Cannot add/search data

[mfasco]

Hi,

Thanks for allowing us to try OntoBrowser.

I'm trying to configure a test installation but I'm having problems getting to a working state.

This is my environment:

• DB version: Oracle Database 11g Express Edition Release 11.2.0.2.0 - 64bit Production
• DB name: "XE"
• OS: Centos7 64bit
• Java: 1.8.0_161
• Wildfly: 11.0.0.Final
• Maven: 3.5.2
• Graphviz: 2.40.1

I installed all the requirements and created a Oracle user with the following commands: create user ontobrowser identified by my_password; grant CREATE SESSION, ALTER SESSION, CREATE DATABASE LINK, CREATE MATERIALIZED VIEW, CREATE PROCEDURE, CREATE PUBLIC SYNONYM, CREATE ROLE, CREATE SEQUENCE, CREATE SYNONYM, CREATE TABLE, CREATE TRIGGER, CREATE TYPE, CREATE VIEW, UNLIMITED TABLESPACE to ontobrowser;

Following the readme, I've tried to import the schema:

sqlplus ontobrowser@XE @create_schema_oracle.sql

but got this error:

(CREATE BITMAP INDEX TERM_IS_ROOT_IDX * ERROR at line 1: ORA-00439: feature not enabled: Bit-mapped indexes )

Then, I've inserted the initial data:

$ sqlplus ontobrowser@XE @insert_initial_data_oracle.sql

no errors here.

At this point, I've tried to load the ontology as described by the docs:

$ curl -s -S -O -L http://purl.obolibrary.org/obo/ma.obo $ curl -s -S -H "Content-Type: application/obo;charset=utf-8" -X PUT --data-binary "@ma.obo" -u SYSTEM "http://ontobrowser.MYDOMAIN.eu:8080/ontobrowser/ontologies/Mouse%20adult%20gross%20anatomy"

But on Wildfly (which has beed started with ./standalone.sh --debug) I can see this on the standard output:

17:13:36,392 INFO [io.undertow.servlet] (default task-1) com.novartis.pcs.ontology.rest.servlet.OntologiesServlet: Failed to import ontology: curator not found in request

Also, if I try to login into the web interface, I can see the webapp, but if I try to perform a search, I get an error 500 caused by this exception on Wildfly:

08:21:07,475 ERROR [org.jboss.as.ejb3.invocation] (default task-6) WFLYEJB0034: EJB Invocation failed on component OntologySearchServiceImpl for method public abstract java.util.List com.novartis.pcs.ontology.service.search.OntologySearchService.search(java.lang.String,boolean) throws com.novartis.pcs.ontology.service.search.result.InvalidQuerySyntaxException: javax.ejb.EJBException: java.lang.RuntimeException: Failed to perform Lucene seach with pattern: asdsa

Any idea to troubleshoot the problem?

Thanks a lot

Matteo

[carloravagli]

Hi Matteo,

The first issue is that the curator username is not being retrieved within the application because user authentication has not been setup. The install docs includes instructions to setup an Apache web server to perform user authentication so the curator username can be passed to Wildfly (and subsequently retrieved by the application). Unfortunately, due to some suspected changes with Wildfly many installers have reported issues with Wildfly not passing on the REMOTE_USER to the application from Apache.

My suggestion for evaluating OntoBrowser would be to setup Basic Authentication directly in Wildfly so the application can retrieve the curator username via the getRemoteUser method. The Wildfly documentation should provide all the instructions required to setup Basic Authentication. Good luck.

Regards, Carlo.