sequenceserver 2.0.0.rc7 → 2.0.0.rc8

data/.csslintrc

@@ -1,2 +0,0 @@
---exclude-exts=.min.css
---ignore=adjoining-classes,box-model,ids,order-alphabetical,unqualified-attributes

data/.dockerignore

@@ -1 +0,0 @@
-_site

data/.eslintignore

@@ -1 +0,0 @@
-**/*{.,-}min.js

data/.eslintrc.json

@@ -1,36 +0,0 @@
-{
-    "env": {
-        "browser": true,
-        "commonjs": true,
-        "es6": true
-    },
-    "extends": "eslint:recommended",
-    "parserOptions": {
-        "ecmaFeatures": {
-            "experimentalObjectRestSpread": true,
-            "jsx": true
-        },
-        "sourceType": "module"
-    },
-    "plugins": [
-        "react"
-    ],
-    "rules": {
-        "indent": [
-            "error",
-            4
-        ],
-        "linebreak-style": [
-            "error",
-            "unix"
-        ],
-        "quotes": [
-            "error",
-            "single"
-        ],
-        "semi": [
-            "error",
-            "always"
-        ]
-    }
-}

data/.gitignore

@@ -1,56 +0,0 @@
-# rcov generated
-coverage
-coverage.data
-
-# rdoc generated
-rdoc
-
-# yard generated
-doc
-.yardoc
-
-# bundler
-.bundle
-
-# jeweler generated
-pkg
-
-# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
-#
-# * Create a file at ~/.gitignore
-# * Include files you want ignored
-# * Run: git config --global core.excludesfile ~/.gitignore
-#
-# After doing this, these files will be ignored in all your git projects,
-# saving you from having to 'pollute' every project you touch with them
-#
-# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
-#
-# For MacOS:
-#
-#.DS_Store
-
-# For TextMate
-#*.tmproj
-#tmtags
-
-# For emacs:
-#*~
-#\#*
-#.\#*
-
-# For vim:
-#*.swp
-
-# For redcar:
-#.redcar
-
-# For rubinius:
-#*.rbc
-
-
-*.swp
-*.~*~
-.gems/*
-Gemfile.lock
-node_modules

data/.mailmap

@@ -1,5 +0,0 @@
-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

@@ -1,3 +0,0 @@
---color
---backtrace
---require spec_helper.rb

data/.rubocop.yml

@@ -1,61 +0,0 @@
-AllCops:
-  TargetRubyVersion: 2.3
-  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/ModuleLength:
-  Exclude:
-    # TODO:
-    #   Revisit later.
-    - 'lib/sequenceserver.rb'
-    - 'spec/blast_spec.rb'
-Metrics/ClassLength:
-  Max: 150
-Metrics/BlockNesting:
-  Exclude:
-    - 'bin/sequenceserver'
-Metrics/BlockLength:
-  Exclude:
-    - 'bin/sequenceserver'
-    - 'sequenceserver.gemspec'
-
-Style/UnlessElse:
-  # TODO:
-  #   Fix in bin/sequenceserver and re-enable.
-  Enabled: false
-Naming/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/AsciiComments:
-  # Nothing wrong with non-ascii chars, like © in comments.
-  Enabled: false
-Style/SignalException:
-  # Roughly, use fail to fail and raise to signal.
-  EnforcedStyle: semantic
-Style/FrozenStringLiteralComment:
-  # Immutability is good. Switching to immutable strings is like a paradigm
-  # shift and should be approached more carefully. Thus, disabling this cop
-  # for now.
-  Enabled: false

data/.travis.yml

@@ -1,74 +0,0 @@
-language: ruby
-
-rvm:
-  - 2.3
-  - 2.5
-
-branches:
-  only:
-    - 1.0.x  # stable
-    - master
-
-cache:
-  directories:
-    - opt
-  bundler: true
-
-before_install:
-  # We will download geckodriver, codeclimate test reporter, and NCBI BLAST+ to
-  # opt/. opt/ is cached to speed up subsequent runs. codeclimate test reporter
-  # and geckodriver contain a single executable and are thus placed in opt/bin,
-  # instead of in their own directory like NCBI BLAST+
-  - mkdir -p opt/bin && cd opt
-  # Download geckodriver and extract to bin
-  - wget -c "https://github.com/mozilla/geckodriver/releases/download/v0.24.0/geckodriver-v0.24.0-linux64.tar.gz" && tar xvf geckodriver-*.tar.gz -C bin
-  # Download codeclimate test reporter to bin and make it executable
-  - wget -c "https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64" -O bin/cc-test-reporter && chmod +x bin/cc-test-reporter
-  # Download and extract NCBI BLAST+ 2.10.0
-  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
-  # Conclude installation by adding opt/bin/ containing codeclimate test reporter
-  # and geckodriver, and opt/ncbi-blast-2.10.0+/bin containing BLAST+ binaries to
-  # PATH.
-  - export PATH="$PWD/bin:$PWD/ncbi-blast-2.10.0+/bin:$PATH"
-  # Reset working directory or subsequent steps may fail.
-  - cd ..
-  # Update bundler. Travis was using bundler 1.16.2 at the time of this writing
-  # and the builds were failing because Gemfile.lock requires bundler > 2.0
-  - gem install bundler -v 2.1.4
-
-env:
-  global:
-    - CC_TEST_REPORTER_ID=ec48bb03c72db6b43ce71fd488110b4707abfde4386c144d886d711378d8db64
-before_script:
-  # Create configuration file for SequenceServer. FIXME: this should not
-  # really be required for running test suite, but it is at the moment
-  - bundle exec bin/sequenceserver -s -d spec/database/sample
-  # Run codeclimate test reporter's before-build hook.
-  - if [ "${TRAVIS_BUILD_STAGE_NAME}" = "Test" ]; then
-      cc-test-reporter before-build;
-    fi
-script:
-  # Run main specs and import spec for BLAST 2.9.0+
-  - bundle exec rspec spec/*_spec.rb spec/blast_versions/blast_2.9.0/*
-after_script:
-  - if [ "${TRAVIS_BUILD_STAGE_NAME}" = "Test" ]; then
-      cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT;
-    fi
-
-jobs:
-  include:
-  # Each script listed below is automatically run by Travis in parallel, and only
-  # against Ruby 2.3 (because it is listed first in the rvm key), and after the
-  # main test stage. We use a glob pattern here instead of specifying just the
-  # directory name because capybara spec files in subfolders don't end with
-  # _spec.rb.
-  - stage: compatibility
-    script: bundle exec rspec spec/blast_versions/diamond_0.9.24/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.2.30/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.2.31/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.3.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.4.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.5.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.6.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.7.1/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.8.1/*

data/AppImage/recipe.yml

@@ -1,15 +0,0 @@
-app: sequenceserver
-
-ingredients:
-  dist: xenial
-  sources:
-    - deb http://us.archive.ubuntu.com/ubuntu/ xenial xenial-updates xenial-security main universe
-  packages:
-    - ruby
-    - ruby-dev
-    - build-essential
-script:
-  - usr/bin/gem install --pre --install-dir var/lib/gems/2.3.0 sequenceserver
-  - cp ${PWD}/../../../AppImage/sequenceserver.sh usr/bin/sequenceserver
-  - cp ${PWD}/../../../AppImage/sequenceserver.desktop .
-  - cp ${PWD}/../../../AppImage/sequenceserver.png .

data/AppImage/sequenceserver.desktop

@@ -1,8 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Type=Application
-Name=SequenceServer
-Icon=sequenceserver
-Exec=sequenceserver
-Terminal=true
-Categories=ConsoleOnly;Science;

data/AppImage/sequenceserver.sh

@@ -1,16 +0,0 @@
-# cd back to the directory where the AppImage was launched from. AppRun changes
-# the working directory so as to work with binaries that have /usr hard-coded;
-# we don't.
-cd $OWD
-
-# Set GEM_PATH to where we installed gems in the AppImage.
-export GEM_PATH=$APPDIR/var/lib/gems/2.3.0
-
-# Get path of sequenceserver executable inside AppImage. Path of bare commands
-# (here ruby) are resolved within AppImage's context. Use of Gem.bin_path lets
-# us avoid hardcoding version number. The file returned is bin/sequenceserver
-# and not the shim that rubygem creates.
-executable=$(ruby -e 'puts Gem.bin_path("sequenceserver", "sequenceserver")')
-
-# Run sequenceserver.
-ruby ${executable} "$@"

