sequenceserver 0.8.9 → 1.0.0.pre.1

metadata

@@ -1,104 +1,163 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 0.8.9
+  version: 1.0.0.pre.1
 platform: ruby
 authors:
 - Anurag Priyam
 - Ben J Woodcroft
+- Vivek Rai
 - Yannick Wurm
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-09 00:00:00.000000000 Z
+date: 2015-01-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: thin
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: 1.6.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: 1.6.2
 - !ruby/object:Gem::Dependency
   name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.0
+        version: 1.4.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.0
+        version: 1.4.5
 - !ruby/object:Gem::Dependency
-  name: ptools
+  name: ox
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.1.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.1.1
 - !ruby/object:Gem::Dependency
-  name: minitest
+  name: slop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
+        version: 3.6.0
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 3.6.0
 - !ruby/object:Gem::Dependency
   name: rack-test
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.6.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.6.2
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 10.3.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 10.3.2
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.26.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.26.1
+- !ruby/object:Gem::Dependency
+  name: capybara
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.4
+- !ruby/object:Gem::Dependency
+  name: capybara-webkit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.3.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.3.0
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
-email: anurag08priyam@gmail.com
+email:
+- anurag08priyam@gmail.com
+- b.woodcroft@uq.edu.au
 executables:
 - sequenceserver
 extensions: []
@@ -107,56 +166,189 @@ files:
 - Gemfile
 - LICENSE.Apache.txt
 - LICENSE.txt
-- README.txt
+- README.md
 - bin/sequenceserver
 - config.ru
-- example.config.yml
 - lib/sequenceserver.rb
 - lib/sequenceserver/blast.rb
-- lib/sequenceserver/customisation.rb
 - lib/sequenceserver/database.rb
-- lib/sequenceserver/database_formatter.rb
-- lib/sequenceserver/helpers.rb
-- lib/sequenceserver/sequencehelpers.rb
-- lib/sequenceserver/sinatralikeloggerformatter.rb
-- lib/sequenceserver/version.rb
-- public/css/beige.css.css
-- public/css/bootstrap.dropdown.css
-- public/css/bootstrap.icons.css
+- lib/sequenceserver/links.rb
+- lib/sequenceserver/logger.rb
+- lib/sequenceserver/sequence.rb
 - public/css/bootstrap.min.css
-- public/css/bootstrap.modal.css
 - public/css/custom.css
+- public/css/font-awesome.min.css
+- public/fonts/FontAwesome.otf
+- public/fonts/fontawesome-webfont.eot
+- public/fonts/fontawesome-webfont.svg
+- public/fonts/fontawesome-webfont.ttf
+- public/fonts/fontawesome-webfont.woff
+- public/fonts/fontawesome-webfont.woff2
 - public/img/glyphicons-halflings-white.png
 - public/img/glyphicons-halflings.png
-- public/js/bootstrap.dropdown.js
-- public/js/bootstrap.modal.js
-- public/js/bootstrap.transition.js
-- public/js/jquery-scrollspy.js
+- public/js/bootstrap.min.js
+- public/js/d3.v3.min.js
+- public/js/html5shiv.min.js
 - public/js/jquery-ui.js
-- public/js/jquery.activity.js
-- public/js/jquery.enablePlaceholder.min.js
 - public/js/jquery.js
+- public/js/jquery.scrollspy.js
+- public/js/jquery.t.js
+- public/js/sequence.js
 - public/js/sequenceserver.blast.js
 - public/js/sequenceserver.js
-- public/js/store.min.js
-- public/sequence.html
+- public/js/underscore.min.js
+- public/js/webshims/polyfiller.js
+- public/js/webshims/shims/FlashCanvas/canvas2png.js
+- public/js/webshims/shims/FlashCanvas/flashcanvas.js
+- public/js/webshims/shims/FlashCanvas/flashcanvas.swf
+- public/js/webshims/shims/FlashCanvasPro/canvas2png.js
+- public/js/webshims/shims/FlashCanvasPro/flash10canvas.swf
+- public/js/webshims/shims/FlashCanvasPro/flash9canvas.swf
+- public/js/webshims/shims/FlashCanvasPro/flashcanvas.js
