Atlas Setup Failing

dramacloak · January 14, 2019, 4:00pm

2019-01-14 09:28:38 Commons Daemon procrun stderr initialized
14-Jan-2019 09:28:39.525 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.14
14-Jan-2019 09:28:39.527 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Dec 6 2018 21:13:53 UTC
14-Jan-2019 09:28:39.528 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.14.0
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Windows 7
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.1
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: C:\Program Files\Java\jre1.8.0_191
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_191-b12
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:28:39.529 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=F:\Program Files\Apache Software Foundation\Tomcat 9.0\temp
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=F:\Program Files\Apache Software Foundation\Tomcat 9.0\conf\logging.properties
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: exit
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: abort
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms128m
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx256m
14-Jan-2019 09:28:39.530 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [F:\Program Files\Apache Software Foundation\Tomcat 9.0\bin;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\Rtools\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;F:\ant\bin;C:\Program Files\Java\jdk1.8.0_191\bin;F:\PostgreSQL\pg11\bin;C:\Program Files (x86)\Integrad.3\MIV;F:\GitHub OHDSI\apache-maven-3.6.0\bin;F:\Program Files\Git\cmd;;.]
14-Jan-2019 09:28:39.622 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:28:39.686 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:28:39.688 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [424] milliseconds
14-Jan-2019 09:28:39.711 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
14-Jan-2019 09:28:39.711 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.14]
14-Jan-2019 09:28:39.745 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war]
14-Jan-2019 09:28:39.755 WARNING [main] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property ‘antiJARLocking’ to ‘true’ did not find a matching property.
14-Jan-2019 09:29:06.761 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war] has finished in [27,016] ms
14-Jan-2019 09:29:06.762 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\Atlas]
14-Jan-2019 09:29:06.778 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\Atlas] has finished in [16] ms
14-Jan-2019 09:29:06.778 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\docs]
14-Jan-2019 09:29:06.792 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\docs] has finished in [13] ms
14-Jan-2019 09:29:06.792 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\host-manager]
14-Jan-2019 09:29:06.814 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\host-manager] has finished in [21] ms
14-Jan-2019 09:29:06.814 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\manager]
14-Jan-2019 09:29:06.831 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\manager] has finished in [17] ms
14-Jan-2019 09:29:06.832 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\ROOT]
14-Jan-2019 09:29:06.844 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\ROOT] has finished in [11] ms
14-Jan-2019 09:29:06.846 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:29:06.854 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:29:06.857 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [27,167] milliseconds
14-Jan-2019 09:31:14.011 INFO [Thread-9] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:31:14.047 INFO [Thread-9] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:31:14.080 INFO [Thread-9] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
14-Jan-2019 09:31:14.183 WARNING [Thread-9] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:31:14.183 WARNING [Thread-9] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [com.microsoft.sqlserver.jdbc.SQLServerDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:31:14.183 WARNING [Thread-9] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [com.amazon.redshift.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:31:14.207 INFO [Thread-9] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:31:14.209 INFO [Thread-9] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler [“ajp-nio-8009”]

