solvebio 1.5.2 → 1.6.1

data/test/test-query.rb

@@ -1,87 +1,70 @@
 $VERBOSE = true
+require 'socket'
 require_relative 'helper'
+require_relative '../lib/resource/main'
 
 class TestQuery < Test::Unit::TestCase
+    def setup
+        @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
+    end
 
-    TEST_DATASET_NAME = 'ClinVar/2.0.0-1/Variants'
+    # When paging is off, results.length should return the number of
+    # results retrieved.
+    def test_limit
+        @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
+        limit = 10
+        results = @dataset.query :paging=>false, :limit => limit
+        assert_equal(limit, results.length,
+                     'limit == results.size, paging = false')
 
-    if SolveBio::api_key
 
-        def setup
-            begin
-                @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
-            rescue SocketError
-                @dataset = nil
-            end
+        results.each_with_index do |val, i|
+            assert results[i], "retrieving value at #{i}"
         end
 
-        # When paging is off, results.length should return the number of
-        # results retrieved.
-        def test_limit
-            skip('Are you connected to the Internet?') unless @dataset
-            @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
-            limit = 10
-            results = @dataset.query :paging=>false, :limit => limit
-            assert_equal(limit, results.length,
-                         'limit == results.size, paging = false')
-
-
-            results.each_with_index do |val, i|
-                assert results[i], "retrieving value at #{i}"
-            end
-
-            assert_raise IndexError do
-                puts results[limit]
-            end
+        assert_raise IndexError do
+            puts results[limit]
         end
+    end
 
-        # test Query when limit is specified and is GREATER THAN total available
-        #  results
-        def test_limit_empty
-            skip('Are you connected to the Internet?') unless @dataset
-            limit = 100
-            results = @dataset.query(:paging=>false, :limit => limit).
-                filter({:hg19_start => 1234})
-            assert_equal(0, results.size)
-
-            assert_raise IndexError do
-                puts results[0]
-            end
+    # test Query when limit is specified and is GREATER THAN total available
+    #  results
+    def test_limit_empty
+        limit = 100
+        results = @dataset.query(:paging=>false, :limit => limit).
+            filter({:omim_ids => 999999})
+        assert_equal(0, results.size)
 
-            results = @dataset.query(:paging=>false, :limit => limit).
-                filter :hg19_start => 148459988
-            assert_equal(1, results.size)
+        assert_raise IndexError do
+            puts results[0]
         end
 
-        # test Filtered Query in which limit is specified but is GREATER THAN
-        #  the number of total available results
-        def test_limit_filter
-            skip('Are you connected to the Internet?') unless @dataset
-            limit = 10
-            num_filters = 3
-
-            filters3 =
-                SolveBio::Filter.new(:hg19_start => 148459988) |
-                SolveBio::Filter.new(:hg19_start => 148562304) |
-                SolveBio::Filter.new(:hg19_start => 148891521)
+        results = @dataset.query(:paging=>false, :limit => limit).
+            filter :omim_ids => 123631
+        assert_equal(1, results.size)
+    end
 
-            results = @dataset.query(:paging=>false, :limit => limit,
-                                     :filters => filters3)
+    # test Filtered Query in which limit is specified but is GREATER THAN
+    #  the number of total available results
+    def test_limit_filter
+        limit = 10
+        num_filters = 2
 
-            num_filters.times do |i|
-                assert results[i]
-            end
+        filters =
+            SolveBio::Filter.new(:omim_ids => 123631) |
+            SolveBio::Filter.new(:omim_ids => 123670)
 
-            assert_equal(num_filters, results.size)
+        results = @dataset.query(:paging=>false, :limit => limit,
+                                 :filters => filters)
 
-            assert_raise IndexError do
-                puts results[num_filters]
-            end
+        num_filters.times do |i|
+            assert results[i]
         end
 
