solvebio 1.5.0

data/.gitignore

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+*~
+.rvmrc
+/Gemfile.lock
+/pkg
+/solvebio-*.gem
+/test/data/.netrc
+Gemfile.lock

data/.travis.yml

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+language: ruby
+before_script:
+  - gem install netrc
+  - touch ~/.netrc
+  - chmod 0600 ~/.netrc
+env:
+  - "COLUMNS=80"
+script: rake
+rvm:
+  - 1.9.3
+  - 2.0.0
+  - 2.1.1
+  - 2.1.2

data/Gemfile

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+# A sample Gemfile
+source "https://rubygems.org"
+
+gem "netrc"

data/Gemspec

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+source 'https://rubygems.org'
+
+gemspec

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2014 Solve, Inc. (https://www.solvebio.com)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/Makefile

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+# I'll admit it -- I'm an absent-minded old-timer who has trouble
+# learning new tricks.
+
+.PHONY: test
+
+RUBY ?= ruby
+RAKE ?= rake
+
+test: check
+
+#: Default target; same as "make check"
+all: check
+	true
+
+#: Same as corresponding rake task
+%:
+	$(RAKE) $@

data/README.md

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+[![Build Status](https://travis-ci.org/solvebio/solvebio-ruby.svg)](https://travis-ci.org/solvebio/solvebio-ruby)
+
+# SolveBio Ruby Client
+
+
+This packages provides a command-line interface (CLI) and Ruby API interface to SolveBio.
+
+For more information about the SolveBio API, https://www.solvebio.com/docs/api/
+For more information about SolveBio, see https://www.solvebio.com
+
+# Installation
+
+Right now we only support installing from git:
+
+    git clone https://github.com/solvebio/solvebio-ruby.git
+	cd solvebio-ruby
+	gem install netrc  # install gem dependencies, may need sudo
+	rake test          # or make test
+    sudo rake install  # or make install
+
+This also builds a *solvebio* gem which you can use elsewhere.
+
+But note, you can also run right inside the git repository without installing anything. For example, running:
+
+    git clone https://github.com/solvebio/solvebio-ruby.git
+	solvebio-ruby/bin/solvebio.rb
+
+will get you into a solvebio irb shell. Just about any Ruby file in the project can be run standalone, and when done so, it demos that Ruby code.
+
+# Optional Gem dependencies
+
+The following optional gems can make your shell experience better
+
+* [bond](http://tagaholic.me/bond/)
+
+    Better command completion
+
+* [launchy](https://github.com/copiousfreetime/launchy)
+
+    Opens help URLs in a web browser tab
+
+* [rb18n-core](https://https://github.com/ai/r18n)
+
+    Localization for number formatting
+
+# Demo code and Documentation
+
+See the [demo folder](https://github.com/solvebio/solvebio-ruby/tree/dev/demo) for ready-to-run examples.
+
+The online [SolveBio Python API documentation](https://www.solvebio.com/docs/api/?python) has additional examples. To use these with the Ruby client,  change `import solvebio` to `require 'solvebio'` and change `solvebio.` to `SolveBio::` everywhere it occurs.
+
+e.g., a Python example:
+
+    solvebio.Depository.retrieve("ClinVar").versions()
+
+the same Python example ported to Ruby:
+
+    SolveBio::Depository.retrieve("ClinVar").versions()
+
+As with any other Ruby method call, you can drop the final parenthesis if you like.
+
+# To Do
+
+This hasn't been extensively field tested yet.

data/Rakefile

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+#!/usr/bin/env rake
+# -*- Ruby -*-
+
+ROOT_DIR         = File.dirname(__FILE__)
+Gemspec_filename = 'solvebio.gemspec'
+
+def gemspec
+  @gemspec ||= eval(File.read(Gemspec_filename), binding, Gemspec_filename)
+end
+
+require 'rubygems/package_task'
+
+desc "Validate the gemspec"
+task :gemspec do
+  gemspec.validate
+end
+
+desc "Build the gem"
+task :package=>:gem
+task :gem=>:gemspec do
+  Dir.chdir(ROOT_DIR) do
+    sh "gem build solvebio.gemspec"
+    FileUtils.mkdir_p 'pkg'
+    FileUtils.mv gemspec.file_name, 'pkg'
+  end
+end
+
+desc "Install the gem locally"
+task :install => :gem do
+  Dir.chdir(ROOT_DIR) do
+    sh %{gem install --both pkg/#{gemspec.file_name}}
+  end
+end
+
+require 'rake/testtask'
+desc "Test everything."
+Rake::TestTask.new(:test) do |t|
+  t.libs << './lib'
+  t.test_files = FileList['test/test-*.rb']
+  t.verbose = true
+end
+
+
+require 'rbconfig'
+RUBY_PATH = File.join(RbConfig::CONFIG['bindir'],
+                      RbConfig::CONFIG['RUBY_INSTALL_NAME'])
+desc "Run all of the demo files."
+task :'run-demo' do
+    FileList['demo/*.rb']+FileList['demo/*/*.rb'].each do |ruby_file|
+        puts(('-' * 20) + ' ' + ruby_file + ' ' + ('-' * 20))
+        system(RUBY_PATH, ruby_file)
+    end
+end
+
+task :test => :lib
+
+desc "same as test"
+task :check => :test
+task :default => :test