2019-01-14 09:32:31 Commons Daemon procrun stderr initialized
14-Jan-2019 09:32:32.167 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.14
14-Jan-2019 09:32:32.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Dec 6 2018 21:13:53 UTC
14-Jan-2019 09:32:32.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.14.0
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Windows 7
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.1
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: C:\Program Files\Java\jre1.8.0_191
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_191-b12
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=F:\Program Files\Apache Software Foundation\Tomcat 9.0\temp
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=F:\Program Files\Apache Software Foundation\Tomcat 9.0\conf\logging.properties
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: exit
14-Jan-2019 09:32:32.172 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: abort
14-Jan-2019 09:32:32.173 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms128m
14-Jan-2019 09:32:32.173 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx256m
14-Jan-2019 09:32:32.173 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [F:\Program Files\Apache Software Foundation\Tomcat 9.0\bin;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\Rtools\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;F:\ant\bin;C:\Program Files\Java\jdk1.8.0_191\bin;F:\PostgreSQL\pg11\bin;C:\Program Files (x86)\Integrad.3\MIV;F:\GitHub OHDSI\apache-maven-3.6.0\bin;F:\Program Files\Git\cmd;;.]
14-Jan-2019 09:32:32.271 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:32:32.344 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:32:32.347 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [428] milliseconds
14-Jan-2019 09:32:32.369 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
14-Jan-2019 09:32:32.369 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.14]
14-Jan-2019 09:32:32.405 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war]
14-Jan-2019 09:32:32.415 WARNING [main] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property ‘antiJARLocking’ to ‘true’ did not find a matching property.
14-Jan-2019 09:32:58.761 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war] has finished in [26,356] ms
14-Jan-2019 09:32:58.762 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\Atlas]
14-Jan-2019 09:32:58.776 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\Atlas] has finished in [13] ms
14-Jan-2019 09:32:58.776 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\docs]
14-Jan-2019 09:32:58.789 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\docs] has finished in [12] ms
14-Jan-2019 09:32:58.789 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\host-manager]
14-Jan-2019 09:32:58.809 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\host-manager] has finished in [19] ms
14-Jan-2019 09:32:58.809 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\manager]
14-Jan-2019 09:32:58.824 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\manager] has finished in [15] ms
14-Jan-2019 09:32:58.824 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\ROOT]
14-Jan-2019 09:32:58.837 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\ROOT] has finished in [13] ms
14-Jan-2019 09:32:58.840 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:32:58.847 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:32:58.851 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [26,502] milliseconds
14-Jan-2019 09:41:07.675 INFO [Thread-9] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:41:07.740 INFO [Thread-9] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:41:07.779 INFO [Thread-9] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
14-Jan-2019 09:41:07.886 WARNING [Thread-9] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:41:07.886 WARNING [Thread-9] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [com.microsoft.sqlserver.jdbc.SQLServerDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:41:07.886 WARNING [Thread-9] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [com.amazon.redshift.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:41:07.908 INFO [Thread-9] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:41:07.909 INFO [Thread-9] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler [“ajp-nio-8009”]

2019-01-14 09:43:27 Commons Daemon procrun stderr initialized
14-Jan-2019 09:43:28.165 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.14
14-Jan-2019 09:43:28.167 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Dec 6 2018 21:13:53 UTC
14-Jan-2019 09:43:28.167 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.14.0
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Windows 7
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.1
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: C:\Program Files\Java\jre1.8.0_191
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_191-b12
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:43:28.169 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=F:\Program Files\Apache Software Foundation\Tomcat 9.0
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=F:\Program Files\Apache Software Foundation\Tomcat 9.0\temp
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=F:\Program Files\Apache Software Foundation\Tomcat 9.0\conf\logging.properties
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: exit
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: abort
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms128m
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx256m
14-Jan-2019 09:43:28.170 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [F:\Program Files\Apache Software Foundation\Tomcat 9.0\bin;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\Rtools\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;F:\ant\bin;C:\Program Files\Java\jdk1.8.0_191\bin;F:\PostgreSQL\pg11\bin;C:\Program Files (x86)\Integrad.3\MIV;F:\GitHub OHDSI\apache-maven-3.6.0\bin;F:\Program Files\Git\cmd;;.]
14-Jan-2019 09:43:28.273 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:43:28.341 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:43:28.344 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [425] milliseconds
14-Jan-2019 09:43:28.367 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
14-Jan-2019 09:43:28.367 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.14]
14-Jan-2019 09:43:28.394 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war]
14-Jan-2019 09:43:28.405 WARNING [main] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property ‘antiJARLocking’ to ‘true’ did not find a matching property.
14-Jan-2019 09:43:57.225 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war] has finished in [28,830] ms
14-Jan-2019 09:43:57.225 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\Atlas]
14-Jan-2019 09:43:57.240 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\Atlas] has finished in [15] ms
14-Jan-2019 09:43:57.240 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\docs]
14-Jan-2019 09:43:57.261 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\docs] has finished in [20] ms
14-Jan-2019 09:43:57.261 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\host-manager]
14-Jan-2019 09:43:57.284 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\host-manager] has finished in [23] ms
14-Jan-2019 09:43:57.284 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\manager]
14-Jan-2019 09:43:57.301 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\manager] has finished in [17] ms
14-Jan-2019 09:43:57.301 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\ROOT]
14-Jan-2019 09:43:57.314 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\ROOT] has finished in [12] ms
14-Jan-2019 09:43:57.316 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [“http-nio-8080”]
14-Jan-2019 09:43:57.324 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [“ajp-nio-8009”]
14-Jan-2019 09:43:57.327 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [28,981] milliseconds
14-Jan-2019 09:44:21.998 WARNING [http-nio-8080-exec-5] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:44:21.999 WARNING [http-nio-8080-exec-5] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [com.microsoft.sqlserver.jdbc.SQLServerDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:44:21.999 WARNING [http-nio-8080-exec-5] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [WebAPI] registered the JDBC driver [com.amazon.redshift.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
14-Jan-2019 09:44:23.527 INFO [http-nio-8080-exec-5] org.apache.catalina.startup.HostConfig.undeploy Undeploying context [/WebAPI]
14-Jan-2019 09:44:54.296 INFO [http-nio-8080-exec-6] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war]
14-Jan-2019 09:44:54.299 WARNING [http-nio-8080-exec-6] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property ‘antiJARLocking’ to ‘true’ did not find a matching property.
14-Jan-2019 09:45:23.259 INFO [http-nio-8080-exec-6] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [F:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\WebAPI.war] has finished in [28,962] ms

