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Is the Bunsen Python API still under maintainence? Is Bunsen in general still maintained?
Description of Issue
We are trying to connect Kafka, Spark (Pyspark) and Bunsen for our project. Reading FHIR resources from kafka into Spark works already - we are getting a pyspark.sql.dataframe.DataFrame. Now we are facing issues with Bunsen when trying to call "extract_entry"
File /usr/local/bunsen/python/bunsen/r4/bundles.py:44, in from_json(df, column)
32 def from_json(df, column):
33 """
34 Takes a dataframe with JSON-encoded bundles in the given column and returns
35 a Java RDD of Bundle records. Note this
(...)
42 :return: a Java RDD of bundles for use with :func:extract_entry
43 """
---> 44 bundles = _bundles(df._sc._jvm)
45 return bundles.fromJson(df._jdf, column)
We were expecting to be able to inspect and load the FHIR bundles with help of Bunsen.
Is the Bunsen Python API still maintained?
The text was updated successfully, but these errors were encountered:
jasminziegler
changed the title
Issues with bunsen Python API (bunsen v 0.5.11) and pyspark v. 3.2.1
Is the Bunsen Python API still maintained? Issues with bunsen Python API (bunsen v 0.5.11) and pyspark v. 3.2.1
Mar 22, 2022
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Is the Bunsen Python API still under maintainence? Is Bunsen in general still maintained?
Description of Issue
We are trying to connect Kafka, Spark (Pyspark) and Bunsen for our project. Reading FHIR resources from kafka into Spark works already - we are getting a pyspark.sql.dataframe.DataFrame. Now we are facing issues with Bunsen when trying to call "extract_entry"
Error Message:
TypeError Traceback (most recent call last)
Input In [14], in <cell line: 1>()
----> 1 bundles = extract_entry(spark, from_json(mydf, 'value'), 'condition')
File /usr/local/bunsen/python/bunsen/r4/bundles.py:44, in from_json(df, column)
32 def from_json(df, column):
33 """
34 Takes a dataframe with JSON-encoded bundles in the given column and returns
35 a Java RDD of Bundle records. Note this
(...)
42 :return: a Java RDD of bundles for use with :func:
extract_entry
43 """
---> 44 bundles = _bundles(df._sc._jvm)
45 return bundles.fromJson(df._jdf, column)
File /usr/local/bunsen/python/bunsen/r4/bundles.py:15, in _bundles(jvm)
14 def _bundles(jvm):
---> 15 return jvm.com.cerner.bunsen.Bundles.forR4()
TypeError: 'JavaPackage' object is not callable
System Configuration
BUNSEN_VERSION=0.5.11
Python 3.8
SPARK_VERSION=3.2.1
SPARK_SCALA_VERSION=2.12
PYSPARK_SUBMIT_ARGS="
--jars /usr/local/bunsen/jars/bunsen-spark-shaded-0.5.11.jar
--packages org.apache.spark:spark-sql-kafka-0-10_2.12:3.2.1
pyspark-shell"
Additional Details (optional)
Expected Outcomes
We were expecting to be able to inspect and load the FHIR bundles with help of Bunsen.
Is the Bunsen Python API still maintained?
The text was updated successfully, but these errors were encountered: