solvebio 1.7.7 → 1.7.8

data/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.7
+current_version = 1.7.8
 files = lib/solvebio/version.rb
 commit = True
 tag = True

data/.gitignore

@@ -2,5 +2,6 @@
 .rvmrc
 pkg
 solvebio-*.gem
+Gemfile.lock
 test/data/.netrc
 *.swp

data/Gemfile

@@ -1,9 +1,7 @@
 # A bundler Gemfile for specifying dependencies. See http://bundler.io/
 source "https://rubygems.org"
+gemspec
 
 gem 'addressable'
-gem 'rest-client'
+gem 'rest-client', '~> 1.7.3'
 gem 'netrc', '~>0.7.7'  # rest-client needs netrc 0.7.7
-group :test do
-    gem 'webmock'
-end

data/README.md

@@ -61,4 +61,4 @@ The following optional gems can make your shell experience better
 Documentation
 -------------
 
-See the [SolveBio API Reference](https://www.solvebio.com/docs/api/?ruby) for more information about using the API.
+See the [SolveBio API Reference](https://docs.solvebio.com/) for more information about using the API.

data/lib/solvebio/dataset.rb

@@ -59,5 +59,47 @@ module SolveBio
             params.merge!(:data_url => self.data_url)
             Query.new(self.id, params)
         end
+
+        def beacon(coordinate, chromosome, genome_build=nil, allele=nil)
+            unless self.respond_to?(:beacon_url)
+                unless self.respond_to?(:id)
+                    raise Exception,
+                    'No Dataset ID was provided. ' +
+                        'Please instantiate the Dataset ' +
+                        'object with an ID or full_name.'
+                end
+                # automatically construct the data_url from the ID
+                self.beacon_url = url + '/beacon'
+            end
+
+            opts = { :params => {
+                       :coordinate => coordinate,
+                       :chromosome => chromosome,
+                       :genome_build => genome_build,
+                       :allele => allele
+                      }
+                    }
+            return Client.request('get', self.beacon_url, opts=opts)
+        end
+
+        def changelog(version=nil, params={})
+            unless self.respond_to?(:changelog_url)
+                unless self.respond_to?(:id)
+                    raise Exception,
+                    'No Dataset ID was provided. ' +
+                        'Please instantiate the Dataset ' +
+                        'object with an ID or full_name.'
+                end
+                # automatically construct the data_url from the ID
+                if version
+                  self.changelog_url = url + '/changelog/' + version
+                else
+                  self.changelog_url = url + '/changelog'
+                end
+            end
+
+            params.merge!(:changelog_url => self.changelog_url)
+            return Client.request('get', self.changelog_url, params)
+        end
     end
 end

data/lib/solvebio/depository_version.rb

@@ -36,5 +36,25 @@ module SolveBio
         def <=>(other)
             self[:full_name] <=> other[:full_name]
         end
+
+        def changelog(version=nil, params={})
+            unless self.respond_to?(:changelog_url)
+                unless self.respond_to?(:id)
+                    raise Exception,
+                    'No Dataset ID was provided. ' +
+                        'Please instantiate the Dataset ' +
+                        'object with an ID or full_name.'
+                end
+                # automatically construct the data_url from the ID
+                if version
+                  self.changelog_url = url + '/changelog/' + version
+                else
+                  self.changelog_url = url + '/changelog'
+                end
+            end
+
+            params.merge!(:changelog_url => self.changelog_url)
+            return Client.request('get', self.changelog_url, params)
+        end
     end
 end

data/lib/solvebio/version.rb

@@ -1,3 +1,3 @@
 module SolveBio
-    VERSION = '1.7.7'
+    VERSION = '1.7.8'
 end

data/test/solvebio/test_dataset.rb

@@ -47,5 +47,17 @@ module SolveBio
             # We can get small or large numbers like 0 or 4902851621.0
             assert(facets['facets'].length >= 0)
         end
+
+# TODO support a Genomic test dataset (grab clinvar one from API build)
+#        def test_dataset_beacon
+#            beacon = @dataset.beacon(234, '6', allele => 'G')
+#            assert(beacon['exist'])
+#        end
+
+# TODO add another version of TEST_DATASET so we can test changelog
+#        def test_dataset_changelog
+#            changelog = @dataset.changelog
+#            assert(changelog['to_version'])
+#        end
     end
 end

data/test/solvebio/test_depositoryversion.rb

@@ -18,5 +18,16 @@ module SolveBio
                        "Should find field #{field} in depo version")
             end
         end
+
+# TODO add another version of TEST_DATASET so we can test changelog
+#        def test_depositoryversion_changelog
+#            dvs = SolveBio::DepositoryVersion.all
+#            dv = dvs.data[0]
+#            assert(dv.respond_to?('id'),
+#                   'Should be able to get id in depositoryversion')
+#
+#            changelog = SolveBio::DepositoryVersion.retrieve(dv.id).changelog
+#            assert(changelog['to_version'])
+#        end
     end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.7.7
+  version: 1.7.8
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-23 00:00:00.000000000 Z
+date: 2015-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc
@@ -143,8 +143,6 @@ files:
 - .gitignore
 - .travis.yml
 - Gemfile
-- Gemfile.lock
-- Gemspec
 - LICENSE
 - README.md
 - Rakefile

data/Gemfile.lock

@@ -1,24 +0,0 @@
-GEM
-  remote: https://rubygems.org/
-  specs:
-    addressable (2.3.7)
-    crack (0.4.2)
-      safe_yaml (~> 1.0.0)
-    mime-types (2.4.3)
-    netrc (0.7.9)
-    rest-client (1.7.3)
-      mime-types (>= 1.16, < 3.0)
-      netrc (~> 0.7)
-    safe_yaml (1.0.4)
-    webmock (1.20.4)
-      addressable (>= 2.3.6)
-      crack (>= 0.3.2)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  addressable
-  netrc (~> 0.7.7)
-  rest-client
-  webmock

data/Gemspec

@@ -1,3 +0,0 @@
-source 'https://rubygems.org'
-
-gemspec