bio-basespace-sdk 0.1.2

data/lib/basespace/model/variant_header.rb

@@ -0,0 +1,44 @@
+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'basespace/model'
+
+module Bio
+module BaseSpace
+
+# Variant header model.
+class VariantHeader < Model
+
+  # Create a new VariantHeader instance.
+  def initialize
+    @swagger_types = {
+      'Metadata'  => 'dict',
+      'Samples'   => 'dict',
+      'Legends'   => 'dict',
+    }
+    @attributes = {
+      'Metadata'  => nil, # dict
+      'Samples'   => nil, # dict
+      'Legends'   => nil, # dict
+    }
+  end
+
+  # Return the sample count as string.
+  def to_s
+    return "VariantHeader: SampleCount=#{get_attr('Samples').length}"
+  end
+end
+
+end # module BaseSpace
+end # module Bio
+

data/lib/basespace/model/variant_info.rb

@@ -0,0 +1,48 @@
+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'basespace/model'
+
+module Bio
+module BaseSpace
+
+# Variant info model.
+class VariantInfo < Model
+
+  # Create a new VariantInfo instance.
+  def initialize
+    @swagger_types = {
+      'CIGAR'        => 'list<Str>',
+      'IDREP'        => 'list<Str>',
+      'REFREP'       => 'list<Str>',
+      'RU'           => 'list<Str>',
+      'VARTYPE_DEL'  => 'list<Str>',
+      'VARTYPE_INS'  => 'list<Str>',
+      'VARTYPE_SNV'  => 'list<Str>',
+    }
+    @attributes = {
+      'CIGAR'        => nil,
+      'IDREP'        => nil,
+      'REFREP'       => nil,
+      'RU'           => nil,
+      'VARTYPE_DEL'  => nil,
+      'VARTYPE_INS'  => nil,
+      'VARTYPE_SNV'  => nil,
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+ 

data/lib/basespace/model/variants_header_response.rb

@@ -0,0 +1,40 @@
+# Copyright 2013 Toshiaki Katayama, Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'basespace/model'
+
+module Bio
+module BaseSpace
+
+# Variants header response model.
+class VariantsHeaderResponse < Model
+
+  # Create a new VariantsHeaderResponse instance.
+  def initialize
+    @swagger_types = {
+      'ResponseStatus'  => 'ResponseStatus',
+      'Response'        => 'VariantHeader',
+      'Notifications'   => 'list<Str>',
+    }
+    @attributes = {
+      'ResponseStatus'  => nil, # ResponseStatus
+      'Response'        => nil, # VariantHeader
+      'Notifications'   => nil, # list<Str>
+    }
+  end
+
+end
+
+end # module BaseSpace
+end # module Bio
+

data/spec/basespaceapi_spec.rb

@@ -0,0 +1,26 @@
+# Copyright 2012-2013 Joachim Baran, Toshiaki Katayama
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'rubygems'
+require 'rspec'
+
+require 'basespace'
+
+describe Bio::BaseSpace::APIClient do
+    describe "initialization" do
+        it "omitting access token" do
+            expect { Bio::BaseSpace::APIClient.new }.to raise_error(Bio::BaseSpace::UndefinedParameterError)
+        end
+    end
+end
+

