genevalidatorapp 1.5.4 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 955fcd74d359c54ce421064d7aced2408857e7dc
-  data.tar.gz: 1c35fb396c2c5a0a059d265944c6e9299e8af259
+SHA256:
+  metadata.gz: 395f62d66b4d5a0afa5d2504f24f8617bd681317ce6a814452b571bd5c6027f4
+  data.tar.gz: afbaf5e9b493f37f6c9ef0678e9e3df88b8faa4a40c45ae255f95eac24c81975
 SHA512:
-  metadata.gz: 0d188f08c4144fa3351c78d2c1e3cde7602dab41fed60c50a60cb371dce1a340852498f738b223aaeca6d9b8d47a99ba1af61f2c1d1b3a9097658df42e8e686c
-  data.tar.gz: c1be3117819f1efdcb9c92150da757e6a9f0daff2062c9e0f25782ae5d21db95335360338cf82f52c76eb539c4f557c87408023224bd74d454c86add87d4c3ab
+  metadata.gz: f516b9f6522c7907e89fae95749aa8b33be3c0bbf970d645aa408feb102971a17e26e6dabb030af1d9c8dbdad19979ab35e006c18b8ea36c4ed778065b12d8af
+  data.tar.gz: e6a83a2c9d22cd18580c232f73a1c44a378f30fca0517849244b49f42c01168d4d505157740ee04dbd5a57ff56c2fdb4b85aced8bc6443c3dd0e471091fd1424

data/README.md

@@ -4,133 +4,10 @@
 [![Scrutinizer Code Quality](https://scrutinizer-ci.com/g/wurmlab/genevalidatorapp/badges/quality-score.png?b=master)](https://scrutinizer-ci.com/g/wurmlab/genevalidatorapp/?branch=master)
 
 
-
-
-
-
-
 ## Introduction
 
-This is a online web application for [GeneValidator](https://github.com/wurmlab/genevalidator). This app is currently hosted at: [genevalidator.sbcs.qmul.ac.uk](http://genevalidator.sbcs.qmul.ac.uk).
-
-GeneValidator helps in identifing problems with gene predictions and provides useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions.
-
-If you use GeneValidator in your work, please cite us as follows:
-> [Dragan M<sup>&Dagger;</sup>, Moghul MI<sup>&Dagger;</sup>, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. <em>Bioinformatics</em>, doi: 10.1093/bioinformatics/btw015](http://bioinformatics.oxfordjournals.org/content/early/2016/01/18/bioinformatics.btw015).
-
-
-
-
-
-
--
-## Installation
-### Installation Requirements
-* Ruby (>= 2.0.0)
-* NCBI BLAST+ (>= 2.2.30+) (download [here](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)).
-* MAFFT installation (>=7.273) (download [here](http://mafft.cbrc.jp/alignment/software/)).
-
-Please see [here](https://gist.github.com/IsmailM/b783e8a06565197084e6) for more help with installing the prerequisites.
-
-### Installation
-Simply run the following command in the terminal.
-
-```bash
-gem install genevalidatorapp
-```
-
-If that doesn't work, try `sudo gem install genevalidatorapp` instead.
-
-##### Running From Source (Not Recommended)
-It is also possible to run from source. However, this is not recommended.
-
-```bash
-# Clone the repository.
-git clone https://github.com/wurmlab/genevalidatorapp.git
-
-# Move into GeneValidatorApp source directory.
-cd GeneValidatorApp
-
-# Install bundler
-gem install bundler
-
-# Use bundler to install dependencies
-bundle install
-
-# Optional: run tests and build the gem from source
-bundle exec rake
-
-# Run GeneValidator.
-bundle exec genevalidatorapp -h
-# note that `bundle exec` executes GeneValidatorApp in the context of the bundle
-
-# Alternativaly, install GeneValidatorApp as a gem
-bundle exec rake install
-genevalidatorapp -h
-```
-
-
-
-
-## Launch GeneValidator
-
-To configure and launch GeneValidatorApp, run the following from a command line.
-
-```bash
-genevalidatorapp
-```
-
-GeneValidatorApp will automatically guide you through an interactive setup process to help locate BLAST+ binaries and ask for the location of BLAST+ databases.
-
-That's it! Open http://localhost:4567/ and start using GeneValidator!
-
-
-
-
-
-
-## Advanced Usage
-
-See `$ genevalidatorapp -h` for more information on all the options available when running GeneValidatorApp.
-
-```bash
-SUMMARY:
-  GeneValidator - Identify problems with predicted genes
-
-USAGE:
-  $ genevalidatorapp [options]
-
-Examples:
-  # Launch GeneValidatorApp with the given config file
-  $ genevalidatorapp --config ~/.genevalidatorapp.conf
-
-  # Launch GeneValidatorApp with 8 threads at port 8888
-  $ genevalidatorapp --num_threads 8 --port 8888
-
-  # Create a config file with the other arguments
-  $ genevalidatorapp -s -d ~/database_dir
-
-    -c, --config_file                Use the given configuration file
-    -b, --bin                        Load BLAST+ and/or MAFFT binaries from this directory
-    -d, --database_dir               Read BLAST database from this directory
-    -f, --default_database_path      The path to the default BLAST database
-    -n, --num_threads                Number of threads to use to run a BLAST search
-    -r, --require                    Load extension from this file
-    -H, --host                       Host to run GeneValidatorApp on
-    -p, --port                       Port to run GeneValidatorApp on
-    -s, --set                        Set configuration value in default or given config file
-    -l, --list_databases             List BLAST databases
-    -D, --devel                      Start GeneValidatorApp in development mode
-    -v, --version                    Print version number of GeneValidatorApp that will be loaded
-    -h, --help                       Display this help message.
-```
-
+This repository is part of the GeneValidator Package and is used internally by GeneValidator - Please see [https://github.com/wurmlab/genevalidator](https://github.com/wurmlab/genevalidator) for more information.
 
