sequenceserver 1.1.0.beta12 → 2.0.0.beta1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rspec

@@ -1,2 +1,3 @@
 --color
 --backtrace
+--require spec_helper.rb

data/.travis.yml

@@ -24,12 +24,12 @@ before_script:
   - ./cc-test-reporter before-build
 script:
   - bundle exec rspec --exclude-pattern 'capybara*' # unit tests
-  - platform='macOS 10.13' browserName=safari browserVersion=11 bundle exec rspec spec/capybara_spec.rb
-  - platform='macOS 10.13' browserName=chrome browserVersion=65 bundle exec rspec spec/capybara_spec.rb
-  - platform='macOS 10.13' browserName=firefox browserVersion=59 bundle exec rspec spec/capybara_spec.rb
+  - platform='macOS 10.14' browserName=safari browserVersion=12 bundle exec rspec spec/capybara_spec.rb
+  - platform='macOS 10.14' browserName=chrome browserVersion=71 bundle exec rspec spec/capybara_spec.rb
+  - platform='macOS 10.14' browserName=firefox browserVersion=64 bundle exec rspec spec/capybara_spec.rb
   - platform='Windows 10' browserName=microsoftedge browserVersion='16.16299' bundle exec rspec spec/capybara_spec.rb
-  - platform='Windows 10' browserName=chrome browserVersion=65 bundle exec rspec spec/capybara_spec.rb
-  - platform='Windows 10' browserName=firefox browserVersion=59 bundle exec rspec spec/capybara_spec.rb
+  - platform='Windows 10' browserName=chrome browserVersion=71 bundle exec rspec spec/capybara_spec.rb
+  - platform='Windows 10' browserName=firefox browserVersion=64 bundle exec rspec spec/capybara_spec.rb
   - platform='Linux' browserName=chrome browserVersion=48 bundle exec rspec spec/capybara_spec.rb
   - platform='Linux' browserName=firefox browserVersion=45 bundle exec rspec spec/capybara_spec.rb
 after_script:

data/README.md

@@ -1,79 +1,122 @@
-[![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
-[![code climate](https://codeclimate.com/github/wurmlab/sequenceserver/badges/gpa.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)
-[![coverage](https://codeclimate.com/github/wurmlab/sequenceserver/badges/coverage.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)
-[![gem version](https://badge.fury.io/rb/sequenceserver.svg)](http://rubygems.org/gems/sequenceserver)
+[![gem version](https://img.shields.io/badge/version-1.0.x%20(old%20stable)-green.svg)](http://rubygems.org/gems/sequenceserver)
+[![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png?branch=1.0.x)](https://travis-ci.org/wurmlab/sequenceserver)
 [![total downloads](http://ruby-gem-downloads-badge.herokuapp.com/sequenceserver?type=total&color=brightgreen)](http://rubygems.org/gems/sequenceserver)
-
 [![gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/wurmlab/sequenceserver)
 
-[![browser matrix](https://saucelabs.com/browser-matrix/yeban.svg)](https://saucelabs.com/u/yeban)
+**Beta version:** 
+[![new gem version](https://img.shields.io/badge/version-1.1.0%20(new%20beta)-yellowgreen.svg)](http://rubygems.org/gems/sequenceserver) **GitHub Master:** [![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
+
+
+
+
+<!--[![code climate](https://codeclimate.com/github/wurmlab/sequenceserver/badges/gpa.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)-->
+<!--[![coverage](https://codeclimate.com/github/wurmlab/sequenceserver/badges/coverage.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)-->
+<!--[![browser matrix](https://saucelabs.com/browser-matrix/yeban.svg)](https://saucelabs.com/u/yeban)-->
 
 # SequenceServer - BLAST searching made easy!
 
-SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use. If you use SequenceServer, please cite our preprint:
+SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use.
 
-> [Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F, Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015. Sequenceserver: A modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142](http://www.biorxiv.org/content/early/2015/11/27/033142).
+## Version 1.0.11
 
-## Install and configure
+- Stable release
+- Release date: June 2017
+- Works with BLAST 2.2.30
 
-To install the old, stable version - 1.0.11 - please see
+For installation instructions and how to use SequenceServer please see
 http://sequenceserver.com.
 
