cerner
Issues while trying to query on Observation resource
Issue Description:
I am trying to explore the Bunsen API and trying to go explore the different functions using 'getting_started.ipynb'. While I am successfully able to successfully run the below example code, the query on observations dataframe is not working. Can someone please help me to understand the issue.
Environment:
Bunsen version: 4.7 Java Version: JDK 8 Spark: 2.3 with Hadoop 2.7
Please note I have tried to run the examples from the bunsen-tutorial sample docker container and I am facing similar issues as well.
Working:
from bunsen.stu3.bundles import load_from_directory, extract_entry, write_to_database
Load and cache the bundles so we don't reload them every time.
bundles = load_from_directory(spark, r'C:\Users\Sumanta\Desktop\Datasets\synthea_sample_data\test',1)
Get the observation and encounters
observations = extract_entry(spark, bundles, 'observation') conditions = extract_entry(spark, bundles, 'condition') encounters = extract_entry(spark, bundles, 'encounter')
from pyspark.sql.functions import col
encounters.select('subject.reference',
'class.code',
'period.start',
'period.end',
)
.where(col('start') > '2013')
.limit(10)
.toPandas()
Not Working:
from pyspark.sql.functions import explode
codes = observations.select('subject',
explode('code.coding').alias('coding'))
.select('subject.reference',
'coding.system',
'coding.code',
'coding.display')
codes.limit(10).toPandas()
Error:
Py4JJavaError Traceback (most recent call last)
E:\Programs\spark-2.4.5-bin-hadoop2.7\python\pyspark\sql\dataframe.py in toPandas(self) 2148 2149 # Below is toPandas without Arrow optimization. -> 2150 pdf = pd.DataFrame.from_records(self.collect(), columns=self.columns) 2151 2152 dtype = {}
E:\Programs\spark-2.4.5-bin-hadoop2.7\python\pyspark\sql\dataframe.py in collect(self) 532 """ 533 with SCCallSiteSync(self._sc) as css: --> 534 sock_info = self._jdf.collectToPython() 535 return list(_load_from_socket(sock_info, BatchedSerializer(PickleSerializer()))) 536
E:\Programs\Anaconda\lib\site-packages\py4j\java_gateway.py in call(self, *args) 1255 answer = self.gateway_client.send_command(command) 1256 return_value = get_return_value( -> 1257 answer, self.gateway_client, self.target_id, self.name) 1258 1259 for temp_arg in temp_args:
E:\Programs\spark-2.4.5-bin-hadoop2.7\python\pyspark\sql\utils.py in deco(*a, **kw) 61 def deco(*a, **kw): 62 try: ---> 63 return f(*a, **kw) 64 except py4j.protocol.Py4JJavaError as e: 65 s = e.java_exception.toString()
E:\Programs\Anaconda\lib\site-packages\py4j\protocol.py in get_return_value(answer, gateway_client, target_id, name) 326 raise Py4JJavaError( 327 "An error occurred while calling {0}{1}{2}.\n". --> 328 format(target_id, ".", name), value) 329 else: 330 raise Py4JError(
Py4JJavaError: An error occurred while calling o2586.collectToPython. : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0 failed 1 times, most recent failure: Lost task 0.0 in stage 2.0 (TID 2, localhost, executor driver): java.lang.NoSuchMethodError: org.apache.spark.sql.catalyst.expressions.codegen.ExprCode.code()Ljava/lang/String; at com.cerner.bunsen.backports.InstanceOf.doGenCode(objects.scala:72) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.If.doGenCode(conditionalExpressions.scala:68) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.IsNull.doGenCode(nullExpressions.scala:329) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.If.doGenCode(conditionalExpressions.scala:68) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.codegen.CodegenContext$$anonfun$generateExpressions$1.apply(CodeGenerator.scala:1102) at org.apache.spark.sql.catalyst.expressions.codegen.CodegenContext$$anonfun$generateExpressions$1.apply(CodeGenerator.scala:1102) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.immutable.List.foreach(List.scala:392) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.immutable.List.map(List.scala:296) at org.apache.spark.sql.catalyst.expressions.codegen.CodegenContext.generateExpressions(CodeGenerator.scala:1102) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.createCode(GenerateUnsafeProjection.scala:288) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.create(GenerateUnsafeProjection.scala:336) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.create(GenerateUnsafeProjection.scala:329) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.create(GenerateUnsafeProjection.scala:33) at org.apache.spark.sql.catalyst.expressions.codegen.CodeGenerator.generate(CodeGenerator.scala:1193) at org.apache.spark.sql.catalyst.expressions.UnsafeProjection$.createCodeGeneratedObject(Projection.scala:120) at org.apache.spark.sql.catalyst.expressions.UnsafeProjection$.createCodeGeneratedObject(Projection.scala:116) at org.apache.spark.sql.catalyst.expressions.CodeGeneratorWithInterpretedFallback.createObject(CodeGeneratorWithInterpretedFallback.scala:52) at org.apache.spark.sql.catalyst.expressions.UnsafeProjection$.create(Projection.scala:159) at org.apache.spark.sql.execution.SerializeFromObjectExec$$anonfun$4.apply(objects.scala:126) at org.apache.spark.sql.execution.SerializeFromObjectExec$$anonfun$4.apply(objects.scala:125) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndexInternal$1$$anonfun$13.apply(RDD.scala:845) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndexInternal$1$$anonfun$13.apply(RDD.scala:845) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:123) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)
Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1891) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1878) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1878) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927) at scala.Option.foreach(Option.scala:257) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:927) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2112) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2061) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2050) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101) at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:365) at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38) at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:3263) at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:3260) at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3370) at org.apache.spark.sql.execution.SQLExecution$$anonfun$withNewExecutionId$1.apply(SQLExecution.scala:80) at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:127) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:75) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3369) at org.apache.spark.sql.Dataset.collectToPython(Dataset.scala:3260) at sun.reflect.GeneratedMethodAccessor48.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.NoSuchMethodError: org.apache.spark.sql.catalyst.expressions.codegen.ExprCode.code()Ljava/lang/String; at com.cerner.bunsen.backports.InstanceOf.doGenCode(objects.scala:72) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.If.doGenCode(conditionalExpressions.scala:68) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.IsNull.doGenCode(nullExpressions.scala:329) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.If.doGenCode(conditionalExpressions.scala:68) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:108) at org.apache.spark.sql.catalyst.expressions.Expression$$anonfun$genCode$2.apply(Expression.scala:105) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.sql.catalyst.expressions.Expression.genCode(Expression.scala:105) at org.apache.spark.sql.catalyst.expressions.codegen.CodegenContext$$anonfun$generateExpressions$1.apply(CodeGenerator.scala:1102) at org.apache.spark.sql.catalyst.expressions.codegen.CodegenContext$$anonfun$generateExpressions$1.apply(CodeGenerator.scala:1102) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.immutable.List.foreach(List.scala:392) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.immutable.List.map(List.scala:296) at org.apache.spark.sql.catalyst.expressions.codegen.CodegenContext.generateExpressions(CodeGenerator.scala:1102) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.createCode(GenerateUnsafeProjection.scala:288) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.create(GenerateUnsafeProjection.scala:336) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.create(GenerateUnsafeProjection.scala:329) at org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeProjection$.create(GenerateUnsafeProjection.scala:33) at org.apache.spark.sql.catalyst.expressions.codegen.CodeGenerator.generate(CodeGenerator.scala:1193) at org.apache.spark.sql.catalyst.expressions.UnsafeProjection$.createCodeGeneratedObject(Projection.scala:120) at org.apache.spark.sql.catalyst.expressions.UnsafeProjection$.createCodeGeneratedObject(Projection.scala:116) at org.apache.spark.sql.catalyst.expressions.CodeGeneratorWithInterpretedFallback.createObject(CodeGeneratorWithInterpretedFallback.scala:52) at org.apache.spark.sql.catalyst.expressions.UnsafeProjection$.create(Projection.scala:159) at org.apache.spark.sql.execution.SerializeFromObjectExec$$anonfun$4.apply(objects.scala:126) at org.apache.spark.sql.execution.SerializeFromObjectExec$$anonfun$4.apply(objects.scala:125) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndexInternal$1$$anonfun$13.apply(RDD.scala:845) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndexInternal$1$$anonfun$13.apply(RDD.scala:845) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346) at org.apache.spark.rdd.RDD.iterator(RDD.scala:310) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:123) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more
@SumantaSa Hi, Is your problem solved? I am trying to extract_entry() for QuestionnaireResponse but it says that FHIR R4 doesn't support this resource.. Why is it so?