-## Using Docker
-```bash
-# With protein database files inside a folder named db
-docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/genevalidator
-```
 
 <hr>
 

data/Rakefile

@@ -1,21 +1,24 @@
-require 'bundler/gem_tasks'
-require 'rspec/core'
-require 'rspec/core/rake_task'
+require 'rake/testtask'
+GEMSPEC = Gem::Specification::load('genevalidatorapp.gemspec')
 
 task default: [:build]
 
 desc 'Builds and installs'
 task install: [:build] do
-  require_relative 'lib/genevalidatorapp/version'
-  sh "gem install ./genevalidatorapp-#{GeneValidatorApp::VERSION}.gem"
+  sh "gem install #{Rake.original_dir}/genevalidatorapp-#{GEMSPEC.version}.gem"
 end
 
 desc 'Runs tests and builds gem (default)'
 task build: [:test] do
-  sh 'gem build genevalidatorapp.gemspec'
+  sh "gem build #{Rake.original_dir}/genevalidatorapp.gemspec"
 end
 
-task test: :spec
-RSpec::Core::RakeTask.new(:spec) do |spec|
-  spec.pattern = FileList['spec/**/*_spec.rb']
+desc 'Runs tests'
+task :test do
+  Rake::TestTask.new do |t|
+    t.libs.push 'lib'
+    t.test_files = FileList['test/test_*.rb']
+    t.verbose = false
+    t.warning = false
+  end
 end

data/genevalidatorapp.gemspec

@@ -3,39 +3,36 @@ lib = File.expand_path('../lib', __FILE__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require 'genevalidatorapp/version'
 
-Gem::Specification.new do |spec|
-  spec.name          = 'genevalidatorapp'
-  spec.version       = GeneValidatorApp::VERSION
-  spec.authors       = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam',
+Gem::Specification.new do |s|
+  s.name          = 'genevalidatorapp'
+  s.version       = GeneValidatorApp::VERSION
+  s.authors       = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam',
                         'Yannick Wurm']
-  spec.email         = 'y.wurm@qmul.ac.uk'
-  spec.summary       = 'A Web App wrapper for GeneValidator.'
-  spec.description   = 'A Web App wrapper for GeneValidator, a program for' \
+  s.email         = 'y.wurm@qmul.ac.uk'
+  s.summary       = 'A Web App wrapper for GeneValidator.'
+  s.description   = 'A Web App wrapper for GeneValidator, a program for' \
                        ' validating gene predictions.'
-  spec.homepage      = 'https://wurmlab.github.io/tools/genevalidator/'
-  spec.license       = 'AGPL'
-
-  spec.files         = `git ls-files -z`.split("\x0")
-  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
-  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
-  spec.require_paths = ['lib']
-
-  spec.required_ruby_version = '>= 2.0.0'
-
-  spec.add_development_dependency 'bundler', '~> 1.6'
-  spec.add_development_dependency 'rake', '~>10.3'
-  spec.add_development_dependency('rspec', '~> 2.8', '>= 2.8.0')
-  spec.add_development_dependency 'rack-test', '~> 0.6'
-  spec.add_development_dependency('capybara', '~> 2.4', '>= 2.4.4')
-  spec.add_development_dependency 'w3c_validators', '~>1.1'
-
-  spec.add_dependency 'genevalidator', '~>1.6'
-  spec.add_dependency 'bio', '~>1.4'
-  spec.add_dependency 'sinatra', '~>1.4'
-  spec.add_dependency 'sinatra-cross_origin', '~> 0.3'
-  spec.add_dependency 'slim', '~>3.0'
-  spec.add_dependency 'slop', '~>3.6'
-  spec.post_install_message = <<INFO
+  s.homepage      = 'https://wurmlab.github.io/tools/genevalidator/'
+  s.license       = 'AGPL'
+
+  s.files         = `git ls-files -z`.split("\x0")
+  s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  s.test_files    = s.files.grep(%r{^(test|spec|features)/})
+  s.require_paths = ['lib']
+
+  s.required_ruby_version = '>= 2.2.0'
+
+  s.add_development_dependency 'bundler', '~> 1.6'
+  s.add_development_dependency 'capybara', '~> 2.4', '>= 2.4.4'
+  s.add_development_dependency 'minitest', '~> 5.10'
+  s.add_development_dependency 'rake', '~> 12.3'
+  # s.add_development_dependency 'w3c_validators', '~>1.1'
+
+  s.add_dependency 'bio', '~>1.4'
+  s.add_dependency 'sinatra', '~>1.4'
+  s.add_dependency 'sinatra-cross_origin', '~> 0.3'
+  s.add_dependency 'slim', '~>3.0'
+  s.post_install_message = <<INFO
 
