solvebio 1.7.3 → 1.7.4

data/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.3
+current_version = 1.7.4
 files = lib/solvebio/version.rb
 commit = True
 tag = False

data/installer

@@ -67,11 +67,13 @@ fi
 GEM_OWNER=`ls -l $GEM | awk '{ print $3 }'`
 
 if [ "$GEM_OWNER" == "root" ]; then
-    GEM="sudo ${GEM}"
+    GEM_SUDO="sudo ${GEM}"
     echo "    IMPORTANT: Your computer's password may be required. It will NOT be sent to SolveBio."
+else
+    GEM_SUDO=$GEM
 fi
 
-$GEM install solvebio 2>&1 >> $LOG
+$GEM_SUDO install solvebio 2>&1 >> $LOG
 
 if [ $? -eq 0 ]; then
     VERSION=`ruby -e "require 'solvebio'; print SolveBio::VERSION"`

data/lib/solvebio.rb

@@ -35,13 +35,14 @@ require 'solvebio/errors'
 
 module SolveBio
     class << self
-        attr_accessor :api_key, :api_host, :logger
+        attr_accessor :access_token, :api_key, :api_host, :logger
     end
 
-    @api_key     = ENV['SOLVEBIO_API_KEY']
-    @api_host    = ENV['SOLVEBIO_API_HOST'] || 'https://api.solvebio.com'
+    @api_key       = ENV['SOLVEBIO_API_KEY']
+    @access_token  = ENV['SOLVEBIO_ACCESS_TOKEN']
+    @api_host      = ENV['SOLVEBIO_API_HOST'] || 'https://api.solvebio.com'
 
-    logfile      =
+    logfile =
         if ENV['SOLVEBIO_LOGFILE']
             ENV['SOLVEBIO_LOGFILE']
         else

data/lib/solvebio/client.rb

@@ -1,7 +1,7 @@
 module SolveBio
     class Client
         attr_reader :headers
-        attr_accessor :api_host, :api_key
+        attr_accessor :api_host, :token
 
         # Add our own kind of Authorization tokens. This has to be
         # done this way, late, because the rest-client gem looks for
@@ -12,8 +12,9 @@ module SolveBio
             end
         end
 
-        def initialize(api_key=nil, api_host=nil)
-            @api_key = api_key
+        def initialize(api_host=nil, token=nil, token_type='Token')
+            @token = token
+            @token_type = token_type
             @api_host = api_host
 
             # Mirroring comments from:
@@ -62,7 +63,6 @@ module SolveBio
 
             # Expand URL with API host if none was given
             api_host = @api_host || SolveBio.api_host
-            api_key = opts[:auth] ? (@api_key || SolveBio.api_key) : nil
 
             if not api_host
                 raise SolveError.new('No SolveBio API host is set')
@@ -72,7 +72,19 @@ module SolveBio
 
             # Handle some default options and add authorization header
             headers = opts[:default_headers] ? @headers.merge(opts[:headers] || {}) : nil
-            authorization = api_key ? "Token #{api_key}" : nil
+
+            if opts[:auth]
+                if token.nil?
+                    if SolveBio.access_token
+                        token = SolveBio.access_token
+                        token_type = 'Bearer'
+                    elsif SolveBio.api_key
+                        token = SolveBio.api_key
+                        token_type = 'Token'
+                    end
+                end
+                authorization = token ? "#{token_type} #{token}" : nil
+            end
 
             # In Rest-Client, GET params are parsed from headers[:params]
             if opts[:params]

data/lib/solvebio/version.rb

@@ -1,3 +1,3 @@
 module SolveBio
-    VERSION = '1.7.3'
+    VERSION = '1.7.4'
 end

data/test/solvebio/test_client.rb

@@ -3,7 +3,7 @@ require File.expand_path('../../helper', __FILE__)
 module SolveBio
     class TestClient < Test::Unit::TestCase
         def test_get
-            client = Client.new(nil, 'http://google.com')
+            client = Client.new('http://google.com')
             assert client, 'Should be able to create a client'
 
             # Can we get something from google?

data/test/solvebio/test_dataset.rb

@@ -45,8 +45,7 @@ module SolveBio
             facets = dataset_field.facets()
 
             # We can get small or large numbers like 0 or 4902851621.0
-            assert(facets['total'] >= 0,
-                   'facets should have a numeric total field >= 0')
+            assert(facets['values'].length >= 0)
         end
     end
 end

data/test/solvebio/test_query_batch.rb

@@ -7,19 +7,11 @@ module SolveBio
         end
 
         def test_invalid_batch_query
-            assert_raise SolveBio::SolveError do
-                SolveBio::BatchQuery
-                    .new([
-                          @dataset.query(:limit => 1, :fields => [:bogus_field]),
-                          @dataset.query(:limit => 10).filter(:bogus_id__gt => 100000)
-                         ]).execute
-            end
-
-            results = SolveBio::BatchQuery
-                .new([
-                      @dataset.query(:limit => 10).filter(:hgnc_id__lt => 100),
-                      @dataset.query(:limit => 10).filter(:hgnc_id__gt => 100)
-                     ]).execute
+            queries = [
+                @dataset.query(:limit => 1, :fields => [:bogus_field]),
+                @dataset.query(:limit => 10).filter(:bogus_id__gt => 100000)
+            ]
+            results = SolveBio::BatchQuery.new(queries).execute
             assert_equal(2, results.length)
 
         end

metadata

@@ -1,118 +1,137 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.7.3
+  version: 1.7.4
+  prerelease: 
 platform: ruby
 authors:
 - SolveBio
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-18 00:00:00.000000000 Z
+date: 2015-01-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.7'
 - !ruby/object:Gem::Dependency
   name: rest_client
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.8'
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.8'
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.1
 - !ruby/object:Gem::Dependency
   name: addressable
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '2.3'
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 2.3.6
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '2.3'
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 2.3.6
 - !ruby/object:Gem::Dependency
   name: rake
   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'
 - !ruby/object:Gem::Dependency
   name: rdoc
   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'
 - !ruby/object:Gem::Dependency
   name: webmock
   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: |
-  SolveBio is a platform for biomedical datasets. With SolveBio you can
+description: ! 'SolveBio is a platform for biomedical datasets. With SolveBio you
+  can
+
   forget about parsing complex flat files and sifting through cryptic
+
   datasets. Just use the Ruby Client and API to explore massive
+
   datasets and automate just about any bioinformatics workflow.
 
+
   See https://www.solvebio.com/ for more information.
+
+'
 email: contact@solvebio.com
 executables:
 - solvebio.rb
@@ -120,9 +139,9 @@ extensions: []
 extra_rdoc_files:
 - LICENSE
 files:
-- ".bumpversion.cfg"
-- ".gitignore"
-- ".travis.yml"
+- .bumpversion.cfg
+- .gitignore
+- .travis.yml
 - Gemfile
 - Gemspec
 - LICENSE
@@ -188,25 +207,26 @@ files:
 homepage: https://www.solvebio.com
 licenses:
 - MIT
-metadata: {}
 post_install_message: 
 rdoc_options:
-- "--charset=UTF-8"
+- --charset=UTF-8
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.9.0
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 2
 summary: Ruby bindings for the SolveBio API

checksums.yaml

@@ -1,7 +0,0 @@
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-  data.tar.gz: 951035287b583008e5351229aa3c46f7ab3e4d7d
-SHA512:
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