bio-ensembl-rest 0.1.0 → 0.2.0

data/.travis.yml

@@ -1,7 +1,6 @@
 language: ruby
 rvm:
   - 1.9.3
-  - 2.0.0
 
 matrix:
   allow_failures:

data/README.md

@@ -3,13 +3,13 @@ Ensembl Rest
 
 A Ruby library for the RESTful Ensembl API.
 
-[![Build Status](https://api.travis-ci.org/ALTree/ensembl-rest.png)](https://travis-ci.org/ALTree/ensembl-rest)
+[![Gem Version](https://badge.fury.io/rb/bio-ensembl-rest.png)](http://badge.fury.io/rb/bio-ensembl-rest)
 
 Obtaining
 ---------
 
 ```sh
-gem install ensembl-rest
+gem install bio-ensembl-rest
 ```
 for the repository:
 ```sh
@@ -43,7 +43,7 @@ See the [ensembl-rest wiki page](https://github.com/ALTree/bio-ensembl-rest/wiki
 
 ### version-specific issues
 
-* On jruby-1.7, methods in the ComparativeGenomics module fail if called with `response: ruby`,
+* On jruby, methods in the ComparativeGenomics module fail if called with `response: ruby`,
 due to a C dependency in the 'bio' gem.
 
 * On rubinius, methods in the ComparativeGenomics module fail if called with `response: ruby`,

data/Rakefile

@@ -14,7 +14,7 @@ require 'rake'
 require 'jeweler'
 Jeweler::Tasks.new do |gem|
   gem.name = "bio-ensembl-rest"
-  gem.version = '0.1.0'
+  gem.version = '0.2.0'
   gem.homepage = "http://github.com/ALTree/bio-ensembl-rest"
   gem.license = "MIT"
   gem.summary = "Ruby Ensembl REST api"

data/lib/bio-ensembl-rest/comparative-genomics.rb

@@ -1,6 +1,38 @@
 module EnsemblRest
   module ComparativeGenomics
 
+    ##
+    # Retrieves genomic alignments as separate blocks based on its location
+    def self.alignment_block(species, region, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/alignment/block/region/#{species}/#{region}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse ComparativeGenomics.alignment_block species, region, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'compara'
+    end
+
+    ##
+    # Retrieves genomic alignments as a single slice based on its location
+    def self.alignment_slice(species, region, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/alignment/slice/region/#{species}/#{region}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse ComparativeGenomics.alignment_slice species, region, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'compara'
+    end
+
+
+
     ##
     # Retrieves Gene Tree dumps for a given Gene Tree stable identifier
     def self.genetree_id(id, opts = {})

data/lib/bio-ensembl-rest/ensembl-rest-main.rb

@@ -52,7 +52,6 @@ module EnsemblRest
     opts
   end
 
-
   ## HTTP request stuff ##
 
   def self.build_path(home, opts) # :nodoc:
@@ -62,7 +61,6 @@ module EnsemblRest
     URI::encode path
   end
 
-  # TODO: add tests to check if this default stuff is ok
   def self.fetch_data(path, opts, mod) # :nodoc:
     # what we should set as content-type in the header
     # to keep ensembl happy when the the user does not

data/lib/bio-ensembl-rest/features.rb

@@ -42,5 +42,22 @@ module EnsemblRest
       return EnsemblRest.fetch_data path, opts, 'features'   
     end
 
+    ##
+    # Uses the given identifier to return translation related features.
+    def self.feature_translation(id, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/feature/translation/#{id}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse feature_translation id, plain_opts
+       end 
+
+       return EnsemblRest.fetch_data path, opts, 'features'
+
+    end
+
   end
+
 end

data/lib/bio-ensembl-rest/information.rb

@@ -33,6 +33,70 @@ module EnsemblRest
     end
 
 
+    ## 
+    # Lists the available analyses by logic name and the database type those logic names are found in.
+    def self.info_analysis(species, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/analysis/#{species}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_analysis species, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information'  
+    end
+
+
+    ## 
+    # Lists all available biotypes for the given species.
+    def self.info_biotypes(species, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/biotypes/#{species}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_biotypes species, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information'  
+    end
+
+    ##
+    # 
+    def self.info_compara_methods(opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/compara/methods", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_compara_methods plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information' 
+    end
+
+
+    ##
+    # 
+    def self.info_compara_species_sets_method(method, opts = {})
+      opts = EnsemblRest.parse_options opts
+      path = EnsemblRest.build_path "/info/compara/species_sets/#{method}", opts
