WebAPI JAR Conflict

Implementers
1

I am new to the ODHSI suite of web tools, and I am having trouble with my installation of the WebAPI (cloned from github 12/5/2017) using PostgreSQL 9.6.6. I am using Java 1.8.0.151, Maven 3.5.0 and Tomcat 8.5.24 on Ubuntu 17.10.

When Accessing http://localhost:8080/WebAPI/source/sources I get the following error:

Type Exception Report

Message Servlet.init() for servlet [org.ohdsi.webapi.JerseyConfig] threw exception

Description The server encountered an unexpected condition that prevented it from fulfilling the request.

Exception

javax.servlet.ServletException: Servlet.init() for servlet [org.ohdsi.webapi.JerseyConfig] threw exception
	org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504)
	org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
	org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
	org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
	org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
	org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
	org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
	org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
	org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	java.lang.Thread.run(Thread.java:748)
Root Cause

java.lang.NoSuchMethodError: javax.ws.rs.core.Application.getProperties()Ljava/util/Map;
	org.glassfish.jersey.server.ApplicationHandler.<init>(ApplicationHandler.java:331)
	org.glassfish.jersey.servlet.WebComponent.<init>(WebComponent.java:392)
	org.glassfish.jersey.servlet.ServletContainer.init(ServletContainer.java:177)
	org.glassfish.jersey.servlet.ServletContainer.init(ServletContainer.java:369)
	javax.servlet.GenericServlet.init(GenericServlet.java:158)
	org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504)
	org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
	org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
	org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
	org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
	org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
	org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
	org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
	org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	java.lang.Thread.run(Thread.java:748)

When ging through the jar files in the web applications’s lib directory I noticed that there are two jar file that contain the class javax.ws.rs.core.Application:

kai@kai-VirtualBox:~/tomcat/webapps/WebAPI/WEB-INF/lib$ grep -lir "javax.ws.rs.core.Application" *.jar
javax.ws.rs-api-2.0.1.jar
jersey-core-1.13.jar

When expanding the source version of jersey-core-1.13.jar I see that its version of javax.rs.core.Application has indeed no getProperties() method. How can I as an implementer resolve this conflict? I am building the WebAPI from source code cloned from github within the past week. Thansk for your help!

2

I think we need to either update the dependency of jersey-core or exclude it. There’s a way to specify this in the maven pom.xml file, but I need to dig into what the solution is. I think this was raised as an issue under the WebAPI repo.

3

Update: I removed the ‘scope’ element from this dependency XML example. Apologies. Please update the POM to the updated form below:

Could you try to modify your local POM.xml file to switch the microsoft JDBC dependency to this:

<dependency>
    <groupId>com.microsoft.sqlserver</groupId>
    <artifactId>mssql-jdbc</artifactId>
    <version>6.2.2.jre8</version>
</dependency>

Then recompile the WAR with the mvn command, and redeploy to tomcat. Let us know if that resolves this.

4

Hi Chris, thank you so much, that worked! Cheers, Kai

5

No Problem. We’ll make an update to the POM for the next release of WebAPI.

6

Hi @kaiwpost @Chris_Knoll

I am having trouble with the deployment of WebAPI war .
I cloned from github on 8th Aug 2018 using postgres 9.6.2 .However when i am deploying the WebAPI war on tomcat i am getting sqlserver exception on startup logs .

SEVERE: Unable to create initial connections of pool.
com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host serverName, port 1433 has failed. Error: "serverName. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.

I am not able to find anything in documentation which states that i need to configure sqlserver apart from the database you are using.

The pom file does mention this however:

<!-- Primary DataSource -->
    <!-- default sql server - TODO How about making postgres the default (e.g. in line with open source tech)? -alexfranken -->
    <datasource.driverClassName>com.microsoft.sqlserver.jdbc.SQLServerDriver</datasource.driverClassName>
    <datasource.url>jdbc:sqlserver://serverName;databaseName=databaseName</datasource.url>
    <datasource.username>user</datasource.username>
    <datasource.password>password</datasource.password>

Am i missing anything.Any help is appreciated.

Edit:I have found a solution for the error i was receiving during startup. :yum:

I build the WebAPI again with webapi-postgresql as profile id.