solvebio 1.6.1 → 1.7.0

data/lib/util.rb

@@ -1,29 +0,0 @@
-module SolveBio
-
-    module_function
-    def pluralize(name)
-           if name.end_with?('y')
-               name = name[0..-2] + 'ie'
-           end
-        return name + "s"
-    end
-
-    # Add underscore before internal uppercase letters. Also, lowercase
-    # all letters.
-    def camelcase_to_underscore(name)
-        # Using [[:upper:]] and [[:lower]] should help with Unicode.
-        s1 = name.gsub(/(.)([[:upper:]])([[:lower:]]+)/){"#{$1}_#{$2}#{$3}"}
-        return (s1.gsub(/([a-z0-9])([[:upper:]])/){"#{$1}_#{$2}"}).downcase
-    end
-end
-
-# Demo code
-if __FILE__ == $0
-    include SolveBio
-    %w(abc abcDef abc01Def aBcDef a1B2C3 ?Foo Dataset).each do |word|
-        puts word + " -> " + camelcase_to_underscore(word)
-    end
-    ['depository',  'dataset'].each do |word|
-        puts word + " -> " + pluralize(word)
-    end
-end

data/test/Makefile

@@ -1,9 +0,0 @@
-# Whatever it is you want to do other run demos, it should be forwarded to the
-# to top-level directory
-.PHONY: all
-
-#: the default target - same as running "check"
-all: check
-
-%:
-	$(MAKE) -C .. $@

data/test/test-annotation.rb

@@ -1,46 +0,0 @@
-require_relative './helper'
-
-class TestAnnotation < Test::Unit::TestCase
-
-    def check_response(response, expect, msg)
-        expect.each do |key, val|
-            assert_equal(val, response[key], msg)
-        end
-    end
-
-    def test_annotation
-        if SolveBio::API_HOST == 'https://api.solvebio.com'
-            skip "Annotation testing only on local/dev environments"
-        end
-
-        vcf_file = File.join(File.dirname(__FILE__), "data/sample.vcf.gz")
-        my_sample = SolveBio::Sample
-                      .create('GRCh37', :vcf_file => vcf_file)
-        assert(my_sample)
-
-        sample_id = my_sample['id']
-        expect = {
-            'class_name' => 'Annotation',
-            'error_message' => '',
-            'sample_id' => sample_id
-        }
-
-        response = SolveBio::Annotation.create(:sample_id => sample_id)
-        check_response(response, expect,
-                       "'Annotation.create(:sample_id=>{#sample_id}")
-
-        ['status', 'user_id', 'created_at', 'updated_at'].each do |field|
-            assert(response.member?(field) ,
-                   "response has field #{field}")
-        end
-
-        all = SolveBio::Annotation.all()
-        assert(all.total > 1,
-               "Annotation.all() returns more than one value")
-
-        response = my_sample.annotate
-        # FIXME: test annotate() more.
-
-        my_sample.delete
-    end
-end

data/test/test-auth.rb

@@ -1,58 +0,0 @@
-#!/usr/bin/env ruby
-$VERBOSE = true
-require 'test/unit'
-require 'rbconfig'
-require_relative '../lib/credentials'
-
-class TestAuth < Test::Unit::TestCase
-
-    include SolveBio::Credentials
-
-    def run_it(cmd)
-        output = `#{cmd}`
-        assert_equal 0, $?.to_i, "Should be able to run #{cmd}"
-        output.chomp
-    end
-
-    def setup
-        ruby=RbConfig.ruby
-        @auth_prog = File.join(File.dirname(__FILE__),
-                               '..', 'lib', 'cli', 'auth.rb')
-        @logout_cmd = "#{ruby} #{@auth_prog} logout"
-        @@whoami_cmd = "#{ruby} #{@auth_prog} whoami"
-
-        # Save who I was so we can compare at the end
-        @i_was = run_it @@whoami_cmd
-
-        begin
-            @@creds = get_credentials
-        rescue CredentialsError
-            @@creds = nil
-        end
-    end
-
-    def teardown
-        # Restore creds to what they were when we started
-        save_credentials(*@@creds) if @@creds
-        netrc_path = SolveBio::Credentials.netrc_path
-        n = Netrc.read(netrc_path)
-        if n[SolveBio::API_HOST]
-            i_am = run_it @@whoami_cmd
-            assert_equal(@i_was, i_am,
-                         'get_credential and save_creditentials be idempotent')
-        end
-    end
-
-    # Integration test of logout
-    def test_logout
-        # Dunno if we are logged in or out - log out
-        output = run_it @logout_cmd
-        # We should be logged out. Try again, and check message.
-        output = run_it @logout_cmd
-        assert_equal 'You are not logged-in.', output
-        # We should be logged out. Try to get status
-        output = run_it @@whoami_cmd
-        assert_equal 'You are not logged-in.', output
-    end
-
-end

