solvebio 1.5.2 → 1.6.1
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/.travis.yml +13 -8
- data/Gemfile +4 -2
- data/README.md +5 -3
- data/demo/cheatsheet.rb +31 -0
- data/lib/cli/auth.rb +6 -6
- data/lib/cli/irbrc.rb +2 -1
- data/lib/cli/options.rb +1 -1
- data/lib/client.rb +85 -83
- data/lib/credentials.rb +2 -2
- data/lib/main.rb +11 -2
- data/lib/query.rb +5 -6
- data/lib/resource/annotation.rb +23 -0
- data/lib/resource/apiresource.rb +241 -0
- data/lib/resource/dataset.rb +91 -0
- data/lib/resource/datasetfield.rb +37 -0
- data/lib/resource/depository.rb +50 -0
- data/lib/resource/depositoryversion.rb +69 -0
- data/lib/resource/main.rb +123 -0
- data/lib/resource/sample.rb +75 -0
- data/lib/{solveobject.rb → resource/solveobject.rb} +43 -22
- data/lib/resource/user.rb +5 -0
- data/lib/solvebio.rb +1 -1
- data/lib/util.rb +29 -0
- data/solvebio.gemspec +7 -4
- data/test/Makefile +9 -0
- data/test/data/sample.vcf.gz +0 -0
- data/test/helper.rb +9 -2
- data/test/test-annotation.rb +46 -0
- data/test/test-auth.rb +8 -4
- data/test/test-client.rb +6 -6
- data/test/test-conversion.rb +13 -0
- data/test/test-dataset.rb +42 -0
- data/test/test-depository.rb +35 -0
- data/test/test-netrc.rb +13 -3
- data/test/test-query-batch.rb +26 -46
- data/test/test-query-paging.rb +77 -98
- data/test/test-query.rb +47 -64
- data/test/test-resource.rb +8 -15
- data/test/test-sample-access.rb +59 -0
- data/test/test-sample-download.rb +20 -0
- data/test/test-tabulate.rb +27 -23
- data/test/{test-solveobject.rb → test-util.rb} +17 -2
- metadata +128 -56
- data/lib/apiresource.rb +0 -130
- data/lib/help.rb +0 -46
- data/lib/resource.rb +0 -414
data/test/test-query.rb
CHANGED
@@ -1,87 +1,70 @@
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$VERBOSE = true
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+
require 'socket'
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require_relative 'helper'
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require_relative '../lib/resource/main'
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5
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class TestQuery < Test::Unit::TestCase
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def setup
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@dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
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end
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-
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# When paging is off, results.length should return the number of
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# results retrieved.
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def test_limit
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@dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
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limit = 10
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results = @dataset.query :paging=>false, :limit => limit
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assert_equal(limit, results.length,
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'limit == results.size, paging = false')
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if SolveBio::api_key
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@dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
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rescue SocketError
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@dataset = nil
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-
end
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results.each_with_index do |val, i|
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assert results[i], "retrieving value at #{i}"
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end
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def test_limit
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skip('Are you connected to the Internet?') unless @dataset
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@dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
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limit = 10
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results = @dataset.query :paging=>false, :limit => limit
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assert_equal(limit, results.length,
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'limit == results.size, paging = false')
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results.each_with_index do |val, i|
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assert results[i], "retrieving value at #{i}"
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end
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assert_raise IndexError do
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puts results[limit]
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end
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assert_raise IndexError do
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puts results[limit]
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end
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end
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assert_equal(0, results.size)
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assert_raise IndexError do
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puts results[0]
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end
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# test Query when limit is specified and is GREATER THAN total available
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# results
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def test_limit_empty
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limit = 100
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results = @dataset.query(:paging=>false, :limit => limit).
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filter({:omim_ids => 999999})
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assert_equal(0, results.size)
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assert_equal(1, results.size)
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assert_raise IndexError do
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puts results[0]
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end
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limit = 10
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num_filters = 3
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filters3 =
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SolveBio::Filter.new(:hg19_start => 148459988) |
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SolveBio::Filter.new(:hg19_start => 148562304) |
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SolveBio::Filter.new(:hg19_start => 148891521)
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results = @dataset.query(:paging=>false, :limit => limit).
