From b4aa01a60f8438271bab827b29715de90146d306 Mon Sep 17 00:00:00 2001
From: Gobbo Alexandre <gobbo_a@gfa-lc6-64.psi.ch>
Date: Wed, 9 Oct 2019 14:08:54 +0200
Subject: [PATCH] Initial commit

---
 pshell | 138 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 138 insertions(+)
 create mode 100755 pshell

diff --git a/pshell b/pshell
new file mode 100755
index 0000000..436579a
--- /dev/null
+++ b/pshell
@@ -0,0 +1,138 @@
+#!/bin/bash
+
+
+
+#Parse JVM arguments, Pshell version and JEP option
+export PSHELL_VER=default
+export JVM_ARGS=
+#export JAVA_VER=/opt/gfa/java/openjdk-1.8.0_40
+#export JAVA_VER=/opt/gfa/java/jdk1.8.0_72
+export JAVA_VER=/opt/gfa/java/openjdk-12_32
+#export JEP=
+
+for i in "$@"
+do
+case $i in
+    -jvmarg=*)
+	JVM_ARGS="${i#*=}"
+	#echo 'JVM args:' ${JVM_ARGS}
+    	shift 
+    ;;
+
+    -version=*|--version=*)
+	export PSHELL_VER="${i#*=}"
+	echo "Using  version " ${PSHELL_VER}
+	#shift
+    ;;
+
+    -test)	
+	export PSHELL_VER=testing
+	echo "Using testing version"
+    	#shift 
+    ;;
+
+    -last)
+	export PSHELL_VER=latest
+	echo "Using latest version"
+       #shift 
+    ;;
+
+    -javaver=*|--javaver=*)
+	export JAVA_VER="${i#*=}"
+	echo "Using  java version " ${JAVA_VER}
+	#shift
+    ;;
+
+#    -py2)
+#	JEP=2
+#	echo "Setting Python 2 for JEP"
+#        shift 
+#    ;;
+
+#    -py3)
+#	JEP=3
+#	echo "Setting Python 3 for JEP"
+#        shift 
+#    ;;
+
+    *)    # unknown option            
+    ;;
+esac
+done
+
+#echo $@
+
+#Parse Pshell version
+#if [[ $@ == **-test** ]] ; then
+#	echo "Using testing version"
+#	export PSHELL_VER=testing
+#else
+# if [[ $@ == **-last** ]] ; then
+#	echo "Using latest version"
+#	export PSHELL_VER=latest
+# fi
+#fi
+
+
+export JVM_EARGS=
+
+
+#Standard startup
+if [[ $@ != **-py** ]] ; then
+#if [[ $JEP == "" ]] ; then
+	${JAVA_VER}/bin/java ${JVM_EARGS} ${JVM_ARGS} -jar /opt/gfa/pshell/${PSHELL_VER} $@
+	exit  
+fi
+
+
+#Using JEP 
+#First clean path and vars
+#unset JCPDS_PATH
+#unset XRF_PEAK_LIBRARY 
+unset PYTHONPATH
+CLEAN_PATH=""	
+for p in $(echo $PATH | sed 's/:/ /g') ; do
+    if [[ $p =~ ^.*/opt/gfa/python.*$ ]] ; then
+        echo 'Remove from path' $p
+    else
+        if [ "$CLEAN_PATH" == "" ] ; then
+            CLEAN_PATH=$p
+        else
+	    CLEAN_PATH=$CLEAN_PATH:$p
+        fi
+    fi
+done
+
+if [[ $@ == **-py3** ]] ; then
+	#Python 3	
+	echo "Setting Python 3 for JEP"
+	#export PYTHONHOME=/opt/gfa/pshell/python/anaconda3
+	#export PYTHONHOME=/exchange/tmp/pshell/python/anaconda3
+	#export PYTHONHOME=/exchange/tmp/pshell/python/latest
+	export PYTHONHOME=/opt/gfa/python-3.5/latest
+	#export JEP_JAR=${PYTHONHOME}/lib/python3.5/site-packages/jep/jep-3.6.1.jar
+	export JEP_JAR=${PYTHONHOME}/lib/python3.5/site-packages/jep/jep-3.6.3.jar		
+	#TODO: Check why had to set library I compiled myself
+        #export LD_LIBRARY_PATH=${PYTHONHOME}/lib/python3.5/site-packages/jep
+	#export LD_LIBRARY_PATH=/opt/gfa/python-3.5/latest/lib:/opt/gfa/pshell/python/jep/py3	
+	
+	#${PYTHONHOME}/lib is for OpenJDK	
+	export LD_LIBRARY_PATH=${PYTHONHOME}/lib:/opt/gfa/pshell/python/jep/py3					
+	export LD_PRELOAD=${PYTHONHOME}/lib/libpython3.5m.so
+else 
+	#Python 2
+	echo "Setting Python 2 for JEP"
+	export PYTHONHOME=/exchange/tmp/pshell/python/anaconda2
+	export LD_LIBRARY_PATH=${PYTHONHOME}/lib/python2.7/site-packages/jep
+	export JEP_JAR=${PYTHONHOME}/lib/python2.7/site-packages/jep/jep-3.5.3.jar
+fi
+
+#If starting with -cp the options in PShell manifest fle are not executed: must be don by command line
+if [[ $JAVA_VER != *"1.8.0"* ]]; then
+    #echo 'Java > 1.8'
+    export JVM_EARGS="--add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.desktop/sun.awt=ALL-UNNAMED --add-opens java.desktop/javax.swing.text.html=ALL-UNNAMED --add-opens java.desktop/sun.swing=ALL-UNNAMED --add-opens java.base/jdk.internal.loader=ALL-UNNAMED"
+fi
+
+export PATH=${PYTHONHOME}/bin:$CLEAN_PATH
+${JAVA_VER}/bin/java  ${JVM_EARGS} ${JVM_ARGS} -cp /opt/gfa/pshell/${PSHELL_VER}:${JEP_JAR} ch.psi.pshell.ui.App $@
+