+
+      if opts['content-type'] == 'ruby'
+        plain_opts = opts.clone
+        plain_opts['content-type'] = 'application/json'
+        return JSON.parse info_compara_species_sets_method method, plain_opts
+      end
+
+      return EnsemblRest.fetch_data path, opts, 'information' 
+    end
+
+
+
     ##
     # Lists all available comparative genomics databases and their data release
     def self.info_comparas(opts = {})

data/test/test-comparative-genomics.rb

@@ -2,6 +2,37 @@ require_relative 'helper'
 
 class TestComparativeGenomics < Test::Unit::TestCase
 
+
+  context 'alignment_block' do 
+
+    setup do
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      align = ComparativeGenomics.alignment_block 'homo sapiens', '2:106040000-106040050:1'
+      assert align.index 'GTAGCAGGAAGAATGTTTATCTCTGTGTCTTGTCTTTCTGGTTAAAGGTAT'
+    end   
+
+    sleep(1)
+
+  end
+
+
+  context 'alignment_slice' do 
+
+    setup do
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      align = ComparativeGenomics.alignment_slice 'homo sapiens', '2:106040000-106040050:1'
+      assert align.index 'GTAGCAGGAAGAATGTTTATCTCTGTGTCTTGTCTTTCTGGTTAAAGGTAT'
+    end   
+
+  end
+
+
   context 'genetree_id' do 
 
     setup do 
@@ -13,6 +44,8 @@ class TestComparativeGenomics < Test::Unit::TestCase
       assert tree.index('Euteleostomi') && tree.index('Sarcopterygii')
     end
 
+    sleep(1)
+
     should 'work with nh response type' do
       tree1 = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
                 response: 'nh',
@@ -25,6 +58,8 @@ class TestComparativeGenomics < Test::Unit::TestCase
       assert tree2.index 'xiphophorus_maculatus'
     end
 
+    sleep(1)
+
     should 'return a Bio::PhyloXML object' do
       tree = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
               response: 'ruby' 
@@ -94,6 +129,8 @@ class TestComparativeGenomics < Test::Unit::TestCase
       assert_nothing_raised { JSON.parse hom }
     end
 
+    sleep(1)
+
     should 'return a xml object' do
       hom = ComparativeGenomics.homology_id 'ENSG00000157764',
               response: 'xml'      

data/test/test-cross-reference.rb

@@ -41,6 +41,8 @@ class TestCrossReference < Test::Unit::TestCase
       assert ref.index 'BROVCA2'
     end
 
+    sleep(1)
+
     should 'return a JSON object' do
       refs = CrossReference.xrefs_name 'human', 'BRCA2', response: 'json'
       assert_nothing_raised { JSON.parse refs }

data/test/test-features.rb

@@ -23,6 +23,8 @@ class TestFeatures < Test::Unit::TestCase
       end
     end
 
+    sleep(1)
+
     should 'raise error if no feature is given' do 
       assert_raises RuntimeError do 
         Features.feature_id 'ENSG00000157764', response: 'json'
@@ -54,6 +56,8 @@ class TestFeatures < Test::Unit::TestCase
       assert fts.index '140624564'         # gene end here
     end
 
+    sleep(1)
+
     should 'support multiple features' do 
       assert_nothing_raised do 
         Features.feature_region 'human', '7:140424943-140624564',
@@ -72,5 +76,18 @@ class TestFeatures < Test::Unit::TestCase
 
   end
 
+  context 'feature_translation' do
+
+    setup do
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do 
+      ft = Features.feature_translation 'ENSP00000288602'
+      assert ft.index('SSF56112')
+    end
+
+  end
+
 
 end

data/test/test-information.rb

@@ -32,8 +32,75 @@ class TestInformation < Test::Unit::TestCase
       assert info.index 'chromosome'        # coordinate_system should be this
     end
 
+    sleep(1)
+
   end
 
+  context 'info_analysis' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      assert_nothing_raised do 
+        info = Information.info_analysis 'homo sapiens'
+      end     
+    end
+
+    sleep(1)
+
+  end
+
+  context 'info_biotypes' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      assert_nothing_raised do 
+        info = Information.info_biotypes 'homo sapiens'
+      end     
+    end
+
+    sleep(1)
+
+  end
+
+  context 'info_compara_methods' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      assert_nothing_raised do 
+        info = Information.info_compara_methods
+      end     
+    end
+
+    sleep(1)
+
+  end
+
+  context 'info_compara_species_sets_method' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      assert_nothing_raised do 
+        info = Information.info_compara_species_sets_method 'EPO'
+      end     
+    end
+
+    sleep(1)
+
+  end
+
+
 
   context 'info_comparas' do
 
@@ -48,6 +115,8 @@ class TestInformation < Test::Unit::TestCase
       assert info.index 'release'      # number of the databases
     end
 
+    sleep(1)
+
   end
 
 