-    else
-        def test_skip
-            skip 'Please set SolveBio::api_key'
+        assert_equal(num_filters, results.size)
+
+        assert_raise IndexError do
+            puts results[num_filters]
         end
     end
 

data/test/test-resource.rb

@@ -1,14 +1,14 @@
 #!/usr/bin/env ruby
 $VERBOSE = true
-require 'test/unit'
-require_relative '../lib/resource'
+require_relative './helper'
+require_relative '../lib/resource/main'
 
 class TestResource < Test::Unit::TestCase
 
     # Do the class FULL_NAME_REGEX contants match what the think they
     # should?
     def test_full_name_regexp
-        assert('Clinvar/2.0.0-1/Variants' =~
+        assert('HGNC/1.0.0-1/HGNC' =~
                 SolveBio::Dataset::FULL_NAME_REGEX,
                 'Dataset regexp')
 
@@ -27,18 +27,11 @@ class TestResource < Test::Unit::TestCase
     def test_Dataset_from_response
         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'
+            'depository' => 'HGNC',
+            'depository_version' => 'HGNC/1.0.0-1',
+            'full_name' => 'HGNC/1.0.0-1/HGNC',
+            'name' => 'HGNC',
+            'title' => 'HGNC'
         }
         so = resp.to_solvebio
         assert_equal SolveBio::Dataset, so.class, 'Hash -> SolveObject'

data/test/test-sample-access.rb

@@ -0,0 +1,59 @@
+require_relative './helper'
+
+class TestSampleAccess < Test::Unit::TestCase
+
+    def check_response(response, expect, msg)
+        expect.each do |key, val|
+            assert_equal(val, response[key], msg)
+        end
+    end
+
+    def test_insert_delete
+        if SolveBio::API_HOST == 'https://api.solvebio.com'
+            skip "Testing only on local/dev environments"
+        end
+
+        all = SolveBio::Sample.all
+        total = all.total
+        vcf_url = 'http://downloads.solvebio.com/vcf/small_sample.vcf.gz'
+        expect = {
+            'class_name'        => 'Sample',
+            'annotations_count' => 0,
+            'description'       =>  '',
+            'genome_build'      => 'GRCh37',
+            'vcf_md5'           => 'a03e39e96671a01208cffd234812556d',
+            'vcf_size'          => 12124
+        }
+
+        response = SolveBio::Sample.create('GRCh37', :vcf_url => vcf_url)
+        check_response(response, expect,
+                       'create sample.vcf.gz from url')
+        all = SolveBio::Sample.all
+        assert_equal(all.total, total + 1, "After uploading an url")
+        total = total + 1
+
+        vcf_file = File.join(File.dirname(__FILE__), 'data/sample.vcf.gz')
+        response = SolveBio::Sample.create('GRCh37', {:vcf_file => vcf_file})
+        expect = {
+            'class_name' => 'Sample',
+            'annotations_count' => 0,
+            'description' => '',
+            'genome_build' => 'GRCh37',
+            'vcf_md5' => '83acd96171c72ab2bb35e9c52961afd9',
+            'vcf_size' => 592
+        }
+
+        check_response(response, expect,
+                       'create sample.vcf.gz from a file')
+
+        # assert_equal(all.total, total, "After uploading a file")
+
+        # sample = SolveBio::Sample.retrieve(response.id)
+        # delete_response = sample.delete
+        # assert_equal(delete_response.deleted, true,
+        #                  'response.deleted should be true')
+
+        # all = SolveBio::Sample.all
+        # assert_equal(all.total, total, "After deleting a file")
+    end
+end

data/test/test-sample-download.rb

@@ -0,0 +1,20 @@
+require 'fileutils'
+require_relative './helper'
+
+class TestSampleDownload < Test::Unit::TestCase
+
+    def test_sample_download
+        if SolveBio::API_HOST == 'https://api.solvebio.com'
+            skip "Testing only on local/dev environments"
+        end
+
+        vcf_file = File.join(File.dirname(__FILE__), 'data/sample.vcf.gz')
+        sample = SolveBio::Sample.create('GRCh37', {:vcf_file => vcf_file})
+        response = sample.download()
+        assert_equal(response['code'], 200,
+                     "Download sample file status ok")
+        assert(File.exist?(response['filename']),
+               "Download sample file on filesystem")
+        FileUtils.rm response['filename']
+    end
+end

