solvebio 1.5.2 → 1.6.1

data/lib/resource/main.rb

@@ -0,0 +1,123 @@
+# -*- coding: utf-8 -*-
+
+require_relative 'solveobject'
+require_relative 'annotation'
+require_relative 'apiresource'
+require_relative 'dataset'
+require_relative 'datasetfield'
+require_relative 'depository'
+require_relative 'depositoryversion'
+require_relative 'sample'
+require_relative 'user'
+
+class SolveBio::ListObject < SolveBio::SolveObject
+
+    include Enumerable
+
+    def all(params={})
+        return request('get', self['url'], {:params => params})
+    end
+
+    def create(params={})
+        return request('post', self['url'], {:params => params})
+    end
+
+    def next_page(params={})
+        if self['links']['next']
+            return request('get', self['links']['next'], {:params => params})
+        end
+        return nil
+    end
+
+    def prev_page(params={})
+        if self['links']['prev']
+            request('get', self['links']['prev'], {:params => params})
+        end
+        return nil
+    end
+
+    def at(i)
+        self.to_a[i]
+    end
+
+    def to_a
+        return to_solve_object(self['data'])
+    end
+
+    def each(*pass)
+        return self unless block_given?
+        i = 0
+        ary = self.dup
+        done = false
+        until done
+            if i >= ary['data'].size
+                ary = next_page
+                break unless ary
+                i = 0
+            end
+            yield(ary.at(i))
+            i += 1
+        end
+        return self
+    end
+
+    def first
+        self['data'][0]
+    end
+
+    # def max
+    #     self['data'][self['total']]
+    # end
+
+end
+
+
+SolveBio::SolveObject::CONVERSION = {
+    'Annotation'        => SolveBio::Annotation,
+    'Depository'        => SolveBio::Depository,
+    'DepositoryVersion' => SolveBio::DepositoryVersion,
+    'Dataset'           => SolveBio::Dataset,
+    'DatasetField'      => SolveBio::DatasetField,
+    'Sample'            => SolveBio::Sample,
+    'User'              => SolveBio::User,
+    'list'              => SolveBio::ListObject
+}
+
+if __FILE__ == $0
+    puts '-' * 50
+    resp = {
+        'class_name' => 'Dataset',
+        'data_url'   => 'https://api.solvebio.com/v1/datasets/25/data',
+        'depository' => 'ClinVar',
+        'depository_id' => 223,
+        'depository_version' => 'ClinVar/2.0.0-1',
+        'depository_version_id' => 15,
+        'description' => '',
+        'fields_url' => 'https://api.solvebio.com/v1/datasets/25/fields',
+        'full_name' => 'ClinVar/2.0.0-1/Variants',
+        'id'  => 25,
+        'name' => 'Variants',
+        'title' => 'Variants',
+        'url' => 'https://api.solvebio.com/v1/datasets/25'
+    }
+    so = to_solve_object(resp)
+    so = resp.to_solvebio
+    puts so.inspect
+    puts so.to_s
+
+    if ARGV[0]
+        require_relative './cli/auth.rb'
+        include SolveBio::Auth
+        login
+        puts '-' * 30, ' HELP ', '-' * 30
+        puts SolveBio::Depository.retrieve('ClinVar').help
+        puts '-' * 30, ' Retrieve ClinVar ','-' * 30
+        puts SolveBio::Depository.retrieve('ClinVar').to_s
+        puts '-' * 30, ' Versions ClinVar ','-' * 30
+        puts SolveBio::Depository.retrieve('Clinvar').versions.to_s
+        puts '-' * 30, ' Dataset  ','-' * 30
+        puts SolveBio::Dataset.retrieve('Clinvar/2.0.0-1/Variants').to_s
+        puts '-' * 30, ' All Depository  ','-' * 30
+        puts SolveBio::Depository.all.to_s
+    end
+end

