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obo-parser

The Obo Parser is build on Scala and Spark

Build

Make sure to import all external libraries by running

`sbt update`.

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-2.12/obo-parser-assembly-0.1.0-SNAPSHOT.jar
  • Spark 3.0.0

Command line arguments

Two arguments is required to executing a build with Obo Parser : obo_file_input_url json_output_local_path . obo_file_input_url is the URL or local path of the input file. json_output_local_path is the local path where the json output will be saved

${SPARK_HOME}/bin/spark-submit --master ${spark_master} --class ${full_main_class_name} ./obo-parser/target/scala-2.12/obo-parser-assembly-0.1.0-SNAPSHOT.jar ${obo_file_input_url} ${json_output_local_path}