Issues while trying to query on Observation resource

[SumantaSa]

No description provided.

[SumantaSa]

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)
in
8 'coding.display')
9
---> 10 codes.limit(10).toPandas()

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

[anam-maker]

@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?