data/test/test-tabulate.rb

@@ -63,6 +63,10 @@ class TestTabulate < Test::Unit::TestCase
     end
 
     def test_tabulate
+        old_verbose = $VERBOSE
+        $VERBOSE=nil
+        SolveBio::Tabulate.const_set(:TTY_COLS, 80)
+        $VERBOSE=old_verbose
         tsv = simple_separated_format("\t")
         expected = <<-EOS
 foo    1
@@ -86,37 +90,37 @@ EOS
         expected = <<-EOS
 | Fields                | Data                        |
 |-----------------------+-----------------------------|
-| rcvaccession_version  | 2                           |
+| alternate_alleles     | T                           |
+| clinical_origin       | somatic                     |
+| clinical_significance | other                       |
+| gene_symbols          | CPB1                        |
 | hg18_chromosome       | 3                           |
+| hg19_chromosome       | 3                           |
 | hg19_start            | 148562304                   |
-| rcvaccession          | RCV000060731                |
 | hg38_start            | 148844517                   |
+| hgvs                  | NC_000003.12:g.148844517C>T |
+| rcvaccession          | RCV000060731                |
+| rcvaccession_version  | 2                           |
 | reference_allele      | C                           |
-| gene_symbols          | CPB1                        |
 | rsid                  | rs150241322                 |
-| hg19_chromosome       | 3                           |
-| hgvs                  | NC_000003.12:g.148844517C>T |
-| clinical_significance | other                       |
-| alternate_alleles     | T                           |
-| clinical_origin       | somatic                     |
 | type                  | SNV                         |
 EOS
 
-        hash = {
-            "rcvaccession_version"=>2,
-            "hg18_chromosome"=>"3",
-            "hg19_start"=>148562304,
-            "rcvaccession"=>"RCV000060731",
-            "hg38_start"=>148844517,
-            "reference_allele"=>"C",
-            "gene_symbols"=>["CPB1"],
-            "rsid"=>"rs150241322",
-            "hg19_chromosome"=>"3",
-            "hgvs"=>["NC_000003.12:g.148844517C>T"],
-            "clinical_significance"=>"other",
-            "alternate_alleles"=>["T"],
-            "clinical_origin"=>["somatic"],
-            "type"=>"SNV"
+         hash = {
+            "alternate_alleles"    => ["T"],
+            "clinical_origin"      => ["somatic"],
+            "clinical_significance"=> "other",
+            "gene_symbols"         => ["CPB1"],
+            "hg18_chromosome"      => "3",
+            "hg19_chromosome"      => "3",
+            "hg19_start"           => 148562304,
+            "hg38_start"           => 148844517,
+            "hgvs"                 => ["NC_000003.12:g.148844517C>T"],
+            "rcvaccession"         => "RCV000060731",
+            "rcvaccession_version" => 2,
+            "reference_allele"     => "C",
+            "rsid"                 => "rs150241322",
+            "type"                 => "SNV"
         }
         assert_equal(expected.chomp, tabulate(hash.to_a,
                                               ['Fields', 'Data'],

data/test/{test-solveobject.rb → test-util.rb}

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 $VERBOSE = true
 require 'test/unit'
-require_relative '../lib/solveobject'
+require_relative '../lib/util'
 
 class TestSolveObject < Test::Unit::TestCase
 
@@ -20,8 +20,23 @@ class TestSolveObject < Test::Unit::TestCase
             ]
         data.each do |triple|
             assert_equal(triple[1],
-                         camelcase_to_underscore(triple[0]),
+                         SolveBio::camelcase_to_underscore(triple[0]),
                          triple[2])
         end
     end
+
+    def test_pluralize
+        data =
+            [
+             ['depository',  'depositories', "ends in 'y'"],
+             ['dataset',     'datasets',     "simply adds an 's'"]
+            ]
+        data.each do |triple|
+            assert_equal(triple[1],
+                         SolveBio::pluralize(triple[0]),
+                         triple[2])
+        end
+
+    end
+
 end

