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-rw-r--r--VERSION2
-rw-r--r--application.rb12
-rwxr-xr-xbin/lazar-start.sh1
-rw-r--r--docker/Dockerfile46
-rwxr-xr-xdocker/start.sh4
-rw-r--r--views/layout.haml4
6 files changed, 32 insertions, 37 deletions
diff --git a/VERSION b/VERSION
index acdfdf4..88c5fb8 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.4.0.pre.0
+1.4.0
diff --git a/application.rb b/application.rb
index fb03a72..e23c042 100644
--- a/application.rb
+++ b/application.rb
@@ -18,16 +18,22 @@ PUBCHEM_CID_URI = PUBCHEM_URI.split("/")[0..-3].join("/")+"/compound/"
"validation.rb"
].each{ |f| require_relative "./lib/#{f}" }
-configure :production, :development do
+configure :production do
STDOUT.sync = true
$logger = Logger.new(STDOUT)
- #$logger.level = Logger::DEBUG
+end
+
+configure :development do
+ STDOUT.sync = true
+ $logger = Logger.new(STDOUT)
+ $logger.level = Logger::DEBUG
end
before do
# use this hostname method instead to('/')
# allowes to set https for xhr requests
- $host_with_port = request.host =~ /localhost/ ? request.host_with_port : request.host
+ #$host_with_port = request.host =~ /localhost/ ? request.host_with_port : request.host
+ $host_with_port = request.host_with_port
$paths = [
"api",
"compound",
diff --git a/bin/lazar-start.sh b/bin/lazar-start.sh
index cf2af36..f83888e 100755
--- a/bin/lazar-start.sh
+++ b/bin/lazar-start.sh
@@ -3,6 +3,7 @@ sudo mongod &
R CMD Rserve --vanilla &
LAZARPATH=$(gem path lazar-gui)
cd $LAZARPATH
+cd $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')
unicorn -c unicorn.rb -E production
exit 0
diff --git a/docker/Dockerfile b/docker/Dockerfile
index a606b9a..b7ba3c1 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -23,12 +23,17 @@ 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
-# mongodb has been removed from main repositories
USER ist
WORKDIR /home/ist
RUN mkdir data
+# mongodb has been removed from main repositories, AUR installation
RUN mkdir src
WORKDIR /home/ist/src
RUN wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz
@@ -36,38 +41,23 @@ RUN tar -xvzf mongodb-bin.tar.gz
WORKDIR /home/ist/src/mongodb-bin
RUN makepkg -s --noconfirm
-# installation requires root
-USER root
-RUN pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz
-
-# install lazar-gui gem
-RUN echo 'gem: --no-document' > /etc/gemrc
-
-#RUN gem install lazar-gui
-RUN gem install lazar
-RUN gem install qsar-report
-RUN gem install sinatra haml sass rdiscount unicorn
-
-USER ist
-WORKDIR /home/ist
-RUN rm -r src
-
-# lazar-gui
-RUN git clone https://git.in-silico.ch/lazar-gui
-WORKDIR lazar-gui
-RUN git checkout prerelease
-
-# SWAGGER for API
+# rest api swagger gui
WORKDIR /home/ist
RUN git clone https://github.com/swagger-api/swagger-ui.git
COPY swagger.html /home/ist/swagger-ui/dist/index.html
-# TODO adjust to lazar-gui gem path
-RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js /home/ist/lazar-gui/public/swagger-ui-bundle.js
-RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js /home/ist/lazar-gui/public/swagger-ui-standalone-preset.js
-RUN ln -s /home/ist/swagger-ui/dist/swagger-ui.css /home/ist/lazar-gui/public/swagger-ui.css
-
# start script
COPY start.sh /home/ist/start.sh
+# mongodb installation requires root
+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
+
+USER ist
+RUN rm -r /home/ist/src
ENTRYPOINT ["/home/ist/start.sh"]
diff --git a/docker/start.sh b/docker/start.sh
index ad40a0e..07fefde 100755
--- a/docker/start.sh
+++ b/docker/start.sh
@@ -5,8 +5,8 @@ mongod --bind_ip 127.0.0.1 --dbpath ~/data &
R CMD Rserve --vanilla &
# import data
-ruby -e "require 'lazar'; include OpenTox; Import.public_data"
+ruby -e "require 'lazar'; include OpenTox; Import.public_data if Model::Validation.all.empty?"
# start lazar service
-cd $HOME/lazar-gui
+cd $(gem which lazar-gui|sed 's#/lib/lazar-gui.rb/##')
unicorn -p 8088 -E production
diff --git a/views/layout.haml b/views/layout.haml
index 8547e13..8cd5dfb 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -34,9 +34,7 @@
%div.container-fluid
%topline.alert
%p
- Problems, bugs, ideas for improvements ? Please report at our
- %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
- , check out the
+ Problems, bugs or ideas for improvements ? Please check the
%a{:href=> "//#{$host_with_port}/predict/faq"} FAQ
page or send us an email.
%a{ :href=>"mailto:info@in-silico.ch?subject=[lazar v#{@version}]", :target=>"_top"}