dev.sh

#!/bin/bash -e

get_script_dir () {
     SOURCE="${BASH_SOURCE[0]}"

     while [ -h "$SOURCE" ]; do
          DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
          SOURCE="$( readlink "$SOURCE" )"
          [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
     done
     cd -P "$( dirname "$SOURCE" )"
     pwd
}

ROOT_DIR="$(get_script_dir)/.."

function cheat_sheet() {

  echo "Cheat sheet - run the following commands:"
  echo
  echo "library(devtools)"
  echo
  echo "devtools::install_github(\"LREN-CHUV/hbplregress\")"
  echo "  # Load the library"
  echo
  echo "source(\"/src/main.R\")"
  echo "  # Perform the computation"
  echo
  echo "lintr::lint(\"/src/main.R\")"
  echo "  # Checks the style of the source code"
  echo
  echo "-----------------------------------------"

}

echo "Starting the results database..."
$ROOT_DIR/tests/analytics-db/start-db.sh
echo
echo "Starting the local database..."
$ROOT_DIR/tests/dummy-ldsm/start-db.sh
echo

sleep 2

if groups $USER | grep &>/dev/null '\bdocker\b'; then
  DOCKER="docker"
else
  DOCKER="sudo docker"
fi

cheat_sheet

$DOCKER run -i -t --rm \
  --link dummyldsm:indb \
  --link analyticsdb:outdb \
  -v $(pwd)/:/src/ \
  -v $(pwd)/tests:/src/tests/ \
  -e JOB_ID=002 \
  -e NODE=dev \
  -e PARAM_query="select feature_name, tissue1_volume from brain_feature order by tissue1_volume" \
  -e PARAM_variable="tissue1_volume" \
  -e PARAM_covariables="feature_name" \
  -e IN_JDBC_DRIVER=org.postgresql.Driver \
  -e IN_JDBC_JAR_PATH=/usr/lib/R/libraries/postgresql-9.4-1201.jdbc41.jar \
  -e IN_JDBC_URL="jdbc:postgresql://indb:5432/postgres" \
  -e IN_JDBC_USER=postgres \
  -e IN_JDBC_PASSWORD=test \
  -e OUT_JDBC_DRIVER=org.postgresql.Driver \
  -e OUT_JDBC_JAR_PATH=/usr/lib/R/libraries/postgresql-9.4-1201.jdbc41.jar \
  -e OUT_JDBC_URL="jdbc:postgresql://outdb:5432/postgres" \
  -e OUT_JDBC_USER=postgres \
  -e OUT_JDBC_PASSWORD=test \
  hbpmip/r-interactive:latest R

$ROOT_DIR/tests/analytics-db/stop-db.sh
$ROOT_DIR/tests/dummy-ldsm/stop-db.sh