bio-old-biofetch-emulator 0.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.document +5 -0
- data/.travis.yml +13 -0
- data/Gemfile +15 -0
- data/LICENSE.txt +20 -0
- data/README.md +47 -0
- data/README.rdoc +48 -0
- data/Rakefile +51 -0
- data/VERSION +1 -0
- data/lib/bio-old-biofetch-emulator.rb +12 -0
- data/lib/bio-old-biofetch-emulator/emulator.rb +415 -0
- data/test/helper.rb +35 -0
- data/test/test_bio-old-biofetch-emulator.rb +96 -0
- metadata +132 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: 1acb392f7fea461ab1f0be3309f787a0bcc12cd7
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data.tar.gz: 7ea00a53bcfb15ff82c7a868bfba893153b50476
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SHA512:
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metadata.gz: b83d93062361505b405e173cc87a955ec946d3111273b278348f20d56ed275650e83f2c4eb7c3ef8f1f861572b06b9c75c82d3f0a8a5cfa8339cdf10999b6f60
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data.tar.gz: ab26f02e799f83c75f7d849572312eca527d648db9f3a1420652c2b5673c134f847ba396852f370c67a08a6bf102d6404101b21b8dc9446290df4fc1f95952a1
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data/.document
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data/.travis.yml
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language: ruby
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rvm:
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- 1.9.2
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- 1.9.3
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- jruby-19mode # JRuby in 1.9 mode
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# - rbx-19mode
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# - 1.8.7
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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gem "bio", ">= 1.4.2"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "rake"
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gem "rdoc"
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gem "jeweler"
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gem "bundler", ">= 1.0.21"
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end
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data/LICENSE.txt
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Copyright (c) 2014 Naohisa Goto
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# bio-old-biofetch-emulator
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[](http://travis-ci.org/ngoto/bioruby-old-biofetch-emulator)
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Full description goes here
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Note: this software is under active development!
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## Installation
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```sh
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gem install bio-old-biofetch-emulator
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```
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## Usage
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```ruby
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require 'bio-old-biofetch-emulator'
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```
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The API doc is online. For more code examples see the test files in
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the source tree.
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## Project home page
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Information on the source tree, documentation, examples, issues and
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how to contribute, see
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http://github.com/ngoto/bioruby-old-biofetch-emulator
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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## Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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## Biogems.info
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This Biogem is published at (http://biogems.info/index.html#bio-old-biofetch-emulator)
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## Copyright
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Copyright (c) 2014 Naohisa Goto. See LICENSE.txt for further details.
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data/README.rdoc
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= bio-old-biofetch-emulator
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{<img
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src="https://secure.travis-ci.org/ngoto/bioruby-old-biofetch-emulator.png"
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/>}[http://travis-ci.org/#!/ngoto/bioruby-old-biofetch-emulator]
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Full description goes here
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Note: this software is under active development!
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== Installation
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gem install bio-old-biofetch-emulator
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== Usage
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== Developers
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To use the library
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require 'bio-old-biofetch-emulator'
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The API doc is online. For more code examples see also the test files in
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the source tree.
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== Project home page
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Information on the source tree, documentation, issues and how to contribute, see
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http://github.com/ngoto/bioruby-old-biofetch-emulator
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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== Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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== Biogems.info
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This Biogem is published at http://biogems.info/index.html#bio-old-biofetch-emulator
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== Copyright
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Copyright (c) 2014 Naohisa Goto. See LICENSE.txt for further details.
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data/Rakefile
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
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gem.name = "bio-old-biofetch-emulator"
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gem.homepage = "http://github.com/ngoto/bioruby-old-biofetch-emulator"
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gem.license = "MIT"
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gem.summary = %Q{Emulates as if old BioRuby BioFetch alives}
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gem.description = %Q{Emulator that emulates Bio::Fetch object in BioRuby as if old BioRuby BioFetch server were still alive. It overrides methods and objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it intercepts all requests and converts them into existing web services such as TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp).}
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gem.email = "ng@bioruby.org"
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gem.authors = ["Naohisa Goto"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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desc "Code coverage detail"
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task :simplecov do
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ENV['COVERAGE'] = "true"
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Rake::Task['test'].execute
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end
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task :default => :test
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require 'rdoc/task'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "bio-old-biofetch-emulator #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
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0.0.0
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# Please require your code below, respecting the naming conventions in the
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# bioruby directory tree.
