pipet 0.0.0 → 0.0.1

data/Gemfile

@@ -1,8 +1,10 @@
 source 'http://rubygems.org'
 
+gem 'thor'
 
 group :development do
   gem 'rspec', '2.14.1'
   gem 'bundler', '1.3.5'
   gem 'jeweler', '1.8.6'
+  gem 'pry'
 end

data/LICENSE.txt

@@ -0,0 +1,22 @@
+The MIT License (MIT)
+
+Copyright (c) [2013] [Austin G. Davis-Richardson]
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Sources/ncbi_nt.rb

@@ -0,0 +1,8 @@
+class NCBINT < Database
+
+  name 'ncbi/nt'
+  url 'ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz'
+  description 'NCBI non-redundant nucleotide database'
+  md5 'f77aff452dd1ba6b0e26b8d6b97b0a62'
+
+end

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.0.1

data/bin/pipet

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib', 'pipet'))
+
+Pipet::CLI.start

data/lib/database.rb

@@ -0,0 +1,12 @@
+class Database
+  class << self
+
+    ##
+    # Returns a list of all objects that inherited from Database
+    #
+    def all
+      ObjectSpace.each_object(Class).select { |klass| klass < self }
+    end
+
+  end
+end

data/lib/database_dsl.rb

@@ -0,0 +1,79 @@
+##
+# Database
+#
+# Creates a DSL for defining Databases
+# which can be downloaded using `pipet pull`
+#
+
+class Database
+
+  class << self
+
+    ##
+    # Specify the URL of a database
+    #
+    def url(url=nil)
+      @url ||= url
+    end
+
+    ##
+    # Specify MD5 checksum of database
+    #
+    def md5(val=nil)
+      @md5 ||= val
+    end
+
+    ##
+    #  Provide a description for the database
+    #
+    def description(val=nil)
+      @description ||= val
+    end
+
+    ##
+    # Name the database. This is used be `pipet pull`
+    #
+    def name(val=nil)
+      @name ||= val
+    end
+
+    ##
+    # Define type of database. This is like a tag.
+    # For example,
+    #
+    # type :nucleotide
+    # for a database of nucleotide sequences
+    #
+    # type :structure
+    # for a database of protein structures
+    #
+    def type(val=nil)
+      @type ||= val
+    end
+
+    ##
+    # Make sure all required attributes have been defined.
+    #
+    def validate
+      required_attributes = [
+        :name,
+        :md5,
+        :description,
+        :type
+      ]
+
+      required_attributes.map do |ra|
+        self.send(ra)
+      end.include? nil
+
+    end
+
+    ##
+    # Downloads the database, checks the MD5 sum.
+    #
+    def pull
+      `wget #{@url}`
+    end
+
+  end # class << self
+end

data/lib/pipet.rb

@@ -0,0 +1,15 @@
+require 'bundler'
+Bundler.require
+
+%w{database database_dsl}.each do |f|
+  require File.join(File.dirname(__FILE__), "#{f}.rb")
+end
+
+
+SOURCES = Dir.glob(File.join(File.dirname(__FILE__), '..', 'Sources', '*.rb'))
+
+SOURCES.each do |sf|
+  require sf
+end
+
+Dir.glob(File.join(File.dirname(__FILE__), 'pipet', '*.rb')).each { |f| require f }

data/lib/pipet/cli.rb

@@ -0,0 +1,6 @@
+module Pipet
+  class CLI < Thor
+  end
+end
+
+Dir.glob(File.join(File.dirname(__FILE__), 'tasks', '*.rb')).each { |f| require f }

data/lib/pipet/tasks/list.rb

@@ -0,0 +1,15 @@
+module Pipet
+  class CLI
+
+    desc 'list', 'list all available databases'
+
+    def list
+      databases = Database.all
+
+      databases.each do |db|
+        puts "#{db.name}"
+      end
+
+    end
+  end
+end

data/lib/pipet/tasks/pull.rb

@@ -0,0 +1,12 @@
+module Pipet
+  class CLI
+
+    desc 'pull', 'download a database'
+
+    def pull(name)
+      match = Database.all.keep_if { |x| x.name == name }.first
+      match.pull
+    end
+
+  end
+end

