cytoscape_requirments_test.sh

#!/bin/bash

####################################
# System checker script for Mac
####################################

# Target Cytoscape version for this script
CYTOSCAPE_VERSION="3.3.0"

# Supported Mac OS versions
SUPPORTED_OS_VERSIONS=("10.8" "10.9" "10.10" "10.11")

# Supported Java verisons
SUPPORTED_JAVA_VERSIONS=("1.8.0")

# Default location for Oracle JDK.
ORACLE_VM_LOCATION="/Library/Java/JavaVirtualMachines"

# This user's shell
shell=$(echo $SHELL | awk -F'/' '{print $(NF)}')

echo "############# Cytoscape System Requirements Checker for Mac ##############"
echo "Target Cytoscape version: $CYTOSCAPE_VERSION"

echo "Your shell is $shell"

# Extract major version
os_version_full=$(sw_vers -productVersion)
os_version=$(echo $os_version_full | awk -F'.' '{print $1 "." $2}')

# Check OS version.
os_pass=0
for os in "${SUPPORTED_OS_VERSIONS[@]}"
do
    if [ "$os" = $os_version ]
    then
        echo "Compatible OS version found: $os_version"
        os_pass=1
        break
    fi
done

if [ "$os_pass" -eq 1 ]
then
    echo " - Pass: OS Version = $os_version_full"
else
    echo "Fail: This version of OS is not supported: $os_version_full"
    echo "Please upgrade your system to ${SUPPORTED_OS_VERSIONS[0]} or newer."
    exit 1
fi

# Check Java Version

# Test 1: Check Oracle Java Machine
jvms=$(find $ORACLE_VM_LOCATION -name jdk1.8.0* -type d)
jvm_test=$(echo $jvms | awk '{if(NF>=1){print 1}else{print 0}}')

if [[ $jvm_test -eq 1 ]]; then
    echo " - Pass: Following Oracle JDK found:"
    echo ""
    echo $jvms | awk '{gsub(/ /, "\n", $0);print}'
else
    echo "- Fail: No Oracle JDK found.  Please download and install Oracle JDK:"
    echo "http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html"
    exit 1
fi

# Test 2: Try java -version command
java_version_original=$(java -version 2>&1)
java_version=$(echo $java_version_original | awk 'NR==1{gsub(/"/,""); print $3}')

java_major_version=$(echo $java_version | awk -F'_' '{print $1}')

if [[ $java_major_version == ${SUPPORTED_JAVA_VERSIONS[0]} ]]
then
    echo " - Pass: Current Java Version = $java_version"
else
    echo "Fail: Java is not reachable."
    echo "Try re-installing Java 8."
    exit 1
fi

# Tets 3: Check Java Home
if [[ $JAVA_HOME != "" ]]; then
    echo " - Pass: JAVA_HOME found: $JAVA_HOME"
else
    echo "JAVA_HOME is not set."
    echo "Please add the following to your .${shell}rc file:"
    echo "export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_*.jdk"
    echo "where * is the latest Java 8 update number."
    echo "And then type 'source ~/.${shell}rc'"
    exit 1
fi

# Test 4: Connect to App Store
NUM_TRY=5
echo "Checking connection to Cytoscape App Store..."
ping_result=$(ping -c $NUM_TRY -t 15 apps.cytoscape.org | grep loss)

num_success=$(echo $ping_result | awk '{print $4}')

echo $ping_result

if [[ $num_success -eq $NUM_TRY ]]; then
    echo "Done!  You are ready to run Cytoscape $CYTOSCAPE_VERSION"
else
    echo "Looks connection to App Store is unstable."
    echo "traceroute result:"
    traceroute apps.cytoscape.org
    exit 1
fi

exit 0