solvebio 1.6.1 → 1.7.0

data/test/solvebio/test_ratelimit.rb

@@ -0,0 +1,31 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class ClientRateLimit < Test::Unit::TestCase
+        def setup
+            WebMock.enable!
+        end
+
+        def teardown
+            WebMock.disable!
+        end
+
+        def test_rate_limit
+
+            responses = [
+                {:body => '{"id": 5}', :status => 429,
+                 :headers => {:retry_after => 1}},
+                {:body => '{"id": 5}', :status => 200},
+            ]
+            depo = SolveBio::Depository.new('HGNC')
+            stub_request(:get, SolveBio.api_host + depo.url).
+                to_return(responses).then.to_raise(Exception)
+            start_time = Time.now()
+            SolveBio::Depository.retrieve('HGNC')
+            elapsed_time = Time.now() - start_time
+            assert(elapsed_time > 1.0,
+                                   "Should have delayed for over a second; " +
+                                   "(was %s)" % elapsed_time)
+        end
+    end
+end

data/test/solvebio/test_resource.rb

@@ -0,0 +1,29 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestResource < Test::Unit::TestCase
+        def test_SolveObject_inspect
+            str = SolveBio::SolveObject.new.inspect
+            assert(str =~ /^#<SolveBio::SolveObject:0x[[:xdigit:]]+>/,
+                   'empty SolveObject inspect')
+            str = SolveBio::SolveObject.new(62).inspect
+            assert(str =~ /^#<SolveBio::SolveObject:0x[[:xdigit:]]+ id=62>/,
+                   "SolveObject inspect with id #{str}")
+
+        end
+
+        def test_Dataset_from_response
+            resp = {
+                :class_name => 'Dataset',
+                :depository => 'HGNC',
+                :depository_version => 'HGNC/1.0.0-1',
+                :full_name => 'HGNC/1.0.0-1/HGNC',
+                :name => 'HGNC',
+                :title => 'HGNC'
+            }
+            so = Util.to_solve_object(resp)
+            assert_equal SolveBio::Dataset, so.class, 'Hash -> SolveObject'
+            resp.keys.each {|k| assert_equal resp[k], so[k]}
+        end
+    end
+end

data/test/solvebio/test_sample_access.rb

@@ -0,0 +1,60 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    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' => '8d6791b0fcd3458105d3f19467ac8686',
+                'vcf_size' => 593
+            }
+
+            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
+end

data/test/solvebio/test_sample_download.rb

@@ -0,0 +1,20 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    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
+end

data/test/solvebio/test_tabulate.rb

@@ -0,0 +1,129 @@
+# -*- coding: utf-8 -*-
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestTabulate < Test::Unit::TestCase
+        include SolveBio::Tabulate
+
+        def test_classify
+            assert_equal true,  '123.45'.number?
+            assert_equal true,  '123'.number?
+            assert_equal false, 'spam'.number?
+            assert_equal true,  '123'.int?
+            assert_equal false, '123.45'.int?
+
+            assert_equal NilClass, _type(nil)
+            assert_equal String, _type('foo')
+            assert_equal Fixnum, _type('1')
+            assert_equal Fixnum, _type(1)
+            assert_equal Fixnum, _type('\x1b[31m42\x1b[0m')
+        end
+
+        def test_align
+            assert_equal( 2, '123.45'.afterpoint)
+            assert_equal(-1, '1001'.afterpoint)
+            assert_equal(-1, 'eggs'.afterpoint)
+            assert_equal( 2, '123e45'.afterpoint)
+
+            assert_equal("  \u044f\u0439\u0446\u0430",
+                         "\u044f\u0439\u0446\u0430".padleft(6))
+            assert_equal("\u044f\u0439\u0446\u0430  ",
+                         "\u044f\u0439\u0446\u0430".padright(6))
+
+            assert_equal(" \u044f\u0439\u0446\u0430 ",
+                         "\u044f\u0439\u0446\u0430".padboth(6))
+
+            assert_equal(" \u044f\u0439\u0446\u0430  ",
+                         "\u044f\u0439\u0446\u0430".padboth(7))
+
+            assert_equal('abc', 'abc'.padright(2))
+            assert_equal('abc', 'abc'.padleft(2))
+            assert_equal('abc', 'abc'.padboth(2))
+
+
+            assert_equal(['   12.345  ', '-1234.5    ', '    1.23   ',
+                          ' 1234.5    ', '    1e+234 ', '    1.0e234'],
+                         align_column(
+                                      ["12.345", "-1234.5", "1.23", "1234.5",
+                                       "1e+234", "1.0e234"], "decimal"))
+        end
+
+        def test_column_type
+            assert_equal(Fixnum, column_type(["1", "2"]))
+            assert_equal(Float,  column_type(["1", "2.3"]))
+            assert_equal(String, column_type(["1", "2.3", "four"]))
+            assert_equal(String,
+                         column_type(["four", '\u043f\u044f\u0442\u044c']))
+            assert_equal(String, column_type([nil, "brux"]))
+            assert_equal(Fixnum, column_type([1, 2, nil]))
+        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
+spam  23
+EOS
+            assert_equal(expected.chomp, tabulate([["foo", 1], ["spam", 23]], [], [],
+                                                  false, tsv),
+                         'simple separated format table')
+            ####################################################################
+            expected = <<-EOS
+| буква   |   цифра |
+|---------+---------|
+| аз      |       2 |
+| буки    |       4 |
+EOS
+            hrow = ["\u0431\u0443\u043a\u0432\u0430", "\u0446\u0438\u0444\u0440\u0430"]
+            tbl = [["\u0430\u0437", 2], ["\u0431\u0443\u043a\u0438", 4]]
+            assert_equal(expected.chomp, SolveBio::Tabulate.tabulate(tbl, hrow),
+                         'org mode with header and unicode')
+
+            ###################################################################
+            expected = <<-EOS
+|                Fields | Data                            |
+|-----------------------+---------------------------------|
+|     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                             |
+EOS
+
+            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'],
+                                                  ['right', 'left']),
+                         'mixed data with arrays; close to actual query output')
+        end
+
+    end
+end

data/test/solvebio/test_util.rb

@@ -0,0 +1,39 @@
+require File.expand_path('../../helper', __FILE__)
+
+module SolveBio
+    class TestSolveObject < Test::Unit::TestCase
+        # Does our kind of camelCasing works?
+        def test_camelcase
+
+            data =
+                [
+                 ['abc',      'abc',        'no camelcase'],
+                 ['aBcDef',   'a_bc_def',   'letters only'],
+                 ['abc01Def', 'abc01_def',  'letters and numbers'],
+                 ['aBcDef',   'a_bc_def',   'multiple letter match'],
+                 ['a1B2C3',   'a1_b2_c3',   'multi letters and numbers'],
+                 ['?Foo',     '?_foo',      'weird symbols, part 1'],
+                 ['Dataset',  'dataset',    'no camelcase with caps'],
+                ]
+            data.each do |triple|
+                assert_equal(triple[1],
+                             Util.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],
+                             Util.pluralize(triple[0]),
+                             triple[2])
+            end
+
+        end
+    end
+end

metadata

@@ -1,15 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.6.1
+  version: 1.7.0
   prerelease: 
 platform: ruby
 authors:
-- solvebio.com
+- SolveBio
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-11-05 00:00:00.000000000 Z
+date: 2014-12-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc
@@ -91,6 +91,22 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: webmock
+  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'
 description: ! 'SolveBio is a platform for biomedical datasets. With SolveBio you
   can
 
@@ -101,7 +117,7 @@ description: ! 'SolveBio is a platform for biomedical datasets. With SolveBio yo
   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.
 
