sequenceserver 1.1.0.beta → 1.1.0.beta2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a57253303745d75b265f72d93f40b063ee76aee3
+  metadata.gz: cccfc5a0df6982dde1187b7f12d043092d6b72c4
+  data.tar.gz: ce2dbf97a61770f721fd3501e150817e4e33f095
 SHA512:
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+  data.tar.gz: 4871277a05d19b600fc2611958623aa38b6328a1e271917aeedf840a0901550f2f76f86e6f59ee31793e95a946ab2ba092308622c8e30290b7065f2913719ccf

data/.travis.yml

@@ -8,25 +8,21 @@ rvm:
 addons:
   firefox: "58.0"
 
-  code_climate:
-    repo_token:
-      secure: "cT2wvWS2Uk2trYGwZ38Qo9XWCeL+OOXH0lVmLfNb1Xy/tWAXycDdZsc9CN8igjhD+/cKvvh529/qdDm2PJnb1Hux1bxHSTuMuE2xQWlfJqaOR/IX0z96MbP1eITKjhGv9vccmIPdV3Rh/OQLeHkyqyHvXio9NXiARMJUZDTpRuA="
-
 branches:
   only:
     - 1.0.x  # stable
     - master
 
 install:
-  - wget -c "https://github.com/mozilla/geckodriver/releases/download/v0.20.0/geckodriver-v0.20.0-macos.tar.gz"
+  - wget -c "https://github.com/mozilla/geckodriver/releases/download/v0.20.0/geckodriver-v0.20.0-linux64.tar.gz"
   - mkdir geckodriver && tar xvf geckodriver-*.tar.gz -C geckodriver
-  - export PATH="geckodriver:$PATH"
+  - export PATH="$PWD/geckodriver:$PATH"
   - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz"
   - tar xvf ncbi-blast-*.tar.gz
   - gem install bundler && bundle
   - bundle exec bin/sequenceserver -s -b ncbi-blast-2.6.0+/bin -d spec/database/sample
 
-script: xvfb-run bundle exec rake spec
+script: xvfb-run bundle exec rspec
 
 cache:
   directories:
@@ -34,3 +30,7 @@ cache:
     - ncbi-blast-2.6.0+
 
 sudo: false
+
+env:
+  global:
+    - CC_TEST_REPORTER_ID=ec48bb03c72db6b43ce71fd488110b4707abfde4386c144d886d711378d8db64

data/README.md

@@ -34,12 +34,6 @@ npm install
 bundle
 ```
 
-We use capybara-webkit for functional testing, which requires [`qt` to be
-installed](https://github.com/thoughtbot/capybara-webkit/wiki/Installing-Qt-and-compiling-capybara-webkit).
-
-We use JSPM (via Node) for front-end package management and building JavaScript
-and CSS files.
-
 If you are deploying SequenceServer from git you can skip `npm install` step
 and skip installing gems used for testing (and `qt`), etc. by running:
 
@@ -53,15 +47,19 @@ logs verbosely and uses raw front-end files.
 bundle exec bin/sequenceserver -D
 ```
 
-Run the specs, lint the code, build front-end and package everything as a gem.
+Run tests:
+```
+bundle exec rspec
+```
+
+Run code style checkers (rubocop, csslint, eslint) -
 ```
-rake
+codeclimate analyze
 ```
 
-Sometimes you may just want to run the specs or lint the code:
+Build minifies JS and CSS bundles:
 ```
-rake spec
-rake lint
+npm run-script build
 ```
 
 ## Using Docker

data/Rakefile

@@ -1,21 +1,8 @@
-require 'rspec/core'
-require 'rspec/core/rake_task'
-
-desc 'Run specs'
-RSpec::Core::RakeTask.new(:spec) do |spec|
-  spec.pattern = FileList['spec/**/*_spec.rb']
-  spec.pattern.exclude(ENV['exclude'])
-end
-
-desc 'Run CodeClimate (rubocop, csslint, eslint)'
-task :lint do
-  sh 'codeclimate analyze'
-end
-
 desc 'Concatenate, minify and gzip JS and CSS files; build gem'
 task :build do
   sh 'npm run-script build'
+  # FIXME: clean up the dir before gem
   sh 'gem build sequenceserver.gemspec'
 end
 
-task :default => [:spec, :lint, :build]
+task :default => [:build]

data/lib/sequenceserver/database.rb

@@ -21,6 +21,11 @@ module SequenceServer
   # and use `parse_seqids` option of `makeblastdb` to format databases.
   Database = Struct.new(:name, :title, :type, :nsequences, :ncharacters,
                         :updated_on) do
+
+    extend Forwardable
+
+    def_delegators SequenceServer, :config, :sys
+
     def initialize(*args)
       args[2].downcase! # database type
       args.each(&:freeze)
@@ -32,7 +37,8 @@ module SequenceServer
     attr_reader :id
 
     def include?(accession)
-      out = `blastdbcmd -entry '#{accession}' -db #{name} 2> /dev/null`
+      cmd = "blastdbcmd -entry '#{accession}' -db #{name}"
+      out, _ = sys(cmd, path: config[:bin])
       !out.empty?
     end
 

data/lib/sequenceserver/routes.rb

@@ -49,6 +49,9 @@ module SequenceServer
         frame_options = SequenceServer.config[:frame_options]
         frame_options && { :frame_options => frame_options }
       }
+
+      # Serve compressed responses.
+      use Rack::Deflater
     end
 