+- public/js/webshims/shims/canvas-blob.js
+- public/js/webshims/shims/color-picker.js
+- public/js/webshims/shims/combos/1.js
+- public/js/webshims/shims/combos/10.js
+- public/js/webshims/shims/combos/11.js
+- public/js/webshims/shims/combos/12.js
+- public/js/webshims/shims/combos/13.js
+- public/js/webshims/shims/combos/14.js
+- public/js/webshims/shims/combos/15.js
+- public/js/webshims/shims/combos/16.js
+- public/js/webshims/shims/combos/17.js
+- public/js/webshims/shims/combos/18.js
+- public/js/webshims/shims/combos/2.js
+- public/js/webshims/shims/combos/21.js
+- public/js/webshims/shims/combos/22.js
+- public/js/webshims/shims/combos/23.js
+- public/js/webshims/shims/combos/25.js
+- public/js/webshims/shims/combos/27.js
+- public/js/webshims/shims/combos/28.js
+- public/js/webshims/shims/combos/29.js
+- public/js/webshims/shims/combos/3.js
+- public/js/webshims/shims/combos/30.js
+- public/js/webshims/shims/combos/31.js
+- public/js/webshims/shims/combos/33.js
+- public/js/webshims/shims/combos/34.js
+- public/js/webshims/shims/combos/4.js
+- public/js/webshims/shims/combos/5.js
+- public/js/webshims/shims/combos/6.js
+- public/js/webshims/shims/combos/7.js
+- public/js/webshims/shims/combos/8.js
+- public/js/webshims/shims/combos/9.js
+- public/js/webshims/shims/combos/97.js
+- public/js/webshims/shims/combos/98.js
+- public/js/webshims/shims/combos/99.js
+- public/js/webshims/shims/details.js
+- public/js/webshims/shims/dom-extend.js
+- public/js/webshims/shims/es5.js
+- public/js/webshims/shims/es6.js
+- public/js/webshims/shims/excanvas.js
+- public/js/webshims/shims/filereader-xhr.js
+- public/js/webshims/shims/form-combat.js
+- public/js/webshims/shims/form-core.js
+- public/js/webshims/shims/form-datalist-lazy.js
+- public/js/webshims/shims/form-datalist.js
+- public/js/webshims/shims/form-fixrangechange.js
+- public/js/webshims/shims/form-inputmode.js
+- public/js/webshims/shims/form-message.js
+- public/js/webshims/shims/form-native-extend.js
+- public/js/webshims/shims/form-number-date-api.js
+- public/js/webshims/shims/form-number-date-ui.js
+- public/js/webshims/shims/form-shim-extend.js
+- public/js/webshims/shims/form-shim-extend2.js
+- public/js/webshims/shims/form-validation.js
+- public/js/webshims/shims/form-validators.js
+- public/js/webshims/shims/forms-picker.js
+- public/js/webshims/shims/geolocation.js
+- public/js/webshims/shims/i18n/formcfg-ar.js
+- public/js/webshims/shims/i18n/formcfg-ch-CN.js
+- public/js/webshims/shims/i18n/formcfg-cs.js
+- public/js/webshims/shims/i18n/formcfg-de.js
+- public/js/webshims/shims/i18n/formcfg-el.js
+- public/js/webshims/shims/i18n/formcfg-en.js
+- public/js/webshims/shims/i18n/formcfg-es.js
+- public/js/webshims/shims/i18n/formcfg-fa.js
+- public/js/webshims/shims/i18n/formcfg-fr.js
+- public/js/webshims/shims/i18n/formcfg-he.js
+- public/js/webshims/shims/i18n/formcfg-hi.js
+- public/js/webshims/shims/i18n/formcfg-hu.js
+- public/js/webshims/shims/i18n/formcfg-it.js
+- public/js/webshims/shims/i18n/formcfg-ja.js
+- public/js/webshims/shims/i18n/formcfg-lt.js
+- public/js/webshims/shims/i18n/formcfg-nl.js
+- public/js/webshims/shims/i18n/formcfg-pl.js
+- public/js/webshims/shims/i18n/formcfg-pt-BR.js
+- public/js/webshims/shims/i18n/formcfg-pt-PT.js
+- public/js/webshims/shims/i18n/formcfg-pt.js
+- public/js/webshims/shims/i18n/formcfg-ru.js
+- public/js/webshims/shims/i18n/formcfg-sv.js
+- public/js/webshims/shims/i18n/formcfg-zh-CN.js
+- public/js/webshims/shims/i18n/formcfg-zh-TW.js
+- public/js/webshims/shims/jme/alternate-media.js
+- public/js/webshims/shims/jme/base.js
+- public/js/webshims/shims/jme/controls.css
+- public/js/webshims/shims/jme/jme.eot
+- public/js/webshims/shims/jme/jme.svg
+- public/js/webshims/shims/jme/jme.ttf
+- public/js/webshims/shims/jme/jme.woff
+- public/js/webshims/shims/jme/mediacontrols-lazy.js
+- public/js/webshims/shims/jme/mediacontrols.js
+- public/js/webshims/shims/jme/playlist.js
+- public/js/webshims/shims/jpicker/images/AlphaBar.png
+- public/js/webshims/shims/jpicker/images/Bars.png
