solvebio 1.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +7 -0
- data/.travis.yml +13 -0
- data/Gemfile +4 -0
- data/Gemspec +3 -0
- data/LICENSE +21 -0
- data/Makefile +17 -0
- data/README.md +64 -0
- data/Rakefile +59 -0
- data/bin/solvebio.rb +36 -0
- data/demo/README.md +14 -0
- data/demo/dataset/facets.rb +13 -0
- data/demo/dataset/field.rb +13 -0
- data/demo/depository/README.md +24 -0
- data/demo/depository/all.rb +13 -0
- data/demo/depository/retrieve.rb +13 -0
- data/demo/depository/versions-all.rb +13 -0
- data/demo/query/query-filter.rb +30 -0
- data/demo/query/query.rb +13 -0
- data/demo/query/range-filter.rb +18 -0
- data/demo/test-api.rb +98 -0
- data/lib/apiresource.rb +130 -0
- data/lib/cli/auth.rb +122 -0
- data/lib/cli/help.rb +13 -0
- data/lib/cli/irb.rb +58 -0
- data/lib/cli/irbrc.rb +53 -0
- data/lib/cli/options.rb +75 -0
- data/lib/client.rb +152 -0
- data/lib/credentials.rb +67 -0
- data/lib/errors.rb +81 -0
- data/lib/filter.rb +312 -0
- data/lib/help.rb +46 -0
- data/lib/locale.rb +47 -0
- data/lib/main.rb +37 -0
- data/lib/query.rb +415 -0
- data/lib/resource.rb +414 -0
- data/lib/solvebio.rb +14 -0
- data/lib/solveobject.rb +101 -0
- data/lib/tabulate.rb +706 -0
- data/solvebio.gemspec +75 -0
- data/test/data/netrc-save +6 -0
- data/test/helper.rb +3 -0
- data/test/test-auth.rb +54 -0
- data/test/test-client.rb +27 -0
- data/test/test-error.rb +36 -0
- data/test/test-filter.rb +70 -0
- data/test/test-netrc.rb +42 -0
- data/test/test-query-batch.rb +60 -0
- data/test/test-query-init.rb +29 -0
- data/test/test-query-paging.rb +123 -0
- data/test/test-query.rb +88 -0
- data/test/test-resource.rb +47 -0
- data/test/test-solveobject.rb +27 -0
- data/test/test-tabulate.rb +127 -0
- metadata +158 -0
data/solvebio.gemspec
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## -*- Ruby -*-
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## This is the rakegem gemspec template. Make sure you read and understand
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## all of the comments. Some sections require modification, and others can
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## be deleted if you don't need them. Once you understand the contents of
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## this file, feel free to delete any comments that begin with two hash marks.
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## You can find comprehensive Gem::Specification documentation, at
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## http://docs.rubygems.org/read/chapter/20
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Gem::Specification.new do |s|
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s.specification_version = 2 if s.respond_to? :specification_version=
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# s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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# s.rubygems_version = '1.3.5'
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## Leave these as is they will be modified for you by the rake gemspec task.
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## If your rubyforge_project name is different, then edit it and comment out
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## the sub! line in the Rakefile
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s.name = 'solvebio'
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s.version = '1.5.0'
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s.date = '2014-08-16'
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## Make sure your summary is short. The description may be as long
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## as you like.
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s.summary = "SolveBio Ruby bindings."
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s.description = <<-EOD
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SolveBio is a platform for biomedical datasets. With SolveBio you can
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forget about parsing complex flat files and sifting through cryptic
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datasets. Just use the Ruby Client and API to explore massive
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datasets and automate just about any bioinformatics workflow.
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See https://www.solvebio.com/docs/api/ for more information.
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EOD
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## List the primary authors. If there are a bunch of authors, it's probably
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## better to set the email to an email list or something. If you don't have
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## a custom homepage, consider using your GitHub URL or the like.
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s.authors = ['solvebio.com']
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s.email = 'contact@solvebio.com'
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s.homepage = 'https://www.solvebio.com'
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## This gets added to the $LOAD_PATH so that 'lib/NAME.rb' can be required as
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## require 'NAME.rb' or'/lib/NAME/file.rb' can be as require 'NAME/file.rb'
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s.require_paths = %w[lib]
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s.required_ruby_version = Gem::Requirement.new(">= 1.9.0")
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## If your gem includes any executables, list them here.
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s.executables = ['solvebio.rb']
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s.default_executable = 'solvebio.rb'
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## Specify any RDoc options here. You'll want to add your README and
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## LICENSE files to the extra_rdoc_files list.