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#
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# For example, say you have a plugin named bio-plugin, the only uncommented
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# line in this file would be
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#
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# require 'bio/bio-plugin/plugin'
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#
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# In this file only require other files. Avoid other source code.
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require 'bio-old-biofetch-emulator/emulator.rb'
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require 'bio'
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require 'cgi'
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module Bio
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module OldBioFetchEmulator
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URL = "http://bioruby.org/cgi-bin/biofetch.rb".freeze
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MAX_ID_NUM = 50
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class Client < Bio::Fetch
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# https://web.archive.org/web/20070803003306/http://www.genome.jp/about_genomenet/service.html
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# https://web.archive.org/web/20110525080429/http://www.genome.jp/dbget/
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# https://web.archive.org/web/20070306215757/http://bioruby.org/cgi-bin/biofetch.rb?info=dbs
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# aa aax bl cpd dgenes dr ec eg emb embu epd est exp
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# gb gbu genes gl gn gp gpu gss htgs ko ld lit mim nt
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# og path pd pdb pdoc pf pir pmd pr prf ps rn rp rs
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# rsaa rsnt sp str sts tr vg
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Databases = {
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# fetching via Bio::PubMed (NCBI E-Utilities)
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"pubmed" => [ :PubMed, true ],
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# fetching via TogoWS REST API
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"genbank" => [ :TogoWS, "ncbi-nucleotide" ],
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"gb" => "genbank",
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"genpept" => [ :TogoWS, "ncbi-protein" ],
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"gp" => "genpept",
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"refseq" => [ :TogoWS, "ncbi-nucleotide", "ncbi-protein" ],
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"rs" => "refseq",
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"refnuc" => [ :TogoWS, "ncbi-nucleotide" ],
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"rsnt" => "refnuc",
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"refpep" => [ :TogoWS, "ncbi-protein" ],
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"rsaa" => "refpep",
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"embl" => [ :TogoWS, "ebi-ena" ],
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"emb" => "embl",
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"uniprot" => [ :TogoWS, true ],
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"up" => "uniprot",
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"swissprot" => "uniprot",
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"sp" => "uniprot",
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"trembl" => "uniprot",
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"tr" => "uniprot",
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"pdb" => [ :TogoWS, true ],
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#"genes" => [ :TogoWS, "kegg-genes" ],
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# fetching via KEGG REST API
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"pathway" => [ :KEGG, true ],
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"path" => "pathway",
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"brite" => [ :KEGG, true ],
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"br" => "brite",
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"module" => [ :KEGG, true ],
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"md" => "module",
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"orthology" => [ :KEGG, true ],
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"ko" => "orthology",
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"genome" => [ :KEGG, true ],
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"genomes" => [ :KEGG, true ],
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"gn" => "genomes",
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"genes" => [ :KEGG, true ],
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"ligand" => [ :KEGG, true ],
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"compound" => [ :KEGG, true ],
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"cpd" => "compound",