dramacloak · January 14, 2019, 4:14pm

I found this error in the tomcat9-stdout log:
2019-01-14 09:29:24.196 INFO http-nio-8080-exec-6 com.odysseusinc.logging.LoggingService - - Could not get JDBC Connection; nested exception is org.postgresql.util.PSQLException: FATAL: database “OHDSI/” does not exist

I updated the source to used database “OHDSI” and now it looks

The vocab is working. Not convinced it’s getting the CDM or Results. How do I debug these tables to see if those are working or accessible in WebAPI?

anthonysena · January 14, 2019, 4:17pm

@dramacloak - if you don’t mind, let’s move this discussion to GitHub: https://github.com/OHDSI/WebAPI/issues/739. It looks like you’ve gotten past the issue but we can use GitHub to track any issues you may have discovered during your setup. Thanks!

dramacloak · January 14, 2019, 4:17pm

I’m not entirely convinced that the CDM and Results tables are working.

Chris_Knoll · January 14, 2019, 4:33pm

You can create a simple cohort definition, and then use the SQL export to pull the query that will generate the cohort. You will need to do a find-replace on the tokens for @cdm_database_schema to use your own schema to your CDM (there may be other tokens starting with @ that you will need to replace). This will verify that your CDM tables are set up correctly. For the results tables, you’ll need to generate the cohort via the Atlas UI and look for errors in your tomcat logs. All the tables required for the results schema are found in this WebAPI endpoint: http://localhost:8080/WebAPI/ddl/results?dialect=postgresql

Look at this script to verify that all the tables created exist in your results schema.

Chris_Knoll · January 14, 2019, 4:35pm

Additionally: there are challenges to setting up Atlas and WebAPI, if you could provide a final list of things that you missed when setting up the application that finally got it working, it would be very helpful to other people who have the same challenges setting up the apps. It might also lead to some clarification in the setup guides.

Thanks.

dramacloak · January 15, 2019, 10:17pm

I’m having troubles defining the cohort definition in Atlas. It looks like it’s trying to build a cohort in the results schema rather than the webapi schema. I have the following in my tomcat stdout log:

