From c9f8cd864a2b72e7330b8095691fa5c16fea83aa Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 30 Aug 2019 11:14:50 +0200
Subject: Dockerfile and start script added

---
 application.rb      |   4 +-
 docker/Dockerfile   |  73 +++++++++++++++++++++++++++++++++++
 docker/start.sh     |  12 ++++++
 docker/swagger.html | 107 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 194 insertions(+), 2 deletions(-)
 create mode 100644 docker/Dockerfile
 create mode 100755 docker/start.sh
 create mode 100644 docker/swagger.html

diff --git a/application.rb b/application.rb
index ef059b2..fb03a72 100644
--- a/application.rb
+++ b/application.rb
@@ -21,7 +21,7 @@ PUBCHEM_CID_URI = PUBCHEM_URI.split("/")[0..-3].join("/")+"/compound/"
 configure :production, :development do
   STDOUT.sync = true  
   $logger = Logger.new(STDOUT)
-  $logger.level = Logger::DEBUG
+  #$logger.level = Logger::DEBUG
 end
 
 before do
@@ -42,7 +42,7 @@ before do
   if request.path =~ /predict/
     @accept = request.env['HTTP_ACCEPT'].split(",").first
     response['Content-Type'] = @accept
-    halt 400, "Mime type #{@accept} is not supported." unless @accept == "text/html" || "*/*"
+    halt 400, "Mime type #{@accept} is not supported." unless @accept == "text/html" or @accept == "*/*"
     @version = File.read("VERSION").chomp
   else
     @accept = request.env['HTTP_ACCEPT'].split(",").first
diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 0000000..a606b9a
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,73 @@
+FROM				archlinux/base
+MAINTAINER  in-silico toxicology Gmbh
+
+RUN         pacman-db-upgrade
+RUN         pacman -Syyu --noconfirm 
+RUN         pacman -S --noconfirm \
+            base-devel \
+            boost-libs \
+            cmake \
+            eigen3 \
+            fontconfig \
+            gcc-fortran \
+            git \
+            gsl \
+            jre10-openjdk-headless \
+            r \
+            ruby \
+            swig \
+            python-pip \
+            catdoc \
+            wget
+RUN         pacman -Scc --noconfirm
+
+RUN         R -e "install.packages('Rserve', repos='http://rforge.net/')"
+RUN         pip install xlsx2csv
+RUN         useradd -ms /bin/bash ist
+
+# mongodb has been removed from main repositories
+USER        ist
+WORKDIR     /home/ist
+RUN         mkdir data
+RUN         mkdir src
+WORKDIR     /home/ist/src
+RUN         wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz
+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
+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
+
+ENTRYPOINT  ["/home/ist/start.sh"]
diff --git a/docker/start.sh b/docker/start.sh
new file mode 100755
index 0000000..ad40a0e
--- /dev/null
+++ b/docker/start.sh
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# start basic services
+mongod --bind_ip 127.0.0.1 --dbpath ~/data &
+R CMD Rserve --vanilla &
+
+# import data
+ruby -e "require 'lazar'; include OpenTox; Import.public_data" 
+
+# start lazar service
+cd $HOME/lazar-gui
+unicorn -p 8088 -E production
diff --git a/docker/swagger.html b/docker/swagger.html
new file mode 100644
index 0000000..239e4f1
--- /dev/null
+++ b/docker/swagger.html
@@ -0,0 +1,107 @@
+<!-- HTML for static distribution bundle build -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8">
+    <title>Swagger UI</title>
+    <link href="https://fonts.googleapis.com/css?family=Open+Sans:400,700|Source+Code+Pro:300,600|Titillium+Web:400,600,700" rel="stylesheet">
+    <link rel="stylesheet" type="text/css" href="./swagger-ui.css" >
+    <link rel="icon" type="image/png" href="./favicon-32x32.png" sizes="32x32" />
+    <link rel="icon" type="image/png" href="./favicon-16x16.png" sizes="16x16" />
+    <style>
+      html
+      {
+        box-sizing: border-box;
+        overflow: -moz-scrollbars-vertical;
+        overflow-y: scroll;
+      }
+
+      *,
+      *:before,
+      *:after
+      {
+        box-sizing: inherit;
+      }
+
+      body
+      {
+        margin:0;
+        background: #fafafa;
+      }
+    </style>
+  </head>
+
+  <body>
+    <div id="swagger-ui"></div>
+
+    <script src="./swagger-ui-bundle.js"> </script>
+    <script src="./swagger-ui-standalone-preset.js"> </script>
+    <script>
+    window.onload = function() {
+
+      // Build a system
+      var base_url = window.location.origin;
+      var swagger_url = base_url + "/api/api.json";
+      const ui = SwaggerUIBundle({
+        url: swagger_url,
+        dom_id: '#swagger-ui',
+        deepLinking: true,
+        presets: [
+          SwaggerUIBundle.presets.apis,
+          SwaggerUIStandalonePreset
+        ],
+        plugins: [
+          SwaggerUIBundle.plugins.DownloadUrl
+        ],
+        layout: "StandaloneLayout"
+      })
+
+      window.ui = ui;
+      document.getElementsByClassName('topbar')[0].style.backgroundColor = "#fafafa";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].alt = "IST";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].src = "./IST_logo_s.png";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].width = "90";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].height = "35";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].style.marginRight = "20px";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('span')[0].innerHTML = "lazar-rest-api";
+    };
+
+    // add link for docs
+    setTimeout(function() {
+      var base_url = window.location.origin;
+      var section = document.getElementsByClassName("info")[0];
+      var node = document.createElement("docs");
+      var heading = document.createElement('h2');
+      var headingtext = document.createTextNode("Documentation");
+      var link = document.createElement('a');
+      var linktext = document.createTextNode("See curl examples for a typical workflow.");
+      heading.appendChild(headingtext);
+      link.appendChild(linktext);
+      link.title = "curl examples";
+      link.href = "https://github.com/OpenRiskNet/home/blob/master/openshift/deployments/lazar#curl-examples";
+      link.target = "javascript:void(0);";
+      node.appendChild(heading);
+      node.appendChild(link);
+      section.appendChild(node);
+    }, 1000);
+    // add link for gui
+    setTimeout(function() {
+      var base_url = window.location.origin;
+      var section = document.getElementsByClassName("info")[0];
+      var node = document.createElement("gui");
+      var heading = document.createElement('h2');
+      var headingtext = document.createTextNode("Lazar Graphical User Interface");
+      var link = document.createElement('a');
+      var linktext = document.createTextNode("Lazar (GUI)");
+      heading.appendChild(headingtext);
+      link.appendChild(linktext);
+      link.title = "GUI link";
+      link.href = base_url = "/predict";
+      link.target = "javascript:void(0);";
+      node.appendChild(heading);
+      node.appendChild(link);
+      section.appendChild(node);
+    }, 1000);
+  </script>
+  </body>
+</html>
-- 
cgit v1.2.3