sequenceserver 1.1.0.beta2 → 1.1.0.beta3

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -6,7 +6,7 @@ rvm:
   - 2.5
 
 addons:
-  firefox: "58.0"
+  sauce_connect: true
 
 branches:
   only:
@@ -14,15 +14,26 @@ branches:
     - master
 
 install:
-  - 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="$PWD/geckodriver:$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 rspec
+before_script:
+  - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter && chmod +x ./cc-test-reporter
+  - ./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='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='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:
+  - ./cc-test-reporter after-build # --exit-code $TRAVIS_TEST_RESULT
 
 cache:
   directories:

data/README.md

@@ -1,4 +1,5 @@
 [![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
+[![Sauce test status](https://saucelabs.com/buildstatus/yeban)](https://saucelabs.com/u/yeban)
 [![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)
@@ -6,6 +7,8 @@
 
 [![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)
+
 # SequenceServer - BLAST searching made easy!
 
 SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user

data/lib/sequenceserver/api_errors.rb

@@ -0,0 +1,67 @@
+module SequenceServer
+
+  # API errors have an http status, title, message, and additional information
+  # like stacktrace or information from program output.
+  class APIError < StandardError
+  end
+
+  # Job not found (404).
+  class NotFound < APIError
+    def http_status
+      404
+    end
+
+    def title
+      'Job not found'
+    end
+
+    def message
+      'The requested job could not be found'
+    end
+  end
+
+  # Errors caused due to incorrect user input.
+  class InputError < APIError
+    def initialize(more_info)
+      @more_info = more_info
+      super
+    end
+
+    def http_status
+      400
+    end
+
+    def title
+      'Input error'
+    end
+
+    def message
+<<MSG
+Looks like there's a problem with one of the query sequences, selected
+databases, or advanced parameters.
+MSG
+    end
+
+    attr_reader :more_info
+  end
+
+  # Errors caused by everything other than invalid user input.
+  class SystemError < APIError
+    def http_status
+      500
+    end
+
+    def title
+      'Job failed'
+    end
+
+    def message
+<<MSG
+Sorry BLAST failed - please try again. If this message persists, there is a
+problem with the server. In this case, please report the bug on our
+<a href="https://github.com/wurmlab/sequenceserver/issues" target="_blank">
+issue tracker</a>.
+MSG
+    end
+  end
+end

data/lib/sequenceserver/blast/constants.rb

@@ -2,7 +2,7 @@
 module SequenceServer
   # Define constanst used by BLAST module.
   module BLAST
-    ERROR_LINE = /\(CArgException.*\)\s(.*)/
+    ERROR_LINE = /Error:\s(.*)/
 
     ALGORITHMS = %w(blastn blastp blastx tblastn tblastx)
 

data/lib/sequenceserver/blast/formatter.rb

@@ -24,7 +24,7 @@ module SequenceServer
       attr_reader :format, :mime, :specifiers
 
       def file
-        @file = File.join(File.dirname(archive_file), filename)
+        @file ||= File.join(File.dirname(archive_file), filename)
       end
 
       def filename
@@ -41,12 +41,14 @@ module SequenceServer
           " -outfmt '#{format} #{specifiers}'" \
           " -out '#{file}'"
         sys(command, path: config[:bin], dir: DOTDIR)
+      rescue CommandFailed => e
+        fail SystemError, e.stderr
       end
 
       def validate
         return true if archive_file && format &&
                        File.exist?(archive_file)
-        fail ArgumentError, <<MSG
+        fail InputError, <<MSG
 Incorrect request parameters. Please ensure that requested file name is
 correct and the file type is either xml or tsv.
 MSG

data/lib/sequenceserver/blast/job.rb

@@ -1,17 +1,10 @@
-require 'sequenceserver/pool'
 require 'sequenceserver/job'
 
-require_relative 'exceptions'
-require_relative 'constants'
-
 module SequenceServer
 
   # BLAST module.
   module BLAST
     # Extends SequenceServer::Job to describe a BLAST job.
-    #
-    # `BLAST::ArgumentError` and `BLAST::RuntimeError` signal errors
-    # encountered when attempting a BLAST search.
     class Job < Job
 
       def initialize(params)
@@ -25,60 +18,23 @@ module SequenceServer
         end
       end
 
-
       attr_reader :advanced_params
+
       # :nodoc:
-      # Attributes used by us.
-      #
-      # Should be considered private.
+      # Attributes used by us - should be considered private.
       attr_reader :method, :qfile, :databases, :options
 
