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shrine-medco/tools/adapter-queries-to-qep/src/main/scala/net/shrine/utilities/adapterqueriestoqep/AdapterQueriesToQep.scala
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AdapterQueriesToQep.scala
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package net.shrine.utilities.adapterqueriestoqep
import java.io.File
import javax.sql.DataSource
import javax.xml.datatype.XMLGregorianCalendar
import com.typesafe.config.{Config, ConfigFactory}
import net.shrine.adapter.dao.AdapterDao
import net.shrine.adapter.dao.model.ShrineQuery
import net.shrine.adapter.dao.squeryl.SquerylAdapterDao
import net.shrine.audit.NetworkQueryId
import net.shrine.dao.squeryl.{DataSourceSquerylInitializer, SquerylInitializer, SquerylDbAdapterSelecter}
import net.shrine.adapter.dao.squeryl.tables.{Tables => AdapterTables}
import net.shrine.protocol.ResultOutputTypes
import net.shrine.qep.QepConfigSource
import net.shrine.qep.queries.{QepQueryDb, QepQuery, QepQueryFlag}
import net.shrine.slick.TestableDataSourceCreator
import org.squeryl.internals.DatabaseAdapter
import net.shrine.config.ConfigExtensions
/**
* @author dwalend
* @since 1.21
*/
object AdapterQueriesToQep {
def main(args: Array[String]): Unit = {
try {
if (args.length != 3) throw new WrongNumberOfArguments("Requires three arguments: the domain to transfer, the full path to the adapter-queries-to-qep.conf file, and the full path to the shrine.conf file.")
val domain = args(0)
val localConfig = args(1)
val shrineConfig = args(2)
val config: Config = ConfigFactory.parseFile(new File(localConfig)).withFallback(ConfigFactory.parseFile(new File(shrineConfig))).withFallback(ConfigFactory.load())
val adapterDataSource: DataSource = TestableDataSourceCreator.dataSource(config.getConfig("shrine.adapter.query.database"))
val squerylAdapter: DatabaseAdapter = SquerylDbAdapterSelecter.determineAdapter(config.getString("shrine.shrineDatabaseType"))
val squerylInitializer: SquerylInitializer = new DataSourceSquerylInitializer(adapterDataSource, squerylAdapter)
val squerylAdapterTables: AdapterTables = new AdapterTables
val breakdownTypes = config.getOptionConfigured("breakdownResultOutputTypes", ResultOutputTypes.fromConfig).getOrElse(Set.empty)
val adapterDao: AdapterDao = new SquerylAdapterDao(squerylInitializer, squerylAdapterTables)(breakdownTypes)
val adapterQueries: Seq[ShrineQuery] = adapterDao.findQueriesByDomain(domain)
println(s"Found ${adapterQueries.size} queries for $domain in the adapter's table")
QepConfigSource.configForBlock(config, getClass.getSimpleName) {
//filter out any queries that already exist
val queriesInQep: Set[NetworkQueryId] = QepQueryDb.db.selectAllQepQueries.map(_.networkId).to[Set]
//turn each ShrineQuery into a QepQuery and store it
val queriesToInsert: Seq[ShrineQuery] = adapterQueries.filterNot(q => queriesInQep.contains(q.networkId))
println(s"Will insert ${queriesToInsert.size} rows into the qep's previousQueries table. (${adapterQueries.size - queriesToInsert.size} have matching network ids.)")
queriesToInsert.map(shrineQueryToQepQuery).foreach(QepQueryDb.db.insertQepQuery)
//only carry over flags for queries that don't already have flag entries
val flagsInQep: Set[NetworkQueryId] = QepQueryDb.db.selectMostRecentQepQueryFlagsFor(adapterQueries.map(q => q.networkId).to[Set]).keySet
val flagsToInsert: Seq[QepQueryFlag] = adapterQueries.filterNot(q => flagsInQep.contains(q.networkId)).flatMap(shrineQueryToQepQueryFlag)
println(s"Will insert ${flagsToInsert.size} rows into the qep's queryFlags table.")
//make flags for each ShrineQuery that has them and store that
flagsToInsert.foreach(QepQueryDb.db.insertQepQueryFlag)
}
println("previousQueries transferred from the local adapter to the QEP cache.")
}
catch {
case wnoa:WrongNumberOfArguments =>
printUsage()
println(wnoa.message)
System.exit(1)
case x: Throwable =>
printUsage()
x.printStackTrace()
System.exit(2)
}
def printUsage(): Unit = {
println(
"""
|Usage: ./adapter-queries-to-qep DOMAIN ADAPTER_CONF SHRINE_CONF
|Copy previous queries from users in DOMAIN from the local shrine_query_history database to the local qepAudit database.
|
|DOMAIN is an I2B2 PM Cell domain name used by the local QEPs researchers.
|ADAPTER_CONF is a configuration file for this tool. This conf file takes precedence over the SHRINE_CONF file.
| See conf/adapter-queries-to-qep.conf for an example.
|SHRINE_CONF is the local configuration file, usually /opt/shrine/tomcat/lib/shrine.conf .
|
|Exit codes: 0 success
| 1 known error
| 2 unknown error (with an accompanying stack trace).
|
|Example: ./adapter-queries-to-qep i2b2demo conf/adapter-queries-to-qep.conf /opt/shrine/tomcat/lib/shrine.conf
""".stripMargin)
}
case class WrongNumberOfArguments(message:String) extends Exception(message)
}
def shrineQueryToQepQuery(shrineQuery: ShrineQuery):QepQuery = {
val date:Long = toMillis(shrineQuery.dateCreated)
new QepQuery(
networkId = shrineQuery.networkId,
userName = shrineQuery.username,
userDomain = shrineQuery.domain,
queryName = shrineQuery.name,
expression = shrineQuery.queryDefinition.expr.map(_.toString),
dateCreated = date,
deleted = false,
queryXml = shrineQuery.queryDefinition.toXml.text,
changeDate = date
)
}
def shrineQueryToQepQueryFlag(shrineQuery: ShrineQuery):Option[QepQueryFlag] = {
if(shrineQuery.isFlagged){
Some(new QepQueryFlag(
networkQueryId = shrineQuery.networkId,
flagged = shrineQuery.isFlagged,
flagMessage = shrineQuery.flagMessage.getOrElse(""),
changeDate = toMillis(shrineQuery.dateCreated)
))
}
else None
}
private def toMillis(xmlGc: XMLGregorianCalendar): Long = xmlGc.toGregorianCalendar.getTimeInMillis
}
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