Merge remote-tracking branch 'origin/master'

deploy/alpha_6.2_58_vcellservice.include

@@ -95,7 +95,7 @@ vcell_I4J_pathto_secretsDir=/usr/local/deploy
 vcell_I4J_use_vagrant=false
 vcell_I4J_install_jres_into_user_home=false
 vcell_I4J_updateSiteBaseUrl=http://vcell.org/webstart/$vcell_site_camel
-vcell_I4J_pathto_mavenRootDir=/opt/build/VCell
+vcell_I4J_pathto_mavenRootDir=/opt/build/vcell
 vcell_I4J_pathto_installerFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/VCell.install4j
 vcell_I4J_pathto_vcellIcnsFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/icons/vcell.icns
 vcell_I4J_pathto_jreDir=$HOME/.install4j6/jres

deploy/alpha_6.2_59_vcellservice.include

@@ -0,0 +1,118 @@
+#!/usr/bin/env bash
+
+shopt -s -o nounset
+
+_site="alpha"
+_version="6.2"
+_build="59"
+vcell_server_os="linux64"
+
+vcell_site_lower=`echo $_site | tr '[:upper:]' '[:lower:]'`
+vcell_site_upper=`echo $_site | tr '[:lower:]' '[:upper:]'`
+vcell_site_camel="${vcell_site_upper:0:1}${vcell_site_lower:1:100}"
+vcell_version=${_version}
+vcell_build=${_build}
+vcell_softwareVersionString="${vcell_site_camel}_Version_${vcell_version}_build_${vcell_build}"
+unset _site
+unset _version
+unset _build
+
+vcell_applicationId="1471-8022-1038-5554"
+vcell_server_sitedir="/share/apps/vcell2/deployed_new/$vcell_site_lower"
+vcell_pathto_sitedir="/share/apps/vcell2/deployed_new/$vcell_site_lower"
+
+vcell_user="vcell"
+vcell_servicehost="vcell-service.cam.uchc.edu"
+vcell_apihost="vcellapi.cam.uchc.edu"
+vcell_apiport=8080
+
+#
+# Nagios monitor port  
+# (rel=33330, beta=33331, alpha=33332, test=-33333, test2=-33334, test3=-33335, test4=-33336)
+#
+vcell_monitor_queryport=33332
+
+vcell_rmihost="vcell-rmi-alpha.cam.uchc.edu"
+vcell_rmiport_low=-1
+vcell_rmiport_high=40106
+vcell_rmihosts="vcell-rmi-alpha.cam.uchc.edu:40106"
+# still using bioformats_ALPHA_6_2_54.jar for later versions ... need to replace with ImageJ support.
+vcell_bioformatsJarFile="bioformats_ALPHA_6_2_54.jar"
+vcell_bioformatsJarDownloadURL="http://vcell.org/webstart/$vcell_site_camel/$vcell_bioformatsJarFile"
+
+vcell_vcellClientJarFileName="vcell-client-0.0.1-SNAPSHOT.jar"
+vcell_vcellServerJarFileName="vcell-server-0.0.1-SNAPSHOT.jar"
+vcell_vcellApiJarFileName="vcell-api-0.0.1-SNAPSHOT.jar"
+vcell_vcellAdminJarFileName="vcell-admin-0.0.1-SNAPSHOT.jar"
+
+vcell_jms_url="failover:(tcp://code2.cam.uchc.edu:61617)?timeout=120000"
+vcell_jms_user=clientUser
+
+#
+# Oracle on server
+#
+vcell_database_url="jdbc:oracle:thin:@VCELL-DB.cam.uchc.edu:1521/vcelldborcl.cam.uchc.edu"
+vcell_database_driver=oracle.jdbc.driver.OracleDriver
+vcell_database_user=vcell
+
+#
+# Postgres on locahost
+#
+#vcell_database_url="jdbc:postgresql://localhost:5432/schaff"
+#vcell_database_driver=org.postgresql.Driver
+#vcell_database_user=schaff
+
+vcell_amplistor_url="http://obj1.cam.uchc.edu:8080/namespace/service_vcell/"
+vcell_amplistor_user=vcell
+
+vcell_mongodb_host=mongo.cam.uchc.edu
+vcell_mongodb_port=27017
+vcell_mongodb_database=$vcell_site_upper
+vcell_mongodb_collection=logging
+
+vcell_smtp_host=vdsmtp.cam.uchc.edu
+vcell_smtp_port=25
+vcell_smtp_email="[email protected]"
+
+vcell_common_jre=/share/apps/vcell2/java/jdk1.8.0_66/bin/java
+vcell_common_jre_rmi=/usr/java/jdk1.8.0_66/jre/bin/java
+
+vcell_rmiservice_high_jmxport=12305
+vcell_rmiservice_http_jmxport=12304
+vcell_vcellservice_jmxport=12360
+
+vcell_primary_datadir=/share/apps/vcell3/users/
+vcell_secondary_datadir=/share/apps/vcell3/users/
+vcell_parallel_datadir=/state/partition1/vcelltemp/
+vcell_export_dir=/share/apps/vcell2/export/
+vcell_export_url=http://vcell.org/export/
+
+vcell_mpich_homedir="/share/apps/vcell2/mpich/"
+
+vcell_secretsDir=/usr/local/deploy
+vcell_I4J_pathto_secretsDir=/usr/local/deploy
+
+vcell_I4J_use_vagrant=false
+vcell_I4J_install_jres_into_user_home=false
+vcell_I4J_updateSiteBaseUrl=http://vcell.org/webstart/$vcell_site_camel
+vcell_I4J_pathto_mavenRootDir=/opt/build/vcell
+vcell_I4J_pathto_installerFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/VCell.install4j
+vcell_I4J_pathto_vcellIcnsFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/icons/vcell.icns
+vcell_I4J_pathto_jreDir=$HOME/.install4j6/jres
+vcell_I4J_jreDir=$HOME/.install4j6/jres
+vcell_I4J_pathto_install4jc=/opt/install4j6/bin/install4jc
+
+vcell_htc_usessh=false
+#
+#if [ "$vcell_htc_usessh" = true ]; then
+#	#
+#	# only define these if using ssh to invoke the htc processes
+#	#
+#	# DSA Keystore is for password-less authentication to HTC host
+#	#
+#	vcell_htc_sshhost="vcell-service.cam.uchc.edu"
+#	vcell_htc_sshuser="vcell"
+#	vcell_htc_sshDsaKeyFile="/Users/schaff/.ssh/schaff_dsa"
+#fi
+#
+