 ------------------------------------------------------------------------
   Thank you for validating your gene predictions with GeneValidator!

data/lib/genevalidatorapp.rb

@@ -57,7 +57,7 @@ module GeneValidatorApp
       puts "   Is GeneValidator already accessible at #{server_url}?"
       puts '   No? Try running GeneValidator on another port, like so:'
       puts
-      puts '       genevalidatorapp -p 4570.'
+      puts '       genevalidator app -p 4570.'
     rescue Errno::EACCES
       puts "** Need root privilege to bind to port #{config[:port]}."
       puts '   It is not advisable to run GeneValidator as root.'
@@ -73,7 +73,7 @@ module GeneValidatorApp
 
     def on_stop
       puts
-      puts '** Thank you for using GeneValidatorApp :).'
+      puts '** Thank you for using GeneValidator :).'
       puts '   Please cite: '
       puts '        Dragan M, Moghul MI, Priyam A, Bustos C, Wurm Y. 2016.'
       puts '        GeneValidator: identify problems with protein-coding gene'

data/lib/genevalidatorapp/config.rb

@@ -76,7 +76,7 @@ module GeneValidatorApp
         :port           => 4567,
         :host           => '0.0.0.0',
         :gv_public_dir  => File.join(Dir.home, '.genevalidatorapp/'),
-        :max_characters => 'undefined',
+        :max_characters => 'undefined'
       }
     end
 

data/lib/genevalidatorapp/database.rb

@@ -73,9 +73,9 @@ module GeneValidatorApp
                ' "%p::%f::%t"'
         list = `#{cmd} 2>&1`
         list.each_line do |line|
-          type, name, title =  line.split('::', 3)
+          type, name, title = line.split('::', 3)
           next if multipart_database_name?(name)
-          next unless type.downcase == 'protein'
+          next unless type.casecmp('protein').zero?
           self << Database.new(name, title, type)
         end
       end
@@ -88,7 +88,7 @@ module GeneValidatorApp
       # /home/ben/pd.ben/sequenceserver/db/nr => no
       # /home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01 => yes
       def multipart_database_name?(db_name)
-        !(db_name.match(/.+\/\S+\d{2}$/).nil?)
+        !db_name.match(%r{.+\/\S+\d{2}$}).nil?
       end
     end
 

data/lib/genevalidatorapp/genevalidator.rb

@@ -44,9 +44,8 @@ module GeneValidatorApp
       def run
         write_seq_to_file
         run_genevalidator
-        copy_json_folder
         { parsed_json: parse_output_json, json_url: @json_url,
-          results_url: @url }
+          results_url: @url, unique_id: @unique_id }
       end
 
       private
@@ -90,24 +89,24 @@ module GeneValidatorApp
       # Simply asserts whether that the seq param is present
       def check_seq_param_present
         return if @params[:seq]
-        fail ArgumentError, 'No input sequence provided.'
+        raise ArgumentError, 'No input sequence provided.'
       end
 
       def check_seq_length
         return unless config[:max_characters] != 'undefined'
         return if @params[:seq].length < config[:max_characters]
-        fail ArgumentError, 'The input sequence is too long.'
+        raise ArgumentError, 'The input sequence is too long.'
       end
 