Caused by: org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [DELETE FROM results.cohort_inclusion WHERE cohort_definition_id = ?;]; nested exception is org.postgresql.util.PSQLException: ERROR: relation “results.cohort_inclusion” does not exist
Position: 13
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:649)
at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:870)
at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:931)
at org.ohdsi.webapi.cohortdefinition.GenerateCohortTasklet.prepareQueries(GenerateCohortTasklet.java:104)
… 23 more
Caused by: org.postgresql.util.PSQLException: ERROR: relation “results.cohort_inclusion” does not exist
Position: 13
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2270)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1998)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:570)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:420)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:366)
at org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:877)
at org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:870)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:633)
… 26 more
2019-01-15 14:15:40.525 DEBUG taskExecutor-2 org.hibernate.engine.transaction.internal.TransactionImpl - - begin
2019-01-15 14:15:40.580 DEBUG taskExecutor-2 org.hibernate.engine.transaction.internal.TransactionImpl - - committing
2019-01-15 14:15:40.581 DEBUG taskExecutor-2 org.hibernate.engine.transaction.internal.TransactionImpl - - begin
2019-01-15 14:15:40.632 DEBUG taskExecutor-2 org.springframework.batch.core.repository.dao.JdbcStepExecutionDao - - Truncating long message before update of StepExecution, original message is: java.lang.RuntimeException: org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [DELETE FROM results.cohort_inclusion WHERE cohort_definition_id = ?;]; nested exception is org.postgresql.util.PSQLException: ERROR: relation “results.cohort_inclusion” does not exist
Position: 13
at org.ohdsi.webapi.cohortdefinition.GenerateCohortTasklet.prepareQueries(GenerateCohortTasklet.java:127)
at org.ohdsi.webapi.common.generation.CancelableTasklet.doTask(CancelableTasklet.java:33)
at org.ohdsi.webapi.common.generation.CancelableTasklet.doTask(CancelableTasklet.java:17)
at org.ohdsi.webapi.common.generation.TransactionalTasklet.lambda$execute$0(TransactionalTasklet.java:37)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)
at org.ohdsi.webapi.common.generation.TransactionalTasklet.execute(TransactionalTasklet.java:37)
at org.springframework.batch.core.step.tasklet.TaskletStep$ChunkTransactionCallback.doInTransaction(TaskletStep.java:406)
at org.springframework.batch.core.step.tasklet.TaskletStep$ChunkTransactionCallback.doInTransaction(TaskletStep.java:330)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)
at org.springframework.batch.core.step.tasklet.TaskletStep$2.doInChunkContext(TaskletStep.java:272)
at org.springframework.batch.core.scope.context.StepContextRepeatCallback.doInIteration(StepContextRepeatCallback.java:81)
at org.springframework.batch.repeat.support.RepeatTemplate.getNextResult(RepeatTemplate.java:374)
at org.springframework.batch.repeat.support.RepeatTemplate.executeInternal(RepeatTemplate.java:215)
at org.springframework.batch.repeat.support.RepeatTemplate.iterate(RepeatTemplate.java:144)
at org.springframework.batch.core.step.tasklet.TaskletStep.doExecute(TaskletStep.java:257)
at org.springframework.batch.core.step.AbstractStep.execute(AbstractStep.java:200)
at org.springframework.batch.core.job.SimpleStepHandler.handleStep(SimpleStepHandler.java:148)
at org.springframework.batch.core.job.AbstractJob.handleStep(AbstractJob.java:392)
at org.springframework.batch.core.job.SimpleJob.doExecute(SimpleJob.java:135)
at org.springframework.batch.core.job.AbstractJob.execute(AbstractJob.java:306)
at org.springframework.batch.core.launch.support.SimpleJobLauncher$1.run(SimpleJobLauncher.java:135)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [DELETE FROM results.cohort_inclusion WHERE cohort_definition_id = ?;]; nested exception is org.postgresql.util.PSQLException: ERROR: relation “results.cohort_inclusion” does not exist
Position: 13
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:649)
at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:870)
at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:931)
at org.ohdsi.webapi.cohortdefinition.GenerateCohortTasklet.prepareQueries(GenerateCohortTasklet.java:104)
… 23 more
Caused by: org.postgresql.util.PSQLException: ERROR: relation “results.cohort_inclusion” does not exist
Position: 13
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2270)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1998)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:570)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:420)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:366)
at org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:877)
at org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:870)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:633)
… 26 more

I’m also getting the following message in cohort definitions:

Some of the reports work (e.g., dashboard, person) but others do not work (e.g., condition, procedure):

Here is how I’ve defined the cohorts:

dramacloak · January 15, 2019, 10:23pm

It was able to manually create the cohort in postgresql using the SQL export to verify the CDM tables are setup correctly.

Chris_Knoll · January 15, 2019, 10:24pm

The results schema is used to store the cohort generation results. The webapi is a completely separate database. You can read the discussion here that talks about the details: Have Some Problmes About Atlas

But in summary, you should have 1 database for webapi, and for each CDM, you have 1 database, each database contains a cdm schema and a results schema. The connection to WebAPI is defined in your settings.xml file you used to build webapi. The CDM connections are stored in the SOURCE table (once WebAPI is installed, it will create the source table).