deploy/deploy.sh

@@ -13,8 +13,10 @@ includefile=$1
 . $vcell_secretsDir/deploySecrets.include
 
 DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+echo "deploy directory is ${DIR}"
 
 projectRootDir=`dirname $DIR`
+echo "project root directory is ${projectRootDir}"
 projectTargetDir=$projectRootDir/target
 
 serverTargetDir=$projectRootDir/vcell-server/target
@@ -31,6 +33,12 @@ clientJarsDir=$clientTargetDir/maven-jars
 
 skip_install4j=false
 skip_build=false
+skip_download_solvers=false
+
+if [ "$skip_download_solvers" = false ]; then
+	installSolversScript="${projectRootDir}/localsolvers/installSolvers.sh"
+	$installSolversScript
+fi
 
 #--------------------------------------------------------------------------
 # build project, generate user help files, gather jar files
@@ -564,4 +572,4 @@ else
 	echo ""
 	echo " then, don't forget to update symbolic links to <latest> installers"
 	echo ""
-fi
+fi

localsolvers/README.md

@@ -0,0 +1,11 @@
+Solvers are no longer included as binary artifacts within this source distribution
+
+please see the vcell-solvers project on github for binaries associated with releases.
+
+The solver archives associated with each platform are available as follows:
+
+linux32.tgz - not yet available from github.
+linux64.tgz - https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/linux64.tgz
+macos.tgz - https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/macos.tgz
+win32.tgz - not yet available from github.
+win64.tgz - https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/win64.tgz

localsolvers/installSolvers.cmd

@@ -0,0 +1,30 @@
+
+@echo "1) download the following urls (one for each platform)
+@echo "2) extract the archive using 7-zip or similar archive utility
+@echo "3) place extracted solver binaries into corresponding subdirectory of localsolvers"
+
+@echo " (for 64-bit Windows)"
+@echo "---win64 url---"
+@type win64/url.txt
+@echo "---end---"
+
+@echo " (for MacOS)"
+@echo "---mac64 url---"
+@type mac64/url.txt
+@echo "---end---"
+
+@echo " (for 64-bit Linux)"
+@echo "---linux64 url---"
+@type linux64/url.txt
+@echo "---end---"
+
+@echo " (for 32-bit Linux)"
+@echo "---linux32 url---"
+@type linux32/url.txt
+@echo "---end---"
+
+@echo " (for 32-bit Windows)"
+@echo "---win32 url---"
+@type win32/url.txt
+@echo "---end---"
+

localsolvers/installSolvers.sh

@@ -0,0 +1,82 @@
+#!/usr/bin/env bash
+
+DIR=${0%/*}
+
+cd $DIR
+#
+# get win64 solver binaries from url stored in win64/url.txt (assumes single archive that is packaged as tar.gz)
+#
+if [ -s "${DIR}/win64/url.txt" ]; then
+	win64_url=$(head -n 1 "${DIR}/win64/url.txt")
+	echo "curl -L -o win64.tgz $win64_url"
+	curl -L -o win64.tgz $win64_url
+	if [ $? -eq 0 ]; then
+		pushd win64
+		tar xzvf ../win64.tgz
+		popd
+		rm win64.tgz
+	fi
+fi
+
+#
+# get win32 solver binaries from url stored in win32/url.txt (assumes single archive that is packaged as tar.gz)
+#
+if [ -s "${DIR}/win32/url.txt" ]; then
+	win32_url=$(head -n 1 "${DIR}/win32/url.txt")
+	echo "curl -L -o win32.tgz $win32_url"
+	curl -L -o win32.tgz $win32_url
+	if [ $? -eq 0 ]; then
+		pushd win32
+		tar xzvf ../win32.tgz
+		popd
+		rm win32.tgz
+	fi
+fi
+
+#
+# get macos (64-bit) solver binaries from url stored in mac64/url.txt (assumes single archive that is packaged as tar.gz)
+#
+if [ -s "${DIR}/mac64/url.txt" ]; then
+	mac64_url=$(head -n 1 "${DIR}/mac64/url.txt")
+	echo "curl -L -o mac64.tgz $mac64_url"
+	curl -L -o mac64.tgz $mac64_url
+	if [ $? -eq 0 ]; then
+		pushd mac64
+		tar xzvf ../mac64.tgz
+		popd
+		rm mac64.tgz
+	fi
+fi
+
+#
+# get linux64 solver binaries from url stored in linux64/url.txt (assumes single archive that is packaged as tar.gz)
+# note that these solvers are the full server-side binaries with the ActiveMQ libraries linked for messaging.
+#
+if [ -s "${DIR}/linux64/url.txt" ]; then
+	linux64_url=$(head -n 1 "${DIR}/linux64/url.txt")
+	echo "curl -L -o linux64.tgz $linux64_url"
+	curl -L -o linux64.tgz $linux64_url
+	if [ $? -eq 0 ]; then
+		pushd linux64
+		tar xzvf ../linux64.tgz
+		popd
+		rm linux64.tgz
+	fi
+fi
+
+#
+# get linux32 solver binaries from url stored in linux32/url.txt (assumes single archive that is packaged as tar.gz)
+#
+if [ -s "${DIR}/linux32/url.txt" ]; then
+	linux32_url=$(head -n 1 "${DIR}/linux32/url.txt")
+	echo "curl -L -o linux32.tgz $linux32_url"
+	curl -L -o linux32.tgz $linux32_url
+	if [ $? -eq 0 ]; then
+		pushd linux32
+		tar xzvf ../linux32.tgz
+		popd
+		rm linux32.tgz
+	fi
+fi
+
+

localsolvers/linux32/url.txt

@@ -0,0 +1 @@
+https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/linux32-historical.tgz

localsolvers/linux64/url.txt

@@ -0,0 +1 @@
+https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/linux64.tgz

localsolvers/mac64/url.txt

@@ -0,0 +1 @@
+https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/macos.tgz

localsolvers/win32/url.txt

@@ -0,0 +1 @@
+

localsolvers/win64/url.txt

@@ -0,0 +1 @@
+https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/win64.tgz