Skip to content
This repository was archived by the owner on May 1, 2024. It is now read-only.
This repository was archived by the owner on May 1, 2024. It is now read-only.

Is the Bunsen Python API still maintained? Issues with bunsen Python API (bunsen v 0.5.11) and pyspark v. 3.2.1 #114

Description

@jasminziegler

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)

image

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?

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions