kf-portal-etl

The Kids-First ETL is built on Scala, Spark, Elasticsearch.

Dependencies

Before building this application, the following dependencies must be built and added to your local maven (.m2) directory.

ES Model

1. Clone from repository

   git clone git@github.com:kids-first/kf-es-model.git

2. Maven install

   cd kf-es-model
   mvn install

Build

To build the application, run the following from the command line in the root directory of the project

sbt ";clean;assembly"

Then get the application jar file from

${root of the project}/target/scala-2.11/kf-portal-etl.jar

Configuration

The Kids-First ETL uses lightbend/config as the configuration library. kf_etl.conf defines all of the configuration objects used by ETL.

The top namespace of the configuration is io.kf.etl. To refer to any specific configuration object, please prefix the namespace string.

• spark defines how the ETL connects to Spark environment
• elasticsearch defines how the ETL connects to the Elasticsearch environment
• processors defines all of the processors. Processors are the basic execution units of the ETL. Each processor has its own configurations, which means a processor could refer to the top level configuration objects or could also customize extra configuration objects to complete its specific job.
  • download dumps clinical data from PostgreSQL and HPO data from MySQL to dump_path
  • file_centric transforms and generates the data for the file-centric index in Elasticsearch.
  • data_path defines where the processor stores both intermediate and output data
  • write_intermediate_data defines if the processor will write the intermediate data into data_path. It is optional; if not available in the file, false will be the default value
  • participant_entric transforms and generates the data for the participant-centric index in Elasticsearch
  • index stores the generated data from the above processors in Elasticsearch

The ETL has a system environment variable called kf.etl.config which define the path to the configuration file.

If kf.etl.config is not provided when the application is submitted to Spark, the ETL will search the root of the class path for the default file with the name kf_etl.conf, otherwise the application will quit.

Running the Application

There are some dependencies to run Kids-First ETL, refer to submit.sh.example

• Spark 2.3.4
• Configuration file: refer to Configuration for the format and contents of the file

To submit the application to Spark, run the following in the command line

${SPARK_HOME}/bin/spark-submit --master spark://${Spark master node name or IP}:7077 --deploy-mode cluster --class io.kf.etl.ETLMain --driver-java-options "-Dkf.etl.config=${URL string for configuration file}" --conf "spark.executor.extraJavaOptions=-Dkf.etl.config=${URL string for configuration file}" ${path to kf-portal-etl.jar} ${command-line arguments}

Command line arguments

Kids-First ETL supports command-line argument -study_id id1 id2. In this case, ETL will filter the dataset retrieved from data service through study_ids.

The third command-line argument is -release_id rid

To submit the application with study_ids, run the following:

${SPARK_HOME}/bin/spark-submit --master spark://${Spark master node name or IP}:7077 --deploy-mode cluster --class io.kf.etl.ETLMain --driver-java-options "-Dkf.etl.config=${URL string for configuration file}" --conf "spark.executor.extraJavaOptions=-Dkf.etl.config=${URL string for configuration file}" ${path to kf-portal-etl.jar} -study_id id1 id2 -release_id rid