data/test/test-client.rb

@@ -1,27 +0,0 @@
-#!/usr/bin/env ruby
-$VERBOSE = true
-require 'test/unit'
-require 'fileutils'
-require_relative '../lib/client'
-
-class TestClient < Test::Unit::TestCase
-
-    def test_get
-        client = SolveBio::Client.new(nil, 'http://google.com')
-        assert client, 'Should be able to create a client'
-
-        # Can we get something from google?
-        output = `curl --silent http://www.google.com`
-        if $?.success? and output
-            assert(client.request('get', 'http://www.google.com',
-                                  {:raw => true, :redirect => true}),
-                                  'HTTP GET, google.com')
-            assert(client.request('get', 'https://www.google.com',
-                                  {:raw => true}),
-                                  'HTTPS GET google.com')
-        else
-            skip('Are you connected to the Internet? www.google.com is unavailable')
-        end
-    end
-
-end

data/test/test-conversion.rb

@@ -1,13 +0,0 @@
-require 'test/unit'
-require_relative  '../lib/resource/apiresource'
-
-class ConversionTest < Test::Unit::TestCase
-    def test_class_to_api_name
-        ar = SolveBio::APIResource
-        [%w(Annotation annotations),
-         %w(DataField  data_fields),
-         %w(Depository depositories)].each do |class_name, expect|
-            assert_equal(expect, ar.class_to_api_name(class_name))
-        end
-    end
-end

data/test/test-dataset.rb

@@ -1,42 +0,0 @@
-# Test Dataset, DatasetField, and Facets
-require_relative './helper'
-require_relative '../lib/resource/main'
-
-class TestDataset < Test::Unit::TestCase
-    def setup
-        @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
-    end
-
-    def test_dataset
-        assert(@dataset.member?('id'),
-               'Should be able to get id in dataset')
-
-        %w(class_name created_at data_url depository depository_id
-           depository_version depository_version_id description
-          fields_url full_name name title updated_at url).each do |field|
-            assert(@dataset.member?(field),
-                   "Should find field #{field} in dataset #{@dataset.id}")
-        end
-
-        fields = @dataset.fields()
-        dataset_field = fields[:data][0]
-        assert(dataset_field.member?('id'),
-               'Should be able to get id in list of dataset fields')
-
-        dataset_field2 = SolveBio::DatasetField.retrieve(dataset_field.id)
-        assert_equal(dataset_field, dataset_field2,
-                     "Retrieving SolveBio::DatasetField id " +
-                     "#{dataset_field[:id]} found by all()")
-
-        %w(class_name created_at dataset dataset_id description facets_url
-          name updated_at url).each do |field|
-            assert(dataset_field.member?(field),
-                   "Should find field #{field} in fields #{dataset_field.id}")
-        end
-        facets = dataset_field.facets()
-
-        # We can get small or large numbers like 0 or 4902851621.0
-        assert(facets['total'] >= 0,
-               'facets should have a numeric total field >= 0')
-    end
-end