     # For any request that hits the app,  log incoming params at debug level.
@@ -58,7 +61,7 @@ module SequenceServer
 
     # Returns base HTML. Rest happens client-side: rendering the search form.
     get '/' do
-      erb :layout
+      erb :search, layout: true
     end
 
     # Returns data that is used to render the search form client side. These
@@ -93,7 +96,7 @@ module SequenceServer
     # Returns base HTML. Rest happens client-side: polling for and rendering
     # the results.
     get '/:jid' do |jid|
-      erb :layout
+      erb :report, layout: true
     end
 
     # @params sequence_ids: whitespace separated list of sequence ids to

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.1.0.beta'
+  VERSION = '1.1.0.beta2'
 end

data/lib/sequenceserver.rb

@@ -96,9 +96,11 @@ module SequenceServer
       temp_stdout_file = Tempfile.new 'sequenceserver-sys'
       temp_stderr_file = Tempfile.new 'sequenceserver-sys'
 
+      # Log the command we are going to run - use -D option to view.
       logger.debug("Executing: #{command}")
 
-      # Fork.
+      # Run command in a child process. This allows us to control PATH
+      # and pwd of the running process.
       child_pid = fork do
         # Set the PATH environment variable to the binary directory or
         # safe directory.

data/package.json

@@ -1,7 +1,7 @@
 {
   "name": "SequenceServer",
   "description": "BLAST searching made easy!",
-  "version": "1.1.0.beta",
+  "version": "1.1.0-beta",
   "homepage": "http://www.sequenceserver.com",
   "repository": "https://github.com/yannickwurm/sequenceserver",
   "author": {
@@ -14,7 +14,7 @@
     "jspm": "^0.16.2"
   },
   "scripts": {
-    "build": "jspm bundle-sfx --minify --skip-source-maps js/sequenceserver.js public/sequenceserver.min.js && cleancss public/css/sequenceserver.css > public/css/sequenceserver.min.css && gzip -kf public/sequenceserver.min.js && gzip -kf public/css/sequenceserver.min.css"
+    "build": "jspm bundle-sfx --minify --skip-source-maps js/search.js public/sequenceserver-search.min.js && jspm bundle-sfx --minify --skip-source-maps js/report.js public/sequenceserver-report.min.js && cleancss public/css/sequenceserver.css > public/css/sequenceserver.min.css"
   },
   "jspm": {
     "directories": {
@@ -29,7 +29,6 @@
       "jquery-ui": "github:components/jqueryui@^1.11.4",
       "nicgirault/circosJs": "github:nicgirault/circosJs@^1.7.0",
       "react": "npm:react@^0.13.3",
-      "react-router": "npm:react-router@^0.13.3",
       "underscore": "npm:underscore@^1.8.3",
       "webshim": "npm:webshim@^1.15.8"
     },

data/public/config.js

@@ -26,7 +26,6 @@ System.config({
     "jquery-ui": "github:components/jqueryui@1.11.4",
     "nicgirault/circosJs": "github:nicgirault/circosJs@1.7.0",
     "react": "npm:react@0.13.3",
-    "react-router": "npm:react-router@0.13.3",
     "underscore": "npm:underscore@1.8.3",
     "webshim": "npm:webshim@1.15.8",
     "github:components/jqueryui@1.11.4": {
@@ -101,12 +100,6 @@ System.config({
     "npm:path-browserify@0.0.0": {
       "process": "github:jspm/nodelibs-process@0.1.1"
     },
-    "npm:react-router@0.13.3": {
-      "object-assign": "npm:object-assign@2.1.1",
-      "process": "github:jspm/nodelibs-process@0.1.1",
-      "qs": "npm:qs@2.4.1",
-      "react": "npm:react@0.13.3"
-    },
     "npm:react@0.13.3": {
       "buffer": "github:jspm/nodelibs-buffer@0.1.0",
       "envify": "npm:envify@3.4.0",

data/public/css/sequenceserver.css

@@ -224,13 +224,6 @@ a.disabled:hover {
   font-weight: normal;
 }
 
-/**
- * Set padding: 10px and 15px on li.
- */
-.list-padded li {
-  padding: 10px 15px;
-}
-
 /**
  * Reset Bootstrap's CSS for pre tags.
  */
@@ -336,14 +329,16 @@ input[name="advanced"] {
 /**********************
         Sidebar
  **********************/
-.sidebar {
-  /* Line up with "Results" on left. */
+.sidebar > div {
+  /* To line up with the results on the right */
   margin-top: 20px;
 }
-.sidebar > .section-header > h4 {
-  padding: 10px 0 0 0;
+.sidebar h4 {
   font-size: 14px;
 }
+.sidebar li a {
+  padding: 7px 10px;
+}
 
 .sidebar.affix {
   margin-top: 0;
@@ -362,14 +357,10 @@ input[name="advanced"] {
   }
 }
 
-.index {
-  max-height: 416px; /* will accomodate 10 elements. IE 7 and above only. */
-  overflow-y: auto;
-}
-
 /* Result per query. */
 .overview {
-  margin: 30px 0;
+  /* To line up with the sidebar on the left */
+  margin: 20px 0;
 }
 .resultn {
   margin-bottom: 50px;