solvebio 1.6.1 → 1.7.0

data/lib/cli/help.rb

@@ -1,13 +0,0 @@
-module SolveBio
-    # Shell help
-    def help
-        puts <<-HELP
-Constants SAMPLE_DEPO, SAMPLE_DEPO_VERSION, and SAMPLE_DATASET are
-available for and example depository, depository_versions or dataset.
-
-By setting environment variable SOLVEBIO_IRBRC, you can add your own
-custom irb profile.
-HELP
-    end
-    module_function :help
-end

data/lib/cli/irbrc.rb

@@ -1,54 +0,0 @@
-# -*- ruby -*-
-# irbrc profile for SolveBio
-IRB.conf[:PROMPT_MODE] = :SIMPLE
-IRB.conf[:PROMPT][:SIMPLE] = {
-  :PROMPT_C => '[SolveBio] In ?: ',  # Prompt when continuing a statement
-  :PROMPT_I => '[SolveBio] In  : ',  # Normal prompt
-  :PROMPT_N => '[SolveBio] In +: ',  # Prompt when indenting code
-  :PROMPT_S => '[SolveBio] In %l: ', # Prompt when continuing a string
-  :RETURN   => "[SolveBio] Out : %s\n"
- }
-
-require_relative '../solvebio'
-require_relative '../resource/apiresource'
-include SolveBio::Auth
-
-# Set some demo names that can be used.
-SAMPLE_DEPO         = 'ClinVar'
-SAMPLE_DEPO_VERSION = "#{SAMPLE_DEPO}/2.0.0-1"
-SAMPLE_DATASET      = "#{SAMPLE_DEPO_VERSION}/Variants"
-
-have_completion = nil
-begin
-    require 'bond' and require 'bond/completion'
-    have_completion = 'bond'
-    rescue LoadError
-      begin
-          have_completion = require 'irb/completion'
-      rescue LoadError
-          have_completion = false
-      end
-    end
-'irb/completion'
-'bond' 'bond/completion'
-
-puts <<-INTRO
-You are in a SolveBio Interactive Ruby (irb) session...
-Type SolveBio::help for help on SolveBio.
-INTRO
-
-unless have_completion
-    if have_completion != 'bond'
-        puts "You might get better completion using the 'bond' gem"
-    end
-end
-
-# Report whether we are logged in.
-include SolveBio::Credentials
-creds = get_credentials()
-if creds
-    puts "You are logged in as #{creds[0]}"
-else
-    puts 'You are not logged in yet. Login using "login [email]"'
-
-end

data/lib/cli/options.rb

@@ -1,75 +0,0 @@
-#!/usr/bin/env ruby
-# -*- coding: utf-8 -*-
-
-# SolveBio Ruby command-line option processing
-
-require 'optparse'
-require_relative '../client'
-
-module SolveBio::CLIOptions
-
-    PROGRAM = 'solvebio.rb'
-
-    def show_version
-        "#{PROGRAM}, version #{SolveBio::VERSION}"
-    end
-
-    # Main parser for the SolveBio command line client
-    def setup_options(options, stdout=$stdout, stderr=$stderr)
-
-        OptionParser.new do |opts|
-            opts.banner = "Usage: solvebio.rb [options] <command> [<args>]"
-            opts.on_tail('-v', '--version',
-                         'print the version') do
-                options[:version] = true
-                stdout.puts "#{PROGRAM}, version #{SolveBio::VERSION}"
-                exit 0
-            end
-
-            opts.on('--api-host NAME', String,
-                    'Override the default SolveBio API host') do
-                |api_host|
-                options[:api_host] = api_host
-            end
-
-            opts.on('--api-key STRING', String,
-                    'Manually provide a SolveBio API key') do
-                |api_key|
-                options[:api_key] = api_key
-            end
-
-            opts.on('-h', '--help', 'Display this screen') do
-                puts opts
-                puts <<-EOH
-
-SolveBio Commands:
-    login [email]       Login and save credentials. Use email if provided.
-    logout              Logout and delete saved credentials
-    whoami              Show your SolveBio email address
-    shell               Open a SolveBio IRB shell
-    test                Make sure the SolveBio API is working correctly
-EOH
-                exit
-            end
-        end
-    end
-
-end
-
-def process_options(argv)
-    options = {}
-    args  = setup_options(options)
-    rest  = args.parse argv
-
-    SolveBio::Client.client.api_host =  options[:api_host] if
-        options[:api_host]
-    SolveBio::Client.client.api_key =  options[:api_key] if
-        options[:api_key]
-    return options, rest, args
-end
-
-if __FILE__ == $0
-    include SolveBio::CLIOptions
-    options, rest, parser  = process_options(ARGV)
-    p options, rest, parser
-end