+- public/js/webshims/shims/jpicker/images/Maps.png
+- public/js/webshims/shims/jpicker/images/NoColor.png
+- public/js/webshims/shims/jpicker/images/bar-opacity.png
+- public/js/webshims/shims/jpicker/images/map-opacity.png
+- public/js/webshims/shims/jpicker/images/mappoint.gif
+- public/js/webshims/shims/jpicker/images/picker.gif
+- public/js/webshims/shims/jpicker/images/preview-opacity.png
+- public/js/webshims/shims/jpicker/images/rangearrows.gif
+- public/js/webshims/shims/jpicker/jpicker.css
+- public/js/webshims/shims/matchMedia.js
+- public/js/webshims/shims/mediacapture-picker.js
+- public/js/webshims/shims/mediacapture.js
+- public/js/webshims/shims/mediaelement-core.js
+- public/js/webshims/shims/mediaelement-debug.js
+- public/js/webshims/shims/mediaelement-jaris.js
+- public/js/webshims/shims/mediaelement-native-fix.js
+- public/js/webshims/shims/mediaelement-yt.js
+- public/js/webshims/shims/moxie/flash/Moxie.cdn.swf
+- public/js/webshims/shims/moxie/flash/Moxie.min.swf
+- public/js/webshims/shims/moxie/js/moxie-html4.js
+- public/js/webshims/shims/moxie/js/moxie-swf.js
+- public/js/webshims/shims/picture.js
+- public/js/webshims/shims/plugins/jquery.ui.position.js
+- public/js/webshims/shims/range-ui.js
+- public/js/webshims/shims/sizzle.js
+- public/js/webshims/shims/sticky.js
+- public/js/webshims/shims/styles/color-picker.png
+- public/js/webshims/shims/styles/forms-ext.css
+- public/js/webshims/shims/styles/forms-picker.css
+- public/js/webshims/shims/styles/progress.gif
+- public/js/webshims/shims/styles/progress.png
+- public/js/webshims/shims/styles/shim-ext.css
+- public/js/webshims/shims/styles/shim.css
+- public/js/webshims/shims/styles/transparent.png
+- public/js/webshims/shims/styles/widget.eot
+- public/js/webshims/shims/styles/widget.svg
+- public/js/webshims/shims/styles/widget.ttf
+- public/js/webshims/shims/styles/widget.woff
+- public/js/webshims/shims/swf/JarisFLVPlayer.swf
+- public/js/webshims/shims/swfmini-embed.js
+- public/js/webshims/shims/swfmini.js
+- public/js/webshims/shims/track-ui.js
+- public/js/webshims/shims/track.js
+- public/js/webshims/shims/url.js
+- public/js/webshims/shims/usermedia-core.js
+- public/js/webshims/shims/usermedia-shim.js
 - public/sequence.min.js
 - sequenceserver.gemspec
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
-- tests/run
-- tests/test_sequencehelpers.rb
-- tests/test_sequenceserver_blast.rb
-- tests/test_ui.rb
-- tests/ui.specs.todo
+- views/400.erb
 - views/500.erb
 - views/_options.erb
+- views/result.erb
 - views/search.erb
 homepage: http://sequenceserver.com
 licenses:
@@ -185,9 +377,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.4.2

data/example.config.yml

@@ -1,39 +0,0 @@
-# Path to the blast executables.
-# 
-# Sequence Server scans the given directory for blast binaries. Ideally it
-# should point the `bin` of your BLAST+ installation. Not setting this
-# value, or setting it to `nil` will default to searching the system `PATH`.
-#
-# Uncomment the following line, and change to appropriate value to use.
-#
-# bin: ~/ncbi-blast-2.2.25+/bin/
-
-# Path to blast database.
-#
-# Sequence Server scans the given directory (including the sub-directories)
-# for blast database. You can not specify more than one top-level directory.
-# Not setting this value, will default to searching `database` directory
-# relative to the current working directory.
-#
-# Uncomment the following line, and change to appropriate value to use.
-#
-# database: ~/blast_databases/
-
-# Port to run Sequence Server on.
-#
-# The app will then be accessible at http://your-ip:port. Defaults to 4567.
-# http://localhost:port is also valid for local access.
-#
-# Uncomment the following line, and change to appropriate value to use.
-#
-# port: 4567
-
-# number of threads to be use when blasting
-#
-# This option is passed directly to BLAST+. Setting this option to more
-# than 1 may crash BLAST+ if it was not compiled with threading support.
-# Default is to use the safe value of 1.
-#
-# Uncomment the following line, and change to appropriate value to use.
-#
-# num_threads: 1