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"glycan" => [ :KEGG, true ],
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"gl" => "glycan",
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"reaction" => [ :KEGG, true ],
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"rn" => "reaction",
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"rpair" => [ :KEGG, true ],
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"rp" => "rpair",
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"rclass" => [ :KEGG, true ],
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"rc" => "rclass",
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"enzyme" => [ :KEGG, true ],
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"ec" => "enzyme",
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"disease" => [ :KEGG, true ],
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"ds" => "disease",
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"drug" => [ :KEGG, true ],
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"dr" => "drug",
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"dgroup" => [ :KEGG, true ],
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"dg" => "dgroup",
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"environ" => [ :KEGG, true ],
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"ev" => "environ",
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"expression" => [ nil ], #[ :KEGG, true ],
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"ex" => "expression",
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"exp" => "expression",
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"dgenes" => [ :KEGG, true ],
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"egenes" => [ :KEGG, true ],
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"eg" => "egenes",
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"mgenes" => [ nil ], #[ :KEGG, true ],
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"mgenome" => [ nil ], #[ :KEGG, true ],
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"mgnm" => "mgenome",
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"vgenome" => [ :KEGG, true ],
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"vgnm" => "vgenome",
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"vgenes" => [ :KEGG, true ],
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"vg" => "vgenes",
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# fetching from GenemeNet
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"aaindex" => [ :DBGET, true ],
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"aax" => "aaindex",
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"aaindex1" => [ :DBGET, true ],
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"aax1" => "aaindex1",
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"aaindex2" => [ :DBGET, true ],
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"aax2" => "aaindex2",
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"aaindex3" => [ :DBGET, true ],
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"aax3" => "aaindex3",
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# formerly can be get from GenomeNet but not available now
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"prf" => [ nil ], #[ :DBGET, true ],
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"litdb" => [ nil ], #[ :DBGET, true ],
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"lit" => [ nil ], #"litdb",
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"pdbstr" => [ nil ], # Protein sequence generated from PDB (GenomeNet)
|
123
|
+
|
124
|
+
"aa" => [ nil ], # nr-aa ???
|
125
|
+
#"aax" # AAindex (KEGG)
|
126
|
+
"bl" => [ nil ], # Blocks (http://blocks.fhcrc.org/)
|
127
|
+
#"cpd" # KEGG Compound
|
128
|
+
#"dgenes" # KEGG DGenes
|
129
|
+
#"dr" # KEGG Drug
|
130
|
+
#"ec" # KEGG Enzyme
|
131
|
+
#"eg" # KEGG EGenes
|
132
|
+
#"emb" # EMBL
|
133
|
+
"embu" => [ nil ], # EMBL UniGene ???
|
134
|
+
"epd" => [ nil ], # The Eukaryotic Promoter Database
|
135
|
+
"est" => [ nil ], # NCBI EST ???
|
136
|
+
#"gb" # GenBank
|
137
|
+
"gbu" => [ nil ], # NCBI UniGene ???
|
138
|
+
#"genes" # KEGG Genes
|
139
|
+
#"gl" # KEGG Glycan
|
140
|
+
#"gn" # KEGG Genomes
|
141
|
+
#"gp" # GenPept ???
|
142
|
+
"gpu" => [ nil ], # ???
|
143
|
+
"gss" => [ nil ], # NCBI GSS ???
|
144
|
+
"htgs" => [ nil ], # NCBI HTGS ???
|
145
|
+
#"ko" # KEGG Orthology
|
146
|
+
"ld" => [ nil ], # ???
|
147
|
+
#"lit" # PRF LitDB
|
148
|
+
"mim" => [ nil ], # ???
|
149
|
+
"nt" => [ nil ], # nr-nt ???
|
150
|
+
"og" => [ nil ], # ???
|
151
|
+
#"path" # KEGG Pathway
|
152
|
+
"pd" => [ nil ], # prodom
|
153
|
+
#"pdb" # PDB
|
154
|
+
"pdoc" => [ nil ], # Prosite literature (GenomeNet)
|
155
|
+
"pf" => [ nil ], # Pfam
|
156
|
+
"pir" => [ nil ], # pir
|
157
|
+
"pmd" => [ nil ], # Protein mutants (DDBJ) (GenomeNet)
|
158
|
+
"pr" => [ nil ], # prints
|
159
|
+
#"prf" # PRF (Protein Research Foundation)
|
160
|
+
"ps" => [ nil ], # prosite
|
161
|
+
#"rn" # KEGG Reaction
|
162
|
+
#"rp" # KEGG RPair
|
163
|
+
#"rs" # NCBI RefSeq
|
164
|
+
#"rsaa" # NCBI RefSeq Amino Acide
|
165
|
+
#"rsnt" # NCBI RefSeq NucleoTide
|
166
|
+
#"sp" # SwissProt
|
167
|
+
"str" => [ nil ], # ???
