sequenceserver 1.0.0.pre.5 → 1.0.0

data/.mailmap

@@ -0,0 +1,5 @@
+Yannick Wurm <y.wurm@qmul.ac.uk> Yannick Wurm <yannick.wurm@unil.ch>
+Ben J Woodcroft <donttrustben@gmail.com> Ben Woodcroft <donttrustben@gmail.com>
+Ben J Woodcroft <donttrustben@gmail.com> Ben J Woodcroft <donttrustben@gmail.com>
+Ben J Woodcroft <donttrustben@gmail.com> Ben J Woodcroft <gmail.com after donttrustben>
+Ben J Woodcroft <donttrustben@gmail.com> Ben J. Woodcroft <donttrustben near gmail.com>

data/.rspec

@@ -0,0 +1,2 @@
+--color
+--backtrace

data/.rubocop.yml

@@ -0,0 +1,51 @@
+AllCops:
+  Exclude:
+    # Because these are vendor files.
+    - 'node_modules/**/*'
+
+Metrics/AbcSize:
+  Exclude:
+    # TODO
+    - 'lib/sequenceserver.rb'
+Metrics/MethodLength:
+  # Because 15 lines in a method is just about as good as 10 (default). And we
+  # have a couple that can't be helped.
+  Max: 15
+  Exclude:
+    # TODO:
+    - 'lib/sequenceserver.rb'
+Metrics/ClassLength:
+  Exclude:
+    # TODO:
+    #   Evaluate whether to make class smaller or to increase 'Max'.
+    - 'lib/sequenceserver/database.rb'
+Metrics/BlockNesting:
+  Exclude:
+    # TODO:
+    #   Fix in bin/sequenceserver and re-enable.
+    - 'bin/sequenceserver'
+
+Lint/Eval:
+  # Used only once. Is rather safe.
+  Enabled: false
+
+Style/UnlessElse:
+  # TODO:
+  #   Fix in bin/sequenceserver and re-enable.
+  Enabled: false
+Style/ClassAndModuleCamelCase:
+  Exclude:
+    # TODO:
+    #   Revisit later.
+    - 'lib/sequenceserver/exceptions.rb'
+Style/Lambda:
+  Exclude:
+    # Because we support 1.8.7.
+    - '**/*.rb'
+Style/EachWithObject:
+  Exclude:
+    # Because we support 1.8.7.
+    - '**/*.rb'
+Style/HashSyntax:
+    # Because we support 1.8.7.
+  EnforcedStyle: hash_rockets

data/.travis.yml

@@ -0,0 +1,18 @@
+language: ruby
+rvm:
+  - 1.9.3
+  - 2.0.0
+  - 2.1.5
+  - 2.2.0
+
+addons:
+  code_climate:
+    repo_token:
+      secure: "cT2wvWS2Uk2trYGwZ38Qo9XWCeL+OOXH0lVmLfNb1Xy/tWAXycDdZsc9CN8igjhD+/cKvvh529/qdDm2PJnb1Hux1bxHSTuMuE2xQWlfJqaOR/IX0z96MbP1eITKjhGv9vccmIPdV3Rh/OQLeHkyqyHvXio9NXiARMJUZDTpRuA="
+
+before_install:
+  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz" && tar xvf ncbi-blast-2.2.30+-x64-linux.tar.gz && export PATH="./ncbi-blast-2.2.30+/bin:$PATH"
+  - sudo apt-get install libqtwebkit-dev xvfb
+  - gem install bundler
+
+script: xvfb-run bundle exec rake

data/COPYRIGHT.txt

@@ -0,0 +1,13 @@
+SequenceServer is copyright Anurag Priyam, Ben J Woodcroft and Yannick Wurm,
+2015, and files herein are licensed under the Affero General Public License
+version 3, the text of which can be found in LICENSE.txt.
+
+Components of SequenceServer, including Sinatra, Ox, Slop, html5shiv,
+Underscore, jQuery, jQuery UI, Bootstrap and Webshim, are licensed under
+the MIT license. D3.js is licensed under BSD license. biojs-vis-sequence
+is licensed under Apache license. Thin and JSON are licensed under Ruby
+license. All unmodified files from these and other sources retain their
+original copyright and license notices, except D3.js whose license can be
+found in LICENSE/d3.txt. We modify biojs-vis-sequence. The modified file
+can be found in public/js/sequence.js. A copy of Apache license can be
+found in LICESNSE/Apache.txt.