data/pipet.gemspec

@@ -5,23 +5,35 @@
 
 Gem::Specification.new do |s|
   s.name = "pipet"
-  s.version = "0.0.0"
+  s.version = "0.0.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin Richardson"]
   s.date = "2013-07-18"
   s.description = "Pipet is a package manager for bioinformatics databases that allows users to easily retrieve databases from their sources using the command line. Pipet also checks for database integrity via checksum"
   s.email = "harekrishna@gmail.com"
+  s.executables = ["pipet"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt"
+  ]
   s.files = [
     ".rspec",
     ".rvmrc",
     "Gemfile",
+    "LICENSE.txt",
     "Rakefile",
+    "Sources/ncbi_nt.rb",
     "VERSION",
+    "bin/pipet",
+    "lib/database.rb",
+    "lib/database_dsl.rb",
     "lib/pipet.rb",
+    "lib/pipet/cli.rb",
+    "lib/pipet/tasks/list.rb",
+    "lib/pipet/tasks/pull.rb",
     "pipet.gemspec",
     "readme.md",
-    "spec/.pipet_spec.rb.swp",
+    "spec/database_spec.rb",
     "spec/pipet_spec.rb",
     "spec/spec_helper.rb"
   ]
@@ -35,18 +47,24 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<thor>, [">= 0"])
       s.add_development_dependency(%q<rspec>, ["= 2.14.1"])
       s.add_development_dependency(%q<bundler>, ["= 1.3.5"])
       s.add_development_dependency(%q<jeweler>, ["= 1.8.6"])
+      s.add_development_dependency(%q<pry>, [">= 0"])
     else
+      s.add_dependency(%q<thor>, [">= 0"])
       s.add_dependency(%q<rspec>, ["= 2.14.1"])
       s.add_dependency(%q<bundler>, ["= 1.3.5"])
       s.add_dependency(%q<jeweler>, ["= 1.8.6"])
+      s.add_dependency(%q<pry>, [">= 0"])
     end
   else
+    s.add_dependency(%q<thor>, [">= 0"])
     s.add_dependency(%q<rspec>, ["= 2.14.1"])
     s.add_dependency(%q<bundler>, ["= 1.3.5"])
     s.add_dependency(%q<jeweler>, ["= 1.8.6"])
+    s.add_dependency(%q<pry>, [">= 0"])
   end
 end
 

data/readme.md

@@ -1,19 +1,29 @@
-= pipet
+# Pipet
 
-Description goes here.
+Bioinformatics Database "Package Manager".
 
-== Contributing to pipet
- 
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
-* Fork the project.
-* Start a feature/bugfix branch.
-* Commit and push until you are happy with your contribution.
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+## Example Usage
 
-== Copyright
+```bash
 
-Copyright (c) 2013 Austin Richardson. See LICENSE.txt for
-further details.
+# List avaiable databases
+darwin@beagle> pipet list
+ncbi/nt
 
+# Download a database
+darwin@beagle> pipet pull ncbi/nt.fasta
+Downloading ncbi/nt.fasta from ftp://ftp.ncbi.nih.gov/blast/db/fasta/nt.gz
+Success!
+nt.fasta located in ~/.pipet/ncbi/nt.fasta
+```
+
+## Installation
+
+```
+# on most 'nix systems
+(sudo) gem install pipet
+```
+
+# Copyright
+
+Copyright (c) 2013 Austin Richardson. See LICENSE.txt for details.

data/spec/database_spec.rb

@@ -0,0 +1,26 @@
+require 'spec_helper'
+
+describe Database do
+
+  let :test_db do
+    class TestDB < Database
+      url 'hello world!'
+      name 'hello world!'
+      md5 '6f5902ac237024bdd0c176cb93063dc4'
+    end
+    TestDB
+  end
+
+  it 'should provide a DSL for defining bioinformatics databases' do
+    test_db.should_not be_nil
+  end
+
+  it '#validate should validate attributes' do
+    test_db.validate.should_not be_false
+  end
+
+  it '#all returns a list of all classes that inherited from Database' do
+    Database.all.include?(test_db).should be_true
+  end
+
+end

data/spec/pipet_spec.rb

@@ -1,7 +1 @@
-require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
-
-describe "Pipet" do
-  it "fails" do
-    fail "hey buddy, you should probably rename this file and start specing for real"
-  end
-end
+require 'spec_helper'

data/spec/spec_helper.rb

@@ -1,13 +1,11 @@
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 
-require 'rspec'
+require 'bundler'
 require 'pipet'
 
-# Requires supporting files with custom matchers and macros, etc,
-# in ./support/ and its subdirectories.
-Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+Bundler.require :development
 
 RSpec.configure do |config|
 
-end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: pipet
 version: !ruby/object:Gem::Version
-  version: 0.0.0
+  version: 0.0.1
   prerelease: 
 platform: ruby
 authors:
@@ -11,6 +11,22 @@ bindir: bin
 cert_chain: []
 date: 2013-07-18 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -59,23 +75,49 @@ dependencies:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.8.6
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Pipet is a package manager for bioinformatics databases that allows users
   to easily retrieve databases from their sources using the command line. Pipet also
   checks for database integrity via checksum
 email: harekrishna@gmail.com
-executables: []
+executables:
+- pipet
 extensions: []
-extra_rdoc_files: []
+extra_rdoc_files:
+- LICENSE.txt
 files:
 - .rspec
 - .rvmrc
 - Gemfile
+- LICENSE.txt
 - Rakefile
+- Sources/ncbi_nt.rb
 - VERSION
+- bin/pipet
+- lib/database.rb
+- lib/database_dsl.rb
 - lib/pipet.rb
+- lib/pipet/cli.rb
+- lib/pipet/tasks/list.rb
+- lib/pipet/tasks/pull.rb
 - pipet.gemspec
 - readme.md
-- spec/.pipet_spec.rb.swp
+- spec/database_spec.rb
 - spec/pipet_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/audy/pipet
@@ -93,7 +135,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -4135599796043976134
+      hash: -106065623171849882
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: