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authorChristoph Helma <helma@in-silico.ch>2019-09-04 12:16:28 +0200
committerChristoph Helma <helma@in-silico.ch>2019-09-04 12:16:28 +0200
commitbd4f62492f217fbc2a2240dcade6452cd5d9b519 (patch)
tree8d3316361fe73898bfee869cdbb2b7fa4cb93afa
parentd1032e4f40d9fbb212e85e0db4f0ecd2e8ac9a88 (diff)
batch mode disabled, lazar-gui gem path and permissions fixed in Dockerfile1.4.1
-rw-r--r--VERSION2
-rwxr-xr-xbin/lazar-start.sh7
-rw-r--r--config.ru2
-rw-r--r--docker/Dockerfile19
-rwxr-xr-xdocker/start.sh2
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