data/test/test-depository.rb

@@ -1,35 +0,0 @@
-# Test Depository, DepositoryVersions
-
-require_relative './helper'
-class TestDepository < Test::Unit::TestCase
-
-    def test_depositories
-        depos = SolveBio::Depository.all()
-
-        depo = depos[:data][0]
-        assert(depo.member?('id'),
-               'Should be able to get id in depository')
-
-        depo2 = SolveBio::Depository.retrieve(depo.id)
-        assert_equal(depo, depo2,
-                         "Retrieving dataset id #{depo.id} found by all()")
-
-        %w(class_name created_at description external_resources
-           full_name id is_private is_restricted latest_version
-           latest_version_id name title updated_at url versions_count
-           versions_url).each do |field|
-            assert(depo.member?(field),
-                   "Should find field #{field} in depo #{depo.id}")
-        end
-
-        depo_version_id = depo.versions()[:data][0].id
-        depo_version = SolveBio::DepositoryVersion.retrieve(depo_version_id)
-
-        %w(class_name created_at datasets_url depository depository_id
-           description full_name id latest name released released_at
-           title updated_at url).each do |field|
-            assert(depo_version.member?(field),
-                   "Should find field #{field} in depo version")
-        end
-    end
-end

data/test/test-error.rb

@@ -1,36 +0,0 @@
-#!/usr/bin/env ruby
-$VERBOSE = true
-require 'test/unit'
-require 'net/http'
-require_relative '../lib/errors'
-
-# require 'trepanning'
-
-$errors = []
-
-class FakeLogger
-    def debug(mess)
-        $errors << mess
-    end
-end
-
-class TestError < Test::Unit::TestCase
-
-    def test_error
-        msg = "hi"
-        assert_equal msg, SolveBio::Error.new(nil, msg).to_s, "Error.to_s fn"
-        response = Net::HTTPUnauthorized.new('HTTP 1.1', '404', 'No creds')
-        old_logger = SolveBio.instance_variable_get('@logger')
-        logger = FakeLogger.new
-        SolveBio.instance_variable_set('@logger', logger)
-        old_verbose = $VERBOSE
-        $VERBOSE=false
-        SolveBio::Error.new(response)
-        $VERBOSE=old_verbose
-        assert_equal ["API Response (404): No content."], $errors
-    ensure
-        $VERBOSE = old_verbose if old_verbose
-        SolveBio.instance_variable_set('@logger', old_logger) if old_logger
-
-    end
-end

data/test/test-filter.rb

@@ -1,70 +0,0 @@
-#!/usr/bin/env ruby
-$VERBOSE = true
-require 'test/unit'
-require_relative '../lib/filter'
-
-class TestFilter < Test::Unit::TestCase
-
-    def test_filter_errors
-        assert_raises TypeError do
-            SolveBio::Filter.new(:style__gtt => 5)
-        end
-        assert_raises TypeError do
-            SolveBio::Filter.new(:style__between => 'a')
-        end
-        assert_raises TypeError do
-            SolveBio::Filter.new(:style__between => [5,10,15])
-        end
-        assert_raises IndexError do
-            SolveBio::Filter.new(:style__range => [10,5])
-        end
-    end
-
-    def test_filter
-        f = SolveBio::Filter.new
-        assert_equal('<SolveBio::Filter []>', f.inspect, 'empty filter')
-        assert_equal('<SolveBio::Filter []>',
-                     (~f).inspect, '"not" of empty filter')
-        f2 = SolveBio::Filter.new({:style => 'Mexican', :price => 'Free'})
-        assert_equal('<SolveBio::Filter [{:and=>[[:price, "Free"], [:style, "Mexican"]]}]>',
-                     f2.inspect, 'Hash to tuple sorting'
-                     )
-        assert_equal('<SolveBio::Filter [{:not=>{:and=>[[:price, "Free"], [:style, "Mexican"]]}}]>',
-                     (~f2).inspect, '~ of a non-nil filter')
-        assert_equal('<SolveBio::Filter [{:and=>[[:price, "Free"], [:style, "Mexican"]]}]>',
-                     (~~f2).inspect, '~~ has no effect')
-
-        filters3 =
-            SolveBio::Filter.new(:omim_id => 144650) |
-            SolveBio::Filter.new(:omim_id => 144600) |
-            SolveBio::Filter.new(:omim_id => 145300)
-
-        assert_equal('<SolveBio::Filter [{:or=>[[:omim_id, 144650], [:omim_id, 144600], [:omim_id, 145300]]}]>',
-                     filters3.inspect,
-                     'combining more than one of a connector (|)')
-
-        assert_equal('<SolveBio::Filter [[:style__between, [5, 10]]]>',
-                     SolveBio::Filter.new(:style__between => (5...11)).inspect)
-        assert_equal('<SolveBio::Filter [[:style__between, [5, 10]]]>',
-                     SolveBio::Filter.new(:style__between => (5..10)).inspect)
-
-    end
-
-    def test_range_filter
-        assert_equal('<RangeFilter [{:and=>[["hg38_start__range", ' +
-                     '[32200000, 32500000]], ' +
-                     '["hg38_end__range", [32200000, 32500000]], ' +
-                     '["hg38_chromosome", "13"]]}]>',
-                     SolveBio::RangeFilter.
-                     new("hg38", "13", 32200000, 32500000).inspect)
-    end
-
-    def test_process_filters
-        # FIXME: add more and put in a loop.
-        filters = [[:omid, nil]]
-        expect  = filters
-        assert_equal(expect.inspect,
-                     SolveBio::Filter.process_filters(filters).inspect)
-    end
-
-end

