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| Code Block | ||||
|---|---|---|---|---|
| ||||
pmEndpoint {
url = "http://localhost:9090/i2b2/services/PMService/getServices"
}
ontEndpoint {
url = "http://localhost:9090/i2b2/services/OntologyService"
} |
- In the adapter {} section:
| Code Block | ||||
|---|---|---|---|---|
| ||||
crcEndpoint {
url = "http://localhost:9090/i2b2/services/QueryToolService"
} |
...
Next, you will need to add the SHRINE project into the pm_project_data table within the i2b2pm schema:
| Code Block | ||||
|---|---|---|---|---|
| ||||
$ 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'); |
...
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:
...
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):
| Code Block | ||||
|---|---|---|---|---|
| ||||
<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> |
...
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:
| Code Block | ||||
|---|---|---|---|---|
| ||||
{
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
}
]
// -------------------------------------------------------------------------------------------
} |
...
Once all of that is done, you will need to restart WildFly and Tomcat.
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