data/lib/client.rb

@@ -1,154 +0,0 @@
-#!/usr/bin/env ruby
-# -*- coding: utf-8 -*-
-require 'openssl'
-require 'rest_client'
-require 'json'
-require 'addressable/uri'
-require_relative 'credentials'
-require_relative 'errors'
-
-# A requests-based HTTP client for SolveBio API resources
-class SolveBio::Client
-
-    attr_reader :headers, :api_host
-    attr_accessor :api_key
-
-    # Add our own kind of Authorization tokens. This has to be
-    # done this way, late, because the rest-client gem looks for
-    # .netrc and will set basic authentication if it finds a match.
-    RestClient.add_before_execution_proc do | req, args |
-        if args[:authorization]
-            req.instance_variable_get('@header')['authorization'] = [args[:authorization]]
-        end
-    end
-
-    def initialize(api_key=nil, api_host=nil)
-        @api_key = api_key || SolveBio::api_key
-        SolveBio::api_key  ||= api_key
-        @api_host = api_host || SolveBio::API_HOST
-
-        # Mirroring comments from:
-        # http://ruby-doc.org/stdlib-2.1.2/libdoc/net/http/rdoc/Net/HTTP.html
-        # gzip compression is used in preference to deflate
-        # compression, which is used in preference to no compression.
-        @headers  = {
-            :content_type     => :json,
-            :accept           => :json,
-            'Accept-Encoding' => 'gzip;q=1.0,deflate;q=0.6,identity;q=0.3',
-            'User-Agent'      => 'SolveBio Ruby Client %s [%s/%s]' % [
-                SolveBio::VERSION,
-                SolveBio::RUBY_IMPLEMENTATION,
-                SolveBio::RUBY_VERSION
-            ]
-        }
-    end
-
-    DEFAULT_REQUEST_OPTS = {
-        :raw             => false,
-        :default_headers => true
-    }
-
-    # Issues an HTTP GET across the wire via the Ruby 'rest-client'
-    # library. See *request()* for information on opts.
-    def get(url, opts={})
-        request('get', url, opts)
-    end
-
-    # Issues an HTTP POST across the wire via the Ruby 'rest-client'
-    # library. See *request* for information on opts.
-    def post(url, data, opts={})
-        opts[:payload] =
-            if opts.member?(:no_json)
-                data
-            else
-                data.to_json
-            end
-        request('post', url, opts)
-    end
-
-    # Issues an HTTP Request across the wire via the Ruby 'rest-client'
-    # library.
-    def request(method, url, opts={})
-
-        opts = DEFAULT_REQUEST_OPTS.merge(opts)
-
-        # Expand URL with API host if none was given
-        api_host = @api_host or SolveBio::API_HOST
-
-        if not api_host
-            raise SolveBio::Error.new('No SolveBio API host is set')
-        elsif not url.start_with?(api_host)
-            url = Addressable::URI.join(api_host, url).to_s
-        end
-
-        # Handle some default options and add authorization header
-        if opts[:default_headers] and @api_key
-            headers = @headers.merge(opts[:headers]||{})
-            authorization = "Token #{@api_key}"
-        else
-            headers = nil
-            authorization = nil
-        end
-
-        SolveBio::logger.debug('API %s Request: %s' % [method.upcase, url])
-
-        response = nil
-        RestClient::Request.
-            execute(:method        => method,
-                    :url           => url,
-                    :headers       => headers,
-                    :authorization => authorization,
-                    :timeout       => opts[:timeout] || 80,
-                    :payload       => opts[:payload]) do
-            |resp, request, result, &block|
-            response = resp
-            if response.code < 200 or response.code >= 400
-                self.handle_api_error(result)
-            end
-        end
-
-        response = JSON.parse(response) unless opts[:raw]
-        response
-    end
-
-    def self.handle_request_error(e)
-        # FIXME: go over this. It is still a rough translation
-        # from the python.
-        err = e.inspect
-        if e.kind_of?(requests.exceptions.RequestException)
-            msg = SolveBio::Error::Default_message
-        else
-            msg = "Unexpected error communicating with SolveBio.\n" +
-                "It looks like there's probably a configuration " +
-                'issue locally.\nIf this problem persists, let us ' +
-                'know at contact@solvebio.com.'
-        end
-        msg = msg + "\n\n(Network error: #{err}"
-        raise SolveBio::Error.new(nil, msg)
-    end
-
-    # SolveBio's API error handler returns a SolveBio::Error.  The
-    # *response* parameter is a (subclass) of Net::HTTPResponse.
-    def handle_api_error(response)
-        SolveBio::logger.info("API Error: #{response.msg}") unless
-            [400, 401, 403, 404].member?(response.code.to_i)
-        raise SolveBio::Error.new(response)
-    end
-
-    def self.client
-        @@client ||= SolveBio::Client.new()
-    end
-
-    def self.get(*args)
-        client.get(*args)
-    end
-
-    def self.post(*args)
-        client.post(*args)
-    end
-
-    def self.request(*args)
-        client.request(*args)
-    end
-
-end