data/spec/basespaceerror_spec.rb

@@ -0,0 +1,87 @@
+# Copyright 2012-2013 Joachim Baran, Toshiaki Katayama
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'rubygems'
+require 'rspec'
+
+require 'basespace'
+
+value = 'testvalue'
+legal = 'legalcases'
+
+describe Bio::BaseSpace::UndefinedParameterError do
+    describe "initialization" do
+        it "passing: #{value}" do
+            Bio::BaseSpace::UndefinedParameterError.new(value).message.should match("The following parameter must be defined: #{value}")
+        end
+        it "raising exception" do
+            expect { raise Bio::BaseSpace::UndefinedParameterError, value }.to raise_exception(Bio::BaseSpace::UndefinedParameterError)
+        end
+    end
+end
+
+describe Bio::BaseSpace::UnknownParameterError do
+    describe "initialization" do
+        it "passing: #{value}" do
+            Bio::BaseSpace::UnknownParameterError.new(value).message.should match("#{value} is not regcognized as a parameter for this call")
+        end
+        it "raising exception" do
+            expect { raise Bio::BaseSpace::UnknownParameterError, value }.to raise_exception(Bio::BaseSpace::UnknownParameterError)
+        end
+    end
+end
+
+describe Bio::BaseSpace::IllegalParameterError do
+    describe "initialization" do
+        it "passing: #{value}" do
+            Bio::BaseSpace::IllegalParameterError.new(value, legal).message.should match("#{value} is not well-defined, legal options are #{legal}")
+        end
+        it "raising exception" do
+            expect { raise Bio::BaseSpace::IllegalParameterError.new(value, legal) }.to raise_exception(Bio::BaseSpace::IllegalParameterError)
+        end
+    end
+end
+
+describe Bio::BaseSpace::WrongFiletypeError do
+    describe "initialization" do
+        it "passing: #{value}" do
+            Bio::BaseSpace::WrongFiletypeError.new(value).message.should match("This data request is not available for file #{value}")
+        end
+        it "raising exception" do
+            expect { raise Bio::BaseSpace::WrongFiletypeError, value }.to raise_exception(Bio::BaseSpace::WrongFiletypeError)
+        end
+    end
+end
+
+describe Bio::BaseSpace::NoResponseError do
+    describe "initialization" do
+        it "passing: #{value}" do
+            Bio::BaseSpace::NoResponseError.new(value).message.should match("No response was returned from the server for this request")
+        end
+        it "raising exception" do
+            expect { raise Bio::BaseSpace::NoResponseError, value }.to raise_exception(Bio::BaseSpace::NoResponseError)
+        end
+    end
+end
+
+describe Bio::BaseSpace::ModelNotInitializedError do
+    describe "initialization" do
+        it "passing: #{value}" do
+            Bio::BaseSpace::ModelNotInitializedError.new(value).message.should match("The request cannot be completed as model has not been initialized - #{value}")
+        end
+        it "raising exception" do
+            expect { raise Bio::BaseSpace::ModelNotInitializedError, value }.to raise_exception(Bio::BaseSpace::ModelNotInitializedError)
+        end
+    end
+end
+

data/spec/basespacemodel_spec.rb

@@ -0,0 +1,57 @@
+# Copyright 2012-2013 Joachim Baran
+#
+#     Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+#     Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'rubygems'
+require 'rspec'
+
+require 'basespace'
+
+attributes = { "Id" => "X10231", "Source" => "Test", "SpeciesName" => "Homo sapiens" }
+
+describe Bio::BaseSpace::Model do
+    describe "initialization" do
+        it "empty model" do
+            expect(Bio::BaseSpace::Model.new).to be_an_instance_of(Bio::BaseSpace::Model)
+        end
+        
+        it "test attributes are nil; tested attributes: #{attributes.keys.join(', ')}" do
+            attributes.keys.each { |attribute|
+              expect(Bio::BaseSpace::Model.new.get_attr(attribute)).to be_nil
+            }
+        end
+    end
+
+    describe "attribute manipulation" do
+        it "getter/setter: consistency" do
+            model = Bio::BaseSpace::Model.new
+            attributes.keys.each { |attribute|
+              expect(model.get_attr(attribute)).to be_nil
+              model.set_attr(attribute, attributes[attribute])
+              expect(model.get_attr(attribute)).to be(attributes[attribute])
+            }
+        end
+
+        it "getter/setter: overwrite attribute value" do
+            model = Bio::BaseSpace::Model.new
+            attributes.keys.each { |attribute|
+              model.set_attr(attribute, attributes[attribute])
+              expect(model.get_attr(attribute)).to be(attributes[attribute])
+              new_value = "#{attributes[attribute]}-modified"
+              model.set_attr(attribute, new_value)
+              expect(model.get_attr(attribute)).to_not be(attributes[attribute])
+              expect(model.get_attr(attribute)).to be(new_value)
+            }
+        end
+    end    
+end
+

