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Problem with starting a new BROADSEA implementation


(Matthew Joss) #1

Hello, we are trying to setup broadsea to run against our MSSQL database and I am experiencing a problem that I hope someone here could assist with. I found that after downloading and configuring the files for MSSQL on github, I executed a ‘docker-compose up -d’ (apparently without error, we think) and then I ran ‘docker-compose down’ as described in the ‘Quickstart BROADSEA deployment’ instructions on github. After this I tried running my edited source-source-daimon.sql script in aqua data studio against our OMOP database, and we discovered that the schema ohdsi and the tables ‘source’ and ‘source-daimon’ were not successfully created when I ran the ‘docker-compose up -d’ command previously. We are unsure why these were not created due to the lack of an error in the log output.

This is what we see when I run the ‘docker-compose up -d’ and then the corresponding docker-compose down:
-bash-4.2$ docker-compose up -d
sqlserver_broadsea-webtools_1 is up-to-date
sqlserver_broadsea-methods-library_1 is up-to-date
-bash-4.2$ docker-compose down
Stopping sqlserver_broadsea-webtools_1 … done
Stopping sqlserver_broadsea-methods-library_1 … done
Removing sqlserver_broadsea-webtools_1 … done
Removing sqlserver_broadsea-methods-library_1 … done
Removing network sqlserver_default

Jeff Klann suggested I run a ‘docker-compose up’ (and then ctrl+c to exit) and this is the log that we see:
-bash-4.2$ docker-compose up
Creating network “sqlserver_default” with the default driver
Creating sqlserver_broadsea-webtools_1 … done
Creating sqlserver_broadsea-methods-library_1 … done
Attaching to sqlserver_broadsea-methods-library_1, sqlserver_broadsea-webtools_1
broadsea-webtools_1 | /usr/lib/python2.7/dist-packages/supervisor/options.py:298: UserWarning: Supervisord is running as root and it is searching for its configuration file in default locations (including its current working directory); you probably want to specify a “-c” argument specifying an absolute path to a configuration file for improved security.
broadsea-webtools_1 | 'Supervisord is running as root and it is searching ’
broadsea-methods-library_1 | 2018-08-13 19:07:22,609 CRIT Supervisor running as root (no user in config file)
broadsea-methods-library_1 | 2018-08-13 19:07:22,644 INFO supervisord started with pid 1
broadsea-webtools_1 | 2018-08-13 19:07:22,745 CRIT Supervisor running as root (no user in config file)
broadsea-webtools_1 | 2018-08-13 19:07:22,745 INFO Included extra file “/etc/supervisor/conf.d/supervisord.conf” during parsing
broadsea-webtools_1 | 2018-08-13 19:07:22,887 INFO RPC interface ‘supervisor’ initialized
broadsea-webtools_1 | 2018-08-13 19:07:22,887 CRIT Server ‘unix_http_server’ running without any HTTP authentication checking
broadsea-webtools_1 | 2018-08-13 19:07:22,889 INFO supervisord started with pid 1
broadsea-methods-library_1 | 2018-08-13 19:07:23,649 INFO spawned: ‘RStudio’ with pid 7
broadsea-methods-library_1 | 2018-08-13 19:07:23,661 INFO spawned: ‘Rserve’ with pid 8
broadsea-webtools_1 | 2018-08-13 19:07:23,895 INFO spawned: ‘deploy-script’ with pid 7
broadsea-methods-library_1 | 2018-08-13 19:07:24,283 INFO reaped unknown pid 38
broadsea-methods-library_1 | 2018-08-13 19:07:24,283 INFO reaped unknown pid 39
broadsea-methods-library_1 | 2018-08-13 19:07:24,500 INFO reaped unknown pid 97
broadsea-methods-library_1 | 2018-08-13 19:07:24,500 INFO reaped unknown pid 98
broadsea-webtools_1 | 2018-08-13 19:07:25,133 INFO success: deploy-script entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
broadsea-methods-library_1 | 2018-08-13 19:07:25,517 INFO success: RStudio entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
broadsea-methods-library_1 | 2018-08-13 19:07:25,518 INFO success: Rserve entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
^CGracefully stopping… (press Ctrl+C again to force)
Stopping sqlserver_broadsea-webtools_1 … done
Stopping sqlserver_broadsea-methods-library_1 … done

we thought, perhaps our configuration is incorrect, however for some reason we are not seeing any errors regarding whether or not we are successfully connecting to our server. When we run docker compose up -d we expect that it is going to try to connect to our server, but the log output has no indication of that.

