NCIP/URI_Resolver

Name: URI_Resolver

Owner: National Cancer Informatics Program

Description: Resolves URIs for CTS2

Created: 2013-06-12 16:55:33.0

Updated: 2013-11-01 18:44:55.0

Pushed: 2015-04-14 21:43:34.0

Homepage: null

Size: 669

Language: Java

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README

URI Resolver REST Interface For CTS2

Table of Contents
Installation Overview
  1. Install war file, URI_Resolver-0.0.1-SNAPSHOT.war to JBOSS or Tomcat server.
  2. Configure database connection values (see below)
  3. Configure user accounts (see below)
  4. Test sample using url: http://localhost/URI_Resolver-0.0.1.SNAPSHOT
Configure Database Connection Values
To use default database connection values
  1. Install MySQL server on the local machine to run on port 3306
  2. Create a MySQL account: uriuser with the password uriuser
  3. Create a MySQL database named uriresolver, give uriuser permissions to write to this database.
  4. Download uriresolver.sql from github project. File is located in src/main/resources
  5. Using MySQL, import data from the uriresolver.sql export file into the uriresolver database
To use user specified database connection values
  1. Create a folder: <USER_HOME>/.cts2_uri
    • USER_HOME refers to the home directory of the account running JBOSS server (i.e. user will be jboss if running on ubuntu)
  2. Create a file: uriresolver.properties and store this file in the USER_HOME/.cts2_uri folder
  3. Edit uriresolver.properties to contain the following:
    db.driverClassName=\
db.url=\
db.username=\
db.password=\
db.editable=false
log.level=0
log.filelocation=
  4. Example uriresolver.properties file:
    jdbc.driverClassName=com.mysql.jdbc.Driver
db.url=jdbc:mysql://localhost:3306/uriresolver
db.username=uriuser
db.password=uriuser
db.editable=false
log.level=0
log.filelocation=
To use In-memory database

An in-memory database will be utilized if the two previous options are not available. Nothing is required to configure this database. It will only exist during the REST connection.

Configure User Accounts
To use default user accounts
  1. Create the uriresolver.properties file, described above, and set db.editable to true.
  2. By default one account will be available with cts2/mayo+nih as the username/password.
To use user specified user accounts
  1. Create the uriresolver.properties file, described above, and set db.editable to true.
  2. Create user.properties (save in USER_HOME/.cts2_uri folder)
  3. Enter username/passwords in user.properties file, one per line with a space seperating the username/password.
  4. Example user.properties file:
    jdoe abcd1234
bspringsteen born2run
  5. If USER_HOME/.cts2_uri/user.properties file exist then only accounts listed in this file will be enabled. The default cts2 account, mentioned above, will not be enabled.
Errors & Warnings
MySQL Errors
13:06:52,434 ERROR [edu.mayo.cts2.uriresolver.dao.UriJDBCTemplate] (http--0.0.0.0-8180-1) Error connecting to data source: Access denied for user 'uriuser'@'localhost' (using password: YES)
13:06:52,438 ERROR [edu.mayo.cts2.uriresolver.controller.ResolveURI] (http--0.0.0.0-8180-1) Unknown error while checking tables exist: Access denied for user 'uriuser'@'localhost' (using password: YES)
13:06:52,439 INFO  [edu.mayo.cts2.uriresolver.controller.ResolveURI] (http--0.0.0.0-8180-1) Creating an in memory database

This error is generated when the program cannot connect a local mysql server with the given credentials. These errors will only be generated when attempting to connect to MySQL, not the in-memory database. Errors can be ignored unless you were expecting the MySQL connection to be successfull. If this is the case check the credentials provided in the error messages.

MySQL Warnings
13:06:52,261 WARN  [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer] (http--0.0.0.0-8180-1) Could not load properties from URL [file:/home/jboss/.cts2_uri/uriresolver.properties]: /home/jboss/.cts2_uri/uriresolver.properties (No such file or directory)

This warning is generated when the user's uriresolver.properties files is not found. At this point the program will use the in-memory database solution.

JBOSS Warnings

Spring Framework Warning (created when war file is loaded into JBoss. This warning can be ignored.)

13:05:56,077 WARN  [org.jboss.as.ee] (MSC service thread 1-3) JBAS011006: Not installing optional component org.springframework.web.context.request.async.StandardServletAsyncWebRequest due to exception: org.jboss.as.server.deployment.DeploymentUnitProcessingException: JBAS011054: Could not find default constructor for class org.springframework.web.context.request.async.StandardServletAsyncWebRequest
at org.jboss.as.ee.component.ComponentDescription$DefaultComponentConfigurator.configure(ComponentDescription.java:606)
at org.jboss.as.ee.component.deployers.EEModuleConfigurationProcessor.deploy(EEModuleConfigurationProcessor.java:81)
at org.jboss.as.server.deployment.DeploymentUnitPhaseService.start(DeploymentUnitPhaseService.java:113) [jboss-as-server-7.1.1.Final.jar:7.1.1.Final]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1811) [jboss-msc-1.0.2.GA.jar:1.0.2.GA]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1746) [jboss-msc-1.0.2.GA.jar:1.0.2.GA]
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [rt.jar:1.6.0_12]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [rt.jar:1.6.0_12]
at java.lang.Thread.run(Thread.java:619) [rt.jar:1.6.0_12]
JBOSS Errors

Sun Rowset ClassNotFound Error (Must be resolved, see below)

12:55:20,312 ERROR [org.apache.catalina.core.ContainerBase.[jboss.web].[default-host].[/URI_Resolver-0.0.1-SNAPSHOT].[uri_resolver]] (http--0.0.0.0-8180-3) Servlet.service() for servlet uri_resolver threw exception: java.lang.ClassNotFoundException: com.sun.rowset.CachedRowSetImpl from [Module "deployment.URI_Resolver-0.0.1-SNAPSHOT.war:main" from Service Module Loader]
at org.jboss.modules.ModuleClassLoader.findClass(ModuleClassLoader.java:190)
at org.jboss.modules.ConcurrentClassLoader.performLoadClassUnchecked(ConcurrentClassLoader.java:468)
at org.jboss.modules.ConcurrentClassLoader.performLoadClassChecked(ConcurrentClassLoader.java:456)
...
You will find more details in the following links:
This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.