+If you want to install and use SequenceServer from source, we recommend the
+use of 'bundler' Ruby gem to install dependencies and to run SequenceServer:
+
+    # Install bundler gem
+    gem install bundler
+
+    # Use bundler to install dependencies
+    cd sequenceserver
+    bundle install --without=development
+
+    # Use bundler command to run SequenceServer
+    bundle exec bin/sequenceserver
+
+If you use SequenceServer, please cite our preprint:
+
+> [Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F, Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015. Sequenceserver: A modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142](http://www.biorxiv.org/content/early/2015/11/27/033142).
+
+## Version 1.1.0-beta12
+
+This is a beta release of SequenceServer 2.0
+
+Here, we have changed the underlying architecture to persist jobs so that
+the results can be bookmarked or shared, and to support integration with
+grid engines such as qsub. Furthermore, the HTML report is now generated
+in the browser by fetching BLAST results in JSON format from the server.
+This facilitates the use of existing JavaScript libraries to visualise
+BLAST results.
+
+The new beta releases are announced on [Google Group](https://groups.google.com/forum/#!forum/sequenceserver) and on the [GitHub release page](https://github.com/wurmlab/sequenceserver/releases).
+
+### Install and configure
+
 To get the latest 1.1.0-beta release, run:
 
     gem install --pre sequenceserver
 
-Version 1.1.0-beta releases are announced on [Google Group](https://groups.google.com/forum/#!forum/sequenceserver). Summary of changes can also be viewed on our [GitHub release
-page](https://github.com/wurmlab/sequenceserver/releases).
+If you are new to the above command, please consult the 'Install or update'
+section on our website http://sequenceserver.com.
 
-## Develop and contribute
+If you want to install and use the beta versions from source, the process is
+the same as for the old stable release (instructions above).
 
-You will need [Ruby](https://www.ruby-lang.org/en/) and [RubyGems](https://rubygems.org/), [Node and npm](https://nodejs.org/), and [CodeClimate](https://codeclimate.com/).
+### Develop and contribute
 
-### Setup
-Get source code and install dependencies.
+In addition to [Ruby](https://www.ruby-lang.org/en/) and [RubyGems](https://rubygems.org/), you will need [Node and npm](https://nodejs.org/) if you want to build JavaScript assets, and [CodeClimate](https://codeclimate.com/) to run static code analysis.
 
-    git clone https://github.com/wurmlab/sequenceserver
-    gem install bundler
-    cd sequenceserver
-    npm install
-    bundle
+If you want to submit a pull-request, you don't need to build JavaScript assets
+(we will do it) or to have run CodeClimate.
 
-If you just want to install and use SequenceServer from source you can skip
-`npm install` step, and skip installing gems used for testing:
+To develop and contribute, you will need to run SequenceServer from source (see
+previous section).
 
-    git clone https://github.com/wurmlab/sequenceserver
-    gem install bundler
-    cd sequenceserver
-    bundle install --without=development
-
-### Run, test, build
+#### Workflow commands
 
 Launch SequenceServer in development mode. In development mode SequenceServer
 logs verbosely and uses raw front-end files.
-```
-bundle exec bin/sequenceserver -D
-```
+
+    bundle exec bin/sequenceserver -D
 
 Run tests:
-```
-bundle exec rspec
-```
+
+    bundle exec rspec
 
 Run code style checkers (rubocop, csslint, eslint) -
-```
-codeclimate analyze
-```
 
-Build minifies JS and CSS bundles:
+    codeclimate analyze
+
+To install JS dependencies to be build JS and CSS bundles:
+
+    npm install
+
+Build minified JS and CSS bundles:
+
+    npm run-script build
+
+## Docker builds
+
+Both the old stable and new beta versions of SequenceServer are available as
+Docker images.
+
 ```
-npm run-script build
+# With database fasta files inside a folder named db
+docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver
 ```
 
