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$ cp /opt/shrine/shrine.keystore /opt/shrine/upgrade-backups/shrine.keystore |
Remove old SHRINE components
SHRINE will use new components, so to avoid conflicts with older files, you can Finally remove the old .war files with this command:
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shrineHubBaseUrl = "https://shrine_hub_url:6443" //The shrine hub's URL as observed from this tomcat server i2b2BaseUrl = "http://localhost:9090" //The local i2b2's URL as observed from this tomcat server i2b2Domain = "i2b2demo" //recommended to change this to a unique domain i2b2ShrineProjectName = "SHRINE" shrine { nodeKey = "unique-node-name" //node key to get information from the hub about this node shrineDatabaseType = "mysql" // default //can be oracle, mysql, sqlserver messagequeue { blockingq { serverUrl = ${shrineHubBaseUrl}/shrine-api/mom //point this to the network hub } } webclient { domain = ${i2b2Domain} name = ${i2b2ShrineProjectName} siteAdminEmail = "shrine-admin@example.com" } pmEndpoint { url = ${i2b2BaseUrl}/i2b2/services/PMService/getServices } ontEndpoint { url = ${i2b2BaseUrl}/i2b2/services/OntologyService/ } hiveCredentials { domain = ${i2b2Domain} username = "demo" password = "demouser" crcProjectId = "Demo" ontProjectId = ${i2b2ShrineProjectName} } breakdownResultOutputTypes { PATIENT_AGE_COUNT_XML { description = "Age patient breakdown" } PATIENT_RACE_COUNT_XML { description = "Race patient breakdown" } PATIENT_VITALSTATUS_COUNT_XML { description = "Vital Status patient breakdown" } PATIENT_GENDER_COUNT_XML { description = "Gender patient breakdown" } } //end breakdown section hub { client { serverUrl = ${shrineHubBaseUrl} } } queryEntryPoint { broadcasterServiceEndpoint { url = ${shrineHubBaseUrl}/shrine/rest/broadcaster/broadcast } } adapter { crcEndpoint { url = ${i2b2BaseUrl}/i2b2/services/QueryToolService/ } adapterMappingsFileName = "AdapterMappings.csv" } //end adapter section keystore { file = "/opt/shrine/shrine.keystore" password = "password" privateKeyAlias = "your_private_key_alias" keyStoreType = "JKS" caCertAliases = ["shrine-hub-ca"] } //end keystore section steward { createTopicsMode = Approved emailDataSteward { //provide the email address of the shrine node system admin, to handle bounces and invalid addresses from = "shrine-admin@example.com" //provide the email address of the shrine node system admin, to handle bounces and invalid addresses to = "shrine-steward@example.com" //provide the externally-reachable URL for the data steward externalStewardBaseUrl = "https://shrine.example.com:6443/steward"${shrineHubBaseUrl}/shrine-api/shrine-steward } database { dataSourceFrom = "JNDI" jndiDataSourceName = "java:comp/env/jdbc/stewardDB" slickProfileClassName = "slick.jdbc.MySQLProfile$" //slick.jdbc.H2Profile$ //slick.jdbc.PostgresProfile$ //slick.jdbc.SQLServerProfile$ //slick.jdbc.JdbcProfile$ //slick.jdbc.OracleProfile$ } //end steward database section } //end steward section } //end shrine |
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Remove the PRIVILEGED_USER table and associated constraints and sequences from your database
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use shrine_query_history;
DROP TABLE PRIVILEGED_USER; |
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use shrine_query_history;
ALTER TABLE COUNT_RESULT DROP COLUMN ORIGINAL_COUNT; |
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use shrine_query_history;
ALTER TABLE BREAKDOWN_RESULT DROP COLUMN ORIGINAL_VALUE; |
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use qepAuditDB; ALTER TABLE previousQueries ADD COLUMN 'status' VARCHAR(255) NOT NULL DEFAULT 'Before V26'; |
MS SQL:
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Added table QUERY_PROBLEM_DIGESTS
MySQL:
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use qepAuditDB; create table `QUERYQUERY_PROBLEM_DIGESTS`DIGESTS (`NETWORKQUERYID`NETWORKQUERYID BIGINT NOT NULL,`CODEC` CODEC TEXT NOT NULL,`STAMP` STAMP TEXT NOT NULL,`SUMMARY` SUMMARY TEXT NOT NULL,`DESCRIPTION` DESCRIPTION TEXT NOT NULL,`DETAILS` DETAILS TEXT NOT NULL,`CHANGEDATE` CHANGEDATE BIGINT NOT NULL); create index queryProblemsNetworkIdIndex on QUERY_PROBLEM_DIGESTS(NETWORKQUERYID); |
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use qepAuditDB; create table `RESULTSRESULTS_OBSERVED`OBSERVED (`NETWORKQUERYID`NETWORKQUERYID BIGINT NOT NULL,`CHECKSUM` CHECKSUM BIGINT NOT NULL,`OBSERVEDTIME` OBSERVEDTIME BIGINT NOT NULL); create index resultsObservedQueryIdIndex on RESULTS_OBSERVED(NETWORKQUERYID); create index resultsObservedChecksumIndex on RESULTS_OBSERVED(CHECKSUM); |
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This is a sample screenshot of the upgraded 2.0.0-PR1 dashboard:
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