diff --git a/commons/protocol/src/main/scala/net/shrine/protocol/QueryMaster.scala b/commons/protocol/src/main/scala/net/shrine/protocol/QueryMaster.scala index 195a7e8ba..b224cd021 100644 --- a/commons/protocol/src/main/scala/net/shrine/protocol/QueryMaster.scala +++ b/commons/protocol/src/main/scala/net/shrine/protocol/QueryMaster.scala @@ -1,23 +1,24 @@ package net.shrine.protocol import javax.xml.datatype.XMLGregorianCalendar /** * @author Bill Simons - * @date 4/2/12 - * @link http://cbmi.med.harvard.edu - * @link http://chip.org + * @since 4/2/12 + * @see http://cbmi.med.harvard.edu + * @see http://chip.org *

* NOTICE: This software comes with NO guarantees whatsoever and is * licensed as Lgpl Open Source - * @link http://www.gnu.org/licenses/lgpl.html + * @see http://www.gnu.org/licenses/lgpl.html */ final case class QueryMaster ( - queryMasterId: String, networkQueryId: Long, + queryMasterId: String, //Outside of tests, this is the networkQueryId as a string + networkQueryId: Long, name: String, userId: String, groupId: String, createDate: XMLGregorianCalendar, held: Option[Boolean] = None, flagged: Option[Boolean] = None, flagMessage: Option[String] = None) \ No newline at end of file diff --git a/qep/service/src/main/scala/net/shrine/service/queries/QepQueryDb.scala b/qep/service/src/main/scala/net/shrine/service/queries/QepQueryDb.scala index a07c46f5c..73baf468a 100644 --- a/qep/service/src/main/scala/net/shrine/service/queries/QepQueryDb.scala +++ b/qep/service/src/main/scala/net/shrine/service/queries/QepQueryDb.scala @@ -1,253 +1,253 @@ package net.shrine.service.queries import java.io.PrintWriter import java.sql.{DriverManager, Connection, SQLException} import java.util.GregorianCalendar import java.util.logging.Logger import javax.naming.InitialContext import javax.sql.DataSource import javax.xml.datatype.{DatatypeFactory} import com.typesafe.config.Config import net.shrine.log.Loggable import net.shrine.protocol.{QueryMaster, ReadPreviousQueriesResponse, ReadPreviousQueriesRequest, RunQueryRequest} import net.shrine.audit.{Time, QueryName, NetworkQueryId, UserName} import net.shrine.service.QepConfigSource import slick.driver.JdbcProfile import scala.concurrent.{Future, Await} import scala.concurrent.duration.{Duration,DurationInt} import scala.language.postfixOps import scala.concurrent.ExecutionContext.Implicits.global import scala.concurrent.blocking /** * DB code for the QEP's query instances and query results. * * @author david * @since 1/19/16 */ case class QepQueryDb(schemaDef:QepQuerySchema,dataSource: DataSource) extends Loggable { import schemaDef._ import jdbcProfile.api._ val database = Database.forDataSource(dataSource) def createTables() = schemaDef.createTables(database) def dropTables() = schemaDef.dropTables(database) def dbRun[R](action: DBIOAction[R, NoStream, Nothing]):R = { val future: Future[R] = database.run(action) blocking { Await.result(future, 10 seconds) } } def insertQepQuery(runQueryRequest: RunQueryRequest):Unit = { debug(s"insertQepQuery $runQueryRequest") insertQepQuery(QepQuery(runQueryRequest)) } def insertQepQuery(qepQuery: QepQuery):Unit = { dbRun(allQepQueryQuery += qepQuery) } def selectAllQepQueries:Seq[QepQuery] = { dbRun(allQepQueryQuery.result) } def selectPreviousQueries(request: ReadPreviousQueriesRequest):ReadPreviousQueriesResponse = { val previousQueries: Seq[QepQuery] = selectPreviousQueriesByUserAndDomain(request.authn.username,request.authn.domain) ReadPreviousQueriesResponse(previousQueries.map(_.toQueryMaster)) } def selectPreviousQueriesByUserAndDomain(userName: UserName,domain: String):Seq[QepQuery] = { dbRun(allQepQueryQuery.filter(_.userName === userName).filter(_.userDomain === domain).result) } } object QepQueryDb extends Loggable { val dataSource:DataSource = { val dataSourceFrom = QepQuerySchema.config.getString("dataSourceFrom") if(dataSourceFrom == "JNDI") { val jndiDataSourceName = QepQuerySchema.config.getString("jndiDataSourceName") val initialContext:InitialContext = new InitialContext() initialContext.lookup(jndiDataSourceName).asInstanceOf[DataSource] } else if (dataSourceFrom == "testDataSource") { val testDataSourceConfig = QepQuerySchema.config.getConfig("testDataSource") val driverClassName = testDataSourceConfig.getString("driverClassName") val url = testDataSourceConfig.getString("url") //Creating an instance of the driver register it. (!) From a previous epoch, but it works. Class.forName(driverClassName).newInstance() object TestDataSource extends DataSource { override def getConnection: Connection = { DriverManager.getConnection(url) } override def getConnection(username: String, password: String): Connection = { DriverManager.getConnection(url, username, password) } //unused methods override def unwrap[T](iface: Class[T]): T = ??? override def isWrapperFor(iface: Class[_]): Boolean = ??? override def setLogWriter(out: PrintWriter): Unit = ??? override def