-## Using Docker
-```bash
+This will use the new beta release of SequenceServer. To use the old stable
+release, add the version tag to the command:
+
+```
 # With database fasta files inside a folder named db
-docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver
+docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver:1.0.11
 ```
 
 ## Contact

data/bin/sequenceserver

@@ -14,8 +14,8 @@ def download_from_url(url)
   archive = File.join('/tmp', File.basename(url))
   # -ip4 is required  to avoid this curl bug http://sourceforge.net/p/curl/bugs/1424/?limit=25
   # see also https://github.com/yannickwurm/sequenceserver/issues/139
-  cmd = "curl -ip4 -C - #{url} -o #{archive} && " \
-        'mkdir -p ~/.sequenceserver && '          \
+  cmd = "curl --ipv4 -C - #{url} -o #{archive} && " \
+        'mkdir -p ~/.sequenceserver && ' \
         "tar xvf #{archive} -C ~/.sequenceserver"
   system(cmd)
 end
@@ -117,6 +117,10 @@ begin
     on 'i', 'interactive',
        'Run SequenceServer in interactive mode'
 
+    on 'x', 'import=',
+       'Import the xml file',
+       argument: true
+
     # on 'doctor',
        # 'Run SequenceServer doctor'
 
@@ -162,27 +166,6 @@ begin
       # working SequenceServer installation. We expect to land following
       # error scenarios either when creating a new SequenceServer (first
       # time or later), or updating config values using -s CLI option.
-      rescue SequenceServer::CONFIG_FILE_ERROR,
-             SequenceServer::BLAST_DATABASE_ERROR => e
-
-        puts e
-        exit!
-      rescue SequenceServer::ENOENT => e
-        puts e
-
-        puts 'Please consult sequenceserver --help for instructions on how to set the correct values.'
-        exit!
-      rescue SequenceServer::NUM_THREADS_INCORRECT => e
-        puts e
-
-        unless num_threads?
-          puts 'You can set the correct value by running:'
-          puts
-          puts '  sequenceserver -s -n <value>'
-          puts
-        end
-
-        exit!
       rescue SequenceServer::BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE,
              SequenceServer::BLAST_NOT_COMPATIBLE => e
 
@@ -198,19 +181,17 @@ begin
         # BLAST+ for her.
         puts
         puts <<~MSG
-          SequenceServer can use NCBI BLAST+ that you may have on your system already, or
-          download the correct package for itself. A recent system update may have broken
-          your NCBI BLAST+ installation.
-
-          Please enter the path to NCBI BLAST+ or press Enter to download.
+          If you have downloaded NCBI BLAST+ already, please enter the path
+          below. Otherwise just press Enter and SequenceServer will download
+          a copy of NCBI BLAST+ for itself.
 
-          Press Ctrl+C to quit.
+          Press Ctrl+C to abort setup.
         MSG
         puts
         response = Readline.readline('>> ').to_s.strip
         if response.empty?
           puts
-          puts 'Installing NCBI BLAST+.'
+          puts 'Downloading NCBI BLAST+.'
           puts "RUBY_PLATFORM #{RUBY_PLATFORM}"
           puts 'Archive will be extracted in ~/.sequenceserver directory.'
           puts
@@ -252,7 +233,7 @@ begin
           unless File.basename(response) == 'bin'
             response = File.join(response, 'bin')
           end
-          fetch_option(:bin).value = File.join(response)
+          fetch_option(:bin).value = response
           puts
         end
         redo
@@ -312,6 +293,14 @@ begin
             exit! unless set?
           end
         end
+      rescue SequenceServer::ENOENT,
+        SequenceServer::CONFIG_FILE_ERROR,
+        SequenceServer::BLAST_DATABASE_ERROR,
+        SequenceServer::NUM_THREADS_INCORRECT => e
+        # Known errors with clear error message are handled here.
+
+        puts e
+        exit!
       rescue => e
         # This will catch any unhandled error and some very special errors.
         # Ideally we will never hit this block. If we do, there's a bug in
@@ -328,7 +317,7 @@ begin
           Error:
             #{e.backtrace.unshift(e.message).join("\n")}
         MSG
-        exit
+        exit!
       end
 
       if doctor?
@@ -375,6 +364,14 @@ begin
         exit
       end
 
+      if import?
+        xml_file = fetch_option(:import).value
+        params = {:xml => xml_file}
+        job = SequenceServer::BLAST::Job.new(params)
+        puts job.id
+        exit
+      end
+
       if set?
         SequenceServer.config.write_config_file
         exit

data/lib/sequenceserver.rb

@@ -1,22 +1,11 @@
 require 'English'
-require 'tempfile'
-
-require 'sequenceserver/version'
-require 'sequenceserver/exceptions'
-require 'sequenceserver/config'
-require 'sequenceserver/logger'
-require 'sequenceserver/server'
-require 'sequenceserver/sequence'
-require 'sequenceserver/database'
-require 'sequenceserver/blast'
-require 'sequenceserver/routes'
-require 'sequenceserver/job_remover'
-require 'sequenceserver/doctor'
+require 'socket'
+require 'resolv'
 