For reference, this is how our 3 files are currently configured (btw they are all in the same directory, with a path that does not have any spaces.):

-bash-4.2$ ls
config-local.js docker-compose.yml source_source_daimon.sql
-bash-4.2$ pwd
/home/maj60/Broadsea/sqlserver
-bash-4.2$

“config-local.js”:

define([], function () {
var configLocal = {};

    // clearing local storage otherwise source cache will obscure the override settings
    localStorage.clear();

    // WebAPI
    configLocal.api = {
            name: 'OHDSI',
            url: 'http://localhost:8080/WebAPI/'
    };

configLocal.cohortComparisonResultsEnabled = false;
    configLocal.userAuthenticationEnabled = false;
    configLocal.plpResultsEnabled = false;

    return configLocal;

});

“docker-compose.yml” : (FYI, User and Password for our db is omitted for security. Also note that we tried our server path with and without the ‘.partners.org’ )

version: ‘2’

services:

broadsea-methods-library:
image: ohdsi/broadsea-methodslibrary
ports:
- “8787:8787”
- “6311:6311”

broadsea-webtools:
image: ohdsi/broadsea-webtools
ports:
- “8080:8080”
volumes:
- .:/tmp/drivers/:ro
- ./config-local.js:/usr/local/tomcat/webapps/atlas/js/config-local.js:ro
environment:
- WEBAPI_URL=http://localhost:8080
- env=webapi-mssql
- datasource.driverClassName=com.microsoft.sqlserver.jdbc.SQLServerDriver
- datasource.url=jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart
- datasource.cdm.schema=dbo
- datasource.ohdsi.schema=ohdsi
- datasource.username=OMITTED
- datasource.password=OMITTED
- spring.jpa.properties.hibernate.default_schema=ohdsi
- spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.SQLServer2008Dialect
- spring.batch.repository.tableprefix=secret-database-name.ohdsi.BATCH_
- flyway.datasource.driverClassName=com.microsoft.sqlserver.jdbc.SQLServerDriver
- flyway.datasource.url=jdbc:sqlserver://192.168.99.100;databasename=secret-database-name
- flyway.schemas=ohdsi
- flyway.placeholders.ohdsiSchema=ohdsi
- flyway.datasource.username=secret-user-name
- flyway.datasource.password=secret-user-password
- flyway.locations=classpath:db/migration/sqlserver

“source-source-daimon.sql” : ( FYI, User and Password for our db is omitted for security.)

– remove any previously added database connection configuration data
truncate ohdsi.source;
truncate ohdsi.source_daimon;

– OHDSI CDM source
INSERT INTO ohdsi.source( source_id, source_name, source_key, source_connection, source_dialect)
VALUES (1, ‘OHDSI CDM V5 Database’, ‘OHDSI-CDMV5’,
‘jdbc:sqlserver://phsqlrpdr322:1433;database=eMERGE_OMOP_Mart;user=OMITTED;password=OMITTED’, ‘sql server’);

– CDM daimon
INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (1, 1, 0, ‘dbo’, 2);

– VOCABULARY daimon
INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (2, 1, 1, ‘dbo’, 2);

– RESULTS daimon
INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (3, 1, 2, ‘ohdsi’, 2);

– EVIDENCE daimon
INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (4, 1, 3, ‘ohdsi’, 2);

Any help in resolving this issue would be greatly appreciated.
Thank you.


(Lee Evans) #2

@mjoss take a look at the troubleshooting section of the Broadsea README page:

It describes how to view the Broadsea-webtools log files which may provide some helpful error messages.


(Taha Abdul-Basser) #3

@mjoss once you follow @lee_evans’s excellent advice please feel free to post the relevant excerpt from the tomcat logs here.

I would just add that this looks very much like a flyway configuration issue. WebAPI uses a package called flyway to manage and execute installation and subsequent modifications to the WebAPI application database. It appears that you did not set the flyway settings in the YAML file and therefore WebAPI does not know how to connect to the database, what schema the application tables should be created in, what the credentials for connecting are, etc. Based on your setting it looks like they should be something like

- flyway.datasource.url=jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart
- flyway.schemas=ohdsi
- flyway.placeholders.ohdsiSchema=ohdsi
- flyway.datasource.username=OMITTED
- flyway.datasource.password=OMITTED

Try adding these settings, restarting with docker-compose and tailing the tomcat logs as per @lee_evans advice.


(Matthew Joss) #4

Hello,

Thank you for your responses. We configured the flyway lines in the YAML file, and discovered a slight error in our prior configuration. We also put the jdbc driver jar files in with docker-compose file. Then I ran the docker-compose up -d, and I see the OHDSI schema and tables are created in our DB. This is good. I was then able to run our modified source source daimon script on our DB, which then inserted values into the source and source-daimon tables. However, when I go to check the status of the containers using a web browser, we see that Atlas and calypso are not working correctly.

Namely when I try these 2 steps, we get errors:
Open the Atlas OHDSI web application at http://your-docker-host-ip-address:8080/atlas
Open the Calypso OHDSI web application at http://your-docker-host-ip-address:8080/calypso

I am using the IP address of the Linux instance that I am using to run docker, where I stored my YAML file etc. from above.