-      # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
-      # rubocop:disable Metrics/MethodLength
-      def run
-        command = "#{method} -db '#{databases.map(&:name).join(' ')}'" \
-                  " -query '#{qfile}' #{options}"
-
-        sys(command, stdout: rfile, stderr: efile, path: config[:bin])
-        done!
-      rescue CommandFailed => e
-        # Capture error.
-        status = e.exitstatus
-        case status
-        when 1 # error in query sequence or options; see [1]
-          efile.open
-
-          # Most of the time BLAST+ generates a verbose error message with
-          # details we don't require.  So we parse out the relevant lines.
-          error = efile.each_line do |l|
-            break Regexp.last_match[1] if l.match(ERROR_LINE)
-          end
-
-          # But sometimes BLAST+ returns the exact/ relevant error message.
-          # Trying to parse such messages returns nil, and we use the error
-          # message from BLAST+ as it is.
-          error = efile.rewind && efile.read unless error.is_a? String
-
-          efile.close
-          fail ArgumentError, error
-        when 2, 3, 4, 255 # see [1]
-          efile.open
-          error = efile.read
-          efile.close
-          fail RuntimeError.new(status, error)
-        end
-
-        success!
-      end
-      # rubocop:enable Metrics/AbcSize, Metrics/CyclomaticComplexity
-      # rubocop:enable Metrics/MethodLength
-
-      def rfile
-        File.join(dir, 'rfile')
+      # Returns the command that will be executed. Job super class takes care
+      # of actual execution.
+      def command
+        @command ||= "#{method} -db '#{databases.map(&:name).join(' ')}'" \
+                     " -query '#{qfile}' #{options}"
       end
 
-      def efile
-        File.join(dir, 'efile')
+      # BLAST's exit status is not definitive of success or error, so we
+      # override success? to define custom criteria. :TODO:
+      def success?
+        super
       end
 
       private
@@ -114,38 +70,37 @@ module SequenceServer
 
       def validate_method(method)
         return true if ALGORITHMS.include? method
-        fail ArgumentError, 'BLAST algorithm should be one of:' \
+        fail InputError, 'BLAST algorithm should be one of:' \
                             " #{ALGORITHMS.join(', ')}."
       end
 
       def validate_sequences(sequences)
         return true if sequences.is_a?(String) && !sequences.empty?
-        fail ArgumentError, 'Sequences should be a non-empty string.'
+        fail InputError, 'Sequences should be a non-empty string.'
       end
 
       def validate_databases(database_ids)
         ids = Database.ids
         return true if database_ids.is_a?(Array) && !database_ids.empty? &&
                        (ids & database_ids).length == database_ids.length
-        fail ArgumentError, 'Database id should be one of:' \
-                            " #{ids.join("\n")}."
+        fail InputError, "Database id should be one of: #{ids.join("\n")}."
       end
 
       # Advanced options are specified by the user. Here they are checked for
       # interference with SequenceServer operations.
       #
-      # Raise ArgumentError if an error has occurred.
+      # Raise InputError if an error has occurred.
       def validate_options(options)
         return true if !options || (options.is_a?(String) &&
                                     options.strip.empty?)
 
         unless allowed_chars.match(options)
-          fail ArgumentError, 'Invalid characters detected in options.'
+          fail InputError, 'Invalid characters detected in options.'
         end
 
         if disallowed_options.match(options)
           failedopt = Regexp.last_match[0]
-          fail ArgumentError, "Option \"#{failedopt}\" is prohibited."
+          fail InputError, "Option \"#{failedopt}\" is prohibited."
         end
 
         true

data/lib/sequenceserver/blast/report.rb

@@ -43,14 +43,27 @@ module SequenceServer
 
       # Generate report.
       def generate
-        xml_ir = parse_xml File.read(Formatter.run(job.rfile, 'xml').file)
-        tsv_ir = parse_tsv File.read(Formatter.run(job.rfile, 'custom_tsv').file)
+        assert_job_completed_successfully
+        xml_ir = parse_xml File.read(Formatter.run(job.stdout, 'xml').file)
+        tsv_ir = parse_tsv File.read(Formatter.run(job.stdout, 'custom_tsv').file)
         extract_program_info xml_ir
         extract_params xml_ir
         extract_stats xml_ir
         extract_queries xml_ir, tsv_ir
       end
 
