solvebio 1.6.1 → 1.7.0

data/.bumpversion.cfg

@@ -0,0 +1,6 @@
+[bumpversion]
+current_version = 1.7.0
+files = lib/solvebio/version.rb
+commit = True
+tag = False
+

data/.gitignore

@@ -1,7 +1,8 @@
 *~
 .rvmrc
-/Gemfile.lock
-/pkg
-/solvebio-*.gem
-/test/data/.netrc
 Gemfile.lock
+pkg
+solvebio-*.gem
+test/data/.netrc
+Gemfile.lock
+*.swp

data/.travis.yml

@@ -1,7 +1,7 @@
 language: ruby
 before_script:
 - gem install netrc --version=0.7.7
-- gem install rest_client addressable
+- gem install rest_client addressable webmock
 - touch ~/.netrc
 - chmod 0600 ~/.netrc
 env:

data/Gemfile

@@ -4,3 +4,6 @@ source "https://rubygems.org"
 gem 'addressable'
 gem 'rest_client'
 gem 'netrc',  '~>0.7.7'  # rest_client needs netrc 0.7.7
+group :test do
+    gem 'webmock'
+end

data/README.md

@@ -1,35 +1,49 @@
 [![Build Status](https://travis-ci.org/solvebio/solvebio-ruby.svg)](https://travis-ci.org/solvebio/solvebio-ruby)
 
-# SolveBio Ruby Client
+SolveBio Ruby Client
+====================
 
+This is the SolveBio Ruby module and command-line interface (CLI).
 
-This packages provides a command-line interface (CLI) and Ruby API interface to SolveBio.
+For more information about SolveBio, see [solvebio.com](https://www.solvebio.com).
 
-For more information about the SolveBio API, https://www.solvebio.com/docs/api/
-For more information about SolveBio, see https://www.solvebio.com
 
-# Installation
+Guided Installation
+-------------------
 
-    gem install solvebio # may need sudo
+To use the guided installer, open up your terminal and paste this:
 
-Installing from git:
+    curl -kL install.solvebio.com/ruby | bash
 
-    git clone https://github.com/solvebio/solvebio-ruby.git
-	cd solvebio-ruby
-	gem install netrc  # install gem dependencies, may need sudo
-	rake test          # or "make test"
-    sudo rake install  # or "make install"
 
-This also builds a *solvebio* gem which you can use elsewhere.
+Manual Installation
+-------------------
+
+    sudo gem install solvebio
+
 
-But note, you can also run right inside the git repository without installing anything. For example, running:
+Installing from Git
+-------------------
+
+First, install dependencies:
+	
+    gem install rest_client
+    gem install addressable
+    gem install netrc
+
+Install from source:
 
     git clone https://github.com/solvebio/solvebio-ruby.git
-	solvebio-ruby/bin/solvebio.rb
+	cd solvebio-ruby
+    rake test
+    sudo rake install
+
 
-will get you into a solvebio irb shell. Just about any Ruby file in the project can be run standalone, and when done so, it demos that Ruby code.
+This will install the `solvebio` gem and the `solvebio.rb` CLI.
 
-# Optional Gem dependencies
+
+Optional Dependencies
+---------------------
 
 The following optional gems can make your shell experience better
 
@@ -45,22 +59,8 @@ The following optional gems can make your shell experience better
 
     Localization for number formatting
 
-# Demo code and Documentation
-
-See the [demo folder](https://github.com/solvebio/solvebio-ruby/tree/master/demo) for ready-to-run examples.
-
-The online [SolveBio Python API documentation](https://www.solvebio.com/docs/api/?python) has additional examples. To use these with the Ruby client,  change `import solvebio` to `require 'solvebio'` and change `solvebio.` to `SolveBio::` everywhere it occurs.
-
-e.g., a Python example:
-
-    solvebio.Depository.retrieve("ClinVar").versions()
-
-the same Python example ported to Ruby:
-
-    SolveBio::Depository.retrieve("ClinVar").versions()
-
-As with any other Ruby method call, you can drop the final parenthesis if you like.
 
-# To Do
+Documentation
+-------------
 
-This hasn't been extensively field tested yet.
+See the [SolveBio API Reference](https://www.solvebio.com/docs/api/?ruby) for more information about using the API.

data/Rakefile

@@ -10,12 +10,10 @@ end
 
 require 'rubygems/package_task'
 
-desc "Validate the gemspec"
 task :gemspec do
   gemspec.validate
 end
 
-desc "Build the gem"
 task :package=>:gem
 task :gem=>:gemspec do
   Dir.chdir(ROOT_DIR) do
@@ -25,7 +23,6 @@ task :gem=>:gemspec do
   end
 end
 
-desc "Install the gem locally"
 task :install => :gem do
   Dir.chdir(ROOT_DIR) do
     sh %{gem install --both pkg/#{gemspec.file_name}}
@@ -33,27 +30,13 @@ task :install => :gem do
 end
 
 require 'rake/testtask'
-desc "Test everything."
 Rake::TestTask.new(:test) do |t|
   t.libs << './lib'
-  t.test_files = FileList['test/test-*.rb']
+  t.pattern = './test/**/test*.rb'
   t.verbose = true
 end
 
-
-require 'rbconfig'
-RUBY_PATH = File.join(RbConfig::CONFIG['bindir'],
-                      RbConfig::CONFIG['RUBY_INSTALL_NAME'])
-desc "Run all of the demo files."
-task :'run-demo' do
-    FileList['demo/*.rb']+FileList['demo/*/*.rb'].each do |ruby_file|
-        puts(('-' * 20) + ' ' + ruby_file + ' ' + ('-' * 20))
-        system(RUBY_PATH, ruby_file)
-    end
-end
-
 task :test => :lib
 
-desc "same as test"
 task :check => :test
 task :default => :test

data/bin/solvebio.rb

@@ -1,36 +1,34 @@
 #!/usr/bin/env ruby
 # -*- coding: utf-8 -*-
 
-# SolveBio Ruby command-line program
-
-require_relative '../lib/solvebio'
-require_relative '../lib/cli/options'
-require_relative '../lib/cli/irb'
+require 'solvebio'
+require 'solvebio/cli'
 
 DIR = File.dirname(__FILE__)
-TEST_PROGRAM = File.join(DIR, %w(.. demo test-api.rb))
-
-include SolveBio::CLIOptions
-options, rest, parser = process_options(ARGV)
 
-rest = ['shell'] if rest.empty?
+include SolveBio
+include SolveBio::CLI
+include SolveBio::CLI::Auth
+include SolveBio::CLI::Credentials
+include SolveBio::CLI::Tutorial
 
-include SolveBio::Auth
+options, argv = process_options(ARGV)
+argv = ['shell'] if argv.empty?
 
-cmd = rest.shift
+cmd = argv.shift
 case cmd
 when 'shell'
     IRB::shell
 when 'login'
-    login *rest
+    login
 when 'logout'
     logout
 when 'whoami'
     whoami
-when 'test'
-    system(TEST_PROGRAM)
+when 'tutorial'
+    tutorial
 else
-    $stderr.puts "Unknown solvbio.rb command: #{cmd}"
+    $stderr.puts "Unknown subcommand command: #{cmd}"
     $stderr.puts parser
     exit 1
 end

