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Unable to setup WebAPI and Atlas

webapi
atlas

(Alberto Gil Jimenez) #1

Hi all,

I have been trying to setup the latest releases of WebAPI and Atlas in my local machine (Ubuntu 18.04.1, java 1.8.0_181-8u181-b13-1ubuntu0.18.04.1-b13) and I found some errors that I did not manage to solve.

In brief: I followed the whole setup, some errors appeared, but once I try to run Atlas nothing happens.

I basically followed all the steps from the WebAPI tutorial in the wiki, and did all the setup on a local database that is populated with a CDM dataset.

The .war file building using maven was successful (BUILD SUCCESS), nevertheless an error showed up in the output:
[ERROR] Critical error: MireDot was unable to process org.ohdsi.webapi.cohortcharacterization.CcController. Interface skipped.
I am not really sure whether this error may be relevant; I could not find anyone in the OHDSI forum that encountered a similar situation.

After that, I deployed the war file using Tomcat. The service created the schema ohdsi, all the related tables, as well as the tables in the webapi schema.
This error showed up in the catalina output:

2018-11-23 12:25:04.121 INFO localhost-startStop-1 org.springframework.jdbc.datasource.DriverManagerDataSource -  - Loaded JDBC driver: org.postgresql.Driver
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.jdbc41.Driver driver.
error loading net.starschema.clouddb.jdbc.BQDriver driver.
error loading org.netezza.Driver driver.

The remaining messages shown in the catalina output are Warnings and Debugs. I did not do any additional setup for the jdbc drivers as I am doing the setup in a Postgres database, and in theory the driver should be available from the Maven repository.

Then, I inserted in the source table (ohdsi schema) the connection details to the server (port, database name, username, passsword) as well as in the source_daimon (webapi schema) (WebAPI SOURCE and SOURE_DAIMON Inserts) the info about the cdm & webapi schemas. After I start Tomcat, I can verify that the configuration worked as I see a response from the API if I try to access it via
http://localhost:8080/WebAPI/source/sources

Subsequently, I tried to launch Atlas using IntelliJ, but once it opens in Firefox, it gets stuck in the Atlas loading page (the one where we can see Atlas as well as the circles moving around). So I guess that a reason for this may be one of the errors that showed up during the installation process.

Has someone here experienced a similar situation, or has any hint about how to tackle this situation?

Thank you very much in advance!

Regards,
Alberto


(Chris Knoll) #2

You can ignore this error, it’s an issue generating documentation that has yet to be resolved.

It looks like your WebAPI install is working if you see a response from the /source/sources endpoint.

For the failure to start up in Firefox. try Chrome 63 or later. Use ctrl-shift-i to bring up the browser’s debug console. if any errors appear during startup, post them here.


(Alberto Gil Jimenez) #3

@Chris_Knoll, thanks a lot for your input, I wasn’t really sure whether these errors might have an impact in the final webapi deployment.

I just realized after checking the browser’s debug, that I forgot to set up the config-local.js file with the api url for my local environment. After doing some modifications, now it works, thank you!


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