 '
 email: contact@solvebio.com
@@ -111,77 +127,73 @@ extensions: []
 extra_rdoc_files:
 - LICENSE
 files:
+- .bumpversion.cfg
 - .gitignore
 - .travis.yml
 - Gemfile
 - Gemspec
 - LICENSE
-- Makefile
 - README.md
 - Rakefile
 - bin/solvebio.rb
-- demo/README.md
-- demo/cheatsheet.rb
-- demo/dataset/facets.rb
-- demo/dataset/field.rb
-- demo/depository/README.md
-- demo/depository/all.rb
-- demo/depository/retrieve.rb
-- demo/depository/versions-all.rb
-- demo/query/query-filter.rb
-- demo/query/query.rb
-- demo/query/range-filter.rb
-- demo/test-api.rb
-- lib/cli/auth.rb
-- lib/cli/help.rb
-- lib/cli/irb.rb
-- lib/cli/irbrc.rb
-- lib/cli/options.rb
-- lib/client.rb
-- lib/credentials.rb
-- lib/errors.rb
-- lib/filter.rb
-- lib/locale.rb
-- lib/main.rb
-- lib/query.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
+- installer
 - lib/solvebio.rb
-- lib/tabulate.rb
-- lib/util.rb
+- lib/solvebio/acccount.rb
+- lib/solvebio/annotation.rb
+- lib/solvebio/api_operations.rb
+- lib/solvebio/api_resource.rb
+- lib/solvebio/cli.rb
+- lib/solvebio/cli/auth.rb
+- lib/solvebio/cli/credentials.rb
+- lib/solvebio/cli/irb.rb
+- lib/solvebio/cli/irbrc.rb
+- lib/solvebio/cli/tutorial.rb
+- lib/solvebio/client.rb
+- lib/solvebio/dataset.rb
+- lib/solvebio/dataset_field.rb
+- lib/solvebio/depository.rb
+- lib/solvebio/depository_version.rb
+- lib/solvebio/errors.rb
+- lib/solvebio/filter.rb
+- lib/solvebio/list_object.rb
+- lib/solvebio/locale.rb
+- lib/solvebio/query.rb
+- lib/solvebio/sample.rb
+- lib/solvebio/singleton_api_resource.rb
+- lib/solvebio/solve_object.rb
+- lib/solvebio/tabulate.rb
+- lib/solvebio/user.rb
+- lib/solvebio/util.rb
+- lib/solvebio/version.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
-- test/test-query-batch.rb
-- test/test-query-init.rb
-- test/test-query-paging.rb
-- test/test-query.rb
-- test/test-resource.rb
-- test/test-sample-access.rb
-- test/test-sample-download.rb
-- test/test-tabulate.rb
-- test/test-util.rb
+- test/solvebio/data/.gitignore
+- test/solvebio/data/.netrc
+- test/solvebio/data/netrc-save
+- test/solvebio/data/sample.vcf.gz
+- test/solvebio/data/test_creds
+- test/solvebio/test_annotation.rb
+- test/solvebio/test_client.rb
+- test/solvebio/test_conversion.rb
+- test/solvebio/test_credentials.rb
+- test/solvebio/test_dataset.rb
+- test/solvebio/test_depository.rb
+- test/solvebio/test_depositoryversion.rb
+- test/solvebio/test_error.rb
+- test/solvebio/test_filter.rb
+- test/solvebio/test_query.rb
+- test/solvebio/test_query_batch.rb
+- test/solvebio/test_query_init.rb
+- test/solvebio/test_query_tabulate.rb
+- test/solvebio/test_ratelimit.rb
+- test/solvebio/test_resource.rb
+- test/solvebio/test_sample_access.rb
+- test/solvebio/test_sample_download.rb
+- test/solvebio/test_tabulate.rb
+- test/solvebio/test_util.rb
 homepage: https://www.solvebio.com
-licenses: []
+licenses:
+- MIT
 post_install_message: 
 rdoc_options:
 - --charset=UTF-8
@@ -204,27 +216,30 @@ rubyforge_project:
 rubygems_version: 1.8.23
 signing_key: 
 specification_version: 2
-summary: SolveBio Ruby bindings.
+summary: Ruby bindings for the SolveBio API
 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
-- test/test-query-batch.rb
-- test/test-query-init.rb
-- test/test-query-paging.rb
-- test/test-query.rb
-- test/test-resource.rb
-- test/test-sample-access.rb
-- test/test-sample-download.rb
-- test/test-tabulate.rb
-- test/test-util.rb
+- test/solvebio/data/.gitignore
+- test/solvebio/data/.netrc
+- test/solvebio/data/netrc-save
+- test/solvebio/data/sample.vcf.gz
+- test/solvebio/data/test_creds
+- test/solvebio/test_annotation.rb
+- test/solvebio/test_client.rb
+- test/solvebio/test_conversion.rb
+- test/solvebio/test_credentials.rb
+- test/solvebio/test_dataset.rb
+- test/solvebio/test_depository.rb
+- test/solvebio/test_depositoryversion.rb
+- test/solvebio/test_error.rb
+- test/solvebio/test_filter.rb
+- test/solvebio/test_query.rb
+- test/solvebio/test_query_batch.rb
+- test/solvebio/test_query_init.rb
+- test/solvebio/test_query_tabulate.rb
+- test/solvebio/test_ratelimit.rb
+- test/solvebio/test_resource.rb
+- test/solvebio/test_sample_access.rb
+- test/solvebio/test_sample_download.rb
+- test/solvebio/test_tabulate.rb
+- test/solvebio/test_util.rb