The ATLAS page has the following error:
application initialization failed
unable to connect to an instance of the webapi.
please contact your administrator to resolve this issue.

and Calypso has the following error:
HTTP Status 404 - /calypso
type Status report
message /calypso
description The requested resource is not available.
Apache Tomcat/7.0.88

We tried troubleshooting by following the instructions in the broadsea quickstart page:
We extracted the tails from stderr and stdout. These did have some vague errors, copid below, however we are not sure how to proceed this this information.

the first notion of an error in stdout:
Unable to translate SQLException with Error code ‘102’, will now try the fallback translator
//
2018-08-30 18:58:49.199 ERROR localhost-startStop-1 org.springframework.boot.SpringApplication - - Application startup failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘webApi’: Invocation of init method failed; nested exception is javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

we also noticed this error:
Error starting ApplicationContext. To display the auto-configuration report re-run your application with ‘debug’ enabled.
2018-09-10 17:09:03.460 ERROR localhost-startStop-1 org.springframework.boot.SpringApplication - - Application startup failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘webApi’: Invocation of init method failed; nested exception is javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

And here was an error we noticed in stderr:
org.apache.catalina.startup.HostConfig deployWAR
SEVERE: Error deploying web application archive /usr/local/tomcat/webapps/WebAPI.war
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]

If the entire tails of each of these would be useful, or if you would like to check our updated YAML file, please let me know and I can copy them into the thread.

Any help with this problem would be greatly appreciated. Thank you.


(Taha Abdul-Basser) #5

Please post relevant excerpts from the supervisor logs as per BroadSea instructions.


(Lee Evans) #6

@mjoss all the Calypso OHDSI web app functionality was incorporated into ATLAS (a couple of years ago), so you can just focus on getting ATLAS up and running.

To debug we need to see the earlier errors in the docker container supervisor log files. Start with the error messages around the point where it tries to load the jdbc drivers.


(Matthew Joss) #7

Hi everyone,

thanks for the tips. Below I have copied the stderr and stdout log files as requested. If you have any idea on how to get ATLAS working from this, any help would be appreciated. Thank you.

root@2e60267eaf26:/var/log/supervisor# tail -1000 stderr

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server version: Apache Tomcat/7.0.88

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server built: May 7 2018 11:12:57 UTC

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server number: 7.0.88.0

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: OS Name: Linux

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: OS Version: 3.10.0-862.2.3.el7.x86_64

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Architecture: amd64

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: JVM Version: 1.8.0_171-8u171-b11-1~deb9u1-b11

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: JVM Vendor: Oracle Corporation

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: CATALINA_BASE: /usr/local/tomcat

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: CATALINA_HOME: /usr/local/tomcat

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dignore.endorsed.dirs=

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dcatalina.base=/usr/local/tomcat

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dcatalina.home=/usr/local/tomcat

Sep 10, 2018 5:08:08 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp

Sep 10, 2018 5:08:08 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent

INFO: Loaded APR based Apache Tomcat Native library 1.2.16 using APR version 1.5.2.

Sep 10, 2018 5:08:08 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent

INFO: APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].

Sep 10, 2018 5:08:08 PM org.apache.catalina.core.AprLifecycleListener initializeSSL

INFO: OpenSSL successfully initialized (OpenSSL 1.1.0f 25 May 2017)

Sep 10, 2018 5:08:09 PM org.apache.coyote.AbstractProtocol init

INFO: Initializing ProtocolHandler [“http-apr-8080”]

Sep 10, 2018 5:08:09 PM org.apache.coyote.AbstractProtocol init

INFO: Initializing ProtocolHandler [“ajp-apr-8009”]

Sep 10, 2018 5:08:09 PM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 3138 ms

Sep 10, 2018 5:08:09 PM org.apache.catalina.core.StandardService startInternal

INFO: Starting service Catalina

Sep 10, 2018 5:08:09 PM org.apache.catalina.core.StandardEngine startInternal

INFO: Starting Servlet Engine: Apache Tomcat/7.0.88

Sep 10, 2018 5:08:09 PM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deploying web application archive /usr/local/tomcat/webapps/WebAPI.war

Sep 10, 2018 5:08:11 PM org.apache.catalina.loader.WebappClassLoaderBase validateJarFile

INFO: validateJarFile(/usr/local/tomcat/webapps/WebAPI/WEB-INF/lib/tomcat-embed-el-8.5.11.jar) - jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending class: javax/el/Expression.class

Sep 10, 2018 5:08:28 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:03 PM org.apache.catalina.core.ContainerBase addChildInternal

SEVERE: ContainerBase.addChild: start:

org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:162)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1017)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:993)

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘webApi’: Invocation of init method failed; nested exception is javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)

at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)

at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:866)

at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542)

at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)

at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:737)

at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:370)

at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)

at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:151)

at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:131)

at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:86)

at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5669)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)

