solvebio 1.5.2 → 1.6.1

data/.travis.yml

@@ -1,13 +1,18 @@
 language: ruby
 before_script:
-  - gem install netrc
-  - touch ~/.netrc
-  - chmod 0600 ~/.netrc
+- gem install netrc --version=0.7.7
+- gem install rest_client addressable
+- touch ~/.netrc
+- chmod 0600 ~/.netrc
 env:
-  - "COLUMNS=80"
+  global:
+  - COLUMNS=80
 script: rake
 rvm:
-  - 1.9.3
-  - 2.0.0
-  - 2.1.1
-  - 2.1.2
+- 1.9.3
+- 2.0.0
+- 2.1.1
+- 2.1.2
+notifications:
+  slack:
+    secure: aIpZOAZwIk/3ZToZqAPEdM4yKyD6UuDmR+KyH2eL+24mTxU+Jp8hum02LlRsdeOXweup9Ov/h7SuDQXfEt506oLmkhfDwk+v2j2RkHmFco4l4M+rI1QAtJw1xhzrscwgnJqkW8n81U5Se84KzU+x7N6EvDcki8G1KlbuU2A9f74=

data/Gemfile

@@ -1,4 +1,6 @@
-# A sample Gemfile
+# A bundler Gemfile for specifying dependencies. See http://bundler.io/
 source "https://rubygems.org"
 
-gem "netrc"
+gem 'addressable'
+gem 'rest_client'
+gem 'netrc',  '~>0.7.7'  # rest_client needs netrc 0.7.7

data/README.md

@@ -10,13 +10,15 @@ For more information about SolveBio, see https://www.solvebio.com
 
 # Installation
 
-Right now we only support installing from git:
+    gem install solvebio # may need sudo
+
+Installing from git:
 
     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
+	rake test          # or "make test"
+    sudo rake install  # or "make install"
 
 This also builds a *solvebio* gem which you can use elsewhere.
 

data/demo/cheatsheet.rb

@@ -0,0 +1,31 @@
+# Cheet sheet for SolveBio API
+require 'solvebio'
+
+# Load the Dataset object
+dataset = SolveBio::Dataset.retrieve('ClinVar/2.0.0-1/Variants')
+
+# Print the Dataset
+puts dataset.query()
+
+# Get help (fields/facets)
+dataset.help()
+
+# Query the dataset (filterless)
+q = dataset.query()
+
+filters = SolveBio::Filter.new :gene_symbols => "BRCA2"
+
+puts dataset.query(:filters => filters)
+
+# Multiple keyword filter (boolean 'or')
+filters = SolveBio::Filter.new :gene_symbols => "BRCA2"
+filters |= SolveBio::Filter.new :gene_symbols => "BRCA1"
+
+# Same as above 'or' in one go using 'in'
+filters = SolveBio::Filter.new :gene_symbols__in => ["BRCA2", "BRCA1"]
+
+puts dataset.query(:filters => filters)
+
+# Range filter. Like 'in' for a contiguous numeric range
+dataset.query(filters =>
+              SolveBio::RangeFilter.new('hg38', "13", 32_200_000, 32_200_500))

data/lib/cli/auth.rb

@@ -37,9 +37,9 @@ module SolveBio::Auth
             :architecture          => SolveBio::ARCHITECTURE,
             # :processor             => processor(),
         }
-        SolveBio::Client.client.request('post',
-                                        '/v1/reports/install',
-                                        data) rescue nil
+        SolveBio::Client.client
+            .request('post', '/v1/reports/install',
+                     {:params => data}) rescue nil
     end
 