data/lib/resource/sample.rb

@@ -0,0 +1,75 @@
+# Solvebio API Resource for Samples
+require_relative 'apiresource'
+require_relative 'solveobject'
+require_relative '../errors'
+
+#  Samples are VCF files uploaded to the SolveBio API. We currently
+#  support uncompressed, extension `.vcf`, and gzip-compressed, extension
+#   `.vcf.gz`, VCF files. Any other extension will be rejected.
+class SolveBio::Sample < SolveBio::APIResource
+
+    include SolveBio::DeletableAPIResource
+    include SolveBio::DownloadableAPIResource
+    include SolveBio::ListableAPIResource
+    include SolveBio::HelpableAPIResource
+
+    def annotate
+        SolveBio::Annotation.create :sample_id => self.id
+    end
+
+    # FIXME: Rubyize APIResource.retrieve
+    def self.retrieve(id, params={})
+        SolveBio::APIResource.retrieve(self, id)
+    end
+
+    def self.create(genome_build, params={})
+        if params.member?(:vcf_url)
+            if params.member?(:vcf_file)
+                raise TypeError,
+                'Specified both vcf_url and vcf_file; use only one'
+            end
+            self.create_from_url(genome_build, params[:vcf_url])
+        elsif params.member?(:vcf_file)
+            return create_from_file(genome_build, params[:vcf_file])
+        else
+            raise TypeError,
+            'Must specify exactly one of vcf_url or vcf_file parameter'
+        end
+    end
+
+    # Creates from the specified file.  The data of the should be in
+    # VCF format.
+    def self.create_from_file(genome_build, vcf_file)
+
+        fh = File.open(vcf_file, 'rb')
+        params = {:genome_build  => genome_build,
+                  :vcf_file => fh}
+        response = SolveBio::Client.client.post(class_url(self), params,
+                                                :no_json => true)
+        to_solve_object(response)
+    end
+
+    # Creates from the specified URL.  The data of the should be in
+    # VCF format.
+    def self.create_from_url(genome_build, vcf_url)
+
+        params = {:genome_build  => genome_build,
+                  :vcf_url       => vcf_url}
+        begin
+            response = SolveBio::Client.client.post class_url(self), params
+        rescue SolveBio::Error => response
+        end
+        to_solve_object(response)
+    end
+end
+
+if __FILE__ == $0
+    unless SolveBio::API_HOST == 'https://api.solvebio.com'
+        SolveBio::SolveObject::CONVERSION = {
+            'Sample' => SolveBio::Sample,
+        } unless defined? SolveBio::SolveObject::CONVERSION
+        url = 'http://downloads.solvebio.com/vcf/small_sample.vcf.gz'
+        response = SolveBio::Sample.create_from_url 'hg19', url
+        puts response
+    end
+end

data/lib/{solveobject.rb → resource/solveobject.rb}

@@ -2,15 +2,7 @@
 
 require 'json'
 require 'set'
-require_relative 'client'
-
-# Add underscore before internal uppercase letters. Also, lowercase
-# all letters.
-def camelcase_to_underscore(name)
-    # 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
+require_relative '../client'
 
 # Base class for all SolveBio API resource objects
 class SolveBio::SolveObject < Hash
@@ -43,13 +35,13 @@ class SolveBio::SolveObject < Hash
     # Note: *key* is turned into a string before access, because the underlying key type
     # is a string.
     def [](key)
-        return super(key.to_s)
+        super(key.to_s)
     end
 
     def self.construct_from(cls, values)
         instance = cls.new(values['id'])
         instance.refresh_from(values)
-        return instance
+        instance
     end
 
     def refresh_from(values)
@@ -58,9 +50,10 @@ class SolveBio::SolveObject < Hash
         values.each { |k, v| self[k] = to_solve_object(v) }
     end
 
-    def request(method, url, params=nil)
-        response = SolveBio::Client.client.request(method, url, params)
-        return to_solve_object(response)
+    def request(method, url, params={})
+        response = SolveBio::Client.client
+            .request method, url, {:params => params}
+        to_solve_object(response)
     end
 
     def inspect
@@ -74,27 +67,55 @@ class SolveBio::SolveObject < Hash
             ident_parts << "full_name=#{self['full_name']}"
         end
 
-        return '<%s:%x> JSON: %s' % [ident_parts.join(' '),
-                                     self.object_id, self.to_json]
+        '<%s:%x> JSON: %s' % [ident_parts.join(' '),
+                              self.object_id, self.to_json]
 
     end
 
     def to_s
         # No equivalent of Python's json sort_keys?
-        return JSON.pretty_generate(self, :indent => '  ')
-        # return self.to_json json.dumps(self, sort_keys=true, indent=2)
+        JSON.pretty_generate(self, :indent => '  ')
+        # self.to_json json.dumps(self, sort_keys=true, indent=2)
     end
 