|
168
|
+
"sts" => [ nil ], # NCBI STS ???
|
169
|
+
#"tr" # TrEMBL
|
170
|
+
#"vg" # KEGG VGenes
|
171
|
+
}
|
172
|
+
|
173
|
+
def initialize(url = URL)
|
174
|
+
super
|
175
|
+
end
|
176
|
+
|
177
|
+
def fetch(db, id, style = 'raw', format = nil)
|
178
|
+
_fetch(:fetch, db, id, style, format)
|
179
|
+
end
|
180
|
+
|
181
|
+
def databases
|
182
|
+
Databases.collect do |key, val|
|
183
|
+
while val && val.is_a?(String)
|
184
|
+
val = Databases[val]
|
185
|
+
end
|
186
|
+
if val && val.is_a?(Array) && val[0] then
|
187
|
+
key
|
188
|
+
else
|
189
|
+
nil
|
190
|
+
end
|
191
|
+
end.compact
|
192
|
+
end
|
193
|
+
|
194
|
+
def formats(database = @database)
|
195
|
+
if database
|
196
|
+
[ "default" ]
|
197
|
+
end
|
198
|
+
end
|
199
|
+
|
200
|
+
def maxids
|
201
|
+
MAX_ID_NUM
|
202
|
+
end
|
203
|
+
|
204
|
+
private
|
205
|
+
def _fetch(cmd, db, id, style, format)
|
206
|
+
db_orig = db
|
207
|
+
db = db.to_s.downcase
|
208
|
+
while a = Databases[db]
|
209
|
+
case a
|
210
|
+
when Array
|
211
|
+
break
|
212
|
+
when String
|
213
|
+
db = a
|
214
|
+
else
|
215
|
+
break
|
216
|
+
end
|
217
|
+
end
|
218
|
+
|
219
|
+
if !a and /[a-z]{3}/ =~ db then
|
220
|
+
remote = :KEGG
|
221
|
+
dbs = [ 'genes' ]
|
222
|
+
id_prefix = db
|
223
|
+
elsif a.is_a?(Array) then
|
224
|
+
remote = a[0]
|
225
|
+
dbs = a[1..-1]
|
226
|
+
dbs.collect! { |x| x == true ? db : x }
|
227
|
+
end
|
228
|
+
|
229
|
+
if !remote then
|
230
|
+
return "ERROR 1 Unknown database [#{db_orig.inspect}]"
|
231
|
+
end
|
232
|
+
|
233
|
+
ids = id.strip.split(/(?:\s*\,\s*|\s+)/)
|
234
|
+
if ids.size > MAX_ID_NUM then
|
235
|
+
return "ERROR 5 Too many IDs [#{ids.size}]. Max [#{MAX_ID_NUM}] allowed."