getLoginTimeout: Int = ??? override def setLoginTimeout(seconds: Int): Unit = ??? override def getParentLogger: Logger = ??? override def getLogWriter: PrintWriter = ??? } TestDataSource } else throw new IllegalArgumentException(s"shrine.steward.database.dataSourceFrom must be either JNDI or testDataSource, not $dataSourceFrom") } val db = QepQueryDb(QepQuerySchema.schema,dataSource) val createTablesOnStart = QepQuerySchema.config.getBoolean("createTablesOnStart") if(createTablesOnStart) QepQueryDb.db.createTables() } /** * Separate class to support schema generation without actually connecting to the database. * * @param jdbcProfile Database profile to use for the schema */ case class QepQuerySchema(jdbcProfile: JdbcProfile) extends Loggable { import jdbcProfile.api._ def ddlForAllTables = { allQepQueryQuery.schema } //to get the schema, use the REPL //println(QepQuerySchema.schema.ddlForAllTables.createStatements.mkString(";\n")) def createTables(database:Database) = { try { val future = database.run(ddlForAllTables.create) Await.result(future,10 seconds) } catch { //I'd prefer to check and create schema only if absent. No way to do that with Oracle. case x:SQLException => info("Caught exception while creating tables. Recover by assuming the tables already exist.",x) } } def dropTables(database:Database) = { val future = database.run(ddlForAllTables.drop) //Really wait forever for the cleanup Await.result(future,Duration.Inf) } /** mysql> describe SHRINE_QUERY; +------------------+--------------+------+-----+-------------------+----------------+ | Field | Type | Null | Key | Default | Extra | +------------------+--------------+------+-----+-------------------+----------------+ | id | int(11) | NO | PRI | NULL | auto_increment | | local_id | varchar(255) | NO | MUL | NULL | | | network_id | bigint(20) | NO | MUL | NULL | | | username | varchar(255) | NO | MUL | NULL | | | domain | varchar(255) | NO | | NULL | | | query_name | varchar(255) | NO | | NULL | | | query_expression | text | YES | | NULL | | | date_created | timestamp | NO | | CURRENT_TIMESTAMP | | | has_been_run | tinyint(1) | NO | | 0 | | | flagged | tinyint(1) | NO | | 0 | | | flag_message | varchar(255) | YES | | NULL | | | query_xml | text | YES | | NULL | | +------------------+--------------+------+-----+-------------------+----------------+ */ class QepQueries(tag:Tag) extends Table[QepQuery](tag,"previousQueries") { def networkId = column[NetworkQueryId]("networkId") def userName = column[UserName]("userName") def userDomain = column[String]("domain") def queryName = column[QueryName]("queryName") def expression = column[String]("expression") def dateCreated = column[Time]("dateCreated") def hasBeenRun = column[Boolean]("hasBeenRun") def flagged = column[Boolean]("flagged") def flagMessage = column[String]("flagMessage") def queryXml = column[String]("queryXml") def * = (networkId,userName,userDomain,queryName,expression,dateCreated,hasBeenRun,flagged,flagMessage,queryXml) <> (QepQuery.tupled,QepQuery.unapply) } val allQepQueryQuery = TableQuery[QepQueries] } object QepQuerySchema { val allConfig:Config = QepConfigSource.config val config:Config = allConfig.getConfig("shrine.queryEntryPoint.audit.database") val slickProfileClassName = config.getString("slickProfileClassName") val slickProfile:JdbcProfile = QepConfigSource.objectForName(slickProfileClassName) val schema = QepQuerySchema(slickProfile) } case class QepQuery( networkId:NetworkQueryId, userName: UserName, userDomain: String, queryName: QueryName, expression: String, dateCreated: Time, hasBeenRun: Boolean, flagged: Boolean, flagMessage: String, queryXml:String ){ def toQueryMaster:QueryMaster = { val gregorianCalendar = new GregorianCalendar() gregorianCalendar.setTimeInMillis(dateCreated) val xmlGregorianCalendar = DatatypeFactory.newInstance().newXMLGregorianCalendar(gregorianCalendar) QueryMaster( - queryMasterId = "?", //todo what is this from? + queryMasterId = networkId.toString, //todo what is this from? networkQueryId = networkId, name = queryName, userId = userName, groupId = userDomain, createDate = xmlGregorianCalendar, held = None, //todo if a query is held at the adapter, how will we know? do we care? flagged = Some(flagged), //todo flagged is boolean, this is tri-state. When is it None vs false flagMessage = Some(flagMessage) //todo this always has a flaggedMessage (empty). When should it be None? ) } } object QepQuery extends ((NetworkQueryId,UserName,String,QueryName,String,Time,Boolean,Boolean,String,String) => QepQuery) { def apply(runQueryRequest: RunQueryRequest):QepQuery = { new QepQuery( runQueryRequest.networkQueryId, runQueryRequest.authn.username, runQueryRequest.authn.domain, runQueryRequest.queryDefinition.name, runQueryRequest.queryDefinition.expr.getOrElse("No Expression").toString, System.currentTimeMillis(), false, false, //todo flagged?? "", //todo flagMessage runQueryRequest.toXmlString ) } }