lazar-gui 1.4.1 → 1.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a0ca50134ea890caa141bbe3d1e24c1c0df610a34164157640a50912c2897806
-  data.tar.gz: 624a704eabec8c163847bdc2bda698f1554c7764572c28aec9ed43d7728e4a05
+  metadata.gz: c549376eed8c822acaa2c0ece7d4abfb45c5cba1658cb2a37e7715bd5ea08815
+  data.tar.gz: c80a58e97beccc882550b831b364f67357d9cf5c1a55e50024dfbcb906668458
 SHA512:
-  metadata.gz: 7ec258039ef43e623613e13398ce20d1c8899a112f9f3dc54576f2b934c5234c17dea91fdf285685a46833dfff9db76c1752d248be09eca8aac7839b9572e0d2
-  data.tar.gz: e0f152007ba1a716425b9e17b034ab26998a95a914fa03f8a991c6ca203f026050731b184a1da1fbb1700370cc353de3e52e3c3e1c560f30a272086d94d6aba1
+  metadata.gz: 7965d14c4d1f8b018efc5765e9ed52a696c2352bbd8ddaed5b19aa9ed8e07f1781e2141ce1466c0d0d9e777bedf3f8d0ed347bba53232a878a7f56c7e1a86761
+  data.tar.gz: 2a21d4022ec21f0ba5ea9ebc9be63bc456bd0fca63e8b6a9df1dbf3389a7b071250b211bb13fcac3e0189d44c282e725dc1a5407232df8a3ff540cd6ea12f1a8

data/VERSION

@@ -1 +1 @@
-1.4.1
+1.4.2

data/docker/Dockerfile

@@ -39,11 +39,6 @@ RUN         tar -xvzf mongodb-bin.tar.gz
 WORKDIR     /home/ist/src/mongodb-bin
 RUN         makepkg -s --noconfirm
 
-# 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
-
 # start script
 COPY        start.sh /home/ist/start.sh
 
@@ -51,20 +46,17 @@ COPY        start.sh /home/ist/start.sh
 USER        root
 RUN         pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz 
 
-# install lazar-gui gem
-# lazar gem (required from lazar-gui) needs mongodb
+# install lazar-gui gem after mongodb: 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
 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
 
+EXPOSE      8088
 ENTRYPOINT  ["/home/ist/start.sh"]

data/docker/start.sh

@@ -5,7 +5,11 @@ mongod --bind_ip 127.0.0.1 --dbpath ~/data &
 R CMD Rserve --vanilla &
 
 # import data
+echo "Importing data and validating models"
 ruby -e "require 'lazar'; include OpenTox; Import.public_data if Model::Validation.all.empty?" 
+# get PubChem cids in advance to avoid timeout issues
+echo "Importing PubChem CID's"
+ruby -e "require 'lazar'; include OpenTox; Compound.all.each{|c| c.cid}"
 
 # start lazar service
 cd `ls -d $(gem environment gemdir)/gems/lazar-gui-*`

data/views/layout.haml

@@ -41,12 +41,10 @@
             %span.fa.fa-envelope
           [version: #{@version}]
         %p
-          A graphical overview of the service API can be found
-          %a{:href => "//#{$host_with_port}/api", :rel => "external"} here.
           Please cite
           %a{ :href=>"https://doi.org/10.3389/fphar.2013.00038", :rel=>"external"}
             %img{ :src=>"https://zenodo.org/badge/DOI/10.3389/zenodo.10.3389.svg", :alt=>"DOI"}
-          in scientific publications.
+          if you use this service for scientific purposes.
           %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=https%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"}
             %span.fa.fa-twitter-square
           %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=https%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=https%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on LinkedIn"}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lazar-gui
 version: !ruby/object:Gem::Version
-  version: 1.4.1
+  version: 1.4.2
 platform: ruby
 authors:
 - Christoph Helma
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-04 00:00:00.000000000 Z
+date: 2019-09-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: lazar
@@ -148,7 +148,6 @@ files:
 - config.ru
 - docker/Dockerfile
 - docker/start.sh
-- docker/swagger.html
 - helper.rb
 - lazar-gui.gemspec
 - lib/api.rb

data/docker/swagger.html

@@ -1,107 +0,0 @@
-<!-- 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>