solvebio 1.6.1 → 1.7.0

data/lib/solvebio/user.rb

@@ -0,0 +1,4 @@
+module SolveBio
+    class User < SingletonAPIResource
+    end
+end

data/lib/solvebio/util.rb

@@ -0,0 +1,59 @@
+module SolveBio
+    module Util
+        def self.object_classes
+          @object_classes ||= {
+            'Depository'        => Depository,
+            'DepositoryVersion' => DepositoryVersion,
+            'Dataset'           => Dataset,
+            'DatasetField'      => DatasetField,
+            'Sample'            => Sample,
+            'Annotation'        => Annotation,
+            'User'              => User,
+            'Account'           => Account,
+            'list'              => ListObject
+          }
+        end
+
+        def self.to_solve_object(resp)
+            case resp
+            when Array
+                resp.map { |i| to_solve_object(i) }
+            when Hash
+                object_classes.fetch(resp[:class_name], SolveObject).construct_from(resp)
+            else
+                resp
+            end
+        end
+        
+        def self.symbolize_names(object)
+            case object
+            when Hash
+                new_hash = {}
+                object.each do |key, value|
+                    key = (key.to_sym rescue key) || key
+                    new_hash[key] = symbolize_names(value)
+                end
+                new_hash
+            when Array
+                object.map { |value| symbolize_names(value) }
+            else
+                object
+            end
+        end
+
+        module_function
+        def pluralize(name)
+               if name.end_with?('y')
+                   name = name[0..-2] + 'ie'
+               end
+            return name + "s"
+        end
+
+        def camelcase_to_underscore(name)
+            # Add underscore before internal uppercase letters.
+            # Using [[:upper:]] and [[:lower]] should help with Unicode.
+            s1 = name.gsub(/(.)([[:upper:]])([[:lower:]]+)/){"#{$1}_#{$2}#{$3}"}
+            return (s1.gsub(/([a-z0-9])([[:upper:]])/){"#{$1}_#{$2}"}).downcase
+        end
+    end
+end

data/lib/solvebio/version.rb

@@ -0,0 +1,3 @@
+module SolveBio
+    VERSION = '1.7.0'
+end

data/solvebio.gemspec

@@ -1,10 +1,8 @@
 ## -*- Ruby -*-
-## This is the rakegem gemspec template. Make sure you read and understand
-## all of the comments. Some sections require modification, and others can
-## be deleted if you don't need them. Once you understand the contents of
-## this file, feel free to delete any comments that begin with two hash marks.
-## You can find comprehensive Gem::Specification documentation, at
-## http://docs.rubygems.org/read/chapter/20
+$:.unshift(File.join(File.dirname(__FILE__), 'lib'))
+
+require 'solvebio/version'
+
 Gem::Specification.new do |s|
   s.specification_version = 2 if s.respond_to? :specification_version=
   # s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
@@ -14,28 +12,27 @@ Gem::Specification.new do |s|
   ## If your rubyforge_project name is different, then edit it and comment out
   ## the sub! line in the Rakefile
   s.name              = 'solvebio'
-  s.version           = '1.6.1'
-  s.date              = '2014-11-05'
+  s.version           = SolveBio::VERSION
 
   ## Make sure your summary is short. The description may be as long
   ## as you like.
-  s.summary     = "SolveBio Ruby bindings."
-
+  s.summary     = "Ruby bindings for the SolveBio API"
   s.description = <<-EOD
 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/docs/api/ for more information.
+See https://www.solvebio.com/ for more information.
 EOD
 
   ## List the primary authors. If there are a bunch of authors, it's probably
   ## better to set the email to an email list or something. If you don't have
   ## a custom homepage, consider using your GitHub URL or the like.
-  s.authors  = ['solvebio.com']
+  s.authors  = ['SolveBio']
   s.email    = 'contact@solvebio.com'
   s.homepage = 'https://www.solvebio.com'
+  s.license = 'MIT'
 