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s.rdoc_options = ["--charset=UTF-8"]
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s.extra_rdoc_files = %w[LICENSE]
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## List your runtime dependencies here. Runtime dependencies are those
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## that are needed for an end user to actually USE your code.
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s.add_dependency('netrc', '>=0.7.7')
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# s.add_dependency('openssl', '>=1.1.0')
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# There is no way to specify optional dependencies.
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# s.add_optional_dependency 'launchy' # opens URL in web browser for help
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# s.add_optional_dependency 'bond' # better shell command completion
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## List your development dependencies here. Development dependencies are
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## those that are only needed during development
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# s.add_development_dependency('DEVDEPNAME', [">= 1.1.0", "< 2.0.0"])
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s.add_development_dependency('rake')
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s.add_development_dependency('rdoc')
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s.files = `git ls-files`.split($/)
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## Test files will be grabbed from the file list. Make sure the path glob
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## matches what you actually use.
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s.test_files = s.files.grep(/^test/)
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end
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data/test/helper.rb
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data/test/test-auth.rb
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#!/usr/bin/env ruby
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$VERBOSE = true
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require 'test/unit'
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require 'rbconfig'
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require_relative '../lib/credentials'
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class TestAuth < Test::Unit::TestCase
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include SolveBio::Credentials
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def run_it(cmd)
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output = `#{cmd}`
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assert_equal 0, $?.to_i, "Should be able to run #{cmd}"
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output.chomp
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end
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def setup
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ruby=RbConfig.ruby
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@auth_prog = File.join(File.dirname(__FILE__),
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'..', 'lib', 'cli', 'auth.rb')
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@logout_cmd = "#{ruby} #{@auth_prog} logout"
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@@whoami_cmd = "#{ruby} #{@auth_prog} whoami"
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# Save who I was so we can compare at the end
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@i_was = run_it @@whoami_cmd
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begin
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@@creds = get_credentials
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rescue CredentialsError
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@@creds = nil
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end
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end
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def teardown
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# Restore creds to what they were when we started
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save_credentials(*@@creds) if @@creds
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i_am = run_it @@whoami_cmd
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assert_equal(@i_was, i_am,
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'get_credential and save_creditentials be idempotent')
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end
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# Integration test of logout
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def test_logout
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# Dunno if we are logged in or out - log out
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output = run_it @logout_cmd
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# We should be logged out. Try again, and check message.
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output = run_it @logout_cmd
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assert_equal 'You are not logged-in.', output
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# We should be logged out. Try to get status
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output = run_it @@whoami_cmd
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assert_equal 'You are not logged-in.', output
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end
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end
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data/test/test-client.rb
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#!/usr/bin/env ruby
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$VERBOSE = true
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require 'test/unit'
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require 'fileutils'
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require_relative '../lib/client'
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# require 'trepanning'
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class TestClient < Test::Unit::TestCase
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def test_get
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client = SolveBio::Client.new(nil, 'http://google.com')
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assert client, 'Should be able to create a client'
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# Can we get something from google?
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output = `curl --silent http://www.google.com`
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if $?.success? and output
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assert(client.request('http', 'http://www.google.com', nil,
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true), 'HTTP GET, google.com')
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assert(client.request('https', 'https://www.google.com', nil,
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true), 'HTTPS GET google.com')
