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To make sure that your new SHRINE instance can communicate with the i2b2 instance, there are a couple of places that we will address. First, you will need to make sure the PM, ONT, CRC cell urls are correctly defined within the shrine.conf file. These urls are what SHRINE uses to communicate with the i2b2 backend:
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After loading the ontology into SHRINE, you will need to add a SHRINE CRC connection to the pm_cell_data table within the i2b2pm schema:
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$ psql -U postgres i2b2
i2b2=# set search_path = i2b2pm;
i2b2=# insert into PM_CELL_DATA (cell_id, project_path, name, method_cd, url, can_override, status_cd) values ('CRC', '/SHRINE', 'SHRINE Federated Query', 'REST', 'https://your_shrine_url:6443/shrine/rest/i2b2/', 1, 'A');
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After doing that, you will also need to add the Shrine Ontology data source (DS) to the ont-ds.xml file within the i2b2 instance. This file should be located within your i2b2 deployments directory (/opt/wildfly/standalone/deployments):
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<datasource jta="false" jndi-name="java:/ShrineOntologyDS" pool-name="ShrineOntologyDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://localhost:5432/i2b2</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>shrine_ont</user-name>
<password>demouser</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource> |
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