+      def assert_job_completed_successfully
+        return true if job.success?
+
+        stderr = File.readlines(job.stderr)
+        if job.exitstatus == 1 # error in query sequence or options; see [1]
+          error = stderr.grep(ERROR_LINE)
+          error = stderr if error.empty?
+          fail InputError, error.join
+        end
+        fail SystemError, stderr.join
+      end
+
       # Make program name and program name + version available via `program`
       # and `program_version` attributes.
       def extract_program_info(ir)

data/lib/sequenceserver/blast.rb

@@ -1,2 +1,3 @@
 require_relative 'blast/job'
 require_relative 'blast/report'
+require_relative 'blast/constants'

data/lib/sequenceserver/exceptions.rb

@@ -148,13 +148,12 @@ MSG
   # Raised if the 'sys' method could not successfully execute a shell command.
   class CommandFailed < StandardError
 
-    def initialize(stdout, stderr, exitstatus)
+    def initialize(exitstatus, stdout: nil, stderr: nil)
+      @exitstatus = exitstatus
       @stdout = stdout
       @stderr = stderr
-      @exitstatus = exitstatus
     end
 
     attr_reader :stdout, :stderr, :exitstatus
-
   end
 end

data/lib/sequenceserver/job.rb

@@ -5,44 +5,46 @@ require 'digest/md5'
 require 'forwardable'
 require 'securerandom'
 
+require 'sequenceserver/pool'
+require 'sequenceserver/api_errors'
+
 module SequenceServer
-  # Job super class.
+  # Abstract job super class.
+  #
+  # Provides a simple framework to store job data, execute shell commands
+  # asynchronously and capture stdout, stderr and exit status. Subclasses
+  # must provide a concrete implementation for `command` and may override
+  # any other methods as required.
   #
-  # Provides access to global `config` and `logger` object as instance methods.
-  # Sub-classes must at least define `run` instance method.
+  # Global `config` and `logger` object are available as instance methods.
+  #
+  # Singleton methods provide the facility to create and queue a job,
+  # fetch a job or all jobs, and delete a job.
   class Job
-    UUID_PATTERN = /[a-f0-9]{8}-[a-f0-9]{4}-4[a-f0-9]{3}-[89aAbB][a-f0-9]{3}-[a-f0-9]{12}/
-
     class << self
       # Creates and queues a job. Returns created job object.
-      #
-      # TODO: Implement dynamic dispatch.
       def create(params)
-        queue BLAST::Job.new(params)
+        job = BLAST::Job.new(params)# TODO: Dynamic dispatch.
+        SequenceServer.pool.queue { job.run }
+        job
       end
 
-      # Fetches job object for the given id.
-      #
-      # TODO: What if the given job id does not exist?
+      # Fetches job with the given id.
       def fetch(id)
-        YAML.load_file(File.join(DOTDIR, id, 'job.yaml'))
-      end
-
-      def all
-        jobdirs = Dir["#{DOTDIR}/*"].select{ |f| f =~ UUID_PATTERN }
-        jobdirs.map{ |fname| fetch File.basename(fname) }
+        job_file = File.join(DOTDIR, id, 'job.yaml')
+        fail NotFound unless File.exist?(job_file)
+        YAML.load_file(job_file)
       end
 
+      # Deletes job with the given id.
       def delete(id)
         FileUtils.rm_r File.join(DOTDIR, id)
       end
 
-      private
-
-      # Queues given job on the thread pool. Returns job.
-      def queue(job)
-        SequenceServer.pool.queue { job.run }
-        job
+      # Returns an Array of all jobs.
+      def all
+        Dir["#{DOTDIR}/**/job.yaml"].
+          map { |f| fetch File.basename File.dirname f }
       end
     end
 
@@ -66,32 +68,49 @@ module SequenceServer
       raise e
     end
 
-    attr_reader :id, :completed_at
+    attr_reader :id, :completed_at, :exitstatus
 
-    # How to execute the job.
+    # Shell out and execute the job.
     #
-    # Subclasses should provide their own implementation.  The method should
-    # call `done!` and `success!`, as appropriate, to indicate if the job is
-    # done and whether it was successful.
+    # NOTE: This method is called asynchronously by thread pool.
     def run
-      raise "To be implemented."
+      sys(command, path: config[:bin], stdout: stdout, stderr: stderr)
+      done!
+    rescue CommandFailed => e
+      done! e.exitstatus
     end
 
-    # Is the job done?
-    def done?
-      !!@done
+    # Returns shell command that will be executed. Subclass needs to provide a
+    # concrete implementation.
+    def command
+      raise "Not implemented."
     end
 