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else
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skip('Are you connected to the Internet? www.google.com is unavailable')
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end
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end
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end
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data/test/test-error.rb
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#!/usr/bin/env ruby
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$VERBOSE = true
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require 'test/unit'
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require 'net/http'
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require_relative '../lib/errors'
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# require 'trepanning'
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$errors = []
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class FakeLogger
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def debug(mess)
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$errors << mess
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end
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end
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class TestError < Test::Unit::TestCase
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def test_error
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msg = "hi"
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assert_equal msg, SolveBio::Error.new(nil, msg).to_s, "Error.to_s fn"
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response = Net::HTTPUnauthorized.new('HTTP 1.1', '404', 'No creds')
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old_logger = SolveBio.instance_variable_get('@logger')
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logger = FakeLogger.new
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SolveBio.instance_variable_set('@logger', logger)
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old_verbose = $VERBOSE
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$VERBOSE=false
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SolveBio::Error.new(response)
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$VERBOSE=old_verbose
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assert_equal ["API Response (404): No content."], $errors
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ensure
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$VERBOSE = old_verbose if old_verbose
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SolveBio.instance_variable_set('@logger', old_logger) if old_logger
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end
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end
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data/test/test-filter.rb
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#!/usr/bin/env ruby
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$VERBOSE = true
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require 'test/unit'
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require_relative '../lib/filter'
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class TestFilter < Test::Unit::TestCase
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def test_filter_errors
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assert_raises TypeError do
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SolveBio::Filter.new(:style__gtt => 5)
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end
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assert_raises TypeError do
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SolveBio::Filter.new(:style__between => 'a')
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end
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assert_raises TypeError do
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SolveBio::Filter.new(:style__between => [5,10,15])
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end
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assert_raises IndexError do
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SolveBio::Filter.new(:style__range => [10,5])
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end
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end
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def test_filter
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f = SolveBio::Filter.new
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assert_equal('<SolveBio::Filter []>', f.inspect, 'empty filter')
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assert_equal('<SolveBio::Filter []>',
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(~f).inspect, '"not" of empty filter')
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f2 = SolveBio::Filter.new({:style => 'Mexican', :price => 'Free'})
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assert_equal('<SolveBio::Filter [{:and=>[[:price, "Free"], [:style, "Mexican"]]}]>',
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f2.inspect, 'Hash to tuple sorting'
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)
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assert_equal('<SolveBio::Filter [{:not=>{:and=>[[:price, "Free"], [:style, "Mexican"]]}}]>',
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(~f2).inspect, '~ of a non-nil filter')
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assert_equal('<SolveBio::Filter [{:and=>[[:price, "Free"], [:style, "Mexican"]]}]>',
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(~~f2).inspect, '~~ has no effect')
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filters3 =
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SolveBio::Filter.new(:omim_id => 144650) |
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SolveBio::Filter.new(:omim_id => 144600) |
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SolveBio::Filter.new(:omim_id => 145300)
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assert_equal('<SolveBio::Filter [{:or=>[[:omim_id, 144650], [:omim_id, 144600], [:omim_id, 145300]]}]>',
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filters3.inspect,
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'combining more than one of a connector (|)')
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assert_equal('<SolveBio::Filter [[:style__between, [5, 10]]]>',
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SolveBio::Filter.new(:style__between => (5...11)).inspect)
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assert_equal('<SolveBio::Filter [[:style__between, [5, 10]]]>',
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SolveBio::Filter.new(:style__between => (5..10)).inspect)
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end
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def test_range_filter
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assert_equal('<RangeFilter [{:and=>[["hg38_start__range", ' +
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'[32200000, 32500000]], ' +
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'["hg38_end__range", [32200000, 32500000]], ' +
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'["hg38_chromosome", "13"]]}]>',