|
236
|
+
end
|
237
|
+
if id_prefix then
|
238
|
+
ids.collect! { |x| "#{id_prefix}:#{x.strip}" }
|
239
|
+
end
|
240
|
+
|
241
|
+
case cmd
|
242
|
+
when :fetch
|
243
|
+
ret = case remote
|
244
|
+
when :TogoWS
|
245
|
+
_fetch_togows(cmd, dbs, ids)
|
246
|
+
when :KEGG
|
247
|
+
_fetch_kegg(cmd, dbs, ids)
|
248
|
+
when :DBGET
|
249
|
+
_fetch_dbget(cmd, dbs, ids)
|
250
|
+
when :PubMed
|
251
|
+
_fetch_pubmed(cmd, dbs, ids)
|
252
|
+
else
|
253
|
+
raise "Bug: unknown remote site #{remote.inspect}"
|
254
|
+
end
|
255
|
+
end
|
256
|
+
ret
|
257
|
+
end
|
258
|
+
|
259
|
+
def _fetch_pubmed(cmd, dbs, ids)
|
260
|
+
a = Bio::PubMed.efetch(ids)
|
261
|
+
if a && a.size > 0 then
|
262
|
+
a.join("\n\n") + "\n"
|
263
|
+
else
|
264
|
+
"Error 4 ID not found [#{ids.inspect}]"
|
265
|
+
end
|
266
|
+
end
|
267
|
+
|
268
|
+
def _fetch_togows(cmd, dbs, ids)
|
269
|
+
all = []
|
270
|
+
ids.each do |id|
|
271
|
+
ret = nil
|
272
|
+
dbs.each do |db|
|
273
|
+
url = "http://togows.org/entry/#{CGI.escape(db)}/#{CGI.escape(id)}"
|
274
|
+
begin
|
275
|
+
ret = Bio::Command.read_uri(url)
|
276
|
+
rescue OpenURI::HTTPError
|
277
|
+
ret = nil
|
278
|
+
end
|
279
|
+
if ret && /\AError/ !~ ret && ret.strip.size > 0 then
|
280
|
+
break
|
281
|
+
else
|
282
|
+
ret = nil
|
283
|
+
end
|
284
|
+
end
|
285
|
+
all.push ret if ret
|
286
|
+
end
|
287
|
+
if all.empty?
|
288
|
+
return "Error 4 ID not found [#{ids.inspect}]"
|
289
|
+
else
|
290
|
+
return all.join("")
|
291
|
+
end
|
292
|
+
end
|
293
|
+
|
294
|
+
def _fetch_kegg(cmd, dbs, ids)
|
295
|
+
all = []
|
296
|
+
ids.each do |id|
|
297
|
+
ret = nil
|
298
|
+
dbs.each do |db|
|
299
|
+
if db == "genes" then
|
300
|
+
url = "http://rest.kegg.jp/get/#{CGI.escape(id)}"
|
301
|
+
else
|
302
|
+
url = "http://rest.kegg.jp/get/#{CGI.escape(db)}:#{CGI.escape(id)}"
|
303
|
+
end
|
304
|
+
begin
|
305
|
+
ret = Bio::Command.read_uri(url)
|
306
|
+
rescue OpenURI::HTTPError
|
307
|
+
ret = nil
|
308
|
+
end
|
309
|
+
if ret && ret.strip.size > 0 then
|
310
|
+
break
|
311
|
+
else
|
312
|
+
ret = nil
|
313
|
+
end
|
314
|
+
end
|
315
|
+
all.push ret if ret
|
316
|
+
end
|
317
|
+
if all.empty?
|
318
|
+
return "Error 4 ID not found [#{ids.inspect}]"
|
319
|
+
else
|
320
|
+
return all.join("")
|
321
|
+
end
|
322
|
+
end
|
323
|
+
|
324
|
+
def _fetch_dbget(cmd, dbs, ids)
|
325
|
+
all = []
|
326
|
+
ids.each do |id|
|
327
|
+
ret = nil
|
328
|
+
dbs.each do |db|
|
329
|
+
url = "http://www.genome.jp/dbget-bin/www_bget?#{CGI.escape(db)}:#{CGI.escape(id)}"
|
330
|
+
begin
|
331
|
+
ret = Bio::Command.read_uri(url)
|
332
|
+
rescue OpenURI::HTTPError
|
333
|
+
ret = nil
|
334
|
+
end
|
335
|
+
if ret then
|
336
|
+
ret = _scrape_dbget(ret)
|
337
|
+
break if ret
|
338
|
+
end
|
339
|
+
ret = nil
|
340
|
+
end
|
341
|
+
all.push ret if ret
|
342
|
+
end
|
343
|
+
if all.empty?