@@ -79,6 +148,8 @@ class TestInformation < Test::Unit::TestCase
       assert info.index '1'            # so we know the server is alive
     end
 
+    sleep(1)
+
   end
 
 
@@ -93,6 +164,8 @@ class TestInformation < Test::Unit::TestCase
       assert info.index 'release'            # we expect a release number
     end
 
+    sleep(1)
+
   end
 
 

data/test/test-lookup.rb

@@ -16,6 +16,8 @@ class TestLookup < Test::Unit::TestCase
       assert look.index 'ENSG00000157764'     # exactly this one
     end
 
+    sleep(1)
+
     should 'support the full parameter' do 
       look_plain = Lookup.lookup_id 'ENSG00000157764'
       look_full = Lookup.lookup_id 'ENSG00000157764', format: 'full'

data/test/test-mapping.rb

@@ -47,6 +47,8 @@ class TestMapping < Test::Unit::TestCase
       assert map.index '-1'                # strand -1
     end
 
+    sleep(1)
+
     should 'return the right mapping' do 
       map = Mapping.map_from_cdna 'ENST00000288602', '100..300',
               response: 'ruby'

data/test/test-ontologies.rb

@@ -61,6 +61,8 @@ class TestOntologies < Test::Unit::TestCase
       assert ont.index 'GO:0043231'       # and this one, too
     end
 
+    sleep(1)
+
     should 'support the subset parameter' do 
       ont1 = Ontologies.ontology_descendents 'GO:0005667', subset: 'goslim_generic'
       ont2 = Ontologies.ontology_descendents 'GO:0005667'
@@ -85,6 +87,8 @@ class TestOntologies < Test::Unit::TestCase
       assert ont.index 'GO:0044451'                      # his parent
     end
 
+    sleep(1)
+
     should 'return a ruby object' do 
       ont = Ontologies.ontology_id 'GO:0005667', response: 'ruby'
       assert_instance_of Hash, ont

data/test/test-sequence.rb

@@ -15,6 +15,8 @@ class TestSequence < Test::Unit::TestCase
       assert_equal seq2.size, 18
     end
 
+    sleep(1)
+
     should 'expand the sequence 10 pairs upstream' do
       seq1 = Sequence.sequence_id 'ENSE00001154485',
               response: 'text',
@@ -35,16 +37,7 @@ class TestSequence < Test::Unit::TestCase
       assert_instance_of Bio::Sequence, seq
     end
 
-    should 'raise an error: ID not found' do
-      assert_raises RuntimeError do
-        Sequence.sequence_id 'CCDS5863.1',
-          response: 'fasta',
-          object_type: 'transcript',
-          db_type: 'otherfeatures',
-          type: 'cds',
-          species: 'human'
-        end
-    end
+    sleep(1)
 
     should 'return multiple sequences' do
       response = Sequence.sequence_id 'ENSG00000157764',
@@ -97,6 +90,8 @@ class TestSequence < Test::Unit::TestCase
       assert_nothing_raised { JSON.parse seq }
     end
 
+    sleep(1)
+
     should 'return a Bio::Sequence object' do
       seq = Sequence.sequence_region 'human',
               'X:1000000..1000100:1',

data/test/test-taxonomy.rb

@@ -41,6 +41,8 @@ class TestTaxonomy < Test::Unit::TestCase
       assert tax.index 'man'            # and this common name
     end
 
+    sleep(1)
+
     should 'work both with name and NBCI taxon id' do
       assert_nothing_raised do 
         Taxonomy.taxonomy_classification 'Homo sapiens'

data/test/test-variation.rb

@@ -14,6 +14,8 @@ class TestVariation < Test::Unit::TestCase
       assert var.index '140453136'   # and starts here
     end
 
+    sleep(1)
+
     should 'return the correct data' do 
       data = JSON.parse Variation.vep_id 'COSM476', 'human'
       var = data['data'].first

metadata

@@ -1,60 +1,68 @@
 --- !ruby/object:Gem::Specification
 name: bio-ensembl-rest
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
+  prerelease: 
 platform: ruby
 authors:
 - Alberto Donizetti
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-28 00:00:00.000000000 Z
+date: 2013-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: libxml-ruby
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '2'
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -62,6 +70,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -69,6 +78,7 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -76,6 +86,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -83,6 +94,7 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -90,6 +102,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -133,25 +146,29 @@ files:
 homepage: http://github.com/ALTree/bio-ensembl-rest
 licenses:
 - MIT
-metadata: {}
 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: -796222272840481707
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 1.8.25
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Ruby Ensembl REST api
 test_files: []

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@@ -1,7 +0,0 @@
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