data/bin/solvebio.rb

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+#!/usr/bin/env ruby
+# -*- coding: utf-8 -*-
+
+# SolveBio Ruby command-line program
+
+require_relative '../lib/solvebio'
+require_relative '../lib/cli/options'
+require_relative '../lib/cli/irb'
+
+DIR = File.dirname(__FILE__)
+TEST_PROGRAM = File.join(DIR, %w(.. demo test-api.rb))
+
+include SolveBio::CLIOptions
+options, rest, parser = process_options(ARGV)
+
+rest = ['shell'] if rest.empty?
+
+include SolveBio::Auth
+
+cmd = rest.shift
+case cmd
+when 'shell'
+    IRB::shell
+when 'login'
+    login *rest
+when 'logout'
+    logout
+when 'whoami'
+    whoami
+when 'test'
+    system(TEST_PROGRAM)
+else
+    $stderr.puts "Unknown solvbio.rb command: #{cmd}"
+    $stderr.puts parser
+    exit 1
+end

data/demo/README.md

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+# Intro
+
+SolveBio aims to provide robust access to highly curated biological datasets. While our datasets do not conform to any proprietary formats, they are organized in a systematic way.
+
+*Depositories* (data repositories) are simply versioned containers of datasets
+
+A depository contains many versions, which in turn contain many datasets. Each dataset represents an independent “datastore”. Datasets store semi-structured data similar to typical “NoSQL” databases.
+
+The [depository folder](https://github.com/solvebio/solvebio-ruby/blob/dev/demo/depository) has examples involving retrieving, getting version information or listing depositories.
+
+*Datasets* are access points to data. Dataset names are unique within versions of a depository. The
+[dataset folder](https://github.com/solvebio/solvebio-ruby/blob/dev/demo/dataset) has programs for retrieving properties of a dataset.
+
+However, issuing queries on a dataset is probably what you will most want to do. The [query folder](https://github.com/solvebio/solvebio-ruby/blob/dev/demo/query) contains examples of queries.

data/demo/dataset/facets.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::DatsetField.retrieve ... facets
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+fields = SolveBio::DatasetField.retrieve(691).facets
+puts fields

data/demo/dataset/field.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::DatsetField.retrieve
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+fields = SolveBio::DatasetField.retrieve(1)
+puts fields

data/demo/depository/README.md

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+# Depositories
+
+A *depository* (or data repository) is like a source code repository,
+but for datasets. Depositories have one or more versions, which in
+turn contain one or more datasets. Typically, depositories contain a
+series of datasets that are compatible with each other (i.e. they come
+from the same data source or project).
+
+Right now, all depositories are curated by the SolveBio team.
+
+* retrieve a depository
+
+    The [retrieve.rb](https://github.com/solvebio/solvebio-ruby/blob/dev/demo/depository/retrieve.rb) Ruby program shows how to retrieve a single depository
+
+* listing a depository
+
+    The [all.rb](https://github.com/solvebio/solvebio-ruby/blob/dev/demo/depository/all.rb) Ruby program shows how to list all depositories
+
+* list all versions of a depository
+
+    The [versions-all.rb](https://github.com/solvebio/solvebio-ruby/blob/dev/demo/depository/all.rb) Ruby program shows how to list all versions
+    of a depository
+
+See also the [SolveBio Depository API](https://www.solvebio.com/docs/api/#depositories)

data/demo/depository/all.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::Depository.all
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio::api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+depo = SolveBio::Depository.all
+puts depo.to_s

data/demo/depository/retrieve.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::Depository.retrieve
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+depo = SolveBio::Depository.retrieve('ClinVar')
+puts depo.to_s

data/demo/depository/versions-all.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::Depository.retrieve({DEPOSITORY_ID}).versions.all
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+depo = SolveBio::Depository.retrieve('ClinVar').versions.all
+puts depo.to_s

data/demo/query/query-filter.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::Query with simple equality tests, sometimes
+# with "and" or "or"
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+ds = SolveBio::Dataset.retrieve('ClinVar/2.0.0-1/Variants')
+
+results = ds.query.filter :hg19_start__in  => [148562304, 148459988]
+
+puts results.to_h  # Show as a hash
+puts '=' * 10
+puts results       # show in a more formatted way
+
+# Here is the same thing but a little more inefficiently
+
+filters2 =
+    SolveBio::Filter.new(:hg19_start => 148459988) |
+    SolveBio::Filter.new(:hg19_start => 148562304) |
+
+results = ds.query(:filters => filters2)
+
+puts '=' * 10
+puts results