data/installer

@@ -0,0 +1,64 @@
+#!/usr/bin/env bash
+#
+# This is the guided installer for the SolveBio Ruby Client:
+#
+#    curl -kL install.solve.bio/ruby | bash
+#
+
+echo
+echo "     ____        _           ____  _"
+echo "    / ___|  ___ | |_   _____| __ )(_) ___"
+echo "    \___ \ / _ \| \ \ / / _ \  _ \| |/ _ \\"
+echo "     ___) | (_) | |\ V /  __/ |_) | | (_) |"
+echo "    |____/ \___/|_| \_/ \___|____/|_|\___/"
+echo
+echo "    Copyright © 2014 Solve, Inc. <https://www.solvebio.com>. All rights reserved."
+echo
+
+shopt -s extglob
+
+function fail_exit() {
+    echo
+    echo "    #####################################"
+    echo
+    echo "    Failed to install SolveBio."
+    echo "    Contact us at support@solvebio.com"
+    echo
+    echo "    #####################################"
+    echo
+    exit
+}
+
+trap ctrl_c INT
+
+function ctrl_c() {
+    echo
+    echo
+    echo "    Installation was aborted..."
+    fail_exit
+}
+
+echo "    Installing SolveBio for Ruby..."
+echo
+echo "    IMPORTANT: Your computer's password may be required. It will NOT be sent to SolveBio."
+
+# Are we installing or upgrading?
+if [ $(gem list | grep solvebio -c) -ne 0 ]; then
+    sudo gem update -q solvebio 2>&1 > /dev/null
+else
+    sudo gem install -q solvebio 2>&1 > /dev/null
+fi
+
+if [ $? -eq 0 ]; then
+    echo
+    echo "    ##############################################"
+    echo
+    echo "    Success! SolveBio for Ruby is now installed."
+    echo
+    echo "    Please run 'solvebio.rb login' to finish the setup."
+    echo
+    echo "    ##############################################"
+    echo
+else
+    fail_exit
+fi

data/lib/solvebio.rb

@@ -1,14 +1,53 @@
-# -*- coding: utf-8 -*-
-# Something to pull in the entire SolveBio API.
+# SolveBio Ruby bindings
+# Learn more at https://www.solvebio.com/docs/api
+require 'logger'
+require 'fileutils'
+require 'json'
+require 'logger'
+require 'netrc'
+require 'openssl'
+require 'rest_client'
+require 'uri'
+require 'addressable/uri'
+require 'set'
 
-require_relative 'resource/main'
-require_relative 'query'
+require 'solvebio/version'
+require 'solvebio/util'
+require 'solvebio/tabulate'
+require 'solvebio/solve_object'
+require 'solvebio/api_resource'
+require 'solvebio/singleton_api_resource'
+require 'solvebio/list_object'
+require 'solvebio/client'
+require 'solvebio/api_operations'
+require 'solvebio/locale'
+require 'solvebio/query'
+require 'solvebio/filter'
+require 'solvebio/acccount'
+require 'solvebio/annotation'
+require 'solvebio/dataset'
+require 'solvebio/dataset_field'
+require 'solvebio/depository'
+require 'solvebio/depository_version'
+require 'solvebio/sample'
+require 'solvebio/user'
+require 'solvebio/errors'
 
-# cli/auth is a little nicer than credentials
-# FIXME: consider moving cli/auth moving out of cli?
-require_relative 'cli/auth'
+module SolveBio
+    class << self
+        attr_accessor :api_key, :api_host, :logger
+    end
 
-# Set authentication if possible
-include SolveBio::Credentials
-creds = get_credentials()
-SolveBio.api_key = SolveBio::Client.client.api_key = creds[1] if creds
+    @api_key     = ENV['SOLVEBIO_API_KEY']
+    @api_host    = ENV['SOLVEBIO_API_HOST'] || 'https://api.solvebio.com'
+
+    logfile      =
+        if ENV['SOLVEBIO_LOGFILE']
+            ENV['SOLVEBIO_LOGFILE']
+        else
+            dir = File::expand_path '~/.solvebio'
+            FileUtils.mkdir_p(dir) unless File.exist? dir
+            File::expand_path File.join(dir, 'solvebio.log')
+        end
+    @logger = Logger.new(logfile)
+end

data/lib/solvebio/acccount.rb

@@ -0,0 +1,4 @@
+module SolveBio
+    class Account < SingletonAPIResource
+    end
+end