... 10 more

Caused by: javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

at org.ohdsi.webapi.job.JobTemplate.launchTasklet(JobTemplate.java:77)

at org.ohdsi.webapi.service.CDMResultsService.warmCache(CDMResultsService.java:155)

at org.ohdsi.webapi.WebApi.lambda$warmCaches$18(WebApi.java:47)

at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)

at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)

at org.ohdsi.webapi.WebApi.warmCaches(WebApi.java:44)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)

... 31 more

Sep 10, 2018 5:09:03 PM org.apache.catalina.startup.HostConfig deployWAR

SEVERE: Error deploying web application archive /usr/local/tomcat/webapps/WebAPI.war

java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1021)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:993)

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

Sep 10, 2018 5:09:03 PM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deployment of web application archive /usr/local/tomcat/webapps/WebAPI.war has finished in 53,948 ms

Sep 10, 2018 5:09:03 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/ROOT

Sep 10, 2018 5:09:04 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:04 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/ROOT has finished in 1,272 ms

Sep 10, 2018 5:09:04 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/docs

Sep 10, 2018 5:09:06 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:06 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/docs has finished in 1,301 ms

Sep 10, 2018 5:09:06 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/examples

Sep 10, 2018 5:09:08 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:08 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/examples has finished in 2,798 ms

Sep 10, 2018 5:09:08 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/host-manager

Sep 10, 2018 5:09:10 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:10 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/host-manager has finished in 1,184 ms

Sep 10, 2018 5:09:10 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/manager

Sep 10, 2018 5:09:11 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:11 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/manager has finished in 1,129 ms

Sep 10, 2018 5:09:11 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/penelope

Sep 10, 2018 5:09:12 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:12 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/penelope has finished in 1,530 ms

Sep 10, 2018 5:09:12 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deploying web application directory /usr/local/tomcat/webapps/atlas

Sep 10, 2018 5:09:13 PM org.apache.catalina.startup.TldConfig execute

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.

Sep 10, 2018 5:09:13 PM org.apache.catalina.startup.HostConfig deployDirectory

INFO: Deployment of web application directory /usr/local/tomcat/webapps/atlas has finished in 1,243 ms

Sep 10, 2018 5:09:13 PM org.apache.coyote.AbstractProtocol start

INFO: Starting ProtocolHandler [“http-apr-8080”]

Sep 10, 2018 5:09:14 PM org.apache.coyote.AbstractProtocol start

INFO: Starting ProtocolHandler [“ajp-apr-8009”]

Sep 10, 2018 5:09:14 PM org.apache.catalina.startup.Catalina start

INFO: Server startup in 64849 ms

root@2e60267eaf26:/var/log/supervisor#


(Matthew Joss) #8

Stdout: beginning with first mention of jdbc
also the forum will not let me post the whole thing so I cut the log up into segments…

2018-09-10 17:08:44.630 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘secondaryDataSource’ of type [org.apache.tomcat.jdbc.pool.DataSource] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:44.672 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration’ of type [org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration$$EnhancerBySpringCGLIB$$f2b2c907] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:45.078 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties’ of type [org.springframework.boot.autoconfigure.jdbc.DataSourceProperties] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:45.147 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘dataSourceInitializer’ of type [org.springframework.boot.autoconfigure.jdbc.DataSourceInitializer] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:46.581 INFO localhost-startStop-1 org.flywaydb.core.internal.dbsupport.DbSupportFactory - - Database: jdbc:sqlserver://phsqlrpdr322.partners.org:1433;jaasConfigurationName=SQLJDBCDriver;serverPreparedStatementDiscardThreshold=10;enablePrepareOnFirstPreparedStatementCall=false;fips=false;socketTimeout=0;authentication=NotSpecified;authenticationScheme=nativeAuthentication;xopenStates=false;sendTimeAsDatetime=true;trustStoreType=JKS;trustServerCertificate=false;TransparentNetworkIPResolution=true;serverNameAsACE=false;sendStringParametersAsUnicode=true;selectMethod=direct;responseBuffering=adaptive;queryTimeout=-1;packetSize=8000;multiSubnetFailover=false;loginTimeout=15;lockTimeout=-1;lastUpdateCount=true;encrypt=false;disableStatementPooling=true;databaseName=eMERGE_OMOP_Mart;columnEncryptionSetting=Disabled;applicationName=Microsoft JDBC Driver for SQL Server;applicationIntent=readwrite; (Microsoft SQL Server 11.0)

2018-09-10 17:08:47.143 INFO localhost-startStop-1 org.flywaydb.core.internal.dbsupport.sqlserver.SQLServerDbSupport - - SQLServer does not support setting the schema for the current session. Default schema NOT changed to [ohdsi]

2018-09-10 17:08:47.491 INFO localhost-startStop-1 org.flywaydb.core.internal.command.DbMigrate - - Current version of schema [ohdsi]: 2.3.0.20180427114800

2018-09-10 17:08:47.491 WARN localhost-startStop-1 org.flywaydb.core.internal.command.DbMigrate - - outOfOrder mode is active. Migration of schema [ohdsi] may not be reproducible.