       # Asserts whether the validations param are specified
       def check_validations_param_present
         return if @params[:validations]
-        fail ArgumentError, 'No validations specified'
+        raise ArgumentError, 'No validations specified'
       end
 
       # Asserts whether the database parameter is present
       def check_database_params_present
-        fail ArgumentError, 'No database specified' unless @params[:database]
+        raise ArgumentError, 'No database specified' unless @params[:database]
       end
 
       def obtain_db_path
@@ -155,17 +154,7 @@ module GeneValidatorApp
       # Asserts that the input file has been generated and is not empty
       def assert_input_file_present
         return if File.exist?(@input_file) && !File.zero?(@input_file)
-        fail 'GeneValidatorApp was unable to create the input file.'
-      end
-
-      # Returns 'blastp' if sequence contains amino acids or returns 'blastx'
-      #   if it contains nucleic acids.
-      def get_blast_type(sequences)
-        (check_seq_type(sequences) == Bio::Sequence::AA) ? 'blastp' : 'blastx'
-      end
-
-      def check_seq_type(sequences)
-        Bio::Sequence.new(Bio::FastaFormat.new(sequences).seq).guess(0.9)
+        raise 'GeneValidatorApp was unable to create the input file.'
       end
 
       # Runs GeneValidator
@@ -178,11 +167,20 @@ module GeneValidatorApp
       end
 
       def run_gv
-        cmd = "genevalidator -v '#{@params[:validations].join(',')}'" \
-              " -d #{@db} -n #{config[:num_threads]} #{@input_file}"
-        logger.debug("GV command: $ #{cmd}")
-        log_file = (logger.debug?) ? '' : "> #{@gv_log_file} 2>&1"
-        `#{cmd} #{log_file}`
+        run_opt = gv_params
+        GeneValidator.init(run_opt)
+        GeneValidator.run
+      end
+
+      def gv_params
+        {
+          validations: @params[:validations],
+          db: @db,
+          num_threads: config[:num_threads],
+          input_fasta_file: @input_file,
+          output_formats: %w[json html],
+          output_dir: File.join(@run_dir, 'output')
+        }
       end
 
       def create_gv_log_file
@@ -192,21 +190,21 @@ module GeneValidatorApp
 
       # Assets whether the results file is produced by GeneValidator.
       def assert_json_output_file_produced
-        @json_file = File.join(@run_dir, 'input_file.fa.json')
+        @json_file = File.join(@run_dir, 'output/input_file_results.json')
         return if File.exist?(@json_file)
-        fail 'GeneValidator did not produce the required output file.'
+        raise 'GeneValidator did not produce the required output file.'
       end
 
       # Reuturns the URL of the results page.
       def produce_result_url_link(url)
         url.gsub(/input/, '').gsub(%r{/*$}, '') +
-          "/GeneValidator/#{@unique_id}/input_file.fa.html/results1.html"
+          "/GeneValidator/#{@unique_id}/output/results.html"
       end
 
       # Reuturns the URL of the results page.
       def produce_json_url_link(url)
         url.gsub(/input/, '').gsub(%r{/*$}, '') +
-          "/GeneValidator/#{@unique_id}/input_file.fa.json"
+          "/GeneValidator/#{@unique_id}/output/input_file_results.json"
       end
 
       def parse_output_json
@@ -215,14 +213,11 @@ module GeneValidatorApp
       end
 
       def output_json_file_path
-        "#{@input_file}.json"
+        File.join(@run_dir, 'output/input_file_results.json')
       end
 
-      def copy_json_folder
-        json_dir = File.join("#{@input_file}.html", 'files/json', '/.')
-        web_dir_json = File.join(public_dir, 'web_files/json')
-        logger.debug("Moving JSON files from #{json_dir} to #{web_dir_json}")
-        FileUtils.cp_r(json_dir, web_dir_json)
+      def individual_json_path
+        "/GeneValidator/#{@unique_id}/output/html_files/json"
       end
     end
   end

data/lib/genevalidatorapp/routes.rb

@@ -30,10 +30,10 @@ module GeneValidatorApp
       set :logging, nil
 
       # This is the app root...
-      set :root,          lambda { GeneValidatorApp.root }
+      set :root,          -> { GeneValidatorApp.root }
 
       # This is the full path to the public folder...
-      set :public_folder, lambda { GeneValidatorApp.public_dir }
+      set :public_folder, -> { GeneValidatorApp.public_dir }
     end
 
     # Set up global variables for the templates...

data/lib/genevalidatorapp/server.rb

@@ -49,7 +49,7 @@ module GeneValidatorApp
     private
 
     def setup_signal_handlers
-      [:INT, :TERM].each do |sig|
+      %i[INT TERM].each do |sig|
         trap sig do
           stop
         end