 # Top level module / namespace.
 module SequenceServer
   # Use a fixed minimum version of BLAST+
-  BLAST_VERSION = '2.6.0+'.freeze
+  BLAST_VERSION = '2.9.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze
@@ -24,133 +13,98 @@ module SequenceServer
   # Constant for denoting the path ~/.sequenceserver
   DOTDIR = File.expand_path('~/.sequenceserver').freeze
 
+  # Load nested class, modules, constants, and files that extend SequenceServer
+  # module (e.g. sys).
+  require 'sequenceserver/version'
+  require 'sequenceserver/logger'
+  require 'sequenceserver/config'
+  require 'sequenceserver/server'
+  require 'sequenceserver/routes'
+  require 'sequenceserver/job_remover'
+  require 'sequenceserver/exceptions'
+  require 'sequenceserver/sys'
+
+  # The singleton methods defined below constitute the "runtime" environment of
+  # SequenceServer.
   class << self
+    # Returns ENV['RACK_ENV']. This environment variable determines if we are
+    # in development on in production mode (default).
     def environment
       ENV['RACK_ENV']
     end
 
-    def verbose?
-      @verbose ||= (environment == 'development')
-    end
-
-    def root
-      File.dirname(File.dirname(__FILE__))
+    # Returns true if RACK_ENV is set to 'development'. Raw JS and CSS files
+    # are served in development mode and the logger is made more verbose.
+    def development?
+      environment == 'development'
     end
+    alias verbose? development?
 
+    # Logger object used in the initialisation routine and throughout the
+    # application.
     def logger
-      @logger ||= Logger.new(STDERR, verbose?)
-    end
-
-    def pool
-      @pool ||= Pool.new(config[:num_threads])
+      @logger ||= case environment
+                  when 'development'
+                    Logger.new(STDERR, Logger::DEBUG)
+                  when 'test'
+                    Logger.new(STDERR, Logger::WARN)
+                  else
+                    Logger.new(STDERR, Logger::INFO)
+                  end
     end
 
+    # SequenceServer initialisation routine.
     def init(config = {})
       # Use default config file if caller didn't specify one.
       config[:config_file] ||= DEFAULT_CONFIG_FILE
+
+      # Initialise global configuration object from the above config hash.
       @config = Config.new(config)
 
-      Thread.abort_on_exception = true if ENV['RACK_ENV'] == 'development'
+      # When in development mode, cause SequenceServer to terminate if any
+      # thread spawned by the main process raises an unhandled exception. In
+      # production mode the expectation is to log at appropriate severity level
+      # and continue operating.
+      Thread.abort_on_exception = true if development?
 
+      # Now locate binaries, scan databases directory, require any plugin files.
       init_binaries
       init_database
       load_extension
+
+      # The above methods validate bin dir, database dir, and path to plugin
+      # files. Port and host settings don't need to be validated: if running
+      # in self-hosted mode, WEBrick will handle incorrect values and if
+      # running via Apache+Passenger host and port settings are not used.
+      # Let's validate remaining configuration keys next.
+
+      # Validate number of threads to use with BLAST.
       check_num_threads
-      @job_remover = JobRemover.new(@config[:job_lifetime])
 
-      self
+      # Doesn't make sense to activate JobRemover when testing. It anyway
+      # keeps stumbling on the mock test jobs that miss a few keys.
+      unless environment == 'test'
+        @job_remover = JobRemover.new(@config[:job_lifetime])
+      end
 
-      # We don't validate port and host settings. If SequenceServer is run
-      # self-hosted, bind will fail on incorrect values. If SequenceServer
-      # is run via Apache+Passenger, we don't need to worry.
+      # 'self' is the most meaningful object that can be returned by this
+      # method.
+      self
     end
 
+    # Holds SequenceServer configuration object for this process. This is
+    # available only after calling SequenceServer.init.
     attr_reader :config
 
-    # 'sys' executes a shell command.
-    #
-    # 'sys' can write the stdout and/or stderr from a shell command to files, or
-    #  return these values.
-    #
-    # 'sys' can get from a failed shell command stdout, stderr, and exit status.
-    #
-    # Supply 'sys' with the shell command and optionally:
-    # dir: A directory to change to for the duration of the execution of
-    # the shell command.
-    # path: A directory to change the PATH environment variable to for the
-    # duration of the execution of the shell command.
-    # stdout: A path to a file to store stdout.
-    # stderr: A path to a file to store stderr.
-    #
-    # Usage:
-    #
-    # sys(command, dir: '/path/to/directory', path: '/path/to/directory',
-    #     stdout: '/path/to/stdout_file', stderr: '/path/to/stderr_file')
+    # Rack-interface.
     #