data/lib/solvebio/annotation.rb

@@ -0,0 +1,11 @@
+#  Annotations are genomic samples that have been annotated.
+#   See https://www.solvebio.com/docs/api/?ruby#annotations
+module SolveBio
+    class Annotation < APIResource
+        include SolveBio::APIOperations::Create
+        include SolveBio::APIOperations::Update
+        include SolveBio::APIOperations::Download
+        include SolveBio::APIOperations::List
+        include SolveBio::APIOperations::Delete
+    end
+end

data/lib/solvebio/api_operations.rb

@@ -0,0 +1,147 @@
+module SolveBio
+    module APIOperations
+        module Create
+            module ClassMethods
+                def create(params={})
+                    response = Client.request('post', url, {:payload => params} )
+                    Util.to_solve_object(response)
+                end
+            end
+
+            def self.included(base)
+                base.extend(ClassMethods)
+            end
+        end
+
+        module Delete
+            def delete(params={})
+                response = Client.request('delete', url, params)
+                refresh_from(response)
+            end
+        end
+        
+        module Update
+            def save
+                refresh_from(request('patch', url,
+                                     {:payload => serialize(self)}))
+                return self
+            end
+
+            def serialize(obj)
+                params = {}
+                if obj.unsaved_values
+                    obj.unsaved_values.each do |k|
+                        next if k == 'id'
+                        params[k] = getattr(obj, k) or ''
+                    end
+                end
+                params
+            end
+        end
+        
+        module Download
+            def download(path=nil)
+                download_url = url + '/download'
+                response = Client.get(download_url, :raw => true)
+
+                if response.code != 302
+                    # Some kind of error. We expect a redirect
+                    raise SolveError('Could not download file: response code' %
+                                     response.status_code)
+                end
+
+                download_url = response.headers[:location]
+                filename = download_url.split('%3B%20filename%3D')[1]
+
+                path = Dir.tmpdir unless path
+                filename = File.join(path, filename)
+                response = nil
+
+                response = Client.get(download_url, :raw => true,
+                                                :default_headers => false)
+
+                File.open(filename, 'wb') do |fh|
+                    fh.write(response.body)
+                end
+
+                self['filename'] = filename
+                self['code'] = response.code
+                self
+            end
+        end
+        
+        module Help
+            attr_reader :have_launchy
+
+            @@have_launchy = false
+            begin
+                @@have_launchy = require 'launchy'
+            rescue LoadError
+            end
+
+            def self.included base
+                base.send :include, InstanceMethods
+            end
+
+            module InstanceMethods
+                def help
+                    open_help(self['full_name'])
+                end
+            end
+
+            def open_help(path)
+                url = URI::join('https://www.solvebio.com/', path)
+                if @@have_launchy
+                    Launchy.open(url)
+                else
+                    puts('The SolveBio Ruby client needs the "launchy" gem to ' +
+                         "open help url: #{url.to_s}")
+                end
+            end
+        end
+        
+        module List
+            module ClassMethods
+                def all(params={})
+                    response = Client.get(url, {:params => params})
+                    Util.to_solve_object(response)
+                end
+            end
+
+            def self.included base
+                base.extend ClassMethods
+            end
+
+            def to_s
+                if self.class.constants.member?(:TAB_FIELDS)
+                    items = self.class.const_get(:TAB_FIELDS).map{
+                        |name| [name, self[name]]
+                    }
+                else
+                    items = self
+                end
+                return Tabulate.tabulate(items, ['Fields', 'Data'],
+                                                   ['right', 'left'], true)
+            end
+
+            def size
+                self[:total]
+            end
+            alias :total :size
+        end
+        
+        module Search
+            module ClassMethods
+                def search(query='', params={})
+                    params['q'] = query
+                    response = Client.get(url, {:params => params})
+                    Util.to_solve_object(response)
+                end
+            end
+
+            def self.included base
+                base.extend ClassMethods
+            end
+        end
+    end
+end