.java:101) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:177) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:137) ~[colfusionserverdal-2.0-SNAPSHOT.jar:?]
... 5 more
Add rest api to get version number
The version should include both the project version number and also maybe a revision number so that later we can refer to specific version for bugs/fixes.
[TODO]: This class might need to be moved to the DAL project or the TransformationUtil should be moved
See class TransformationTest seems that either it is in the wrong place or the functionality that it tests e.g. RelationshipTransofmationUtil is in the wrong place (e.g. it is in DAL project currently)
Write a wiki page on how to deal with database changes
[ImportWizard][Dataverse] Propagate error 403 error from dataverse API as response error (currently we return 404)
Currently we return 404 for any status code except 200 that we receive from dataverse when send our request to download a datafile.
At least error 403 should be propagated back to our clients to let them know what happened.
Update code to use new version of Neo4j
If the code is not yet moved from PHP to java, then first move the code to Java and use latest Neo4j version
Problem accessing kettle transformaiton
After submitting an excel file, see this error in the log column in execinfo table:
Finished to prepare Carte Server Url for the /Users/Evgeny/Documents/Colfusion/Colfusion/assets/www/temp/1/Sheet1-1819591982.ktr file. KtrFileURL is http%3A%2F%2F192.168.33.11%2F%2Ftemp%2F1%2FSheet1-1819591982.ktr
at Mon Sep 07 20:09:49 EDT 2015:
Starting HTTP call to Carte Server http://192.168.33.11:8081/kettle/executeTrans/?trans=http%3A%2F%2F192.168.33.11%2F%2Ftemp%2F1%2FSheet1-1819591982.ktr&Sid=1&Eid=1
at Mon Sep 07 20:09:49 EDT 2015:
Got the following status code in response 401:
at Mon Sep 07 20:09:49 EDT 2015:
Got This contect as the result of the call to carte <html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Error 401 UNAUTHORIZED</title>
</head>
<body>
<h2>HTTP ERROR: 401</h2>
<p>Problem accessing /kettle/executeTrans/. Reason:
<pre> UNAUTHORIZED</pre></p>
<hr /><i><small>Powered by Jetty://</small></i>
</body>
</html>
BLL should know nothing about REST API and view models
Some of the BLL Services create view model instances that also include adding extra stuff like error message or XML attributes, etc. BLL should not know all that stuff and instead return it's models. REST controllers (our view) will be responsible to convert BLL models into viewmodels that then send back to clients in JSON.
Move all ViewModels into War project
Currently there are view models in colfusionserver project and ...dal project and it is a mess. Move them all to the ...war project and refactor according to #34
Mark database based tests as integration tests
Mark database based tests as integration tests so when running mvn test we could select whether to run or not
Exception ColumnToColumnDataMatching Process
See the exception below. Simply uploaded two files that have similar variables. When second file was uploaded and when story page was opened, so this exception in eclipse.
org.hibernate.PropertyValueException: not-null property references a null or transient value : edu.pitt.sis.exp.colfusion.dal.orm.ColfusionRelationshipsColumnsDataMathingRatios.colfusionProcesses
at org.hibernate.engine.internal.Nullability.checkNullability(Nullability.java:106) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:309) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:160) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:231) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:102) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:55) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1222) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:425) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.beforeTransactionCommit(JdbcTransaction.java:101) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:177) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:137) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dal.managers.GeneralManagerImpl.saveOrUpdate(GeneralManagerImpl.java:82) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.bll.relationships.ColumnToColumnDataMatchingProcess.execute(ColumnToColumnDataMatchingProcess.java:174) [colfusionserverbll-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.bll.process.ProcessBase.run(ProcessBase.java:174) [colfusionserverbll-2.0-SNAPSHOT.jar:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
10:47:04.443 [-1] INFO edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil - commitTransaction: commited trasaction org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction@5f3687f3
10:47:04.443 [-1] ERROR edu.pitt.sis.exp.colfusion.dal.managers.GeneralManagerImpl - save failed HibernateException
org.hibernate.HibernateException: org.hibernate.PropertyValueException: not-null property references a null or transient value : edu.pitt.sis.exp.colfusion.dal.orm.ColfusionRelationshipsColumnsDataMathingRatios.colfusionProcesses
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:165) ~[colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.dal.managers.GeneralManagerImpl.saveOrUpdate(GeneralManagerImpl.java:82) [colfusionserverdal-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.bll.relationships.ColumnToColumnDataMatchingProcess.execute(ColumnToColumnDataMatchingProcess.java:174) [colfusionserverbll-2.0-SNAPSHOT.jar:?]
at edu.pitt.sis.exp.colfusion.bll.process.ProcessBase.run(ProcessBase.java:174) [colfusionserverbll-2.0-SNAPSHOT.jar:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
Caused by: org.hibernate.PropertyValueException: not-null property references a null or transient value : edu.pitt.sis.exp.colfusion.dal.orm.ColfusionRelationshipsColumnsDataMathingRatios.colfusionProcesses
at org.hibernate.engine.internal.Nullability.checkNullability(Nullability.java:106) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:309) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:160) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:231) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:102) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:55) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1222) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:425) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.beforeTransactionCommit(JdbcTransaction.java:101) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:177) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.commitTransaction(HibernateUtil.java:137) ~[colfusionserverdal-2.0-SNAPSHOT.jar:?]
... 4 more
NullPointerException on first two request to openrefine to check if table is locked
Seems like there is a race condition on ConfigManager instance so one of the request see that ConfigManager was initialized, but the properties were not loaded and it tries to access properties and that's why we see null pointer exception.
Missing column: did in colfusion.colfusion_charts
Just start the server and then try to open any page on Colfusion Web
SEVERE: Servlet.service() for servlet [Jersey Web Application] in context with path [/ColFusionServer] threw exception [Filter execution threw an exception] with root cause
org.hibernate.HibernateException: Missing column: did in colfusion.colfusion_charts
at org.hibernate.mapping.Table.validateColumns(Table.java:365)
at org.hibernate.cfg.Configuration.validateSchema(Configuration.java:1336)
at org.hibernate.tool.hbm2ddl.SchemaValidator.validate(SchemaValidator.java:155)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:525)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1857)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:66)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40)
at edu.pitt.sis.exp.colfusion.war.infra.LoggingFilter.doFilter(LoggingFilter.java:47)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.logging.log4j.core.web.Log4jServletFilter.doFilter(Log4jServletFilter.java:66)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:516)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1086)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:659)
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:223)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1558)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1515)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
[Dataverse] Api's base url should be provided by user since there are more than one dataverse server
Dataverse exposes much of its functionality via REST api in a form $SERVER/api. We currently use dataverse.harvard.edu for CHIA's data, however some other users might have their data on other dataverse servers.
Consider making JerseyClientUtil do async requests
Currently doGet, doPost, doPut, etc. do sync request. Consider either replacing them with async versions, or just add a async versions
[Dataverse] Use dataverse token associated with user acount
Currently we use hardcoded dataverse token, but instead each user who wants to interact with dataverse needs to have their own token. Is seems that currently there is no way to automate token generation and retrieval process because Dataverse API doesn't provide such functionality.
However, see the issue #11, once that issue is done, this one should be read to be implemented
Exception when trying to init hibernate from call to openrefine
Tried to click edit data link and got the following exception.
09:13:14.835 [pool-1-thread-10] INFO edu.pitt.sis.exp.colfusion.dal.managers.SourceInfoManagerImpl - Getting story source into db for sid '5'
09:13:15.149 [..otations.common.Version] HCANN000001: Hibernate Commons Annotations {4.0.4.Final} (3791ms)
09:13:15.165 [ org.hibernate.Version] HHH000412: Hibernate Core {4.3.4.Final} (16ms)
09:13:15.171 [..bernate.cfg.Environment] HHH000206: hibernate.properties not found (6ms)
09:13:15.175 [..bernate.cfg.Environment] HHH000021: Bytecode provider name : javassist (4ms)
09:13:15.236 [..rnate.cfg.Configuration] HHH000042: Configuring from file: colfusion3821110165452862697hibernateProp (61ms)
09:13:15.285 [pool-1-thread-10] ERROR edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil - sessionFactory initialization failed!
org.hibernate.HibernateException: Could not parse configuration: /var/folders/sj/5sbln_7s4rbbf0ggt_dry4dm0000gn/T/colfusion3821110165452862697hibernateProp
at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:2163) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at org.hibernate.cfg.Configuration.configure(Configuration.java:2133) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:55) [classes/:?]
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40) [classes/:?]
at edu.pitt.sis.exp.colfusion.dal.managers.SourceInfoManagerImpl.getStorySourceInfoDB(SourceInfoManagerImpl.java:833) [classes/:?]
at edu.pitt.sis.exp.colfusion.dal.databaseHandlers.DatabaseHandlerFactory.getTargetDatabaseHandler(DatabaseHandlerFactory.java:74) [classes/:?]
at edu.pitt.sis.exp.colfusion.ColFusionOpenRefineProjectManager.createProjectToOpenRefine(ColFusionOpenRefineProjectManager.java:85) [classes/:?]
at com.google.refine.commands.colfusion.CreateProjectFromColfusionStoryCommand.doGet(CreateProjectFromColfusionStoryCommand.java:77) [classes/:?]
at com.google.refine.RefineServlet.service(RefineServlet.java:173) [classes/:?]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820) [servlet-api-2.5.jar:2.5]
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81) [jetty-util-6.1.22.jar:6.1.22]
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:132) [jetty-util-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.Server.handle(Server.java:326) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) [jetty-6.1.22.jar:6.1.22]
at org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228) [jetty-6.1.22.jar:6.1.22]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_45]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_45]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_45]
Caused by: org.dom4j.DocumentException: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory Nested exception: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory
at org.dom4j.io.SAXReader.read(SAXReader.java:484) ~[dom4j-1.6.1.jar:1.6.1]
at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:2155) ~[hibernate-core-4.3.4.Final.jar:4.3.4.Final]
... 30 more
09:13:15.293 [ org.mortbay.log] Error for /command/core/create-project-from-colfusion-story (57ms)
java.lang.ExceptionInInitializerError
at edu.pitt.sis.exp.colfusion.dal.managers.SourceInfoManagerImpl.getStorySourceInfoDB(SourceInfoManagerImpl.java:833)
at edu.pitt.sis.exp.colfusion.dal.databaseHandlers.DatabaseHandlerFactory.getTargetDatabaseHandler(DatabaseHandlerFactory.java:74)
at edu.pitt.sis.exp.colfusion.ColFusionOpenRefineProjectManager.createProjectToOpenRefine(ColFusionOpenRefineProjectManager.java:85)
at com.google.refine.commands.colfusion.CreateProjectFromColfusionStoryCommand.doGet(CreateProjectFromColfusionStoryCommand.java:77)
at com.google.refine.RefineServlet.service(RefineServlet.java:173)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:132)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923)
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: org.hibernate.HibernateException: Could not parse configuration: /var/folders/sj/5sbln_7s4rbbf0ggt_dry4dm0000gn/T/colfusion3821110165452862697hibernateProp
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:70)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40)
... 27 more
Caused by: org.hibernate.HibernateException: Could not parse configuration: /var/folders/sj/5sbln_7s4rbbf0ggt_dry4dm0000gn/T/colfusion3821110165452862697hibernateProp
at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:2163)
at org.hibernate.cfg.Configuration.configure(Configuration.java:2133)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:55)
... 28 more
Caused by: org.dom4j.DocumentException: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory Nested exception: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory
at org.dom4j.io.SAXReader.read(SAXReader.java:484)
at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:2155)
... 30 more
09:13:15.296 [ org.mortbay.log] Nested in java.lang.ExceptionInInitializerError: (3ms)
java.lang.RuntimeException: org.hibernate.HibernateException: Could not parse configuration: /var/folders/sj/5sbln_7s4rbbf0ggt_dry4dm0000gn/T/colfusion3821110165452862697hibernateProp
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:70)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.<clinit>(HibernateUtil.java:40)
at edu.pitt.sis.exp.colfusion.dal.managers.SourceInfoManagerImpl.getStorySourceInfoDB(SourceInfoManagerImpl.java:833)
at edu.pitt.sis.exp.colfusion.dal.databaseHandlers.DatabaseHandlerFactory.getTargetDatabaseHandler(DatabaseHandlerFactory.java:74)
at edu.pitt.sis.exp.colfusion.ColFusionOpenRefineProjectManager.createProjectToOpenRefine(ColFusionOpenRefineProjectManager.java:85)
at com.google.refine.commands.colfusion.CreateProjectFromColfusionStoryCommand.doGet(CreateProjectFromColfusionStoryCommand.java:77)
at com.google.refine.RefineServlet.service(RefineServlet.java:173)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:132)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923)
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.hibernate.HibernateException: Could not parse configuration: /var/folders/sj/5sbln_7s4rbbf0ggt_dry4dm0000gn/T/colfusion3821110165452862697hibernateProp
at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:2163)
at org.hibernate.cfg.Configuration.configure(Configuration.java:2133)
at edu.pitt.sis.exp.colfusion.dal.utils.HibernateUtil.initiSessionFactory(HibernateUtil.java:55)
... 28 more
Caused by: org.dom4j.DocumentException: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory Nested exception: org.dom4j.DocumentFactory cannot be cast to org.dom4j.DocumentFactory
at org.dom4j.io.SAXReader.read(SAXReader.java:484)
at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:2155)
... 30 more
Rename ColfusionServer to ColfusionServerBLL
Allow users to link their dataverse token to Colfusion account
It seems that Daverse API doesn't support OAuth and uses in house implemented token based REST API (see this for changes: IQSS/dataverse#1818 and IQSS/dataverse#1935). So for now at least users should be able to update their dataverse token manually that we can use to interact with dataverse API.
[StoryRestService] MineRelationships does more than one thing
The MineRelaitonship method does more than one thing. Particularly it triggers the process to mine new relationships and also query the database to get the list of already found relationships. This functionality needs to be splitted into two separate methods. One should simply be GET return and return the list of relationships, while other should be POST to trigger relationship mining.
Update Apache POI to newest version
[Dataverse] Figure out if dataverse api always accessible via 'https' or not
Currently in DataverseContextImpl we hard wire protocol to talk to dataverse api as https. Figure out if it should be configurable or it can stay as a constant
Refactor ExcelImporter
Excel importer class is currently doing at least two separate things: first handling the excel file and constructing required models by extracting some data from the file. Better separate those two function, to have one class that is responsible to open and read excel and other class that have logic related to Colfusion
Where to save uploaded files
Uploaded files should be stored separately from coflusion front end, but they need to be accessible via HTTP for carte server and also for download. But need to add more security to make some files not available to the general public (e.g. private datasets)
Move IOUtilsTest from ColfusionServer project to ColfusionServerUtils
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