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Lock wait timeout exceeded when using the entity import api & UI

timdeftimdef Cambridge, MAMember, Broadie

Sometimes when trying to import entities, I get a "lock wait timeout exceeded" error and a stack trace. I've gotten this from using FISS and from the UI:

firecloud.errors.FireCloudServerError: 500: {
"statusCode": 500,
"source": "rawls",
"timestamp": 1477588111702,
"causes": [],
"stackTrace": [{
"className": "sun.reflect.NativeConstructorAccessorImpl",
"methodName": "newInstance0",
"fileName": "NativeConstructorAccessorImpl.java",
"lineNumber": -2
}, {
"className": "sun.reflect.NativeConstructorAccessorImpl",
"methodName": "newInstance",
"fileName": "NativeConstructorAccessorImpl.java",
"lineNumber": 62
}, {
"className": "sun.reflect.DelegatingConstructorAccessorImpl",
"methodName": "newInstance",
"fileName": "DelegatingConstructorAccessorImpl.java",
"lineNumber": 45
}, {
"className": "java.lang.reflect.Constructor",
"methodName": "newInstance",
"fileName": "Constructor.java",
"lineNumber": 423
}, {
"className": "com.mysql.jdbc.Util",
"methodName": "handleNewInstance",
"fileName": "Util.java",
"lineNumber": 404
}, {
"className": "com.mysql.jdbc.Util",
"methodName": "getInstance",
"fileName": "Util.java",
"lineNumber": 387
}, {
"className": "com.mysql.jdbc.SQLError",
"methodName": "createSQLException",
"fileName": "SQLError.java",
"lineNumber": 946
}, {
"className": "com.mysql.jdbc.MysqlIO",
"methodName": "checkErrorPacket",
"fileName": "MysqlIO.java",
"lineNumber": 3878
}, {
"className": "com.mysql.jdbc.MysqlIO",
"methodName": "checkErrorPacket",
"fileName": "MysqlIO.java",
"lineNumber": 3814
}, {
"className": "com.mysql.jdbc.MysqlIO",
"methodName": "sendCommand",
"fileName": "MysqlIO.java",
"lineNumber": 2478
}, {
"className": "com.mysql.jdbc.MysqlIO",
"methodName": "sqlQueryDirect",
"fileName": "MysqlIO.java",
"lineNumber": 2625
}, {
"className": "com.mysql.jdbc.ConnectionImpl",
"methodName": "execSQL",
"fileName": "ConnectionImpl.java",
"lineNumber": 2551
}, {
"className": "com.mysql.jdbc.PreparedStatement",
"methodName": "executeInternal",
"fileName": "PreparedStatement.java",
"lineNumber": 1861
}, {
"className": "com.mysql.jdbc.PreparedStatement",
"methodName": "execute",
"fileName": "PreparedStatement.java",
"lineNumber": 1192
}, {
"className": "com.zaxxer.hikari.proxy.PreparedStatementProxy",
"methodName": "execute",
"fileName": "PreparedStatementProxy.java",
"lineNumber": 44
}, {
"className": "com.zaxxer.hikari.proxy.PreparedStatementJavassistProxy",
"methodName": "execute",
"fileName": "PreparedStatementJavassistProxy.java",
"lineNumber": -1
}, {
"className": "slick.jdbc.StatementInvoker",
"methodName": "results",
"fileName": "StatementInvoker.scala",
"lineNumber": 39
}, {
"className": "slick.jdbc.StatementInvoker",
"methodName": "iteratorTo",
"fileName": "StatementInvoker.scala",
"lineNumber": 22
}, {
"className": "slick.jdbc.Invoker$class",
"methodName": "foreach",
"fileName": "Invoker.scala",
"lineNumber": 48
}, {
"className": "slick.jdbc.StatementInvoker",
"methodName": "foreach",
"fileName": "StatementInvoker.scala",
"lineNumber": 16
}, {
"className": "slick.jdbc.StreamingInvokerAction$class",
"methodName": "run",
"fileName": "StreamingInvokerAction.scala",
"lineNumber": 22
}, {
"className": "slick.jdbc.SQLActionBuilder$$anon$1",
"methodName": "run",
"fileName": "StaticQuery.scala",
"lineNumber": 100
}, {
"className": "slick.jdbc.SQLActionBuilder$$anon$1",
"methodName": "run",
"fileName": "StaticQuery.scala",
"lineNumber": 100
}, {
"className": "slick.dbio.SynchronousDatabaseAction$FusedAndThenAction$$anonfun$run$4",
"methodName": "apply",
"fileName": "DBIOAction.scala",
"lineNumber": 508
}, {
"className": "slick.dbio.SynchronousDatabaseAction$FusedAndThenAction$$anonfun$run$4",
"methodName": "apply",
"fileName": "DBIOAction.scala",
"lineNumber": 508
}, {
"className": "scala.collection.Iterator$class",
"methodName": "foreach",
"fileName": "Iterator.scala",
"lineNumber": 742
}, {
"className": "scala.collection.AbstractIterator",
"methodName": "foreach",
"fileName": "Iterator.scala",
"lineNumber": 1194
}, {
"className": "scala.collection.IterableLike$class",
"methodName": "foreach",
"fileName": "IterableLike.scala",
"lineNumber": 72
}, {
"className": "scala.collection.AbstractIterable",
"methodName": "foreach",
"fileName": "Iterable.scala",
"lineNumber": 54
}, {
"className": "slick.dbio.SynchronousDatabaseAction$FusedAndThenAction",
"methodName": "run",
"fileName": "DBIOAction.scala",
"lineNumber": 508
}, {
"className": "slick.dbio.SynchronousDatabaseAction$$anon$6",
"methodName": "run",
"fileName": "DBIOAction.scala",
"lineNumber": 444
}, {
"className": "slick.backend.DatabaseComponent$DatabaseDef$$anon$2",
"methodName": "liftedTree1$1",
"fileName": "DatabaseComponent.scala",
"lineNumber": 237
}, {
"className": "slick.backend.DatabaseComponent$DatabaseDef$$anon$2",
"methodName": "run",
"fileName": "DatabaseComponent.scala",
"lineNumber": 237
}, {
"className": "java.util.concurrent.ThreadPoolExecutor",
"methodName": "runWorker",
"fileName": "ThreadPoolExecutor.java",
"lineNumber": 1142
}, {
"className": "java.util.concurrent.ThreadPoolExecutor$Worker",
"methodName": "run",
"fileName": "ThreadPoolExecutor.java",
"lineNumber": 617
}, {
"className": "java.lang.Thread",
"methodName": "run",
"fileName": "Thread.java",
"lineNumber": 745
}],
"message": "Lock wait timeout exceeded; try restarting transaction"
}

What is causing this, and what can I do to address the issue? I've encountered this error twice in the past week, and the first time it was resolved by waiting (not sure exactly how long).

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Answers

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