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filter :omim_ids => 123631
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assert_equal(1, results.size)
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end
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-
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-
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# test Filtered Query in which limit is specified but is GREATER THAN
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# the number of total available results
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def test_limit_filter
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limit = 10
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num_filters = 2
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filters =
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SolveBio::Filter.new(:omim_ids => 123631) |
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SolveBio::Filter.new(:omim_ids => 123670)
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-
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results = @dataset.query(:paging=>false, :limit => limit,
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:filters => filters)
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-
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end
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num_filters.times do |i|
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assert results[i]
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end
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-
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assert_equal(num_filters, results.size)
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assert_raise IndexError do
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puts results[num_filters]
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end
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end
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data/test/test-resource.rb
CHANGED
@@ -1,14 +1,14 @@
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#!/usr/bin/env ruby
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$VERBOSE = true
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-
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require_relative '../lib/resource'
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require_relative './helper'
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require_relative '../lib/resource/main'
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class TestResource < Test::Unit::TestCase
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# Do the class FULL_NAME_REGEX contants match what the think they
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# should?
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def test_full_name_regexp
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assert('
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assert('HGNC/1.0.0-1/HGNC' =~
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SolveBio::Dataset::FULL_NAME_REGEX,
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'Dataset regexp')
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@@ -27,18 +27,11 @@ class TestResource < Test::Unit::TestCase
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def test_Dataset_from_response
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resp = {
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'class_name' => 'Dataset',
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'
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'
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'
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'
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'
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'description' => '',
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'fields_url' => 'https://api.solvebio.com/v1/datasets/25/fields',
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'full_name' => 'ClinVar/2.0.0-1/Variants',
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'id' => 25,
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'name' => 'Variants',
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'title' => 'Variants',
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'url' => 'https://api.solvebio.com/v1/datasets/25'
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'depository' => 'HGNC',
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'depository_version' => 'HGNC/1.0.0-1',
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'full_name' => 'HGNC/1.0.0-1/HGNC',
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'name' => 'HGNC',
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'title' => 'HGNC'
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}
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so = resp.to_solvebio
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assert_equal SolveBio::Dataset, so.class, 'Hash -> SolveObject'
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@@ -0,0 +1,59 @@
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require_relative './helper'
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class TestSampleAccess < Test::Unit::TestCase