data/test/test-netrc.rb

@@ -1,52 +0,0 @@
-#!/usr/bin/env ruby
-$VERBOSE = true
-require 'test/unit'
-require 'fileutils'
-require_relative '../lib/credentials'
-
-# Does .netrc reading and manipulation work?
-class TestNetrc < Test::Unit::TestCase
-
-
-    def setup
-        @netrc_path_save = ENV["NETRC_PATH"]
-        path = ENV['NETRC_PATH'] = File.join(File.dirname(__FILE__), 'data')
-        FileUtils.cp(File.join(path, 'netrc-save'), File.join(path, '.netrc'))
-        File.chmod(0600, "#{path}/.netrc")
-        @old_warn_level = $VERBOSE
-        @old_api_host = SolveBio::API_HOST
-        $VERBOSE = nil
-        SolveBio.const_set(:API_HOST, 'https://api.solvebio.com')
-        $VERBOSE = @old_warn_level
-    end
-
-    def teardown
-        ENV["NETRC_PATH"] = @netrc_path_save
-        $VERBOSE = nil
-        SolveBio.const_set(:API_HOST, @old_api_host)
-        $VERBOSE = @old_warn_level
-    end
-
-    include SolveBio::Credentials
-
-    def test_netrc
-        assert netrc_path, 'Should get a location for .netrc'
-    end
-
-    def test_get_credentials
-        assert_equal ['rocky@example.com', 'shhhh'], get_credentials.to_a
-    end
-
-    def test_save_credentials
-        new_values = get_credentials.map{|x| x+"abc"}
-        save_credentials(*new_values)
-        assert_equal(new_values, get_credentials.to_a,
-                     'Should append "abc" to creds')
-    end
-
-    def test_delete_credentials
-        delete_credentials
-        assert_equal nil, get_credentials, 'Should be able to delete credentials'
-    end
-
-end

data/test/test-query-batch.rb

@@ -1,40 +0,0 @@
-#!/usr/bin/env ruby
-$VERBOSE = true
-require 'socket'
-require_relative 'helper'
-require_relative '../lib/resource/main'
-
-class TestQueryBatch < Test::Unit::TestCase
-    def setup
-        @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
-    end
-
-    def test_invalid_batch_query
-        assert_raise SolveBio::Error do
-            SolveBio::BatchQuery
-                .new([
-                      @dataset.query(:limit => 1, :fields => [:bogus_field]),
-                      @dataset.query(:limit => 10).filter(:bogus_id__gt => 100000)
-                     ]).execute
-        end
-
-        results = SolveBio::BatchQuery
-            .new([
-                  @dataset.query(:limit => 10).filter(:hgnc_id__lt => 100),
-                  @dataset.query(:limit => 10).filter(:hgnc_id__gt => 100)
-                 ]).execute
-        assert_equal(2, results.length)
-
-    end
-
-    def test_batch_query
-        queries = [
-                   @dataset.query(:limit => 1),
-                   @dataset.query(:limit => 10).filter(:hgnc_id__gt => 100)
-                  ]
-        results = SolveBio::BatchQuery.new(queries).execute
-        assert_equal(2, results.size)
-        assert_equal(1, results[0]['results'].length)
-        assert_equal(10, results[1]['results'].size)
-    end
-end