-    # Was the job success?
+    # Where will the stdout be written to during execution and read from later.
+    def stdout
+      File.join(dir, 'stdout')
+    end
+
+    # Where will the stderr be written to during execution and read from later.
+    def stderr
+      File.join(dir, 'stderr')
+    end
+
+    # Was the job successful?
     def success?
-      !!@success
+      exitstatus == 0
+    end
+
+    # Is the job done? Yes if exitstatus of the job is available. No otherwise.
+    def done?
+      !!@exitstatus
     end
 
     private
 
-    # Save job state.
+    # Saves job object to a YAML file in job directory.
     def save
-      File.write(File.join(dir, 'job.yaml'), to_yaml)
+      File.write(yfile, to_yaml)
     end
 
     # Save arbitrary blob of data for this job to a file. Returns absolute path
@@ -108,16 +127,20 @@ module SequenceServer
       filename
     end
 
-    # Marks the job as done.
-    def done!
-      @completed_at = Time.now
-      @done = true
-      save
+    # Retrieve file from job dir with the given name. Raises RuntimeError if
+    # the file can't be found.
+    #
+    # NOTE: Not used.
+    def fetch(key)
+      filename = File.join(dir, key)
+      raise if !File.exist? filename
+      filename
     end
 
-    # Marks the job as success.
-    def success!
-      @success = true
+    # Marks the job as done and save its exitstatus.
+    def done!(status = 0)
+      @completed_at = Time.now
+      @exitstatus = status
       save
     end
 
@@ -125,5 +148,10 @@ module SequenceServer
     def dir
       File.join(DOTDIR, id)
     end
+
+    # Where to write serialised job object.
+    def yfile
+      File.join(dir, 'job.yaml')
+    end
   end
 end

data/lib/sequenceserver/routes.rb

@@ -12,16 +12,11 @@ module SequenceServer
       disable :method_override
 
       # Ensure exceptions never leak out of the app. Exceptions raised within
-      # the app must be handled by the app. We do this by attaching error
-      # blocks to exceptions we know how to handle and attaching to Exception
-      # as fallback.
+      # the app must be handled by the app.
       disable :show_exceptions, :raise_errors
 
       # Make it a policy to dump to 'rack.errors' any exception raised by the
-      # app so that error handlers don't have to do it themselves. But for it
-      # to always work, Exceptions defined by us should not respond to `code`
-      # or `http_status` methods. Error blocks must explicitly set http
-      # status, if needed, by calling `status` method.
+      # app.
       enable :dump_errors
 
       # We don't want Sinatra do setup any loggers for us. We will use our own.
@@ -89,8 +84,7 @@ module SequenceServer
     get '/:jid.json' do |jid|
       job = Job.fetch(jid)
       halt 202 unless job.done?
-      rep = Report.generate job
-      rep.to_json
+      Report.generate(job).to_json
     end
 
     # Returns base HTML. Rest happens client-side: polling for and rendering
@@ -132,24 +126,34 @@ module SequenceServer
       send_file out.file, :filename => out.filename, :type => out.mime
     end
 
-    # This error block will only ever be hit if the user gives us a funny
-    # sequence or incorrect advanced parameter. Well, we could hit this block
-    # if someone is playing around with our HTTP API too.
-    error BLAST::ArgumentError do
-      status 400
+    # Catches any exception raised within the app and returns error message and
+    # the backtrace as response body. If the error class defines `http_status`
+    # instance method, its return value will be used to set HTTP status. HTTP
+    # status is set to 500 otherwise.
+    error 400..500 do
       error = env['sinatra.error']
-      erb :'400', :layout => nil, :locals => { :error => error }
-    end
 
-    # 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 SequenceServer
-    # or something really weird going on. If we hit this error block we show
-    # the stacktrace to the user requesting them to post the same to our Google
-    # Group.
-    error Exception, BLAST::RuntimeError do
-      status 500
-      error = env['sinatra.error']
-      erb :'500', :layout => nil, :locals => { :error => error }
+      # All errors will have a message.
+      error_data = {message: error.message}
+
+      # If error object has a title method, use that, or use error class for
+      # title.
+      if error.respond_to? :title
+        error_data[:title] = error.title
+      else
+        error_data[:title] = error.class.to_s
+      end
+
+      # If error object has a more_info method, use that. If the error does
+      # not have more_info and the error is not APIError, use backtrace as
+      # more_info.
+      if error.respond_to? :more_info
+        error_data[:more_info] = error.more_info
+      else
+        error_data[:more_info] = error.backtrace.join("\n")
+      end
+
+      error_data.to_json
     end
   end
 end

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.1.0.beta2'
+  VERSION = '1.1.0.beta3'
 end