lazar-gui 1.4.0.pre.0 → 1.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: b62bd400db67c63890b87da66fd39a5c409ae608
-  data.tar.gz: 846c1c3f564c6591b82ccede408f211a7ca66aaf
+SHA256:
+  metadata.gz: ad561aa97606a3fea005b3093d9b8bdd0ccb7246564f1124f5f70cbd3f9a5a67
+  data.tar.gz: 736f17abe8d0c6df86e256f37dffdffddd4e367adbb5db322aa8cfad5463db11
 SHA512:
-  metadata.gz: 7d0b13b9618aa506941ea3a99ee59ee4e70ff7e539c3936562ae5b5ea23d4f68221bd41109947dd5b1b3255d6134abe21e227729632c0ae92afe914be1bf6ec7
-  data.tar.gz: 8d75947e07ef2754bcdd9d318212f4696e1a6b6ec87cc6d330cb333dbb0c253399b84c6518fa704a8c729ce4f7dd97592ae75cf601b69046023fe54c2ba89f1a
+  metadata.gz: 3c918b6a66502ef6c9652a7fa40fa99abf6a5c12d51752cb36feea1cc58b267b37171cf4965d5074b9f9bf896d04ad69a1ee295b87ee8e7326622195b9b42c45
+  data.tar.gz: 96343339b9ed6326fb0bc525ea860ff07d184d39d9aadafea3916ea00106657b052828f674efad23b6c8ab29102ca8ed577d3552eb4c7b32832f84e7f5513507

data/VERSION

@@ -1 +1 @@
-1.4.0.pre.0
+1.4.0

data/application.rb

@@ -27,7 +27,8 @@ 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",

data/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

data/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"]

data/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

data/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"}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lazar-gui
 version: !ruby/object:Gem::Version
-  version: 1.4.0.pre.0
+  version: 1.4.0
 platform: ruby
 authors:
 - Christoph Helma
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-02 00:00:00.000000000 Z
+date: 2019-09-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: lazar
@@ -393,12 +393,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
-rubyforge_project: lazar-gui
-rubygems_version: 2.5.2.3
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: lazar-gui