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SolveBio::RangeFilter.
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new("hg38", "13", 32200000, 32500000).inspect)
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end
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def test_process_filters
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# FIXME: add more and put in a loop.
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filters = [[:omid, nil]]
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expect = filters
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assert_equal(expect.inspect,
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SolveBio::Filter.process_filters(filters).inspect)
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end
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end
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data/test/test-netrc.rb
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#!/usr/bin/env ruby
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$VERBOSE = true
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require 'test/unit'
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require 'fileutils'
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require_relative '../lib/credentials'
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# Does .netrc reading and manipulation work?
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class TestNetrc < Test::Unit::TestCase
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def setup
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@netrc_path_save = ENV["NETRC_PATH"]
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path = ENV["NETRC_PATH"] = File.join(File.dirname(__FILE__), 'data')
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FileUtils.cp(File.join(path, 'netrc-save'), File.join(path, '.netrc'))
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File.chmod(0600, "#{path}/.netrc")
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end
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def teardown
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ENV["NETRC_PATH"] = @netrc_path_save
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end
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include SolveBio::Credentials
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def test_netrc
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assert netrc_path, 'Should get a location for .netrc'
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end
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def test_get_credentials
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assert_equal ['rocky@example.com', 'shhhh'], get_credentials
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end
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def test_save_credentials
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new_values = get_credentials.map{|x| x+"abc"}
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save_credentials(*new_values)
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assert_equal new_values, get_credentials, 'Should append "abc" to creds'
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end
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def test_delete_credentials
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delete_credentials
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assert_equal nil, get_credentials, 'Should be able to delete credentials'
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end
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end
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#!/usr/bin/env ruby
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$VERBOSE = true
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require_relative 'helper'
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class TestQueryBatch < Test::Unit::TestCase
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TEST_DATASET_NAME = 'ClinVar/2.0.0-1/Variants'
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if SolveBio::api_key
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def setup
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12
|
+
begin
|
13
|
+
@dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
|
14
|
+
rescue SocketError
|
15
|
+
@dataset = nil
|
16
|
+
end
|
17
|
+
end
|
18
|
+
|
19
|
+
def test_invalid_batch_query
|
20
|
+
skip('Are you connected to the Internet?') unless @dataset
|
21
|
+
assert_raise SolveBio::Error do
|
22
|
+
SolveBio::BatchQuery
|
23
|
+
.new([
|
24
|
+
@dataset.query(:limit => 1, :fields => [:bogus_field]),
|
25
|
+
@dataset.query(:limit => 10).filter(:hg19_start__gt => 100000)
|
26
|
+
]).execute
|
27
|
+
end
|
28
|
+
|
29
|
+
dataset2 = SolveBio::Dataset.retrieve('HGNC/1.0.0-1/HGNC')
|
30
|
+
results = SolveBio::BatchQuery
|
31
|
+
.new([
|
32
|
+
dataset2.query(:limit => 1),
|
33
|
+
@dataset.query(:limit => 10).filter(:hg19_start => 100000)
|
34
|
+
]).execute
|
35
|
+
assert_equal(2, results.length)
|
36
|
+
|
37
|
+
|
38
|
+
|
39
|
+
end
|
40
|
+
|
41
|
+
def test_batch_query
|
42
|
+
skip('Are you connected to the Internet?') unless @dataset
|
43
|
+
queries = [
|
44
|
+
@dataset.query(:limit => 1),
|
45
|
+
@dataset.query(:limit => 10).filter(:hg19_start__gt => 100000)
|
46
|
+
]
|
47
|
+
results = SolveBio::BatchQuery.new(queries).execute
|
48
|
+
assert_equal(2, results.size)
|
49
|
+
assert_equal(1, results[0]['results'].length)
|
50
|
+
assert_equal(10, results[1]['results'].size)
|
51
|
+
end
|
52
|
+
|
53
|
+
|
54
|
+
else
|
55
|
+
def test_skip
|
56
|
+
skip 'Please set SolveBio::api_key'
|
57
|
+
end
|
58
|
+
end
|
59
|
+
|
60
|
+
end
|
@@ -0,0 +1,29 @@
|
|
1
|
+
$VERBOSE = true
|
2
|
+
require 'test/unit'
|
3
|
+
require_relative '../lib/query'
|
4
|
+
|
5
|
+
class TestQuery < Test::Unit::TestCase
|
6
|
+
|
7
|
+
def test_query_initialize
|
8
|
+
[SolveBio::PagingQuery, SolveBio::Query].each do |klass|
|
9
|
+
assert klass.new(5)
|
10
|
+
assert klass.new('5')
|
11
|
+
assert_raises TypeError do
|
12
|
+
# dataset id should be an Fixnum
|
13
|
+
klass.new(:limit => 10)
|
14
|
+
end
|
15
|
+
assert klass.new(5, :limit => 10)
|
16
|
+
assert klass.new(5.0, :limit => 10.0)
|
17
|
+
assert_raises RangeError do
|
18
|
+
# limit should be > 0
|
19
|
+
assert klass.new(5, :limit => -1)
|
20
|
+
end
|
21
|
+
assert_raises TypeError do
|
22
|
+
# limit should be a Fixnum
|
23
|
+
assert klass.new(5, :limit => 'a')
|
24
|
+
end
|
25
|
+
end
|
26
|
+
end
|
27
|
+
|
28
|
+
|
29
|
+
end
|
@@ -0,0 +1,123 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
$VERBOSE = true
|
3
|
+
require_relative 'helper'
|
4
|
+
|
5
|
+
class TestQueryPaging < Test::Unit::TestCase
|
6
|
+
|
7
|
+
TEST_DATASET_NAME = 'ClinVar/2.0.0-1/Variants'
|
8
|
+
|
9
|
+
if SolveBio::api_key
|
10
|
+
|
11
|
+
def setup
|
12
|
+
begin
|
13
|
+
@dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
|
14
|
+
rescue SocketError
|
15
|
+
@dataset = nil
|
16
|
+
end
|
17
|
+
end
|
18
|
+
|
19
|
+
def test_query
|
20
|
+
skip('Are you connected to the Internet?') unless @dataset
|
21
|
+
results = @dataset.query(:paging=>true, :limit => 10)