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def check_response(response, expect, msg)
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expect.each do |key, val|
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assert_equal(val, response[key], msg)
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end
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end
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def test_insert_delete
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if SolveBio::API_HOST == 'https://api.solvebio.com'
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skip "Testing only on local/dev environments"
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end
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all = SolveBio::Sample.all
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total = all.total
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vcf_url = 'http://downloads.solvebio.com/vcf/small_sample.vcf.gz'
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expect = {
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'class_name' => 'Sample',
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'annotations_count' => 0,
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'description' => '',
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'genome_build' => 'GRCh37',
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'vcf_md5' => 'a03e39e96671a01208cffd234812556d',
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'vcf_size' => 12124
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}
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response = SolveBio::Sample.create('GRCh37', :vcf_url => vcf_url)
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check_response(response, expect,
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'create sample.vcf.gz from url')
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all = SolveBio::Sample.all
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assert_equal(all.total, total + 1, "After uploading an url")
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total = total + 1
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vcf_file = File.join(File.dirname(__FILE__), 'data/sample.vcf.gz')
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response = SolveBio::Sample.create('GRCh37', {:vcf_file => vcf_file})
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expect = {
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'class_name' => 'Sample',
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'annotations_count' => 0,
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'description' => '',
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'genome_build' => 'GRCh37',
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'vcf_md5' => '83acd96171c72ab2bb35e9c52961afd9',
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'vcf_size' => 592
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}
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check_response(response, expect,
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'create sample.vcf.gz from a file')
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# assert_equal(all.total, total, "After uploading a file")
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# sample = SolveBio::Sample.retrieve(response.id)
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# delete_response = sample.delete
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# assert_equal(delete_response.deleted, true,
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# 'response.deleted should be true')
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# all = SolveBio::Sample.all
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# assert_equal(all.total, total, "After deleting a file")
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end
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end
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@@ -0,0 +1,20 @@
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require 'fileutils'
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require_relative './helper'
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class TestSampleDownload < Test::Unit::TestCase
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def test_sample_download
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if SolveBio::API_HOST == 'https://api.solvebio.com'
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skip "Testing only on local/dev environments"
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end
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vcf_file = File.join(File.dirname(__FILE__), 'data/sample.vcf.gz')
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sample = SolveBio::Sample.create('GRCh37', {:vcf_file => vcf_file})
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response = sample.download()
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assert_equal(response['code'], 200,
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"Download sample file status ok")
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assert(File.exist?(response['filename']),
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"Download sample file on filesystem")
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FileUtils.rm response['filename']
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end
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end
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data/test/test-tabulate.rb
CHANGED
@@ -63,6 +63,10 @@ class TestTabulate < Test::Unit::TestCase
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end
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def test_tabulate
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old_verbose = $VERBOSE
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$VERBOSE=nil
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SolveBio::Tabulate.const_set(:TTY_COLS, 80)
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$VERBOSE=old_verbose
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tsv = simple_separated_format("\t")
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expected = <<-EOS
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foo 1
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@@ -86,37 +90,37 @@ EOS
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expected = <<-EOS
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| Fields | Data |
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|-----------------------+-----------------------------|
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-
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| alternate_alleles | T |
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| clinical_origin | somatic |
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| clinical_significance | other |
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| gene_symbols | CPB1 |
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| hg18_chromosome | 3 |
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| hg19_chromosome | 3 |
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| hg19_start | 148562304 |
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| rcvaccession | RCV000060731 |
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| hg38_start | 148844517 |
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| hgvs | NC_000003.12:g.148844517C>T |
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| rcvaccession | RCV000060731 |
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| rcvaccession_version | 2 |
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| reference_allele | C |
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| gene_symbols | CPB1 |
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| rsid | rs150241322 |
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| hg19_chromosome | 3 |
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| hgvs | NC_000003.12:g.148844517C>T |
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| clinical_significance | other |
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| alternate_alleles | T |
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| clinical_origin | somatic |
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| type | SNV |
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EOS
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"
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"
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"
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"
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"
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"
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"
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"
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"
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"
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"
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"
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"type"=>"SNV"
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hash = {
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"alternate_alleles" => ["T"],
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"clinical_origin" => ["somatic"],
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"clinical_significance"=> "other",
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"gene_symbols" => ["CPB1"],
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"hg18_chromosome" => "3",
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"hg19_chromosome" => "3",
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"hg19_start" => 148562304,
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"hg38_start" => 148844517,
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"hgvs" => ["NC_000003.12:g.148844517C>T"],
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"rcvaccession" => "RCV000060731",
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"rcvaccession_version" => 2,
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"reference_allele" => "C",
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"rsid" => "rs150241322",
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"type" => "SNV"
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}
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assert_equal(expected.chomp, tabulate(hash.to_a,
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['Fields', 'Data'],
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@@ -1,7 +1,7 @@
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1
1