2018-09-10 17:08:47.498 INFO localhost-startStop-1 org.flywaydb.core.internal.command.DbMigrate - - Schema [ohdsi] is up to date. No migration necessary.

2018-09-10 17:08:47.508 INFO localhost-startStop-1 org.flywaydb.core.internal.dbsupport.sqlserver.SQLServerDbSupport - - SQLServer does not support setting the schema for the current session. Default schema NOT changed to [dbo]

2018-09-10 17:08:47.510 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘flyway’ of type [org.flywaydb.core.Flyway] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:47.530 DEBUG localhost-startStop-1 org.ohdsi.webapi.ShiroConfiguration - - DisabledSecurity module loaded

2018-09-10 17:08:47.545 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘security’ of type [org.ohdsi.webapi.shiro.management.DisabledSecurity] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:47.566 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘noLockoutPolicy’ of type [org.ohdsi.webapi.shiro.lockout.NoLockoutPolicy] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:47.724 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘securityManager’ of type [org.ohdsi.webapi.shiro.lockout.LockoutWebSecurityManager] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:47.950 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘integrationGlobalProperties’ of type [org.springframework.beans.factory.config.PropertiesFactoryBean] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:47.951 INFO localhost-startStop-1 org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - - Bean ‘integrationGlobalProperties’ of type [java.util.Properties] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2018-09-10 17:08:48.072 INFO localhost-startStop-1 org.springframework.web.context.ContextLoader - - Root WebApplicationContext: initialization completed in 16401 ms

2018-09-10 17:08:51.337 INFO localhost-startStop-1 org.springframework.boot.web.servlet.ServletRegistrationBean - - Mapping servlet: ‘org.ohdsi.webapi.JerseyConfig’ to [/*]

2018-09-10 17:08:51.338 INFO localhost-startStop-1 org.springframework.boot.web.servlet.ServletRegistrationBean - - Mapping servlet: ‘dispatcherServlet’ to [/]

2018-09-10 17:08:51.339 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘errorPageFilter’ to: [/*]

2018-09-10 17:08:51.339 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘characterEncodingFilter’ to: [/*]

2018-09-10 17:08:51.339 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘hiddenHttpMethodFilter’ to: [/*]

2018-09-10 17:08:51.339 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘httpPutFormContentFilter’ to: [/*]

2018-09-10 17:08:51.339 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘requestContextFilter’ to: [/*]

2018-09-10 17:08:51.340 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘corsFilter’ to: [/*]

2018-09-10 17:08:51.340 INFO localhost-startStop-1 org.springframework.boot.web.servlet.FilterRegistrationBean - - Mapping filter: ‘shiroFilter’ to: [/*]

2018-09-10 17:08:51.520 INFO localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource - - Loaded JDBC driver: com.microsoft.sqlserver.jdbc.SQLServerDriver

driver loaded: org.postgresql.Driver

driver loaded: com.microsoft.sqlserver.jdbc.SQLServerDriver

error loading oracle.jdbc.driver.OracleDriver driver.

driver loaded: com.amazon.redshift.jdbc.Driver

error loading com.cloudera.impala.jdbc4.Driver driver.

error loading net.starschema.clouddb.jdbc.BQDriver driver.

error loading org.netezza.Driver driver.

2018-09-10 17:08:52.462 INFO localhost-startStop-1 org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean - - Building JPA container EntityManagerFactory for persistence unit ‘default’

2018-09-10 17:08:52.528 INFO localhost-startStop-1 org.hibernate.jpa.internal.util.LogHelper - - HHH000204: Processing PersistenceUnitInfo [

name: default

...]

(Matthew Joss) #9

stdout continued:

2018-09-10 17:08:52.769 INFO localhost-startStop-1 org.hibernate.Version - - HHH000412: Hibernate Core {5.0.12.Final}

2018-09-10 17:08:52.771 INFO localhost-startStop-1 org.hibernate.cfg.Environment - - HHH000206: hibernate.properties not found

2018-09-10 17:08:52.779 INFO localhost-startStop-1 org.hibernate.cfg.Environment - - HHH000021: Bytecode provider name : javassist

2018-09-10 17:08:52.983 INFO localhost-startStop-1 org.hibernate.annotations.common.Version - - HCANN000001: Hibernate Commons Annotations {5.0.1.Final}

2018-09-10 17:08:53.745 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource - - Creating new JDBC DriverManager Connection to [jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart]

2018-09-10 17:08:53.802 INFO localhost-startStop-1 org.hibernate.dialect.Dialect - - HHH000400: Using dialect: org.hibernate.dialect.SQLServer2008Dialect

2018-09-10 17:08:54.659 WARN localhost-startStop-1 org.hibernate.boot.internal.IdGeneratorInterpreterImpl - - HHH000392: Hibernate does not support SequenceGenerator.initialValue() unless ‘hibernate.id.new_generator_mappings’ set