|
22
|
+
# When paging is on, results.size should return the number
|
23
|
+
# of total number of results.
|
24
|
+
assert_equal(results.size, results.total,
|
25
|
+
'results.size == results.total, paging=true')
|
26
|
+
end
|
27
|
+
|
28
|
+
# In paging queries, results.size should return the total number of
|
29
|
+
# results that exist. Yes, this is the same as test_query, but
|
30
|
+
# we revers the order of access, to make sure "warmup" is called.
|
31
|
+
def test_limit
|
32
|
+
skip('Are you connected to the Internet?') unless @dataset
|
33
|
+
limit = 10
|
34
|
+
results = @dataset.query(:paging=>true, :limit => limit)
|
35
|
+
assert_equal(results.total, results.length,
|
36
|
+
'results.total == results.length, paging = true')
|
37
|
+
end
|
38
|
+
|
39
|
+
|
40
|
+
def test_paging
|
41
|
+
skip('Are you connected to the Internet?') unless @dataset
|
42
|
+
limit = 100
|
43
|
+
total = 7
|
44
|
+
results = @dataset.query(:paging => true, :limit => limit).
|
45
|
+
filter(:hg19_start__range => [140000000, 140050000])
|
46
|
+
|
47
|
+
assert_equal(total, results.size)
|
48
|
+
|
49
|
+
# Make sure we can iterate over the entire result set
|
50
|
+
i = 0
|
51
|
+
results.each_with_index do |val, j|
|
52
|
+
assert val, "Can retrieve filter item #{i}"
|
53
|
+
i = j
|
54
|
+
end
|
55
|
+
assert_equal(i, total-1)
|
56
|
+
end
|
57
|
+
|
58
|
+
|
59
|
+
def test_range
|
60
|
+
skip('Are you connected to the Internet?') unless @dataset
|
61
|
+
limit = 100
|
62
|
+
results = @dataset.query(:paging => true, :limit => limit).
|
63
|
+
filter(:hg19_start__range => [140000000, 140050000])[2..5]
|
64
|
+
assert_equal(3, results.size)
|
65
|
+
|
66
|
+
results = @dataset.query(:paging => true, :limit => limit).
|
67
|
+
filter(:hg19_start__range => [140000000, 140050000])[0..8]
|
68
|
+
assert_equal(7, results.size)
|
69
|
+
end
|
70
|
+
|
71
|
+
def test_paging_and_slice_equivalence
|
72
|
+
skip('Are you connected to the Internet?') unless @dataset
|
73
|
+
idx0 = 3
|
74
|
+
idx1 = 5
|
75
|
+
|
76
|
+
query = proc{
|
77
|
+
@dataset.query( :paging => true, :limit => 20).
|
78
|
+
filter(:hg19_start__range => [140000000, 140060000])[2..10]
|
79
|
+
}
|
80
|
+
|
81
|
+
results_slice = query.call()[idx0...idx1]
|
82
|
+
results_paging = []
|
83
|
+
query.call.each_with_index do |r, i|
|
84
|
+
break if i == idx1
|
85
|
+
results_paging << r if i >= idx0
|
86
|
+
end
|
87
|
+
|
88
|
+
assert_equal(results_slice.size, results_paging.size)
|
89
|
+
|
90
|
+
results_paging.size.times do |i|
|
91
|
+
id_a = results_paging[i][:hg19_start]
|
92
|
+
id_b = results_slice[i][:hg19_start]
|
93
|
+
assert_equal(id_a, id_b)
|
94
|
+
end
|
95
|
+
end
|
96
|
+
|
97
|
+
|
98
|
+
def test_caching
|
99
|
+
skip('Are you connected to the Internet?') unless @dataset
|
100
|
+
idx0 = 60
|
101
|
+
idx1 = 81
|
102
|
+
|
103
|
+
q = @dataset.query(:paging => true, :limit => 100)
|
104
|
+
# q = self.dataset.query(paging=True, limit=100) \
|
105
|
+
# .filter(omim_id__in=range(100000, 120000))
|
106
|
+
results_slice = q[idx0..idx1]
|
107
|
+
results_cached = q[idx0..idx1]
|
108
|
+
|
109
|
+
assert_equal(results_slice.size, results_cached.size)
|
110
|
+
results_slice.size-1.times do |i|
|
111
|
+
id_a = results_slice[i]['reference_allele']
|
112
|
+
id_b = results_cached[i]['reference_allele']
|
113
|
+
assert_equal(id_b, id_a)
|
114
|
+
end
|
115
|
+
end
|
116
|
+
|
117
|
+
else
|
118
|
+
def test_skip
|
119
|
+
skip 'Please set SolveBio::api_key'
|
120
|
+
end
|
121
|
+
end
|
122
|
+
|
123
|
+
end
|