metadata

@@ -1,66 +1,116 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: solvebio
-version: !ruby/object:Gem::Version 
+version: !ruby/object:Gem::Version
+  version: 1.6.1
   prerelease: 
-  version: 1.5.2
 platform: ruby
-authors: 
+authors:
 - solvebio.com
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2014-10-01 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2014-11-05 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: netrc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.7.7
+  type: :runtime
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.7.7
+- !ruby/object:Gem::Dependency
+  name: rest_client
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.1
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: rake
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.1
+- !ruby/object:Gem::Dependency
+  name: addressable
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.3.6
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.3.6
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: rdoc
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    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
+        version: '0'
   type: :development
-  version_requirements: *id003
-description: |
-  SolveBio is a platform for biomedical datasets. With SolveBio you can
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: ! '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.
 
+'
 email: contact@solvebio.com
-executables: 
+executables:
 - solvebio.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
-files: 
+files:
 - .gitignore
 - .travis.yml
 - Gemfile
@@ -71,6 +121,7 @@ files:
 - Rakefile
 - bin/solvebio.rb
 - demo/README.md
+- demo/cheatsheet.rb
 - demo/dataset/facets.rb
 - demo/dataset/field.rb
 - demo/depository/README.md
@@ -81,7 +132,6 @@ files:
 - demo/query/query.rb
 - demo/query/range-filter.rb
 - demo/test-api.rb
-- lib/apiresource.rb
 - lib/cli/auth.rb
 - lib/cli/help.rb
 - lib/cli/irb.rb
@@ -91,19 +141,33 @@ files:
 - lib/credentials.rb
 - lib/errors.rb
 - lib/filter.rb
-- lib/help.rb
 - lib/locale.rb
 - lib/main.rb
 - lib/query.rb
-- lib/resource.rb
+- lib/resource/annotation.rb
+- lib/resource/apiresource.rb
+- lib/resource/dataset.rb
+- lib/resource/datasetfield.rb
+- lib/resource/depository.rb
+- lib/resource/depositoryversion.rb
+- lib/resource/main.rb
+- lib/resource/sample.rb
+- lib/resource/solveobject.rb
+- lib/resource/user.rb
 - lib/solvebio.rb
-- lib/solveobject.rb
 - lib/tabulate.rb
+- lib/util.rb
 - solvebio.gemspec
+- test/Makefile
 - test/data/netrc-save
+- test/data/sample.vcf.gz
 - test/helper.rb
+- test/test-annotation.rb
 - test/test-auth.rb
 - test/test-client.rb
+- test/test-conversion.rb
+- test/test-dataset.rb
+- test/test-depository.rb
 - test/test-error.rb
 - test/test-filter.rb
 - test/test-netrc.rb
@@ -112,40 +176,46 @@ files:
 - test/test-query-paging.rb
 - test/test-query.rb
 - test/test-resource.rb
-- test/test-solveobject.rb
+- test/test-sample-access.rb
+- test/test-sample-download.rb
 - test/test-tabulate.rb
+- test/test-util.rb
 homepage: https://www.solvebio.com
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --charset=UTF-8
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
       version: 1.9.0
-required_rubygems_version: !ruby/object:Gem::Requirement 
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
 rubygems_version: 1.8.23
 signing_key: 
 specification_version: 2
 summary: SolveBio Ruby bindings.
-test_files: 
+test_files:
+- test/Makefile
 - test/data/netrc-save
+- test/data/sample.vcf.gz
 - test/helper.rb
+- test/test-annotation.rb
 - test/test-auth.rb
 - test/test-client.rb
+- test/test-conversion.rb
+- test/test-dataset.rb
+- test/test-depository.rb
 - test/test-error.rb
 - test/test-filter.rb
 - test/test-netrc.rb
@@ -154,5 +224,7 @@ test_files:
 - test/test-query-paging.rb
 - test/test-query.rb
 - test/test-resource.rb
-- test/test-solveobject.rb
+- test/test-sample-access.rb
+- test/test-sample-download.rb
 - test/test-tabulate.rb
+- test/test-util.rb