 
@@ -51,7 +51,7 @@ module SolveBio::Auth
     # Prompt user for login information (email/password).
     # Email and password are used to get the user's auth_token key.
     #
-    def login(email=nil, password=nil)
+    def login(email=nil)
         delete_credentials
 
         email, password = ask_for_credentials email unless
@@ -65,8 +65,8 @@ module SolveBio::Auth
         # code.  Not sure if it's valid here, or what the equivalent
         # is.
         begin
-            response = SolveBio::Client.
-                client.request('post', '/v1/auth/token', data)
+            response = SolveBio::Client.client
+                .request 'post', '/v1/auth/token', {:payload => data}
         rescue SolveBio::Error => e
             puts "Login failed: #{e.to_s}"
             return false

data/lib/cli/irbrc.rb

@@ -10,6 +10,7 @@ IRB.conf[:PROMPT][:SIMPLE] = {
  }
 
 require_relative '../solvebio'
+require_relative '../resource/apiresource'
 include SolveBio::Auth
 
 # Set some demo names that can be used.
@@ -48,6 +49,6 @@ 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 [, password]]"'
+    puts 'You are not logged in yet. Login using "login [email]"'
 
 end

data/lib/cli/options.rb

@@ -46,7 +46,7 @@ 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 the SolveBio Python shell
+    shell               Open a SolveBio IRB shell
     test                Make sure the SolveBio API is working correctly
 EOH
                 exit

data/lib/client.rb

@@ -1,30 +1,39 @@
 #!/usr/bin/env ruby
 # -*- coding: utf-8 -*-
 require 'openssl'
-require 'net/http'
+require 'rest_client'
 require 'json'
+require 'addressable/uri'
 require_relative 'credentials'
 require_relative 'errors'
 
-# import textwrap
-
 # 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'    => 'application/json',
-            'Accept'          => 'application/json',
+            :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,
@@ -34,119 +43,112 @@ class SolveBio::Client
         }
     end
 
-    def request(method, url, params=nil, raw=false)
+    DEFAULT_REQUEST_OPTS = {
+        :raw             => false,
+        :default_headers => true
+    }
 
-        if not @api_host
-            raise SolveBio::Error.new(nil, 'No SolveBio API host is set')
-        elsif not url.start_with?(@api_host)
-            url = URI.join(@api_host, url).to_s
-        end
+    # 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
 
-        uri  = URI.parse(url)
-        http = Net::HTTP.new(uri.host, uri.port)
+    # 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
 
-        # Note: there's also read_timeout and ssl_timeout
-        http.open_timeout = 80 # in seconds
+    # Issues an HTTP Request across the wire via the Ruby 'rest-client'
+    # library.
+    def request(method, url, opts={})
 
-        if uri.scheme == 'https'
-            http.use_ssl = true
-            # FIXME? Risky - see
-            # http://www.rubyinside.com/how-to-cure-nethttps-risky-default-https-behavior-4010.html
-            http.verify_mode = OpenSSL::SSL::VERIFY_NONE
-        end
+        opts = DEFAULT_REQUEST_OPTS.merge(opts)
 
-        http.set_debug_output($stderr) if $DEBUG
-        SolveBio::logger.debug('API %s Request: %s' % [method.upcase, url])
+        # Expand URL with API host if none was given
+        api_host = @api_host or SolveBio::API_HOST
 
-        request = nil
-        if ['POST', 'PUT', 'PATCH'].member?(method.upcase)
-            # FIXME? do we need to do something different for
-            # PUT and PATCH?
-            request = Net::HTTP::Post.new(uri.request_uri)
-            request.body = params.to_json
-        else
-            request = Net::HTTP::Get.new(uri.request_uri)
-        end
-        @headers.each { |k, v| request.add_field(k, v) }
-        request.add_field('Authorization', "Token #{@api_key}") if @api_key
-        response = http.request(request)
-
-        # FIXME: There's probably gzip decompression built in to
-        # net/http. Until I figure out how to get that to work, the
-        # below works.
-        case response
-        when Net::HTTPSuccess then
-            begin
-                if response['Content-Encoding'].eql?( 'gzip' ) then
-                    puts "Performing gzip decompression for response body." if $DEBUG
-                    sio = StringIO.new( response.body )
-                    gz = Zlib::GzipReader.new( sio )
-                    response.body = gz.read()
-                end
-            rescue Exception
-                puts "Error occurred (#{$!.message})" if $DEBUG
-                # handle errors
-                raise $!.message
-            end
+        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
 
-        status_code = response.code.to_i
-        if status_code < 200 or status_code >= 300
-            handle_api_error(response)
+        # 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
 
-        if raw
-            return response.body
-        else
-            return JSON.parse(response.body)
+        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 handle_request_error(e)
+    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. ' +
+            msg = "Unexpected error communicating with SolveBio.\n" +
                 "It looks like there's probably a configuration " +
-                'issue locally. If this problem persists, let us ' +
+                '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)
-        if [400, 401, 403, 404].member?(response.code.to_i)
-            raise SolveBio::Error.new(response)
-        else
-            SolveBio::logger.info("API Error: #{response.msg}")
-            raise SolveBio::Error.new(response)
-        end
+        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
-
-if __FILE__ == $0
-    puts SolveBio::Client.client.headers
-    puts SolveBio::Client.client.api_host
-    client = SolveBio::Client.new(nil, 'http://google.com')
-    response = client.request('http', 'http://google.com') rescue 'no good'
-    puts response.inspect
-    puts '-' * 30
-    response = client.request('http', 'http://www.google.com') rescue 'nope'
-    puts response.inspect
-    puts '-' * 30
-    response = client.request('http', 'https://www.google.com') rescue 'nope'
-    puts response.inspect
-end

data/lib/credentials.rb

@@ -3,7 +3,7 @@
 # Deals with reading netrc credentials
 require_relative 'main'
 require 'netrc'
-require 'uri'
+require 'addressable/uri'
 
 #
 #    Raised if the credentials are not found.
@@ -17,7 +17,7 @@ module SolveBio::Credentials
 
     # SolveBio API host -- just the hostname
     def api_host
-        URI(SolveBio::API_HOST).host
+        Addressable::URI.parse(SolveBio::API_HOST).host
     end
 
     def netrc_path

data/lib/main.rb

@@ -7,12 +7,21 @@
 # Have questions or comments? email us at: contact@solvebio.com
 
 require 'logger'
+require 'fileutils'
 
 module SolveBio
 
-    VERSION      = '1.5.0'
+    VERSION      = '1.6.1'
     @api_key     = ENV['SOLVEBIO_API_KEY']
-    @logger      = Logger.new('/tmp/solvebio.log')
+    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)
     API_HOST     = ENV['SOLVEBIO_API_HOST'] || 'https://api.solvebio.com'
 
     # Config info in reports and requests. Encapsulate more?

data/lib/query.rb

@@ -118,11 +118,11 @@ class SolveBio::PagingQuery
             return 'query returned 0 results'
         end
 
+        sorted_items = SolveBio::Tabulate.
+            tabulate(self[0].to_a.sort_by{|x| x[0]})
         msg =
             "\n%s\n\n... %s more results." %
-            [SolveBio::Tabulate.tabulate(self[0].to_a,
-                                         ['Fields', 'Data'],
-                                         ['right', 'left']),
+            [sorted_items, ['Fields', 'Data'], ['right', 'left'],
              (@total - 1).pretty_int]
         return msg
     end
@@ -283,7 +283,7 @@ class SolveBio::PagingQuery
         _params.merge!(params)
         SolveBio::logger.debug("querying dataset: #{_params}")
 
-        @response = SolveBio::Client.client.request('post', @data_url, _params)
+        @response = SolveBio::Client.client.post(@data_url, _params)
         @total    = @response['total']
         SolveBio::logger.
             debug("query response took: #{@response['took']} ms, " +
@@ -379,8 +379,7 @@ class SolveBio::BatchQuery
     def execute(params={})
         _params = build_query()
         _params.merge!(params)
-        response = SolveBio::Client.
-            client.request('post', '/v1/batch_query', _params)
+        response = SolveBio::Client.client.post('/v1/batch_query', _params)
         return response
     end
 end