-Chris

dramacloak · January 17, 2019, 6:55pm

The DDL script generated by Atlas for Postgresql has been running for over 43 hours now to create and index the additional tables required by Atlas in the results schema. I’m not seeing any errors from Postgresql for this step. Is this long amount of run time common on this step?

Chris_Knoll · January 18, 2019, 3:03am

No, 43 hours does not sound right to create indexes on newly created tables. But, maybe there’s either some sort of table lock in your environment that may be active, or some other resource contention is leading to the delay. I can’t recall exactly how to determine table locks or blocked processes via PG Admin III, but if you can execute the statements in sequence, you can narrow down which index is taking so long.

dramacloak · February 25, 2019, 10:42pm

Here’s an accounting of all of the issues we’ve had so far, as requested, which we hope will help with the setup guides, etc.

OHDSI OMOP Install Notes_25Feb2019.pdf (135.9 KB)

ambuj · April 2, 2019, 11:55am

@Chris_Knoll @Ajit_Londhe

Hello Guys,

I have been trying to run Atlas in house using postgresql as my CDM database. I have 2 schemas:
Schema 1: CDM
tables: omop_cdm (contains omop schema and vocabularies)
results
Schema 2: OHDSI
tables: webapi

select * from webapi.source_daimon looks like -
source_daimon_id | source_id | daimon_type | table_qualifier | priority
------------------±----------±------------±----------------±---------
1 | 1 | 0 | omop_cdm | 0
3 | 1 | 2 | results | 2
2 | 1 | 1 | vocab | 1
(3 rows)

I prepared build for Atlas using “npm run build” and copied all files to the webapps folder under tomcat directory and able to host the files.
But getting the following errors as shown in screenshot below:
Atlas version : 2.7.0

Please let me know how can I fix this issue as I am unable to find any solution to these issues.

Thank you
Ambuj S

DTorok · April 2, 2019, 12:19pm

In webapi.source_daimon the table_qualifier should be the schema name. So what you are telling web_api that your vocabulary files are in the schema vocab, but in your explanation the vocabulary files are in ‘omop_cdm’. See https://github.com/OHDSI/WebAPI/wiki/Source-Configuration for an explanation for populating source and source_daimon.

ambuj · April 2, 2019, 12:24pm

@DTorok
I added vocab just to do some RnD to figure out the cause of it. however keeping it omop_cdm instead of vocab is giving me the same issue.
source_daimon_id | source_id | daimon_type | table_qualifier | priority
------------------±----------±------------±----------------±---------
1 | 1 | 0 | omop_cdm | 0
3 | 1 | 2 | results | 2
2 | 1 | 1 | omop_cdm | 1
(3 rows)

After making the change, restarted webapi service. Still same window I get with same errors.

DTorok · April 2, 2019, 12:27pm

Rather than showing the network tab, what is displayed in the Console tab?

smanikonda · April 2, 2019, 2:58pm

@ambuj,
Couple of observations I could see (these might not have any impact, but to be consistent with the documentation):

The priority has to be 0 for all three of the them (as they are 3 different entities - i.e. omop data, vocab data, and results)
Did you create a separate schema for Results?

ambuj · April 3, 2019, 11:22am

@DTorok @smanikonda
Atlas is up and running now, the issue was within Source table, had to update the JDBC connection. So , I am all set with this.

@Ajit_Londhe @Chris_Knoll
Just one quick question, if I create a new cohort from Atlas, will it be creating the entries in CDM Cohort tables?

Thank you.

Chris_Knoll · April 3, 2019, 1:34pm

No, there are 2 cohort tables: one in the CDM schema (for cdm standard cohorts), and there’s a cohort in the results schema (where WebAPI writes the cohort results). You did make separate schema for your cdm and results scehma, right?

ambuj · April 3, 2019, 1:47pm

yes, there are 2 separate schemas for CDM and webapi. and I found the entries created in webapi cohort tables for the cohorts generated via Atlas.

Doubt is, if I manually make entries in cdm cohort tables, how will it reflect in Atlas? will it run the analysis based upon the subject id? or shall we just those table blank.