bioswr Files

This is a BioSWR 1.0 Web application.
BioSWR uses JAX-RS 1.1, JSF 2.0 and CDI 1.0 and developed for JAVA EE6 Application Servers (i.e. JBoss 7.1.1)
BioSWR also uses JDBC connection for ontologies storage.

web.xml
--------------------------------------------------
<resource-ref>
  <res-ref-name>jdbc/bio_swr</res-ref-name>
  <res-type>javax.sql.DataSource</res-type>
  <res-auth>Container</res-auth>
  <res-sharing-scope>Shareable</res-sharing-scope>
</resource-ref>

This connection must be configured for the concrete AS

jboss-web.xml
--------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<jboss-web>
  <context-root>/BioSWR</context-root>
  <security-domain>bioswr</security-domain>
  <resource-ref>
    <res-ref-name>jdbc/bio_swr</res-ref-name>
    <jndi-name>java:/jdbc/bio_swr</jndi-name>
  </resource-ref>
</jboss-web>

BioSWR also relies on Application Server security mechanism

web.xml
--------------------------------------------------
<login-config>
  <auth-method>BASIC</auth-method>
</login-config>

This username is used to keep track of registered services and annotations owner.

All ontologies are stored in one table:

CREATE TABLE IF NOT EXISTS "file" (
  "id" CHAR(32) NOT NULL,
  "type" VARCHAR(256) NOT NULL,
  "url" VARCHAR(256) DEFAULT NULL,
  "file" MEDIUMTEXT NOT NULL,
  "crc32" INTEGER(11) UNSIGNED DEFAULT NULL,
  "user" VARCHAR(32) DEFAULT NULL,
  "locked" BOOLEAN NOT NULL DEFAULT TRUE,
  "status" INTEGER(11) UNSIGNED DEFAULT NULL,
  "checkdate" DATETIME DEFAULT NULL,
  PRIMARY KEY ("id", "type"),
)