     # @property
     def id
-        return self['id']
+        self['id']
     end
 end
 
-if __FILE__ == $0
-    %w(abc abcDef abc01Def aBcDef a1B2C3 ?Foo Dataset).each do |word|
-        puts word + " -> " + camelcase_to_underscore(word)
+class Hash
+    def to_solvebio(klass=nil)
+        resp = self.dup()
+        if ! klass
+            klass_name ||= resp['class_name']
+            if klass_name.kind_of?(String)
+                klass = SolveBio::SolveObject::CONVERSION[klass_name] ||
+                        SolveBio::SolveObject
+            else
+                klass = SolveBio::SolveObject
+            end
+        end
+        SolveBio::SolveObject::construct_from(klass, resp)
+    end
+end
+
+class Array
+    def to_solvebio
+        return self.map{|i| to_solve_object(i)}
     end
+end
+
+def to_solve_object(resp)
+    if resp.kind_of?(Array) or
+            (not resp.kind_of? SolveBio::SolveObject and resp.kind_of?(Hash))
+        resp.to_solvebio
+    else
+        return resp
+    end
+end
+
+if __FILE__ == $0
     puts SolveBio::SolveObject.new.inspect
     puts SolveBio::SolveObject.new(64).inspect
 

data/lib/resource/user.rb

@@ -0,0 +1,5 @@
+require_relative 'apiresource'
+
+class SolveBio::User < SolveBio::APIResource
+    include SolveBio::SingletonAPIResource
+end

data/lib/solvebio.rb

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # Something to pull in the entire SolveBio API.
 
-require_relative 'resource'
+require_relative 'resource/main'
 require_relative 'query'
 
 # cli/auth is a little nicer than credentials

data/lib/util.rb

@@ -0,0 +1,29 @@
+module SolveBio
+
+    module_function
+    def pluralize(name)
+           if name.end_with?('y')
+               name = name[0..-2] + 'ie'
+           end
+        return name + "s"
+    end
+
+    # Add underscore before internal uppercase letters. Also, lowercase
+    # all letters.
+    def camelcase_to_underscore(name)
+        # 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
+
+# Demo code
+if __FILE__ == $0
+    include SolveBio
+    %w(abc abcDef abc01Def aBcDef a1B2C3 ?Foo Dataset).each do |word|
+        puts word + " -> " + camelcase_to_underscore(word)
+    end
+    ['depository',  'dataset'].each do |word|
+        puts word + " -> " + pluralize(word)
+    end
+end

data/solvebio.gemspec

@@ -14,8 +14,8 @@ 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           = '1.5.2'
-  s.date              = '2014-10-01'
+  s.version           = '1.6.1'
+  s.date              = '2014-11-05'
 
   ## Make sure your summary is short. The description may be as long
   ## as you like.
@@ -54,9 +54,12 @@ EOD
 
   ## List your runtime dependencies here. Runtime dependencies are those
   ## that are needed for an end user to actually USE your code.
-  s.add_dependency('netrc',   '>=0.7.7')
-  # s.add_dependency('openssl', '>=1.1.0')
 
+  s.add_dependency('netrc',   '>=0.7.7')      # handling .netrc
+  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

data/test/Makefile

@@ -0,0 +1,9 @@
+# Whatever it is you want to do other run demos, it should be forwarded to the
+# to top-level directory
+.PHONY: all
+
+#: the default target - same as running "check"
+all: check
+
+%:
+	$(MAKE) -C .. $@

data/test/helper.rb

@@ -1,3 +1,10 @@
 require 'test/unit'
-require_relative '../lib/resource'
-SolveBio.api_key = 'ce68f783a65275d3e81463621d825bad20eb20b0'
+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/test-annotation.rb

@@ -0,0 +1,46 @@
+require_relative './helper'
+
+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.member?(field) ,
+                   "response has field #{field}")
+        end
+
+        all = SolveBio::Annotation.all()
+        assert(all.total > 1,
+               "Annotation.all() returns more than one value")
+
+        response = my_sample.annotate
+        # FIXME: test annotate() more.
+
+        my_sample.delete
+    end
+end