   ## This gets added to the $LOAD_PATH so that 'lib/NAME.rb' can be required as
   ## require 'NAME.rb' or'/lib/NAME/file.rb' can be as require 'NAME/file.rb'
@@ -59,17 +56,12 @@ EOD
   s.add_dependency('rest_client', '>=1.8.1')  # better URI handler
   s.add_dependency('addressable', '>=2.3.6')  # better URI parsing
 
-  # s.add_dependency('openssl', '>=1.1.0')
-
-  # There is no way to specify optional dependencies.
-  # s.add_optional_dependency 'launchy' # opens URL in web browser for help
-  # s.add_optional_dependency 'bond'    # better shell command completion
-
   ## List your development dependencies here. Development dependencies are
   ## those that are only needed during development
   # s.add_development_dependency('DEVDEPNAME', [">= 1.1.0", "< 2.0.0"])
   s.add_development_dependency('rake')
   s.add_development_dependency('rdoc')
+  s.add_development_dependency('webmock')
   s.files = `git ls-files`.split($/)
 
   ## Test files will be grabbed from the file list. Make sure the path glob

data/test/helper.rb

@@ -1,10 +1,14 @@
+require 'solvebio'
+require 'solvebio/cli'
+
 require 'test/unit'
+require 'webmock/test_unit'
+require 'net/http'
+
 ENV['SOLVEBIO_API_HOST'] ||= 'https://api.solvebio.com'
-require_relative '../lib/main'
 
 TEST_DATASET_NAME = 'HGNC/1.0.0-1/HGNC'
 
-
 def local_api?
     ENV['SOLVEBIO_LOCAL_API']
 end

data/test/solvebio/data/.gitignore

@@ -0,0 +1 @@
+/.solvebio

data/test/solvebio/data/.netrc

@@ -0,0 +1,6 @@
+machine foo.bar
+	login a@example.com
+	password secret
+machine api.solvebio.com
+	login rocky@example.comabc
+	password shhhhabc

data/test/solvebio/data/test_creds

@@ -0,0 +1,3 @@
+machine api.solvebio.com
+	login testing@solvebio.com
+	password badcafebabe0feeddeadbeefeee111eee1110000

data/test/solvebio/test_annotation.rb

@@ -0,0 +1,45 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestAnnotation < Test::Unit::TestCase
+        def check_response(response, expect, msg)
+            expect.each do |key, val|
+                assert_equal(val, response[key], msg)
+            end
+        end
+
+        def test_annotation
+            if SolveBio.api_host == 'https://api.solvebio.com'
+                skip "Annotation testing only on local/dev environments"
+            end
+
+            vcf_file = File.join(File.dirname(__FILE__), "data/sample.vcf.gz")
+            my_sample = SolveBio::Sample
+                          .create('GRCh37', :vcf_file => vcf_file)
+            assert(my_sample)
+
+            sample_id = my_sample['id']
+            expect = {
+                'class_name' => 'Annotation',
+                'error_message' => '',
+                'sample_id' => sample_id
+            }
+
+            response = SolveBio::Annotation.create(:sample_id => sample_id)
+            check_response(response, expect,
+                           "'Annotation.create(:sample_id=>{#sample_id}")
+
+            ['status', 'user_id', 'created_at', 'updated_at'].each do |field|
+                assert(response.respond_to?(field) ,
+                       "response has field #{field}")
+            end
+
+            all = SolveBio::Annotation.all()
+            assert(all.total > 1,
+                   "Annotation.all() returns more than one value")
+
+            my_sample.delete
+            assert my_sample.deleted
+        end
+    end
+end