|
344
|
+
return "Error 4 ID not found [#{ids.inspect}]"
|
345
|
+
else
|
346
|
+
return all.join("")
|
347
|
+
end
|
348
|
+
end
|
349
|
+
|
350
|
+
def _scrape_dbget(orig_str)
|
351
|
+
a = orig_str.split(/^\s*\<\!\-\- bget\:result \-\-\>$\s*/)
|
352
|
+
if a[1] then
|
353
|
+
str = a[1]
|
354
|
+
str.sub!(/\A\s*\<pre\>$\s*/, "")
|
355
|
+
str.sub!(/^\s*\<\/pre\>.*/m, "")
|
356
|
+
str.gsub!(/\<[^\>]+\>/, "")
|
357
|
+
return str
|
358
|
+
end
|
359
|
+
nil
|
360
|
+
end
|
361
|
+
|
362
|
+
end #class Client
|
363
|
+
|
364
|
+
module Query
|
365
|
+
# Shortcut for using BioRuby's BioFetch server. You can fetch an entry
|
366
|
+
# without creating an instance of BioFetch server. This method uses the
|
367
|
+
# default dbfetch server, which is http://bioruby.org/cgi-bin/biofetch.rb
|
368
|
+
#
|
369
|
+
# Example:
|
370
|
+
# puts Bio::Fetch.query('refseq','NM_123456')
|
371
|
+
#
|
372
|
+
# ---
|
373
|
+
# *Arguments*:
|
374
|
+
# * _database_: name of database to query (see Bio::Fetch#databases to get list of supported databases)
|
375
|
+
# * _id_: single ID or ID list separated by commas or white space
|
376
|
+
# * _style_: [raw|html] (default = 'raw')
|
377
|
+
# * _format_: name of output format (see Bio::Fetch#formats)
|
378
|
+
def query(*args)
|
379
|
+
Client.new.fetch(*args)
|
380
|
+
end
|
381
|
+
end #module Query
|
382
|
+
|
383
|
+
DONT_OVERRIDE = ::Bio::Fetch.const_defined?(:EBI) ?
|
384
|
+
[ Client, ::Bio::Fetch::EBI ] : [ Client ]
|
385
|
+
|
386
|
+
class << ::Bio::Fetch
|
387
|
+
|
388
|
+
alias_method :new_without_old_biofetch_emulator, :new
|
389
|
+
|
390
|
+
def new_with_old_biofetch_emulator(*arg)
|
391
|
+
tmp = self.ancestors
|
392
|
+
if (tmp - DONT_OVERRIDE).size == tmp.size then
|
393
|
+
$stderr.puts self
|
394
|
+
case arg.size
|
395
|
+
when 0
|
396
|
+
return Client.new
|
397
|
+
when 1
|
398
|
+
case arg[0]
|
399
|
+
when URL
|
400
|
+
return Client.new(*arg)
|
401
|
+
end
|
402
|
+
end
|
403
|
+
end
|
404
|
+
new_without_old_biofetch_emulator(*arg)
|
405
|
+
end
|
406
|
+
|
407
|
+
alias_method :new, :new_with_old_biofetch_emulator
|
408
|
+
|
409
|
+
include Query
|
410
|
+
|
411
|
+
end #class << Bio::Fetch
|
412
|
+
|
413
|
+
end #module OldBioFetchEmulator
|
414
|
+
|
415
|
+
end #module Bio
|
data/test/helper.rb
ADDED
@@ -0,0 +1,35 @@
|
|
1
|
+
#
|
2
|
+
#require 'simplecov'
|
3
|
+
#
|
4
|
+
#module SimpleCov::Configuration
|
5
|
+
# def clean_filters
|
6
|
+
# @filters = []
|
7
|
+
# end
|
8
|
+
#end
|
9
|
+
#
|
10
|
+
#SimpleCov.configure do
|
11
|
+
# clean_filters
|
12
|
+
# load_adapter 'test_frameworks'
|
13
|
+
#end
|
14
|
+
#
|
15
|
+
#ENV["COVERAGE"] && SimpleCov.start do
|
16
|
+
# add_filter "/.rvm/"
|
17
|
+
#end
|
18
|
+
require 'rubygems'
|
19
|
+
#require 'bundler'
|
20
|
+
#begin
|
21
|
+
# Bundler.setup(:default, :development)
|
22
|
+
#rescue Bundler::BundlerError => e
|
23
|
+
# $stderr.puts e.message
|
24
|
+
# $stderr.puts "Run `bundle install` to install missing gems"
|
25
|
+
# exit e.status_code
|
26
|
+
#end
|
27
|
+
require 'test/unit'
|
28
|
+
#require 'shoulda'
|
29
|
+
|
30
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
31
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
32
|
+
require 'bio-old-biofetch-emulator'
|
33
|
+
|
34
|
+
class Test::Unit::TestCase
|
35
|
+
end
|
@@ -0,0 +1,96 @@
|
|
1
|
+
require 'helper'
|
2
|
+
|
3
|
+
module FuncTestBioOldBiofetchEmulator
|
4
|
+
|
5
|
+
module CommonTestMethods
|
6
|
+
|
7
|
+
def fetch_and_check_ids(db, ids, regexp)
|
8
|
+
tmp_ids = ids.dup
|
9
|
+
str = @bf.fetch(db, ids.join(","))
|
10
|
+
str.scan(regexp) do |x|
|
11
|
+
assert_equal(tmp_ids.shift.to_s, $1)
|
12
|
+
end
|
13
|
+
assert(tmp_ids.empty?)
|
14
|
+
|
15
|
+
str2 = @bf.fetch(db, ids.join(" "))
|
16
|
+
assert_equal(str, str2)
|
17
|
+
end
|
18
|
+
private :fetch_and_check_ids
|
19
|
+
|
20
|
+
def test_fetch_pubmed
|
21
|
+
db = "pubmed"
|
22
|
+
ids = [ 20739307, 22332238 ]
|
23
|
+
regexp = /^PMID- +(\d+)/
|
24
|
+
fetch_and_check_ids(db, ids, regexp)
|
25
|
+
end
|
26
|
+
|
27
|
+
def test_fetch_refseq
|
28
|
+
db = "rs"
|
29
|
+
ids = [ "NM_123456", "NP_198907" ]
|
30
|
+
regexp = /^ACCESSION +([\_A-Z0-9]+)/
|
31
|
+
fetch_and_check_ids(db, ids, regexp)
|
32
|
+
end
|
33
|
+
|
34
|
+
def test_fetch_kegg_genes
|
35
|
+
db = "hal"
|
36
|
+
ids = [ "VNG1467G", "VNG6476G", "VNG2243G" ]
|
37
|
+
regexp = /^ENTRY +([A-Z0-9]+)/
|
38
|
+
fetch_and_check_ids(db, ids, regexp)
|
39
|
+
end
|
40
|
+
|
41
|
+
def test_fetch_aaindex
|
42
|
+
db = "aax"
|
43
|
+
ids = [ "PRAM900102", "DAYM780301" ] # (aaindex1, aaindex2)
|
44
|
+
regexp = /^H +([A-Z0-9]+)$/
|
45
|
+
fetch_and_check_ids(db, ids, regexp)
|
46
|
+
end
|
47
|
+
|
48
|
+
def test_class
|
49
|
+
assert_instance_of(Bio::OldBioFetchEmulator::Client, @bf)
|
50
|
+
assert_equal(Bio::OldBioFetchEmulator::Client, @bf.class)
|
51
|
+
end
|
52
|
+
end #module CommonTestMethods
|
53
|
+
|
54
|
+
class TestClient < Test::Unit::TestCase
|
55
|
+
include CommonTestMethods
|
56
|
+
|
57
|
+
def setup
|
58
|
+
Bio::NCBI.default_email ||= "staff@bioruby.org"
|
59
|
+
@bf = Bio::OldBioFetchEmulator::Client.new
|
60
|
+
end
|
61
|
+
end #class TestClient
|
62
|
+
|
63
|
+
class TestBioFetch < Test::Unit::TestCase
|
64
|
+
include CommonTestMethods
|
65
|
+
|
66
|
+
def setup
|
67
|
+
Bio::NCBI.default_email ||= "staff@bioruby.org"
|
68
|
+
@bf = Bio::Fetch.new
|
69
|
+
end
|
70
|
+
|
71
|
+
end #class TestClient
|
72
|
+
|
73
|
+
class TestBioFetchWithURL < Test::Unit::TestCase
|
74
|
+
include CommonTestMethods
|
75
|
+
|
76
|
+
def setup
|
77
|
+
Bio::NCBI.default_email ||= "staff@bioruby.org"
|
78
|
+
@bf = Bio::Fetch.new("http://bioruby.org/cgi-bin/biofetch.rb")
|
79
|
+
end
|
80
|
+
|
81
|
+
end #class TestClient
|
82
|
+
|
83
|
+
class TestBioFetchWithOtherURL < Test::Unit::TestCase
|
84
|
+
def setup
|
85
|
+
Bio::NCBI.default_email ||= "staff@bioruby.org"
|
86
|
+
@bf = Bio::Fetch.new("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch")
|
87
|
+
end
|
88
|
+
|
89
|
+
def test_class
|
90
|
+
assert_instance_of(Bio::Fetch, @bf)
|
91
|
+
assert_equal(Bio::Fetch, @bf.class)
|
92
|
+
end
|
93
|
+
end #class TestClient
|
94
|
+
|
95
|
+
end #module FuncTestBioOldBiofetchEmulator
|
96
|
+
|
metadata
ADDED
@@ -0,0 +1,132 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-old-biofetch-emulator
