travis-test

#!/bin/bash -e

set -x

source vars

function apt_install {
  sudo apt-get install -qq -y "$@"
}

function minimal_ts_etl_checkout {
  test -d env/tranSMART-ETL || svn checkout --depth immediates \
    https://github.com/transmart/tranSMART-ETL/trunk env/tranSMART-ETL
  svn up --set-depth infinity env/tranSMART-ETL/{Postgres,Kettle-GPL}
}

function postgres_target_deps {
  apt_install php5-cli php5-json
  minimal_ts_etl_checkout

  sudo make -C env /var/lib/postgresql/tablespaces
}

function test_main_pg {
  postgres_target_deps
  apt_install rsync #solr needs it

  make -j4 postgres

  test_clinical_load
  test_clinical_load_tsbatch
  test_solr
}

function customize_vars_oracle {
  local readonly port=$1
  echo "export ORACLE=1" >> vars
  echo "export ORAHOST=$ORACLE_MACHINE" >> vars
  echo "export ORAPORT=$port" >> vars
  echo "export ORASID=ORCL" >> vars
  echo "export ORAUSER=system" >> vars
  echo "export ORAPASSWORD=manager" >> vars
  echo "export ORACLE_MANAGE_TABLESPACES=1" >> vars
# The pool process seems flaky at this point. Most builds fail
#  echo "export USE_POOL_PROCESS=1" >> vars
  echo "export export _JAVA_OPTIONS='-Djava.security.egd=file:///dev/urandom'" >> vars
}

function test_main_ora {
  local port
  if [[ -z "$ORACLE_SECRET" ]]; then
    echo "Skipping because \$ORACLE_SECRET is not set"
    return 0
  fi

  apt_install nmap

  source ~/ts-travis/oracle_database.sh
  port=$(get_oracle_db)
  customize_vars_oracle "$port"
  source vars

  make -C data/oracle start_pool &
  make oracle
}

function test_clinical_load {
  make -C env data-integration
  make -C samples/postgres load_clinical_GSE8581
  make -C samples/postgres showdblog
}

function test_clinical_load_tsbatch {
  USE_TRANSMART_BATCH=1 make -C samples/postgres load_clinical_GSE27831
}

function test_solr {
  local solr_pid

  make -C solr solr_home
  make -C solr start > /tmp/solr_log 2>&1 &
  if ! timeout 30s bash -c 'while ! lsof -iTCP:8983 -sTCP:LISTEN; do sleep 1; done'; then
    echo "Solr didn't start within 30 seconds!" >&2
    cat /tmp/solr_log
    exit 1
  fi
  make -C solr browse_full_import

  solr_pid=%1
  kill -HUP $solr_pid
  if ! timeout 15s bash -c "while test -d /proc/$solr_pid; do sleep 1; done"; then
    echo "Solr didn't exit within 15 seconds!" >&2
    cat /tmp/solr_log
    exit 1
  fi
}

function test_load_dump_load_pg {
  postgres_target_deps

  make -j4 postgres

  # ddl
  make -C ddl/postgres clean_all
  make -C ddl/postgres dump
  make -C ddl/postgres files_all

  # data
  make -C data/common clean_dumps
  make -C data/postgres dump

  make postgres_drop

  make -j4 postgres

  # ideally, there should be no diff, but...
  git diff --shortstat ddl/postgres/ data/common/
}

function test_R {
  apt_install libcairo-dev clang gfortran g++ libreadline-dev

  export CC=clang
  export CXX=clang++
  export R_FLAGS=-O0
  export TRANSMART_USER=$USER

  make -C R -j3 root/bin/R
  make -C R install_packages

  sudo -E make -C R install_rserve_upstart

  sudo initctl start rserve

  if ! sudo initctl status rserve | grep 'start/running'; then
    echo "Rserve not running!" >&2
    exit 1
  fi
}

function test_configuration_syntax {
  make -C config install

  groovy -e 'new ConfigSlurper().parse(new File('\
'System.getProperty("user.home"),'\
'".grails/transmartConfig/Config.groovy").toURL())'
}

case $1 in
  main_pg)
    test_main_pg
    ;;
  main_oracle)
    test_main_ora
    ;;
  load_dump_load_pg)
    test_load_dump_load_pg
    ;;
  configuration_syntax)
    test_configuration_syntax
    ;;
  R)
    test_R
    ;;
  *)
    echo "Unknown test suite: $1" >&2
    ;;
esac

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