data/lib/credentials.rb

@@ -1,67 +0,0 @@
-#!/usr/bin/env ruby
-# -*- coding: utf-8 -*-
-# Deals with reading netrc credentials
-require_relative 'main'
-require 'netrc'
-require 'addressable/uri'
-
-#
-#    Raised if the credentials are not found.
-#
-class CredentialsError < RuntimeError
-end
-
-module SolveBio::Credentials
-
-    module_function
-
-    # SolveBio API host -- just the hostname
-    def api_host
-        Addressable::URI.parse(SolveBio::API_HOST).host
-    end
-
-    def netrc_path
-        path =
-            if ENV['NETRC_PATH']
-                File.join(ENV['NETRC_PATH'], ".netrc")
-            else
-                Netrc.default_path
-            end
-        if not File.exist?(path)
-            raise IOError, "netrc file #{path} not found"
-        end
-        path
-    end
-
-    #
-    #    Returns the tuple user / password given a path for the .netrc file.
-    #    Raises CredentialsError if no valid netrc file is found.
-    #
-    def get_credentials
-        n = Netrc.read(netrc_path)
-        return n[api_host]
-    rescue Netrc::Error => e
-        raise CredentialsError, "Could not read .netrc file: #{e}"
-    end
-    module_function :get_credentials
-
-    def delete_credentials
-        n = Netrc.read(netrc_path)
-        n.delete(api_host)
-        n.save
-    end
-
-    def save_credentials(email, api_key)
-        n = Netrc.read(netrc_path)
-        # Overwrites any existing credentials
-        n[api_host] = email, api_key
-        n.save
-    end
-end
-
-# Demo code
-if __FILE__ == $0
-    include SolveBio::Credentials
-    puts "authentication: #{netrc_path}"
-    puts "creds", get_credentials
-end

data/lib/errors.rb

@@ -1,81 +0,0 @@
-#!/usr/bin/env ruby
-# -*- coding: utf-8 -*-
-require_relative 'main'
-
-class SolveBio::Error < RuntimeError
-    Default_message =
-        'Unexpected error communicating with SolveBio. ' +
-        'If this problem persists, let us know at ' +
-        'contact@solvebio.com.'
-
-    attr_reader :json_body
-    attr_reader :status_code
-    attr_reader :message
-    attr_reader :field_errors
-
-    def initialize( response=nil, message=nil)
-        @json_body = nil
-        @status_code = nil
-        @message = message or Default_message
-        @field_errors = []
-
-        if response
-            @status_code = response.code.to_i
-            @message     = response.message
-            begin
-                @json_body = JSON.parse(response.body)
-            rescue
-                @message = '404 Not Found.' if @status_code == 404
-                SolveBio.logger.debug(
-                    "API Response (%d): No content." % @status_code)
-            else
-                SolveBio.logger.debug(
-                    "API Response (#{@status_code}): #{@json_body}")
-
-                if [400, 401, 403, 404].member?(@status_code)
-                    @message = 'Bad request.'
-
-                    if @json_body.member?('detail')
-                        @message = '%s' % @json_body['detail']
-                    end
-
-                    if @json_body.member?('non_field_errors')
-                        @message = '%s.' % \
-                            @json_body['non_field_errors'].join(', ')
-                    end
-
-                    @json_body.each do |k, v|
-                        unless ['detail', 'non_field_errors'].member?(k)
-                            v = v.join(', ') if v.kind_of?(Array)
-                            @field_errors << ('%s (%s)' % [k, v])
-                        end
-                    end
-
-                    unless @field_errors.empty?
-                        @message += (' The following fields were missing ' +
-                            'or invalid: %s' %
-                                         @field_errors.join(', '))
-                    end
-                end
-            end
-        end
-        self
-    end
-
-    def to_s
-        @message
-    end
-end
-
-# Demo code
-if __FILE__ == $0
-    puts SolveBio::Error.new
-    puts SolveBio::Error.new(nil, 'Hi there').inspect
-    puts SolveBio::Error.new(nil, 'Hi there').to_s
-    puts SolveBio::Error.new(nil, ['Hello, ', 'again.']).inspect
-
-    require 'net/http'
-    response = Net::HTTPUnauthorized.new('HTTP 1.1', '404', 'No creds')
-    puts SolveBio::Error.new(response).to_s
-
-end