data/test/solvebio/test_client.rb

@@ -0,0 +1,29 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestClient < Test::Unit::TestCase
+        def test_get
+            client = Client.new(nil, 'http://google.com')
+            assert client, 'Should be able to create a client'
+
+            # Can we get something from google?
+            output = `curl --silent http://www.google.com`
+            if $?.success? and output
+                assert(client.request('get', 'http://www.google.com',
+                                      {:raw => true, :redirect => true}),
+                                      'HTTP GET, google.com')
+                assert(client.request('get', 'https://www.google.com',
+                                      {:raw => true}),
+                                      'HTTPS GET google.com')
+                assert(Client.request('get', 'http://www.google.com',
+                                      {:raw => true, :redirect => true}),
+                                      'HTTP GET, google.com')
+                assert(Client.request('get', 'https://www.google.com',
+                                      {:raw => true}),
+                                      'HTTPS GET google.com')
+            else
+                skip('Are you connected to the Internet? www.google.com is unavailable')
+            end
+        end
+    end
+end

data/test/solvebio/test_conversion.rb

@@ -0,0 +1,14 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class ConversionTest < Test::Unit::TestCase
+        def test_class_to_api_name
+            klass = SolveBio::Annotation
+            assert_equal('/v1/annotations', klass.url)
+            klass = SolveBio::DatasetField
+            assert_equal('/v1/dataset_fields', klass.url)
+            klass = SolveBio::Depository
+            assert_equal('/v1/depositories', klass.url)
+        end
+    end
+end

data/test/solvebio/test_credentials.rb

@@ -0,0 +1,67 @@
+require File.expand_path('../../helper', __FILE__)
+
+def silence_output(&block)
+    original_stdout = $stdout
+    $stdout = fake = StringIO.new
+    begin
+        yield
+    ensure
+        $stdout = original_stdout
+    end
+   fake.string
+end
+
+module SolveBio
+    class TestNetrc < Test::Unit::TestCase
+        include SolveBio::CLI::Credentials
+        include SolveBio::CLI::Auth
+
+        def setup
+            @home_path_save = ENV['HOME']
+            home_path = ENV['HOME'] = File.join(File.dirname(__FILE__), 'data')
+            credentials_file = netrc_path
+            FileUtils.cp(File.join(home_path, 'netrc-save'), credentials_file)
+            File.chmod(0600, credentials_file)
+            @old_warn_level = $VERBOSE
+            @old_api_host = SolveBio.api_host
+            $VERBOSE = nil
+            SolveBio.api_host = 'https://api.solvebio.com'
+            $VERBOSE = @old_warn_level
+        end
+
+        def teardown
+            ENV["HOME"] = @home_path_save
+            $VERBOSE = nil
+            SolveBio.api_host = @old_api_host 
+            $VERBOSE = @old_warn_level
+        end
+
+        def test_netrc
+            assert(netrc_path,
+                   "Should get a location for SolveBio's credentials")
+        end
+
+        def test_get_credentials
+            assert_equal ['rocky@example.com', 'shhhh'], get_credentials.to_a
+        end
+
+        def test_save_credentials
+            new_values = get_credentials.map{|x| x+"abc"}
+            save_credentials(*new_values)
+            assert_equal(new_values, get_credentials.to_a,
+                         'Should append "abc" to creds')
+        end
+
+        def test_delete_credentials
+            delete_credentials
+            assert_equal(nil, get_credentials,
+                         'Should be able to delete credentials')
+            pair = ['testagain@solvebio.com', 'b00b00']
+            save_credentials(*pair)
+            auths = get_credentials()
+            assert_equal(pair, auths,
+                         "Should get newly set credentials for host #{SolveBio.api_host}")
+        end
+
+    end
+end