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#!/usr/bin/env ruby
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2
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$VERBOSE = true
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3
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require 'test/unit'
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-
require_relative '../lib/
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+
require_relative '../lib/util'
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5
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6
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class TestSolveObject < Test::Unit::TestCase
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7
7
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@@ -20,8 +20,23 @@ class TestSolveObject < Test::Unit::TestCase
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20
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]
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data.each do |triple|
|
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assert_equal(triple[1],
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-
camelcase_to_underscore(triple[0]),
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SolveBio::camelcase_to_underscore(triple[0]),
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triple[2])
|
25
25
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end
|
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26
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end
|
27
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+
|
28
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+
def test_pluralize
|
29
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+
data =
|
30
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+
[
|
31
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['depository', 'depositories', "ends in 'y'"],
|
32
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+
['dataset', 'datasets', "simply adds an 's'"]
|
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+
]
|
34
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+
data.each do |triple|
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35
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+
assert_equal(triple[1],
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36
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+
SolveBio::pluralize(triple[0]),
|
37
|
+
triple[2])
|
38
|
+
end
|
39
|
+
|
40
|
+
end
|
41
|
+
|
27
42
|
end
|
metadata
CHANGED
@@ -1,66 +1,116 @@
|
|
1
|
-
--- !ruby/object:Gem::Specification
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
2
|
name: solvebio
|
3
|
-
version: !ruby/object:Gem::Version
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 1.6.1
|
4
5
|
prerelease:
|
5
|
-
version: 1.5.2
|
6
6
|
platform: ruby
|
7
|
-
authors:
|
7
|
+
authors:
|
8
8
|
- solvebio.com
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
|
13
|
-
|
14
|
-
|
15
|
-
- !ruby/object:Gem::Dependency
|
12
|
+
date: 2014-11-05 00:00:00.000000000 Z
|
13
|
+
dependencies:
|
14
|
+
- !ruby/object:Gem::Dependency
|
16
15
|
name: netrc
|
16
|
+
requirement: !ruby/object:Gem::Requirement
|
17
|
+
none: false
|
18
|
+
requirements:
|
19
|
+
- - ! '>='
|
20
|
+
- !ruby/object:Gem::Version
|
21
|
+
version: 0.7.7
|
22
|
+
type: :runtime
|
17
23
|
prerelease: false
|
18
|
-
|
24
|
+
version_requirements: !ruby/object:Gem::Requirement
|
19
25
|
none: false
|
20
|
-
requirements:
|
21
|
-
- -
|
22
|
-
- !ruby/object:Gem::Version
|
26
|
+
requirements:
|
27
|
+
- - ! '>='
|
28
|
+
- !ruby/object:Gem::Version
|
23
29
|
version: 0.7.7
|
30
|
+
- !ruby/object:Gem::Dependency
|
31
|
+
name: rest_client
|
32
|
+
requirement: !ruby/object:Gem::Requirement
|
33
|
+
none: false
|
34
|
+
requirements:
|
35
|
+
- - ! '>='
|
36
|
+
- !ruby/object:Gem::Version
|
37
|
+
version: 1.8.1
|
24
38
|
type: :runtime
|
25
|
-
version_requirements: *id001
|
26
|
-
- !ruby/object:Gem::Dependency
|
27
|
-
name: rake
|
28
39
|
prerelease: false
|
29
|
-
|
40
|
+
version_requirements: !ruby/object:Gem::Requirement
|
41
|
+
none: false
|
42
|
+
requirements:
|
43
|
+
- - ! '>='
|
44
|
+
- !ruby/object:Gem::Version
|
45
|
+
version: 1.8.1
|
46
|
+
- !ruby/object:Gem::Dependency
|
47
|
+
name: addressable
|
48
|
+
requirement: !ruby/object:Gem::Requirement
|
30
49
|
none: false
|
31
|
-
requirements:
|
32
|
-
- -
|
33
|
-
- !ruby/object:Gem::Version
|
34
|
-
version:
|
50
|
+
requirements:
|
51
|
+
- - ! '>='
|
52
|
+
- !ruby/object:Gem::Version
|
53
|
+
version: 2.3.6
|
54
|
+
type: :runtime
|
55
|
+
prerelease: false
|
56
|
+
version_requirements: !ruby/object:Gem::Requirement
|
57
|
+
none: false
|
58
|
+
requirements:
|
59
|
+
- - ! '>='
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: 2.3.6
|
62
|
+
- !ruby/object:Gem::Dependency
|
63
|
+
name: rake
|
64
|
+
requirement: !ruby/object:Gem::Requirement
|
65
|
+
none: false
|
66
|
+
requirements:
|
67
|
+
- - ! '>='
|
68
|
+
- !ruby/object:Gem::Version
|
69
|
+
version: '0'
|
35
70
|
type: :development
|
36
|
-
version_requirements: *id002
|
37
|
-
- !ruby/object:Gem::Dependency
|
38
|
-
name: rdoc
|
39
71
|
prerelease: false
|
40
|
-
|
72
|
+
version_requirements: !ruby/object:Gem::Requirement
|
41
73
|
none: false
|
42
|
-
requirements:
|
43
|
-
- -
|
44
|
-
- !ruby/object:Gem::Version
|
45
|
-
