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pmEndpoint { url = "http://localhost:9090/i2b2/services/PMService/getServices" } ontEndpoint { url = "http://localhost:9090/i2b2/services/OntologyService" } |
- In the adapter {} section:
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crcEndpoint { url = "http://localhost:9090/i2b2/services/QueryToolService" } |
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Next, you will need to add the SHRINE project into the pm_project_data table within the i2b2pm schema:
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$ psql -U postgres i2b2 i2b2=# set search_path = i2b2pm; i2b2=# insert into PM_PROJECT_DATA (project_id, project_name, project_wiki, project_path, status_cd) values ('SHRINE', 'SHRINE', 'http://open.med.harvard.edu/display/SHRINE', '/SHRINE', 'A'); |
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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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This should result in something that looks like this:
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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Next, you will need to template the i2b2_config_data.js file to reflect the correct PM cell url for logging into the SHRINE webclient. The file is located in /opt/shrine/tomcat/webapps/shrine-webclient/i2b2_config_data.js. It should look like this:
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{ urlProxy: "/shrine-proxy/request", urlFramework: "js-i2b2/", loginTimeout: 15, // in seconds username_label:"SHRINE Username:", //Username Label password_label:"SHRINE Password:", //Password Label clientHelpUrl: 'help/pdf/shrine-client-guide.pdf', networkHelpUrl:'help/pdf/shrine-network-guide.pdf', wikiBaseUrl: 'https://open.med.harvard.edu/wiki/display/SHRINE/', obfuscation: 10, resultName: "patients", // ------------------------------------------------------------------------------------------- // THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO lstDomains: [ { domain: "i2b2demo", name: "SHRINE", urlCellPM: "http://localhost:9090/i2b2/services/PMService/", allowAnalysis: false, debug: true, isSHRINE: true } ] // ------------------------------------------------------------------------------------------- } |
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Once all of that is done, you will need to restart WildFly and Tomcat.