2018-09-10 17:08:54.813 WARN localhost-startStop-1 org.hibernate.boot.internal.IdGeneratorInterpreterImpl - - HHH000392: Hibernate does not support SequenceGenerator.initialValue() unless ‘hibernate.id.new_generator_mappings’ set

2018-09-10 17:08:54.979 WARN localhost-startStop-1 org.hibernate.boot.internal.IdGeneratorInterpreterImpl - - HHH000392: Hibernate does not support SequenceGenerator.initialValue() unless ‘hibernate.id.new_generator_mappings’ set

2018-09-10 17:08:55.037 WARN localhost-startStop-1 org.hibernate.boot.internal.IdGeneratorInterpreterImpl - - HHH000392: Hibernate does not support SequenceGenerator.initialValue() unless ‘hibernate.id.new_generator_mappings’ set

2018-09-10 17:08:55.181 WARN localhost-startStop-1 org.hibernate.boot.internal.IdGeneratorInterpreterImpl - - HHH000392: Hibernate does not support SequenceGenerator.initialValue() unless ‘hibernate.id.new_generator_mappings’ set

2018-09-10 17:08:55.348 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.353 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.353 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.354 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.355 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.356 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.357 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.357 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.358 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.358 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.374 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.375 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.375 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.376 WARN localhost-startStop-1 org.hibernate.orm.deprecation - - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceHiLoGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

2018-09-10 17:08:55.511 WARN localhost-startStop-1 org.hibernate.mapping.RootClass - - HHH000038: Composite-id class does not override equals(): org.ohdsi.webapi.conceptset.ConceptSetGenerationInfoKey

2018-09-10 17:08:55.512 WARN localhost-startStop-1 org.hibernate.mapping.RootClass - - HHH000039: Composite-id class does not override hashCode(): org.ohdsi.webapi.conceptset.ConceptSetGenerationInfoKey

2018-09-10 17:08:58.337 INFO localhost-startStop-1 org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean - - Initialized JPA EntityManagerFactory for persistence unit ‘default’

2018-09-10 17:08:59.714 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:08:59.862 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:08:59.864 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:08:59.865 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:08:59.865 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:08:59.865 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:08:59.886 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:08:59.890 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:08:59.952 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:08:59.952 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.123 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.124 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.137 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.137 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.138 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.138 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.245 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.246 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.248 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.248 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.249 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.249 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.335 INFO localhost-startStop-1 org.hibernate.hql.internal.QueryTranslatorFactoryInitiator - - HHH000397: Using ASTQueryTranslatorFactory

2018-09-10 17:09:00.714 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.715 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.716 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.716 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.736 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.736 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.772 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.773 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.774 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.774 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:00.775 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:00.776 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:01.231 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:01.232 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:01.233 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

2018-09-10 17:09:01.233 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:01.234 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation


(Matthew Joss) #10

stdout continued:

2018-09-10 17:09:01.234 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:01.503 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DataSourceUtils - - Fetching JDBC Connection from DataSource

2018-09-10 17:09:01.504 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource - - Creating new JDBC DriverManager Connection to [jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart]

2018-09-10 17:09:01.527 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DataSourceUtils - - Returning JDBC Connection to DataSource

2018-09-10 17:09:01.528 INFO localhost-startStop-1 org.springframework.batch.core.repository.support.JobRepositoryFactoryBean - - No database type set, using meta data indicating: SQLSERVER

2018-09-10 17:09:01.983 INFO localhost-startStop-1 org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor - - Initializing ExecutorService

2018-09-10 17:09:02.028 INFO localhost-startStop-1 org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor - - Initializing ExecutorService ‘taskExecutor’

2018-09-10 17:09:02.054 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Creating new transaction with name [org.springframework.data.jpa.repository.support.SimpleJpaRepository.findAll]: PROPAGATION_REQUIRED,ISOLATION_DEFAULT,readOnly; ‘’

2018-09-10 17:09:02.055 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Opened new EntityManager [org.hibernate.jpa.internal.EntityManagerImpl@7a9a47bc] for JPA transaction

2018-09-10 17:09:02.071 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource - - Creating new JDBC DriverManager Connection to [jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart]

2018-09-10 17:09:02.097 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DataSourceUtils - - Setting JDBC Connection [ConnectionID:13 ClientConnectionId: 54412804-1092-4a8a-a2ff-e14afb292f42] read-only

2018-09-10 17:09:02.101 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Exposing JPA transaction as JDBC transaction [org.springframework.orm.jpa.vendor.HibernateJpaDialect$HibernateConnectionHandle@3e546ee2]

Hibernate: select source0_.SOURCE_ID as SOURCE_I1_34_, source0_.SOURCE_CONNECTION as SOURCE_C2_34_, source0_.SOURCE_DIALECT as SOURCE_D3_34_, source0_.SOURCE_KEY as SOURCE_K4_34_, source0_.SOURCE_NAME as SOURCE_N5_34_ from ohdsi.source source0_

Hibernate: select daimons0_.SOURCE_ID as SOURCE_I5_35_0_, daimons0_.SOURCE_DAIMON_ID as SOURCE_D1_35_0_, daimons0_.SOURCE_DAIMON_ID as SOURCE_D1_35_1_, daimons0_.DAIMON_TYPE as DAIMON_T2_35_1_, daimons0_.PRIORITY as PRIORITY3_35_1_, daimons0_.SOURCE_ID as SOURCE_I5_35_1_, daimons0_.TABLE_QUALIFIER as TABLE_QU4_35_1_ from ohdsi.source_daimon daimons0_ where daimons0_.SOURCE_ID=?

2018-09-10 17:09:02.308 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Initiating transaction commit

2018-09-10 17:09:02.308 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Committing JPA transaction on EntityManager [org.hibernate.jpa.internal.EntityManagerImpl@7a9a47bc]

2018-09-10 17:09:02.319 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Closing JPA EntityManager [org.hibernate.jpa.internal.EntityManagerImpl@7a9a47bc] after transaction

2018-09-10 17:09:02.319 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:02.353 DEBUG localhost-startStop-1 org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler - - Creating new EntityManager for shared EntityManager invocation

Hibernate: select source0_.SOURCE_ID as SOURCE_I1_34_, source0_.SOURCE_CONNECTION as SOURCE_C2_34_, source0_.SOURCE_DIALECT as SOURCE_D3_34_, source0_.SOURCE_KEY as SOURCE_K4_34_, source0_.SOURCE_NAME as SOURCE_N5_34_ from ohdsi.source source0_ where source0_.SOURCE_KEY=?

2018-09-10 17:09:02.394 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource - - Creating new JDBC DriverManager Connection to [jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart]

Hibernate: select daimons0_.SOURCE_ID as SOURCE_I5_35_0_, daimons0_.SOURCE_DAIMON_ID as SOURCE_D1_35_0_, daimons0_.SOURCE_DAIMON_ID as SOURCE_D1_35_1_, daimons0_.DAIMON_TYPE as DAIMON_T2_35_1_, daimons0_.PRIORITY as PRIORITY3_35_1_, daimons0_.SOURCE_ID as SOURCE_I5_35_1_, daimons0_.TABLE_QUALIFIER as TABLE_QU4_35_1_ from ohdsi.source_daimon daimons0_ where daimons0_.SOURCE_ID=?


(Matthew Joss) #11

stdout continued:

2018-09-10 17:09:02.442 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:02.517 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Creating new transaction with name [org.springframework.batch.core.repository.support.SimpleJobRepository.getLastJobExecution]: PROPAGATION_REQUIRES_NEW,ISOLATION_READ_COMMITTED

2018-09-10 17:09:02.518 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Opened new EntityManager [org.hibernate.jpa.internal.EntityManagerImpl@559dae00] for JPA transaction

2018-09-10 17:09:02.518 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource - - Creating new JDBC DriverManager Connection to [jdbc:sqlserver://phsqlrpdr322.partners.org:1433;databasename=eMERGE_OMOP_Mart]

2018-09-10 17:09:02.543 DEBUG localhost-startStop-1 org.springframework.jdbc.datasource.DataSourceUtils - - Changing isolation level of JDBC Connection [ConnectionID:15 ClientConnectionId: 60c9cf59-354b-462b-b079-a9c76c06fc27] to 2

2018-09-10 17:09:02.545 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Exposing JPA transaction as JDBC transaction [org.springframework.orm.jpa.vendor.HibernateJpaDialect$HibernateConnectionHandle@6cfac632]

2018-09-10 17:09:02.570 DEBUG localhost-startStop-1 org.springframework.jdbc.core.JdbcTemplate - - Executing prepared SQL query

2018-09-10 17:09:02.572 DEBUG localhost-startStop-1 org.springframework.jdbc.core.JdbcTemplate - - Executing prepared SQL statement [SELECT JOB_INSTANCE_ID, JOB_NAME from secret-database-name.ohdsi.BATCH_JOB_INSTANCE where JOB_NAME = ? and JOB_KEY = ?]

2018-09-10 17:09:02.626 INFO localhost-startStop-1 org.springframework.beans.factory.xml.XmlBeanDefinitionReader - - Loading XML bean definitions from class path resource [org/springframework/jdbc/support/sql-error-codes.xml]

2018-09-10 17:09:02.849 INFO localhost-startStop-1 org.springframework.jdbc.support.SQLErrorCodesFactory - - SQLErrorCodes loaded: [DB2, Derby, H2, HSQL, Informix, MS-SQL, MySQL, Oracle, PostgreSQL, Sybase, Hana]


(Matthew Joss) #12

stdout continued:

2018-09-10 17:09:02.849 DEBUG localhost-startStop-1 org.springframework.jdbc.support.SQLErrorCodesFactory - - Looking up default SQLErrorCodes for DataSource [org.springframework.jdbc.datasource.DriverManagerDataSource@52d33912]