data/test/solvebio/test_dataset.rb

@@ -0,0 +1,52 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestDataset < Test::Unit::TestCase
+        def setup
+            @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
+        end
+
+        def test_dataset_retrieval
+            assert(@dataset.id,
+                   'Should be able to get id in dataset')
+            assert(@dataset[:id],
+                   'Should be able to get id in dataset')
+
+            %w(class_name created_at data_url depository depository_id
+               depository_version depository_version_id description
+              fields_url full_name genome_builds is_genomic
+              name title updated_at url).each do |field|
+                assert(@dataset.respond_to?(field),
+                       "Should find field #{field} in dataset #{@dataset.id}")
+            end
+        end
+
+        def test_dataset_fields
+            fields = @dataset.fields
+            dataset_field = fields[:data][0]
+            assert(dataset_field.id,
+                   'Should be able to get id in list of dataset fields')
+
+            dataset_field2 = SolveBio::DatasetField.retrieve(dataset_field.id)
+            assert_equal(dataset_field.id, dataset_field2.id,
+                         "Retrieving SolveBio::DatasetField id " +
+                         "#{dataset_field.id} found by all()")
+
+            %w(class_name created_at dataset dataset_id description facets_url
+              name updated_at url).each do |field|
+                assert(dataset_field.respond_to?(field),
+                       "Should find field #{field} in fields #{dataset_field.id}")
+            end
+        end
+
+        def test_dataset_facets
+            fields = @dataset.fields
+            dataset_field = fields[:data][0]
+            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')
+        end
+    end
+end

data/test/solvebio/test_depository.rb

@@ -0,0 +1,24 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestDepository < Test::Unit::TestCase
+        def test_depositories
+            depos = SolveBio::Depository.all
+
+            depo = depos.data[0]
+            assert(depo.id,
+                   'Should be able to get id in depository')
+
+            depo2 = SolveBio::Depository.retrieve(depo.id)
+            assert_equal(depo.id, depo2.id,
+                         "Retrieving dataset id #{depo.id} found by all()")
+            %w(class_name created_at description external_resources
+               full_name id is_private is_restricted latest_version
+               latest_version_id name title updated_at url versions_count
+               versions_url).each do |field|
+                assert(depo.respond_to?(field),
+                       "Should find field #{field} in depo #{depo.id}")
+            end
+        end
+    end
+end

data/test/solvebio/test_depositoryversion.rb

@@ -0,0 +1,22 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestDepository < Test::Unit::TestCase
+        def test_depositoryversion
+            dvs = SolveBio::DepositoryVersion.all
+            dv = dvs.data[0]
+            assert(dv.respond_to?('id'),
+                   'Should be able to get id in depositoryversion')
+
+            dv2 = SolveBio::DepositoryVersion.retrieve(dv.id)
+            assert_equal(dv.id, dv2.id,
+                         "Retrieving dataset id #{dv.id} found by all()")
+            %w(class_name created_at datasets_url depository depository_id
+               description full_name id latest name is_released released_at
+               title updated_at url).each do |field|
+                assert(dv.respond_to?(field),
+                       "Should find field #{field} in depo version")
+            end
+        end
+    end
+end

data/test/solvebio/test_error.rb

@@ -0,0 +1,31 @@
+require File.expand_path('../../helper', __FILE__)
+
+$errors = []
+
+class FakeLogger
+    def debug(mess)
+        $errors << mess
+    end
+end
+
+module SolveBio
+    class TestError < Test::Unit::TestCase
+        def test_error
+            msg = "hi"
+            assert_equal msg, SolveBio::SolveError.new(nil, msg).to_s, "Error.to_s fn"
+            response = Net::HTTPUnauthorized.new('HTTP 1.1', '404', 'No creds')
+            old_logger = SolveBio.instance_variable_get('@logger')
+            logger = FakeLogger.new
+            SolveBio.instance_variable_set('@logger', logger)
+            old_verbose = $VERBOSE
+            $VERBOSE=false
+            SolveBio::SolveError.new(response)
+            $VERBOSE=old_verbose
+            assert_equal ["API Response (404): No content."], $errors
+        ensure
+            $VERBOSE = old_verbose if old_verbose
+            SolveBio.instance_variable_set('@logger', old_logger) if old_logger
+
+        end
+    end
+end