safrant/evsrestapi

EVSRESTAPI

Information on the build and deployment process for the EVSRESTAPI project

Prerequisites

• Install Docker and ensure it is configured to allow (Docker -> Settings -> Resources)

  • Memory = 7G
  • Swap = 1G

• Clone the project - https://github.com/NCIEVS/evsrestapi

  • Before cloning the repo, make sure that the command git config core.autocrlf returns false. Change it to false using git config --global core.autocrlf false if necessary

• Choose a local directory $dir (e.g. c:/evsrestapi)

• mkdir -p $dir/elasticsearch/data

• Download latest ThesaurusInf_*OWL.zip, unpack to $dir/ThesaurusInferred.owl (see https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/)

Steps for Loading NCI Thesaurus Data and Indexes Locally

• Launch Stardog and load NCI Thesaurus data - (see Stardog Resources)

• Launch Elasticsearch docker container - (see Elasticsearch Resources)

• Load/Compute Indexes (for NCI Thesaurus)

  Build the project - From the root of cloned https://github.com/NCIEVS/evsrestapi

  gradlew clean build -x test

  version=ncit_21.08d export EVS_SERVER_PORT=8083 export NCI_EVS_BULK_LOAD_DOWNLOAD_BATCH_SIZE=500 export NCI_EVS_BULK_LOAD_INDEX_BATCH_SIZE=100 java -Dspring.profiles.active=local -jar build/libs/evsrestapi-*.jar --terminology $version --forceDeleteIndex > log 2>&1 & tail -f log

Steps for Building and Running EVSRESTAPI locally

• Launch Stardog and Elasticsearch (as described above)

  • If loaded properly, the loaded artifacts should be persistent and you can take down and restart the docker processes and the data will still be there.
  • NOTE: both services must be loaded and running for the application tests to run properly

• Configure application

  • see src/main/resources/application-local.yml file for local setup (these settings should be suitable for local deployment)

• Build the application (MUST DO BEFORE RUNNING if using "external tools configuration")

  • ./gradlew clean build -x test
  • Executable war file present in build/libs

• Run application in Eclipse (SpringBoot)

  • Click "Run" -> "External Tools" -> "External Tools Configurations"

  • Create a new entry under "Program" and configure it as follows:

    • location = <path to java executable, e.g. 'C:/Program Files/Java/jdk1.8.0_191/bin/java.exe'>
    • working dir = <path to project, e.g. 'C:/Users/bcarl/Desktop/workspace/evsrestapi'>
    • Arguments = command line args
      • '-Xmx4096M' - ensure enough memory usage
      • '-Dspring.profiles.active=local' - make sure to use application-local.yml
      • '-jar *.war' - point to the war file

  • Test that it's up by looking for swagger docs: http://localhost:8080/swagger-ui.html#/

Steps for Loading NCI Metathesaurus Indexes Locally

• Download the NCI Metathesaurus to a local directory

• Properly configure the environment variables needed by ncim.sh

• Run ncim.sh

    dir=c:/evsrestapi/NCIM_202008/META
    export NCI_EVS_BULK_LOAD_DOWNLOAD_BATCH_SIZE=500
    export NCI_EVS_BULK_LOAD_INDEX_BATCH_SIZE=50
    src/main/bin/ncim.sh --noconfig $dir