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create table `previousQueries` (`networkId` BIGINT NOT NULL,`userName` TEXT NOT NULL,`domain` TEXT NOT NULL,`queryName` TEXT NOT NULL,`expression` TEXT,`dateCreated` BIGINT NOT NULL,`deleted` BOOLEAN NOT NULL,`queryXml` TEXT NOT NULL,`changeDate` BIGINT NOT NULL); create table `queryFlags` (`networkId` BIGINT NOT NULL,`flagged` BOOLEAN NOT NULL,`flagMessage` TEXT NOT NULL,`changeDate` BIGINT NOT NULL); create table `queryResults` (`resultId` BIGINT NOT NULL,`networkQueryId` BIGINT NOT NULL,`instanceId` BIGINT NOT NULL,`adapterNode` TEXT NOT NULL,`resultType` TEXT,`size` BIGINT NOT NULL,`startDate` BIGINT,`endDate` BIGINT,`status` TEXT NOT NULL,`statusMessage` TEXT,`changeDate` BIGINT NOT NULL); create table `queryBreakdownResults` (`networkQueryId` BIGINT NOT NULL,`adapterNode` TEXT NOT NULL,`resultId` BIGINT NOT NULL,`resultType` TEXT NOT NULL,`dataKey` TEXT NOT NULL,`value` BIGINT NOT NULL,`changeDate` BIGINT NOT NULL); create table `queryResultProblemDigests` (`networkQueryId` BIGINT NOT NULL,`adapterNode` TEXT NOT NULL,`codec` TEXT NOT NULL,`stamp` TEXT NOT NULL,`summary` TEXT NOT NULL,`description` TEXT NOT NULL,`details` TEXT NOT NULL,`changeDate` BIGINT NOT NULL); |
shrine.conf changes
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Configure the SHRINE Data Steward
Database - i2b2
The SHRINE Data Steward is typically backed by the i2b2 PM cell used by SHRINE. From the steward application's point of view, all users on the SHRINE project are considered Researchers. However, there is some additional work that has to be done to the i2b2 user list to accommodate the SHRINE Data Steward.
QEP User
The Steward application requires set of user credentials that it will use to submit queries through to SHRINE. It is recommended that this be a dedicated user separate from any other account. Additionally, it will need to have the parameter "qep" defined (name: qep, value: true, type: text), which can be set in the Manage Users section of the i2b2 Admin Panel.
In shrine.conf, make sure there is a shrineSteward block in the queryEntryPoint section, and that the qepUserName and qepPassword properties match the user with the qep parameter.
Steward User
In Steward application deployments that require manual topic approval, a trusted user will have to be given permission to review proposed research topics and approve/reject them. To mark a user as such, add the "DataSteward" parameter (name: DataSteward, value: true, type: text) to that user in the Manage Users section of the i2b2 Admin Panel.
Changes to shrine.conf
Consolidation of .conf files
The dashboard.conf, steward.conf, and shrine.conf files have been consolidated into a single shrine.conf file. (The three files had several sections that were duplicated and had to be identical. This should make managing SHRINE's configuration simpler.) All services expect to find all the configuration values they need inside shrine.conf. steward.conf and dashboard.conf will be ignored.
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trustModelIsHub = true attachSigningCert = true |
Node Meta Data Service
SHRINE networks now include a JSON api at every node that reports about the contents of the metaData section. What belongs in the metaData section is completely configurable, and we recommend that it be used as a means for serving relevant contact information. Bear in mind that this information is publicly available. For more information on interacting with the Node Data Service, please see the wiki page.
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shrine {
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adapter {
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// obfuscation {
// binSize = 5 //by default. //Round to the nearest binSize. Use 1 for no effect (to match SHRINE 1.21 and earlier).
// sigma = 6.5 //by default. //Noise to inject. Use 0 for no effect. (Use 1.33 to match SHRINE 1.21 and earlier).
// clamp = 10 //by default. //Maximum ammount of noise to inject. (Use 3 to match SHRINE 1.21 and earlier).
// }
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<?xml version='1.0' encoding='utf-8'?>
<!-- The contents of this file will be loaded for each web application -->
<Context>
<WatchedResource>WEB-INF/web.xml</WatchedResource>
<Resource name="jdbc/problemDB" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/shrine_query_history"
testOnBorrow="true" validationQuery="SELECT 1"/>
<Resource name="jdbc/shrineDB" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="SHRINE_MYSQL_USERshrine" password="SHRINE_MYSQL_PASSWORDdemouser" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://SHRINE_MYSQL_HOSTlocalhost:3306/SHRINEshrine_DBquery_NAMEhistory"
testOnBorrow="true" validationQuery="SELECT 1"/>
<Resource name="jdbc/adapterAuditDB" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/adapterAuditDB"
testOnBorrow="true" validationQuery="SELECT 1"/>
<Resource name="jdbc/qepAuditDB" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="shrine" password="demouser" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/qepAuditDB"
testOnBorrow="true" validationQuery="SELECT 1"/>
<Resource name="jdbc/stewardDB" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="SHRINE_STEWARD_MYSQL_USERshrine" password="SHRINE_STEWARD_MYSQL_PASSWORDdemouser" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://SHRINE_STEWARD_MYSQL_HOSTlocalhost:3306/SHRINE_STEWARD_DB_NAMEstewardDB"
testOnBorrow="true" validationQuery="SELECT 1"/>
</Context> |
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