data/Dockerfile

@@ -1,25 +0,0 @@
-FROM debian:buster-slim
-
-LABEL Description="Intuitive local web frontend for the BLAST bioinformatics tool"
-LABEL MailingList="https://groups.google.com/forum/#!forum/sequenceserver"
-LABEL Website="http://www.sequenceserver.com"
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-        ruby ruby-dev build-essential curl gnupg git wget \
-        zlib1g-dev && rm -rf /var/lib/apt/lists/*
-
-VOLUME ["/db"]
-EXPOSE 4567
-
-COPY . /sequenceserver
-WORKDIR /sequenceserver
-# Install bundler, then use bundler to install SequenceServer's dependencies,
-# and then use SequenceServer to install BLAST. In the last step, -s is used
-# so that SequenceServer will exit after writing configuration file instead
-# of starting up, while -d is used to suppress questions about database dir.
-RUN gem install bundler && \
-        bundle install --without=development && \
-        yes '' | bundle exec bin/sequenceserver -s -d spec/database/sample
-RUN touch ~/.sequenceserver/asked_to_join
-
-CMD ["bundle", "exec", "bin/sequenceserver", "-d", "/db"]

data/LICENSE.txt

@@ -1,661 +0,0 @@
-                    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.
-
-                            Preamble
-
-  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 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.
-
-  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.
-
-  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.
-
-  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.
-
-  The precise terms and conditions for copying, distribution and
-modification follow.
-
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-  9. Acceptance Not Required for Having Copies.
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-(such as an express permission to practice a patent or covenant not to
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-and the Corresponding Source of the work is not available for anyone
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-then you must either (1) cause the Corresponding Source to be so
-available, or (2) arrange to deprive yourself of the benefit of the
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-consistent with the requirements of this License, to extend the patent
-license to downstream recipients.  "Knowingly relying" means you have
-actual knowledge that, but for the patent license, your conveying the
-covered work in a country, or your recipient's use of the covered work
-in a country, would infringe one or more identifiable patents in that
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-  If, pursuant to or in connection with a single transaction or
-arrangement, you convey, or propagate by procuring conveyance of, a
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-receiving the covered work authorizing them to use, propagate, modify
-or convey a specific copy of the covered work, then the patent license
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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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-in the business of distributing software, under which you make payment
-to the third party based on the extent of your activity of conveying
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-parties who would receive the covered work from you, a discriminatory
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-conveyed by you (or copies made from those copies), or (b) primarily
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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.
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-  Nothing in this License shall be construed as excluding or limiting
-any implied license or other defenses to infringement that may
-otherwise be available to you under applicable patent law.
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-  12. No Surrender of Others' Freedom.
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-  If conditions are imposed on you (whether by court order, agreement or
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-excuse you from the conditions of this License.  If you cannot convey a
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-to collect a royalty for further conveying from those to whom you convey
-the Program, the only way you could satisfy both those terms and this
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-  13. Remote Network Interaction; Use with the GNU General Public License.
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-  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
-supports such interaction) an opportunity to receive the Corresponding
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-from a network server at no charge, through some standard or customary
-means of facilitating copying of software.  This Corresponding Source
-shall include the Corresponding Source for any work covered by version 3
-of the GNU General Public License that is incorporated pursuant to the
-following paragraph.
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-  Notwithstanding any other provision of this License, you have
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-under version 3 of the GNU General Public License into a single
-combined work, and to convey the resulting work.  The terms of this
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-but the work with which it is combined will remain governed by version
-3 of the GNU General Public License.
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-  14. Revised Versions of this License.
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-  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.
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-  Each version is given a distinguishing version number.  If the
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-option of following the terms and conditions either of that numbered
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-Foundation.  If the Program does not specify a version number of the
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-by the Free Software Foundation.
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-  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
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
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-  Later license versions may give you additional or different
-permissions.  However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
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-  15. Disclaimer of Warranty.
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-  16. Limitation of Liability.
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-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
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-  17. Interpretation of Sections 15 and 16.
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-  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
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-
-                     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/>.