solvebio 1.5.0

data/test/test-query.rb

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+$VERBOSE = true
+require_relative 'helper'
+
+class TestQuery < Test::Unit::TestCase
+
+    TEST_DATASET_NAME = 'ClinVar/2.0.0-1/Variants'
+
+    if SolveBio::api_key
+
+        def setup
+            begin
+                @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
+            rescue SocketError
+                @dataset = nil
+            end
+        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
+        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
+
+            results = @dataset.query(:paging=>false, :limit => limit).
+                filter :hg19_start => 148459988
+            assert_equal(1, results.size)
+        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,
+                                     :filters => filters3)
+
+            num_filters.times do |i|
+                assert results[i]
+            end
+
+            assert_equal(num_filters, results.size)
+
+            assert_raise IndexError do
+                puts results[num_filters]
+            end
+        end
+
+    else
+        def test_skip
+            skip 'Please set SolveBio::api_key'
+        end
+    end
+
+end

data/test/test-resource.rb

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+#!/usr/bin/env ruby
+$VERBOSE = true
+require 'test/unit'
+require_relative '../lib/resource'
+
+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' =~
+                SolveBio::Dataset::FULL_NAME_REGEX,
+                'Dataset regexp')
+
+    end
+
+    def test_SolveObject_inspect
+        str = SolveBio::SolveObject.new.inspect
+        assert(str =~ /^<SolveBio::SolveObject:[[:xdigit:]]+> JSON: {}/,
+               'empty SolveObject inspect')
+        str = SolveBio::SolveObject.new(62).inspect
+        assert(str =~ /^<SolveBio::SolveObject id=62:[[:xdigit:]]+> JSON: {"id":62}/,
+               "SolveObject inspect with id #{str}")
+
+    end
+
+    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'
+        }
+        so = resp.to_solvebio
+        assert_equal SolveBio::Dataset, so.class, 'Hash -> SolveObject'
+        resp.keys.each {|k| assert_equal resp[k], so[k]}
+    end
+end

data/test/test-solveobject.rb

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+#!/usr/bin/env ruby
+$VERBOSE = true
+require 'test/unit'
+require_relative '../lib/solveobject'
+
+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],
+                         camelcase_to_underscore(triple[0]),
+                         triple[2])
+        end
+    end
+end

data/test/test-tabulate.rb

@@ -0,0 +1,127 @@
+#!/usr/bin/env ruby
+# -*- coding: utf-8 -*-
+require_relative '../lib/tabulate'
+$VERBOSE = true
+require 'test/unit'
+
+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
+        tsv = simple_separated_format("\t")
+        expected = <<-EOS
+foo    1
+spam  23
+EOS
+        assert_equal(expected.chomp, tabulate([["foo", 1], ["spam", 23]], [], 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                        |
+|-----------------------+-----------------------------|
+| 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                         |
+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"
+        }
+        assert_equal(expected.chomp, tabulate(hash.to_a,
+                                              ['Fields', 'Data'],
+                                              ['right', 'left']),
+                     'mixed data with arrays; close to actual query output')
+    end
+
+end

metadata

@@ -0,0 +1,158 @@
+--- !ruby/object:Gem::Specification 
+name: solvebio
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 1.5.0
+platform: ruby
+authors: 
+- solvebio.com
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2014-08-16 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: netrc
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.7.7
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rake
+  prerelease: false
+  requirement: &id002 !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 
+    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
+  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: 
+- solvebio.rb
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+files: 
+- .gitignore
+- .travis.yml
+- Gemfile
+- Gemspec
+- LICENSE
+- Makefile
+- README.md
+- Rakefile
+- bin/solvebio.rb
+- demo/README.md
+- 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/apiresource.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/help.rb
+- lib/locale.rb
+- lib/main.rb
+- lib/query.rb
+- lib/resource.rb
+- lib/solvebio.rb
+- lib/solveobject.rb
+- lib/tabulate.rb
+- solvebio.gemspec
+- test/data/netrc-save
+- test/helper.rb
+- test/test-auth.rb
+- test/test-client.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-solveobject.rb
+- test/test-tabulate.rb
+homepage: https://www.solvebio.com
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: 1.9.0
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  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/data/netrc-save
+- test/helper.rb
+- test/test-auth.rb
+- test/test-client.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-solveobject.rb
+- test/test-tabulate.rb