metadata

@@ -0,0 +1,239 @@
+--- !ruby/object:Gem::Specification
+name: bio-basespace-sdk
+version: !ruby/object:Gem::Version
+  version: 0.1.2
+  prerelease: 
+platform: ruby
+authors:
+- Joachim Baran
+- Raoul Bonnal
+- Eri Kibukawa
+- Francesco Strozzi
+- Toshiaki Katayama
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-07-20 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: getopt
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+- !ruby/object:Gem::Dependency
+  name: addressable
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.5
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: ! "Bio::BaseSpace is a Ruby based SDK ported from the Python based BaseSpacePy
+  SDK to be used in the development of Apps and scripts for working with Illumina's
+  BaseSpace cloud-computing solution for next-gen sequencing data analysis.\n\n  The
+  primary purpose of the SDK is to provide an easy-to-use Ruby environment enabling
+  developers to authenticate a user, retrieve data, and upload data/results from their
+  own analysis to BaseSpace.\n\n  If you haven't already done so, you may wish to
+  familiarize yourself with the general BaseSpace developers documentation (https://developer.basespace.illumina.com/)
+  and create a new BaseSpace App to be used when working through the examples provided
+  in 'examples' folder."
+email: joachim.baran@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- README.md
+files:
+- .document
+- .rspec
+- .travis.yml
+- Gemfile
+- License.txt
+- README.md
+- Rakefile
+- VERSION
+- examples/0_app_triggering.rb
+- examples/1_authentication.rb
+- examples/2_browsing.rb
+- examples/3_accessing_files.rb
+- examples/4_app_result_upload.rb
+- examples/5_purchasing.rb
+- lib/basespace.rb
+- lib/basespace/api/api_client.rb
+- lib/basespace/api/base_api.rb
+- lib/basespace/api/basespace_api.rb
+- lib/basespace/api/basespace_error.rb
+- lib/basespace/api/billing_api.rb
+- lib/basespace/model.rb
+- lib/basespace/model/app_result.rb
+- lib/basespace/model/app_result_response.rb
+- lib/basespace/model/app_session.rb
+- lib/basespace/model/app_session_compact.rb
+- lib/basespace/model/app_session_launch_object.rb
+- lib/basespace/model/app_session_response.rb
+- lib/basespace/model/application.rb
+- lib/basespace/model/application_compact.rb
+- lib/basespace/model/basespace_model.rb
+- lib/basespace/model/coverage.rb
+- lib/basespace/model/coverage_meta_response.rb
+- lib/basespace/model/coverage_metadata.rb
+- lib/basespace/model/coverage_response.rb
+- lib/basespace/model/file.rb
+- lib/basespace/model/file_response.rb
+- lib/basespace/model/genome_response.rb
+- lib/basespace/model/genome_v1.rb
+- lib/basespace/model/list_response.rb
+- lib/basespace/model/multipart_upload.rb
+- lib/basespace/model/product.rb
+- lib/basespace/model/project.rb
+- lib/basespace/model/project_response.rb
+- lib/basespace/model/purchase.rb
+- lib/basespace/model/purchase_response.rb
+- lib/basespace/model/purchased_product.rb
+- lib/basespace/model/query_parameters.rb
+- lib/basespace/model/query_parameters_purchased_product.rb
+- lib/basespace/model/refund_purchase_response.rb
+- lib/basespace/model/resource_list.rb
+- lib/basespace/model/response_status.rb
+- lib/basespace/model/run_compact.rb
+- lib/basespace/model/sample.rb
+- lib/basespace/model/sample_response.rb
+- lib/basespace/model/user.rb
+- lib/basespace/model/user_compact.rb
+- lib/basespace/model/user_response.rb
+- lib/basespace/model/variant.rb
+- lib/basespace/model/variant_header.rb
+- lib/basespace/model/variant_info.rb
+- lib/basespace/model/variants_header_response.rb
+- spec/basespaceapi_spec.rb
+- spec/basespaceerror_spec.rb
+- spec/basespacemodel_spec.rb
+homepage: https://github.com/joejimbo/basespace-ruby-sdk
+licenses:
+- Apache, Version 2.0
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -907772599930210264
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Bio::BaseSpace is a Ruby based SDK to be used in the development of Apps
+  and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen
+  sequencing data analysis.
+test_files: []