solvebio 1.7.5 → 1.7.6

data/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.5
+current_version = 1.7.6
 files = lib/solvebio/version.rb
 commit = True
 tag = False

data/.travis.yml

@@ -2,7 +2,7 @@ language: ruby
 sudo: false
 before_script:
 - gem install netrc --version=0.7.7
-- gem install rest_client addressable webmock
+- gem install rest-client addressable webmock
 - touch ~/.netrc
 - chmod 0600 ~/.netrc
 env:

data/Gemfile

@@ -2,8 +2,8 @@
 source "https://rubygems.org"
 
 gem 'addressable'
-gem 'rest_client'
-gem 'netrc', '~>0.7.7'  # rest_client needs netrc 0.7.7
+gem 'rest-client'
+gem 'netrc', '~>0.7.7'  # rest-client needs netrc 0.7.7
 group :test do
     gem 'webmock'
 end

data/README.md

@@ -27,7 +27,7 @@ Installing from Git
 
 First, install dependencies:
 	
-    gem install rest_client addressable netrc
+    gem install rest-client addressable netrc
 
 Install from source:
 

data/lib/solvebio.rb

@@ -6,7 +6,7 @@ require 'json'
 require 'logger'
 require 'netrc'
 require 'openssl'
-require 'rest_client'
+require 'rest-client'
 require 'uri'
 require 'addressable/uri'
 require 'set'

data/lib/solvebio/filter.rb

@@ -287,15 +287,17 @@ module SolveBio
             end
 
             if exact or start.nil?
-                f = SolveBio::Filter.new({FIELD_START => start, FIELD_STOP  => stop})
+                # Handle the case where start is None because sometimes
+                # a record will have only the chromosome set (no positions).
+                f = SolveBio::Filter.new({FIELD_START => start, FIELD_STOP => stop})
             else
                 f = SolveBio::Filter.new({"#{FIELD_START}__lte" => start,
-                                          "#{FIELD_START}__gte" => stop})
+                                          "#{FIELD_STOP}__gte" => stop})
                 if start != stop
                     f |= SolveBio::Filter.new({"#{FIELD_START}__range" =>
-                                               [start, stop + 1]})
+                                               [start, stop]})
                     f |= SolveBio::Filter.new({"#{FIELD_STOP}__range" =>
-                                               [start, stop + 1]})
+                                               [start, stop]})
                 end
             end
 

data/lib/solvebio/version.rb

@@ -1,3 +1,3 @@
 module SolveBio
-    VERSION = '1.7.5'
+    VERSION = '1.7.6'
 end

data/solvebio.gemspec

@@ -53,7 +53,7 @@ EOD
   ## that are needed for an end user to actually USE your code.
 
   s.add_dependency('netrc', '~> 0.7')
-  s.add_dependency('rest_client', '~> 1.8', '>= 1.8.1')
+  s.add_dependency('rest-client', '~> 1.8', '>= 1.8.1')
   s.add_dependency('addressable', '~> 2.3', '>= 2.3.6')
 
   ## List your development dependencies here. Development dependencies are

data/test/solvebio/test_dataset.rb

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

data/test/solvebio/test_filter.rb

@@ -49,9 +49,9 @@ module SolveBio
 
         def test_genomic_filter
             assert_equal(
-                '<GenomicFilter [{:and=>[["genomic_coordinates.start", 13], ["genomic_coordinates.stop", 32200000], ["genomic_coordinates.chromosome", "hg38"]]}]>',
+                '<GenomicFilter [{:and=>[["genomic_coordinates.start", 32200000], ["genomic_coordinates.stop", 32500000], ["genomic_coordinates.chromosome", "13"]]}]>',
                          SolveBio::GenomicFilter.
-                         new("hg38", "13", 32200000, 32500000).inspect)
+                         new("13", 32200000, 32500000, exact: true).inspect)
         end
 
         def test_process_filters
@@ -65,7 +65,7 @@ module SolveBio
         def test_genomic_single_position
             f = SolveBio::GenomicFilter.new('chr1', 100)
             assert_equal(
-                '<GenomicFilter [{:and=>[["genomic_coordinates.start__gte", 100.0], ["genomic_coordinates.start__lte", 100.0], ["genomic_coordinates.chromosome", "1"]]}]>',
+                '<GenomicFilter [{:and=>[["genomic_coordinates.start__lte", 100.0], ["genomic_coordinates.stop__gte", 100.0], ["genomic_coordinates.chromosome", "1"]]}]>',
                 f.inspect)
 
             f = SolveBio::GenomicFilter.new('chr1', 100, 100, true)
@@ -76,7 +76,7 @@ module SolveBio
 
         def test_range
             f = SolveBio::GenomicFilter.new('chr1', 100, 200)
-            assert_equal('<GenomicFilter [{:and=>[{:or=>[{:and=>[["genomic_coordinates.start__gte", 200.0], ["genomic_coordinates.start__lte", 100.0]]}, ["genomic_coordinates.start__range", [100, 201]], ["genomic_coordinates.stop__range", [100, 201]]]}, ["genomic_coordinates.chromosome", "1"]]}]>',
+            assert_equal('<GenomicFilter [{:and=>[{:or=>[{:and=>[["genomic_coordinates.start__lte", 100.0], ["genomic_coordinates.stop__gte", 200.0]]}, ["genomic_coordinates.start__range", [100, 200]], ["genomic_coordinates.stop__range", [100, 200]]]}, ["genomic_coordinates.chromosome", "1"]]}]>',
                          f.inspect)
             f = SolveBio::GenomicFilter.new('chr1', 100, 200, true)
             assert_equal('<GenomicFilter [{:and=>[["genomic_coordinates.start", 100], ["genomic_coordinates.stop", 200], ["genomic_coordinates.chromosome", "1"]]}]>',

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.7.5
+  version: 1.7.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-06 00:00:00.000000000 Z
+date: 2015-02-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc
@@ -28,7 +28,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0.7'
 - !ruby/object:Gem::Dependency
-  name: rest_client
+  name: rest-client
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements: