Changes to scripts

.gitignore

@@ -77,3 +77,4 @@ Thumbs.db
 Configurations/
 isatab files/
 src/main/resources/Configurations/
+Plugins/

bundler.py

@@ -38,7 +38,7 @@
         '<key>Java</key>'\
         '<dict>'\
         '<key>VMOptions</key>'\
-        '<string>-Xms256m -Xmx1024m</string>'\
+        '<string>-Xms256mm -Xmx1024mm</string>'\
         '<key>MainClass</key>'\
         '<string>org.isatools.isacreator.launch.ISAcreatorApplication</string>'\
         '<key>JVMVersion</key>'\

compile.sh

@@ -43,6 +43,13 @@ fi
 
 curl -L -O http://bitbucket.org/eamonnmag/isatools-downloads/downloads/"$CONFIG_FILES"
 
+mkdir Configurations
+cp $CONFIG_FILES ./Configurations
+cd Configurations
+unzip $CONFIG_FILES
+rm -f $CONFIG_FILES
+cd ..
+
 mv $CONFIG_FILES src/main/resources/Configurations/
 
 WD=$(pwd)
@@ -76,7 +83,7 @@ then
     rm -f $MIXS_DATASETS
     cd ../
 else
-    cp -r src/test/resources/test-data/* "isatab files"/
+    cp -r src/test/resources/test-data/ "isatab files"/
 fi
 
 

package.sh

@@ -68,19 +68,28 @@ fi
 
 curl -L -O http://bitbucket.org/eamonnmag/isatools-downloads/downloads/"$CONFIGURATION"
 
+mkdir Configurations
+cp $CONFIGURATION
+cd Configurations
+unzip $CONFIGURATION
+rm -f $CONFIGURATION
+cd ..
+
+#back to project folder
 
 cp $CONFIGURATION src/main/resources/Configurations/
 
+#project folder
 WD=$(pwd)
 
 pwd
 cd src/main/resources/Configurations/
 unzip $CONFIGURATION
-
 rm -f $CONFIGURATION
 pwd
+
 cd $WD
-echo "Changing back to target..."
+echo "Changing back to project folder..."
 pwd
 
 ##Building ISAcreator
@@ -91,7 +100,6 @@ if [ "$?" -ne 0 ]; then
     exit 1
 fi
 
-
 mkdir target/Configurations
 cp $CONFIGURATION target/Configurations/
 rm -f $CONFIGURATION
@@ -100,9 +108,11 @@ cd target/Configurations/
 unzip $CONFIGURATION
 rm -f $CONFIGURATION
 
-# Now package up the tools
-cd ../
+cd ..
 
+#in target folder
+
+# Now package up the tools
 mkdir "isatab files"
 if [ "$PACKAGE_TYPE" = "scidata" ]
 then
@@ -120,7 +130,7 @@ then
     rm -f $MIXS_DATASETS
     cd ../
 else
-    cp -r ../"isatab files"/* "isatab files"
+     cp -r ../src/test/resources/test-data/ ./"isatab files"
 fi
 
 pwd
@@ -137,6 +147,6 @@ echo "Packaging completed successfully!"
 mkdir ISAcreator-$VERSION-dmg-folder/
 mkdir ISAcreator-$VERSION-dmg-folder/ISAcreator-$VERSION
 mv ISAcreator.app ISAcreator-$VERSION-dmg-folder/ISAcreator-$VERSION
-cp -r Configurations ISAcreator-$VERSION-dmg-folder/ISAcreator-$VERSION
+cp -r ../src/main/resources/Configurations ISAcreator-$VERSION-dmg-folder/ISAcreator-$VERSION
 cp -r ../ProgramData ISAcreator-$VERSION-dmg-folder/ISAcreator-$VERSION
 cp -r "isatab files" ISAcreator-$VERSION-dmg-folder/ISAcreator-$VERSION

run.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+
+get_tag_data () {
+    local tag=$1
+    local xml_file=$2
+
+    # Find tag in the xml, convert tabs to spaces, remove leading spaces, remove the tag.
+    grep $tag $xml_file | \
+        tr '\011' '\040' | \
+        sed -e 's/^[ ]*//' \
+            -e 's/^<.*>\([^<].*\)<.*>$/\1/'
+
+}
+
+
+ALLVERSIONS=`get_tag_data \<version\> pom.xml  2>/dev/null`
+
+VERSIONSPLIT=(`echo $ALLVERSIONS | tr ' ' ' '`)
+# get first version number referenced. Should always be the version of the project, since it's always the first
+VERSION=${VERSIONSPLIT[0]}
+
+if [ "$VERSION" = "" ]
+then
+  echo "Couldn't extract version from pom.xml. Exiting."
+  exit 1
+fi
+
+java -cp target/ISAcreator-$VERSION.jar org.isatools.isacreator.launch.ISAcreatorApplication