data/Gruntfile.js

@@ -0,0 +1,133 @@
+module.exports = function (grunt) {
+    grunt.initConfig({
+        pkg: grunt.file.readJSON('package.json'),
+        prefix: 'public/dist/',
+        name: '<%= pkg.name.toLowerCase() %>',
+        //htmllint: {
+            //options: {
+            //},
+            //all: 'views/*'
+        //},
+        bootlint: {
+            options: {
+                stoponerror: false
+            },
+            main: {
+                src: 'views/search.erb'
+            },
+            partials: {
+                options: {
+                    relaxerror: [
+                        'E001', 'W001', 'W002', 'W003', 'W005',
+                        'E013', 'E014' // for result.erb only
+                    ]
+                },
+                src: [
+                    'views/_options.erb',
+                    'views/result.erb',
+                    'views/400.erb',
+                    'views/500.erb'
+                ]
+            }
+        },
+        csslint: {
+            files: 'public/css/custom.css'
+        },
+        jshint: {
+            options: {
+                force: true
+            },
+            files: [
+                'Gruntfile.js',
+                'public/js/sequenceserver.js',
+                'public/js/sequenceserver.blast.js',
+                'public/js/jquery.t.js',
+            ]
+        },
+        cssmin: {
+            options: {
+                keepSpecialComments: 0
+            },
+            main: {
+                files: {
+                    '<%= prefix %>/css/<%= name %>.min.css':
+                        [
+                            'public/css/bootstrap.min.css',
+                            'public/css/font-awesome.min.css',
+                            'public/css/custom.css'
+                        ]
+                }
+            }
+        },
+        uglify: {
+            options: {
+            },
+            main: {
+                files: {
+                    '<%= prefix %>/js/<%= name %>.min.js':
+                        [
+                            // Base.
+                            'public/js/underscore.min.js',
+                            'public/js/jquery.min.js',
+                            'public/js/jquery-ui.min.js',
+                            'public/js/bootstrap.min.js',
+                            'public/js/webshims/polyfiller.js',
+
+                            // d3 - for visualisation.
+                            'public/js/d3.v3.min.js',
+
+                            // Our stuff.
+                            'public/js/sequence.js',
+                            'public/js/sequenceserver.js',
+                            'public/js/jquery.t.js',
+                            'public/js/sequenceserver.blast.js',
+                        ]
+                }
+            }
+        },
+        copy: {
+            shims: {
+                expand: true,
+                cwd:    'public/js/webshims/shims/',
+                src:    '**',
+                dest:   '<%= prefix %>/js/shims/'
+            },
+            fonts: {
+                expand: true,
+                cwd:    'public/fonts/',
+                src:    '**',
+                dest:   '<%= prefix %>/fonts'
+            }
+        },
+        compress: {
+            options: {
+                mode: 'gzip'
+            },
+            js: {
+                files: {
+                    '<%= prefix %>/js/<%= name %>.min.js.gz':
+                        '<%= prefix %>/js/<%= name %>.min.js'
+                }
+            },
+            css: {
+                files: {
+                    '<%= prefix %>/css/<%= name %>.min.css.gz':
+                        '<%= prefix %>/css/<%= name %>.min.css'
+                }
+            }
+        }
+    });
+
+    //grunt.loadNpmTasks('grunt-html');
+    grunt.loadNpmTasks('grunt-bootlint');
+    grunt.loadNpmTasks('grunt-contrib-csslint');
+    grunt.loadNpmTasks('grunt-contrib-jshint');
+    grunt.loadNpmTasks('grunt-contrib-cssmin');
+    grunt.loadNpmTasks('grunt-contrib-uglify');
+    grunt.loadNpmTasks('grunt-contrib-copy');
+    grunt.loadNpmTasks('grunt-contrib-compress');
+
+    //grunt.registerTask('cop', ['htmllint', 'bootlint', 'csslint', 'jshint']);
+    grunt.registerTask('cop', ['bootlint', 'csslint', 'jshint']);
+    grunt.registerTask('build', ['cssmin', 'uglify', 'copy', 'compress']);
+};