-    # rubocop:disable Metrics/CyclomaticComplexity
-    def sys(command, options = {})
-      # Available output channels
-      channels = %i[stdout stderr]
-
-      # Make temporary files to store output from stdout and stderr.
-      temp_files = {
-        stdout: Tempfile.new('sequenceserver-sys'),
-        stderr: Tempfile.new('sequenceserver-sys')
-      }
-
-      # Log the command we are going to run - use -D option to view.
-      logger.debug("Executing: #{command}")
-
-      # 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.
-        ENV['PATH'] = options[:path] if options[:path]
-
-        # Change to the specified directory.
-        Dir.chdir(options[:dir]) if options[:dir] && Dir.exist?(options[:dir])
-
-        # Execute the shell command, redirect stdout and stderr to the
-        # temporary files.
-        exec("#{command} 1>#{temp_files[:stdout].path}" \
-             " 2>#{temp_files[:stderr].path}")
-      end
-
-      # Wait for the termination of the child process.
-      _, status = Process.wait2(child_pid)
-
-      # If a full path was given for stdout and stderr files, move the
-      # temporary files to this path. If the path given does not exist,
-      # create it.
-      channels.each do |channel|
-        filename = options[channel]
-        break unless filename
-
-        # If the given path has a directory component, ensure it exists.
-        file_dir = File.dirname(filename)
-        FileUtils.mkdir_p(file_dir) unless File.directory?(file_dir)
-
-        # Now move the temporary file to the given path.
-        # TODO: don't we need to explicitly close the temp file here?
-        FileUtils.mv(temp_files.delete(channel), filename)
-      end
-
-      # Read the remaining temp files into memory. For large outputs,
-      # the caller should supply a file path to prevent loading the
-      # output in memory.
-      temp_files.each do |channel, tempfile|
-        temp_files[channel] = tempfile.read
-      end
-
-      # Finally, return contents of the remaining temp files if the
-      # command completed successfully or raise CommandFailed error.
-      return temp_files.values if status.success?
-      raise CommandFailed.new(status.exitstatus, **temp_files)
+    # Add our logger to Rack env and let Routes do the rest.
+    def call(env)
+      env['rack.logger'] = logger
+      Routes.call(env)
     end
-    # rubocop:enable Metrics/CyclomaticComplexity
 
-    # Run SequenceServer as a self-hosted server using Thin webserver.
+    # Run SequenceServer using WEBrick.
     def run
       check_host
       Server.run(self)
@@ -167,13 +121,19 @@ module SequenceServer
       puts '   Instructions available on http://sequenceserver.com.'
     end
 
+    # This method is called after WEBrick has bound to the host and port and is
+    # ready to accept connections.
     def on_start
       puts '** SequenceServer is ready.'
       puts "   Go to #{server_url} in your browser and start BLASTing!"
+      puts '   To share your setup, please try one of the following: '
+      puts "     -  http://#{ip_address}:#{config[:port]}"
+      puts "     -  http://#{hostname}:#{config[:port]}" if hostname
       puts '   Press CTRL+C to quit.'
       open_in_browser(server_url)
     end
 
+    # This method is called when WEBrick is terminated.
     def on_stop
       puts
       puts '** Thank you for using SequenceServer :).'
@@ -184,16 +144,8 @@ module SequenceServer
       puts '       custom BLAST databases. biorxiv doi: 10.1101/033142.'
     end
 
-    # Rack-interface.
-    #
-    # Inject our logger in the env and dispatch request to our
-    # controller.
-    def call(env)
-      env['rack.logger'] = logger
-      Routes.call(env)
-    end
-
-    # Run SequenceServer interactively.
+    # This method is invoked by the -i switch to start an IRB shell with
+    # SequenceServer loaded.
     def irb
       ARGV.clear
       require 'irb'
@@ -229,7 +181,7 @@ module SequenceServer
         fail ENOENT.new('database dir', config[:database_dir])
       end
 
-      logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}")
+      logger.debug("Will look for BLAST+ databases in: #{config[:database_dir]}")
       Database.scan_databases_dir
       Database.each do |database|
         logger.debug("Found #{database.type} database '#{database.title}'" \
@@ -287,6 +239,17 @@ module SequenceServer
       "http://#{host}:#{config[:port]}"
     end
 
+    # Returns a local ip adress
+    def ip_address
+      Socket.ip_address_list.find { |ai| ai.ipv4? && !ai.ipv4_loopback? }.ip_address
+    end
+
+    # Returns machine's hostname based on the local ip;
+    # If hostname cannot be determined then print nothing
+    def hostname
+      Resolv.getname(ip_address) rescue nil
+    end
+
     # Uses `open` on Mac or `xdg-open` on Linux to opens the search form in
     # user's default browser. This function is called when SequenceServer
     # is launched from the terminal. Errors, if any, are silenced.