2018-09-10 17:09:02.850 DEBUG localhost-startStop-1 org.springframework.jdbc.support.SQLErrorCodesFactory - - SQL error codes for ‘Microsoft SQL Server’ found

2018-09-10 17:09:02.850 DEBUG localhost-startStop-1 org.springframework.jdbc.support.SQLErrorCodesFactory - - Caching SQL error codes for DataSource [org.springframework.jdbc.datasource.DriverManagerDataSource@52d33912]: database product name is ‘Microsoft SQL Server’

2018-09-10 17:09:02.853 DEBUG localhost-startStop-1 org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator - - Unable to translate SQLException with Error code ‘102’, will now try the fallback translator

2018-09-10 17:09:02.854 DEBUG localhost-startStop-1 org.springframework.jdbc.support.SQLStateSQLExceptionTranslator - - Extracted SQL state class ‘S0’ from value ‘S0001’

2018-09-10 17:09:02.854 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Initiating transaction rollback

2018-09-10 17:09:02.854 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Rolling back JPA transaction on EntityManager [org.hibernate.jpa.internal.EntityManagerImpl@559dae00]

2018-09-10 17:09:02.862 DEBUG localhost-startStop-1 org.springframework.orm.jpa.JpaTransactionManager - - Closing JPA EntityManager [org.hibernate.jpa.internal.EntityManagerImpl@559dae00] after transaction

2018-09-10 17:09:02.862 DEBUG localhost-startStop-1 org.springframework.orm.jpa.EntityManagerFactoryUtils - - Closing JPA EntityManager

2018-09-10 17:09:03.394 WARN localhost-startStop-1 org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext - - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘webApi’: Invocation of init method failed; nested exception is javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

2018-09-10 17:09:03.395 INFO localhost-startStop-1 org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor - - Shutting down ExecutorService ‘taskExecutor’

2018-09-10 17:09:03.439 INFO localhost-startStop-1 org.springframework.boot.autoconfigure.logging.AutoConfigurationReportLoggingInitializer - -


(Matthew Joss) #13

stdout continued:

Error starting ApplicationContext. To display the auto-configuration report re-run your application with ‘debug’ enabled.

2018-09-10 17:09:03.460 ERROR localhost-startStop-1 org.springframework.boot.SpringApplication - - Application startup failed

org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘webApi’: Invocation of init method failed; nested exception is javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)

at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)

at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)

at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)

at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)

at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:866)

at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542)

at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)

at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:737)

at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:370)

at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)

at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:151)

at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:131)

at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:86)

at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5669)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1017)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:993)

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2021)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

Caused by: javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error

at org.ohdsi.webapi.job.JobTemplate.launchTasklet(JobTemplate.java:77)

at org.ohdsi.webapi.service.CDMResultsService.warmCache(CDMResultsService.java:155)

at org.ohdsi.webapi.WebApi.lambda$warmCaches$18(WebApi.java:47)

at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)

at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)

at org.ohdsi.webapi.WebApi.warmCaches(WebApi.java:44)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)

at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)

... 31 more

root@2e60267eaf26:/var/log/supervisor#


(Lee Evans) #14

@mjoss did you do a docker-compose down and docker-compose up -d after running the source/source-daimon table row inserts? That’s required for ATLAS to load the rows from those tables.


(Matthew Joss) #15

Yes I did that a couple of times as I recall. Shall I try again and re-post the error logs?


(Lee Evans) #16

@mjoss OK, try doing that one more time and then try to connect to ATLAS in the Chrome browser and see what messages you get in the Chrome developer tools console.

On the Chrome developer tools networking tab you should see a reference to ‘sources/’ it’s a HTTP GET to ‘host ip address/WebAPI/source/sources’. Please post the output from that call here.

Another thing to verify is that your docker-compose.yml WEBAPI_URL references the correct server domain name or ip address where the Broadsea container is running - it may not be recognized when referenced as ‘localhost’.

Similarly verify in your Atlas config-local.js file that the configLocal.api url in config-local.js references the Broadsea container server host domain name or ip address.

Also, you might want to try changing the broadsea-webtools ports statement to use port 80 in the docker-compose.yml file:

ports:
- “80:8080”

and change the two above mentioned WEBAPI urls to use port 80. In some cases organizations have an internal proxy server or firewall config that only allows through port 80 traffic.


(Taha Abdul-Basser) #17

Just the relevant snippets would have been fine :slight_smile:

It is appears that WebAPI is failing to during the cache warm up phase of the WebAPI start up sequence, which is fairly far along. It appears that query associated with creating the jobs cache is failing.
Can you confirm that the table BATCH_JOB_INSTANCE does in fact exist in the OHDSI application (aka WebAPI) database and test run a query similar to

SELECT JOB_INSTANCE_ID, JOB_NAME from secret-database-name.ohdsi.BATCH_JOB_INSTANCE where JOB_NAME = ? and JOB_KEY = ?

against your database?


t