data/LICENSE.txt

@@ -1,69 +1,661 @@
-SequenceServer (http://sequenceserver.com) 
-Copyright (c) 2010-2011  Yannick Wurm, Benjamin J. Woodcroft, Anurag Priyam. 
+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
 
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
 
-1.  Definitions 
+                            Preamble
 
-The software: the SequenceServer software and associated documentation. The
-term does not extend to unmodified open source software components used within
-SequenceServer which are governed by their own license agreements. However,
-modfications to such components shall be deemed a part of the SequenceServer
-software.
+  The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
 
-The authors: Yannick Wurm, Anurag Priyam, Benjamin J. Woodcroft. 
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.
 
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
 
-2. Fair usage
+  Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
 
-Within not-for-profit and educational organizations the software can 
-be freely used by individuals and on internal and public websites.
+  A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate.  Many developers of free software are heartened and
+encouraged by the resulting cooperation.  However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
 
-Installation of the software or use of the software by for-profit 
-organizations (including but not limited to companies, service providers 
-and consultancies) requires purchase of a usage license or other specific
-arrangements with the authors.
+  The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community.  It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server.  Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
 
+  An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals.  This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
 
-3. Modifications
+  The precise terms and conditions for copying, distribution and
+modification follow.
 
-Modifications can be made by not-for-profit and educational organizations. 
-However, citation requests and links to sequenceserver.com must remain
-visible and unaltered. 
+                       TERMS AND CONDITIONS
 
+  0. Definitions.
 
-4. Redistribution of the software
+  "This License" refers to version 3 of the GNU Affero General Public License.
 
-Redistribution without modification is permitted unless associated to 
-a financial transaction. In particular, the software may not be 
-distributed with nor installed via a commercial software package, nor 
-be made available by commercial service providers.  
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
 
-Redistribution with modification is permitted only if ALL of the 
-following conditions are respected:
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
 
-   a. no financial transaction is associated (see above). 
-   b. This license and copyright notices are included and remain
-      unchanged; citation requests and links to sequenceserver.com 
-      remain visible and unaltered. 
-   c. Modifications are made freely available on github.com (or an 
-      equivalent medium) and the authors are allowed to freely 
-      incorporate modifications into the software.
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
 
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
 
-5. Specific needs
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
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+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
 
-The authors reserve the right to make specific licensing, modification 
-and distribution  arrangements with interested parties. 
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
 
+  An interactive user interface displays "Appropriate Legal Notices"
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-6. Disclaimer
+  1. Source Code.
 
-THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
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+  However, if you cease all violation of this License, then your
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+  9. Acceptance Not Required for Having Copies.
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+  You are not required to accept this License in order to receive or
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+sale, or importing the Program or any portion of it.
+
+  11. Patents.
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+  A "contributor" is a copyright holder who authorizes use under this
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+
+  A contributor's "essential patent claims" are all patent claims
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+  If you convey a covered work, knowingly relying on a patent license,
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+consistent with the requirements of this License, to extend the patent
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+
+  If, pursuant to or in connection with a single transaction or
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+  A patent license is "discriminatory" if it does not include within
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+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
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+parties who would receive the covered work from you, a discriminatory
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+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
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+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
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+
+  13. Remote Network Interaction; Use with the GNU General Public License.
+
+  Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
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+following paragraph.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
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+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time.  Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU Affero General
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+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
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+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
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+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source.  For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code.  There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.