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Naohisa Goto
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-11-13 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bio
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ">="
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: 1.4.2
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ">="
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: 1.4.2
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rdoc
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ">="
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ">="
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: jeweler
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: bundler
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 1.0.21
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ">="
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 1.0.21
|
83
|
+
description: Emulator that emulates Bio::Fetch object in BioRuby as if old BioRuby
|
84
|
+
BioFetch server were still alive. It overrides methods and objects in Bio::Fetch,
|
85
|
+
and if the old BioRuby BioFetch server's URL is given, it intercepts all requests
|
86
|
+
and converts them into existing web services such as TogoWS, KEGG REST API, NCBI
|
87
|
+
E-Utilities, and GenomeNet(genome.jp).
|
88
|
+
email: ng@bioruby.org
|
89
|
+
executables: []
|
90
|
+
extensions: []
|
91
|
+
extra_rdoc_files:
|
92
|
+
- LICENSE.txt
|
93
|
+
- README.md
|
94
|
+
- README.rdoc
|
95
|
+
files:
|
96
|
+
- ".document"
|
97
|
+
- ".travis.yml"
|
98
|
+
- Gemfile
|
99
|
+
- LICENSE.txt
|
100
|
+
- README.md
|
101
|
+
- README.rdoc
|
102
|
+
- Rakefile
|
103
|
+
- VERSION
|
104
|
+
- lib/bio-old-biofetch-emulator.rb
|
105
|
+
- lib/bio-old-biofetch-emulator/emulator.rb
|
106
|
+
- test/helper.rb
|
107
|
+
- test/test_bio-old-biofetch-emulator.rb
|
108
|
+
homepage: http://github.com/ngoto/bioruby-old-biofetch-emulator
|
109
|
+
licenses:
|
110
|
+
- MIT
|
111
|
+
metadata: {}
|
112
|
+
post_install_message:
|
113
|
+
rdoc_options: []
|
114
|
+
require_paths:
|
115
|
+
- lib
|
116
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
117
|
+
requirements:
|
118
|
+
- - ">="
|
119
|
+
- !ruby/object:Gem::Version
|
120
|
+
version: '0'
|
121
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
122
|
+
requirements:
|
123
|
+
- - ">="
|
124
|
+
- !ruby/object:Gem::Version
|
125
|
+
version: '0'
|
126
|
+
requirements: []
|
127
|
+
rubyforge_project:
|
128
|
+
rubygems_version: 2.2.2
|
129
|
+
signing_key:
|
130
|
+
specification_version: 4
|
131
|
+
summary: Emulates as if old BioRuby BioFetch alives
|
132
|
+
test_files: []
|