data/demo/query/query.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::Query
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+dataset = SolveBio::Dataset.retrieve('ClinVar/2.0.0-1/Variants')
+puts dataset.query

data/demo/query/range-filter.rb

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+#!/usr/bin/env ruby
+# Simple use of SolveBio::Query
+
+require 'solvebio'
+
+# SolveBio.api_key = 'set-me-correctly'
+unless SolveBio.api_key
+    puts 'Please set SolveBio.api_key. Hint: solvebio.rb login'
+    exit 1
+end
+
+filters = SolveBio::RangeFilter.
+    new "hg38", "13", 32200000, 32500000
+
+ds = SolveBio::Dataset.retrieve 'ClinVar/2.0.0-1/Variants'
+
+results = ds.query(:filters => filters)
+puts results

data/demo/test-api.rb

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+#!/usr/bin/env ruby
+# Test SolveBio API
+require_relative  '../lib/solvebio'
+
+DEPOSITORY         = 'ClinVar'
+DEPOSITORY_VERSION = "#{DEPOSITORY}/2.0.0-1"
+DATASET            = "#{DEPOSITORY_VERSION}/Variants"
+
+# Custom Exception class for running basic tests
+class TestFail < RuntimeError
+end
+
+DEBUG = ARGV.size > 1
+
+# Function for running small tests with nice printing and checks
+def run_and_verify(func, title='run a test', check_func_symbols)
+    puts "Trying to #{title}..."
+    response = func.call
+    check_func_symbols.each do |sym|
+        unless response.send(sym)
+            raise TestFail, "Failed on #{DATASET} using #{sym}"
+        end
+    end
+    puts "\x1b[32mOK!\x1b[39m\n"
+    return response
+end
+
+creds = SolveBio::Credentials.get_credentials
+unless creds
+    puts 'You must be logged in as a SolveBio user ' +
+        'in order to run the test suite!'
+    exit(1)
+end
+
+SolveBio::Client.client.api_key = creds[1]
+
+begin
+    # depository things
+    load_depo = proc { SolveBio::DepositoryVersion.
+        retrieve(DEPOSITORY_VERSION) }
+    begin
+        dataset = run_and_verify(load_depo, 'load a depository version',
+                                 [:id, :to_s, :inspect, :instance_url])
+    rescue SolveBio::Error => exc
+        raise TestFail, "Loading #{DEPOSITORY_VERSION} failed! (#{exc})"
+    end
+
+    # depository things
+    load_depo = proc { SolveBio::Depository.retrieve(DEPOSITORY) }
+    begin
+        dataset = run_and_verify(load_depo, 'load a depository',
+                                 [:to_s, :versions, :versions_url,
+                                 :first, :max, :min])
+    rescue SolveBio::Error => exc
+        raise TestFail, "Loading #{DEPOSITORY} failed! (#{exc})"
+    end
+
+    # try loading a Dataset
+    load_dataset = proc { SolveBio::Dataset.retrieve(DATASET) }
+    begin
+        dataset = run_and_verify(load_dataset, 'load a dataset',
+                                 [:depository, :depository_version, :fields])
+    rescue SolveBio::Error => exc
+        raise TestFail, "Loading #{DATASET} failed! (#{exc})"
+    end
+
+    # try loading a DatasetField
+    load_dataset = proc { SolveBio::DatasetField.retrieve(1) }
+    begin
+        dataset = run_and_verify(load_dataset, 'load a dataset field',
+                                 [:facets, :instance_url])
+    rescue SolveBio::Error => exc
+        raise TestFail, "Loading DataSetField 1 failed! (#{exc})"
+    end
+
+    # run a basic query
+    query_dataset = proc {
+        dataset = SolveBio::Dataset.retrieve(DATASET)
+        dataset.query({:paging=>true, :limit => 10})
+    }
+    query = run_and_verify(query_dataset, 'run a basic query',
+                           [:size, :inspect, :clone])
+
+    # # run a basic filter
+    # basic_filter = proc { query.filter(clinical_significance='Pathogenic') }
+    # run_and_verify(basic_filter, 'run a basic filter')
+
+    # # run a range filter
+    # range_filter = solvebio.RangeFilter(build="hg19",
+    #                                     chromosome=1,
+    #                                     start=100000,
+    #                                     last=900000)
+    # run_and_verify(proc { query.filter(range_filter) },
+    #                'run a range filter')
+
+rescue TestFail, exc
+    puts "\n\n\x1b[31mFAIL!\x1b[39m #{exc}"
+end