version:
|
74
|
+
requirements:
|
75
|
+
- - ! '>='
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: '0'
|
78
|
+
- !ruby/object:Gem::Dependency
|
79
|
+
name: rdoc
|
80
|
+
requirement: !ruby/object:Gem::Requirement
|
81
|
+
none: false
|
82
|
+
requirements:
|
83
|
+
- - ! '>='
|
84
|
+
- !ruby/object:Gem::Version
|
85
|
+
version: '0'
|
46
86
|
type: :development
|
47
|
-
|
48
|
-
|
49
|
-
|
87
|
+
prerelease: false
|
88
|
+
version_requirements: !ruby/object:Gem::Requirement
|
89
|
+
none: false
|
90
|
+
requirements:
|
91
|
+
- - ! '>='
|
92
|
+
- !ruby/object:Gem::Version
|
93
|
+
version: '0'
|
94
|
+
description: ! 'SolveBio is a platform for biomedical datasets. With SolveBio you
|
95
|
+
can
|
96
|
+
|
50
97
|
forget about parsing complex flat files and sifting through cryptic
|
98
|
+
|
51
99
|
datasets. Just use the Ruby Client and API to explore massive
|
100
|
+
|
52
101
|
datasets and automate just about any bioinformatics workflow.
|
53
|
-
|
102
|
+
|
103
|
+
|
54
104
|
See https://www.solvebio.com/docs/api/ for more information.
|
55
105
|
|
106
|
+
'
|
56
107
|
email: contact@solvebio.com
|
57
|
-
executables:
|
108
|
+
executables:
|
58
109
|
- solvebio.rb
|
59
110
|
extensions: []
|
60
|
-
|
61
|
-
extra_rdoc_files:
|
111
|
+
extra_rdoc_files:
|
62
112
|
- LICENSE
|
63
|
-
files:
|
113
|
+
files:
|
64
114
|
- .gitignore
|
65
115
|
- .travis.yml
|
66
116
|
- Gemfile
|
@@ -71,6 +121,7 @@ files:
|
|
71
121
|
- Rakefile
|
72
122
|
- bin/solvebio.rb
|
73
123
|
- demo/README.md
|
124
|
+
- demo/cheatsheet.rb
|
74
125
|
- demo/dataset/facets.rb
|
75
126
|
- demo/dataset/field.rb
|
76
127
|
- demo/depository/README.md
|
@@ -81,7 +132,6 @@ files:
|
|
81
132
|
- demo/query/query.rb
|
82
133
|
- demo/query/range-filter.rb
|
83
134
|
- demo/test-api.rb
|
84
|
-
- lib/apiresource.rb
|
85
135
|
- lib/cli/auth.rb
|
86
136
|
- lib/cli/help.rb
|
87
137
|
- lib/cli/irb.rb
|
@@ -91,19 +141,33 @@ files:
|
|
91
141
|
- lib/credentials.rb
|
92
142
|
- lib/errors.rb
|
93
143
|
- lib/filter.rb
|
94
|
-
- lib/help.rb
|
95
144
|
- lib/locale.rb
|
96
145
|
- lib/main.rb
|
97
146
|
- lib/query.rb
|
98
|
-
- lib/resource.rb
|
147
|
+
- lib/resource/annotation.rb
|
148
|
+
- lib/resource/apiresource.rb
|
149
|
+
- lib/resource/dataset.rb
|
150
|
+
- lib/resource/datasetfield.rb
|
151
|
+
- lib/resource/depository.rb
|
152
|
+
- lib/resource/depositoryversion.rb
|
153
|
+
- lib/resource/main.rb
|
154
|
+
- lib/resource/sample.rb
|
155
|
+
- lib/resource/solveobject.rb
|
156
|
+
- lib/resource/user.rb
|
99
157
|
- lib/solvebio.rb
|
100
|
-
- lib/solveobject.rb
|
101
158
|
- lib/tabulate.rb
|
159
|
+
- lib/util.rb
|
102
160
|
- solvebio.gemspec
|
161
|
+
- test/Makefile
|
103
162
|
- test/data/netrc-save
|
163
|
+
- test/data/sample.vcf.gz
|
104
164
|
- test/helper.rb
|
165
|
+
- test/test-annotation.rb
|
105
166
|
- test/test-auth.rb
|
106
167
|
- test/test-client.rb
|
168
|
+
- test/test-conversion.rb
|
169
|
+
- test/test-dataset.rb
|
170
|
+
- test/test-depository.rb
|
107
171
|
- test/test-error.rb
|
108
172
|
- test/test-filter.rb
|
109
173
|
- test/test-netrc.rb
|
@@ -112,40 +176,46 @@ files:
|
|
112
176
|
- test/test-query-paging.rb
|
113
177
|
- test/test-query.rb
|
114
178
|
- test/test-resource.rb
|
115
|
-
- test/test-
|
179
|
+
- test/test-sample-access.rb
|
180
|
+
- test/test-sample-download.rb
|
116
181
|
- test/test-tabulate.rb
|
182
|
+
- test/test-util.rb
|
117
183
|
homepage: https://www.solvebio.com
|
118
184
|
licenses: []
|
119
|
-
|
120
185
|
post_install_message:
|
121
|
-
rdoc_options:
|
186
|
+
rdoc_options:
|
122
187
|
- --charset=UTF-8
|
123
|
-
require_paths:
|
188
|
+
require_paths:
|
124
189
|
- lib
|
125
|
-
required_ruby_version: !ruby/object:Gem::Requirement
|
190
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
126
191
|
none: false
|
127
|
-
requirements:
|
128
|
-
- -
|
129
|
-
- !ruby/object:Gem::Version
|
192
|
+
requirements:
|
193
|
+
- - ! '>='
|
194
|
+
- !ruby/object:Gem::Version
|
130
195
|
version: 1.9.0
|
131
|
-
required_rubygems_version: !ruby/object:Gem::Requirement
|
196
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
132
197
|
none: false
|
133
|
-
requirements:
|
134
|
-
- -
|
135
|
-
- !ruby/object:Gem::Version
|
136
|
-
version:
|
198
|
+
requirements:
|
199
|
+
- - ! '>='
|
200
|
+
- !ruby/object:Gem::Version
|
201
|
+
version: '0'
|
137
202
|
requirements: []
|
138
|
-
|
139
203
|
rubyforge_project:
|
140
204
|
rubygems_version: 1.8.23
|
141
205
|
signing_key:
|
142
206
|
specification_version: 2
|
143
207
|
summary: SolveBio Ruby bindings.
|
144
|
-
test_files:
|
208
|
+
test_files:
|
209
|
+
- test/Makefile
|
145
210
|
- test/data/netrc-save
|
211
|
+
- test/data/sample.vcf.gz
|
146
212
|
- test/helper.rb
|
213
|
+
- test/test-annotation.rb
|
147
214
|
- test/test-auth.rb
|
148
215
|
- test/test-client.rb
|
216
|
+
- test/test-conversion.rb
|
217
|
+
- test/test-dataset.rb
|
218
|
+
- test/test-depository.rb
|
149
219
|
- test/test-error.rb
|
150
220
|
- test/test-filter.rb
|
151
221
|
- test/test-netrc.rb
|
@@ -154,5 +224,7 @@ test_files:
|
|
154
224
|
- test/test-query-paging.rb
|
155
225
|
- test/test-query.rb
|
156
226
|
- test/test-resource.rb
|
157
|
-
- test/test-
|
227
|
+
- test/test-sample-access.rb
|
228
|
+
- test/test-sample-download.rb
|
158
229
|
- test/test-tabulate.rb
|
230
|
+
- test/test-util.rb
|