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From "Eskala, Nagakalyana" <nagakalyana.esk...@anthem.com>
Subject RE: cTakes on Apache Spark - Error
Date Tue, 01 May 2018 16:40:16 GMT
More update on the issue:

We have extracted the lvg related files in the exact folder structure, and are copying all
the folders recursively in the spark executor working directory using addFiles option. But
the LvgAnnotator is not able to find the lvg.properties file in the classpath of the spark
executor even though we have set up using the configuration spark.executor.extraClassPath

Code snippet:
sc.addFile("hdfs:///ctakes_4.0.0/resources", true);
sparkConf.set("spark.executor.extraClassPath", "./resources/");
sparkConf.set("spark.driver.extraClassPath", "./resources/");

From: Eskala, Nagakalyana
Sent: Monday, April 30, 2018 8:50 PM
To: 'dev@ctakes.apache.org' <dev@ctakes.apache.org>
Subject: cTakes on Apache Spark - Error

We are trying to run the Apache ctakes Default clinical pipeline in a spark streaming application.
We intend to parse all input text sent to a socket on spark streaming by executing a default
clinical pipeline in individual executors of a spark application.

The ctakes pipeline requires external resources to be available in the classpath. We have
used JavaSparkContext.addFiles to provide all the resources (dictionaries) recursively from
HDFS to each individual executor working directory. Once the addFiles copies the resources
to each executor, we try to include it in the classpath of each executor using the configuration.

sc.addFile("hdfs:///ctakes_4.0.0/resources", true);
sparkConf.set("spark.executor.extraClassPath", "./resources/");
sparkConf.set("spark.driver.extraClassPath", "./resources/");

The error occurs in LvgAnnotator class which tries to access the lvg.properties file through
the lookup. It is not able to locate the file and hence there is an error.

18/04/30 15:55:50 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost,
executor driver, partition 0, ANY, 4744 bytes)
18/04/30 15:55:50 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
18/04/30 15:55:51 INFO ae.LvgAnnotator: URL==null
18/04/30 15:55:51 INFO ae.LvgAnnotator: Unable to find org/apache/ctakes/lvg/data/config/lvg.properties.
18/04/30 15:55:51 INFO ae.LvgAnnotator: Copying files and directories to under /tmp/
18/04/30 15:55:51 INFO ae.LvgAnnotator: Copying lvg-related file to /tmp/data/config/lvg.properties
18/04/30 15:55:51 ERROR executor.Executor: Exception in task 0.0 in stage 1.0 (TID 1)
at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1792)
at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1769)
at org.apache.commons.io.IOUtils.copy(IOUtils.java:1744)
at org.apache.commons.io.FileUtils.copyInputStreamToFile(FileUtils.java:1512)
at org.apache.ctakes.lvg.ae.LvgAnnotator.copyLvgFiles(LvgAnnotator.java:620)
at org.apache.ctakes.lvg.ae.LvgAnnotator.createAnnotatorDescription(LvgAnnotator.java:649)
at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenProcessingPipeline(ClinicalPipelineFactory.java:110)
at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getDefaultPipeline(ClinicalPipelineFactory.java:68)

Ideally, since the resources folder has been recursively added to each executor node and the
classpath has been set, the internal executor should be able to locate the properties and
other resource files. However, that is not the case. Is there something we should be differently
doing (configuration, classpath, etc) so that the ctakes pipeline can be run in a spark executor
with all the resources and classpath set appropriately.

Thanks for the help.

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