From bd4f62492f217fbc2a2240dcade6452cd5d9b519 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 4 Sep 2019 12:16:28 +0200
Subject: batch mode disabled, lazar-gui gem path and permissions fixed in
 Dockerfile

---
 VERSION            |  2 +-
 bin/lazar-start.sh |  7 ++++---
 config.ru          |  2 +-
 docker/Dockerfile  | 19 +++++++++++++------
 docker/start.sh    |  2 +-
 5 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/VERSION b/VERSION
index 88c5fb8..347f583 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.4.0
+1.4.1
diff --git a/bin/lazar-start.sh b/bin/lazar-start.sh
index f83888e..a7852d3 100755
--- a/bin/lazar-start.sh
+++ b/bin/lazar-start.sh
@@ -1,9 +1,10 @@
 #!/bin/bash
 sudo mongod &
 R CMD Rserve --vanilla &
-LAZARPATH=$(gem path lazar-gui)
-cd $LAZARPATH
-cd $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')
+#LAZARPATH=$(gem path lazar-gui)
+#cd $LAZARPATH
+#cd $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')
+cd `ls -d $(gem environment gemdir)/gems/lazar-gui-*`
 unicorn -c unicorn.rb -E production
 
 exit 0
diff --git a/config.ru b/config.ru
index 559491d..0ac80ec 100644
--- a/config.ru
+++ b/config.ru
@@ -1,4 +1,4 @@
-ENV["BATCH_MODE"] = "true"
+ENV["BATCH_MODE"] = "false"
 ENV["LAZAR_ENV"] = "production"
 require "lazar"
 require "qsar-report"
diff --git a/docker/Dockerfile b/docker/Dockerfile
index b7ba3c1..34c99f7 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -24,9 +24,7 @@ RUN         pacman -Scc --noconfirm
 RUN         R -e "install.packages('Rserve', repos='http://rforge.net/')"
 RUN         pip install xlsx2csv
 
-# install lazar-gui gem
 RUN         echo 'gem: --no-document' > /etc/gemrc
-RUN         gem install lazar-gui
 
 RUN         useradd -ms /bin/bash ist
 
@@ -53,11 +51,20 @@ COPY        start.sh /home/ist/start.sh
 USER        root
 RUN         pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz 
 
-# swagger links
-RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-bundle.js
-RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-standalone-preset.js
-RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui.css $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui.css
+# install lazar-gui gem
+# lazar gem (required from lazar-gui) needs mongodb
+RUN         gem install lazar-gui 
+
+# change owners (temporary workaround)
+RUN         chown ist `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public
+RUN         chown ist `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/tmp
+RUN         chown ist `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/api/api.json
 
 USER        ist
 RUN         rm -r /home/ist/src
+# swagger links
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public/swagger-ui-bundle.js
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public/swagger-ui-standalone-preset.js
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui.css `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public/swagger-ui.css
+
 ENTRYPOINT  ["/home/ist/start.sh"]
diff --git a/docker/start.sh b/docker/start.sh
index 07fefde..e223878 100755
--- a/docker/start.sh
+++ b/docker/start.sh
@@ -8,5 +8,5 @@ R CMD Rserve --vanilla &
 ruby -e "require 'lazar'; include OpenTox; Import.public_data if Model::Validation.all.empty?" 
 
 # start lazar service
-cd $(gem which lazar-gui|sed 's#/lib/lazar-gui.rb/##')
+cd `ls -d $(gem environment gemdir)/gems/lazar-gui-*`
 unicorn -p 8088 -E production
-- 
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