solvebio 1.6.1 → 1.7.0

data/Makefile

@@ -1,17 +0,0 @@
-# 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/demo/README.md

@@ -1,14 +0,0 @@
-# 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/master/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/master/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/master/demo/query) contains examples of queries.

data/demo/cheatsheet.rb

@@ -1,31 +0,0 @@
-# Cheet sheet for SolveBio API
-require 'solvebio'
-
-# Load the Dataset object
-dataset = SolveBio::Dataset.retrieve('ClinVar/2.0.0-1/Variants')
-
-# Print the Dataset
-puts dataset.query()
-
-# Get help (fields/facets)
-dataset.help()
-
-# Query the dataset (filterless)
-q = dataset.query()
-
-filters = SolveBio::Filter.new :gene_symbols => "BRCA2"
-
-puts dataset.query(:filters => filters)
-
-# Multiple keyword filter (boolean 'or')
-filters = SolveBio::Filter.new :gene_symbols => "BRCA2"
-filters |= SolveBio::Filter.new :gene_symbols => "BRCA1"
-
-# Same as above 'or' in one go using 'in'
-filters = SolveBio::Filter.new :gene_symbols__in => ["BRCA2", "BRCA1"]
-
-puts dataset.query(:filters => filters)
-
-# Range filter. Like 'in' for a contiguous numeric range
-dataset.query(filters =>
-              SolveBio::RangeFilter.new('hg38', "13", 32_200_000, 32_200_500))

data/demo/dataset/facets.rb

@@ -1,13 +0,0 @@
-#!/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

@@ -1,13 +0,0 @@
-#!/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

@@ -1,24 +0,0 @@
-# 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/master/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/master/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/master/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

@@ -1,13 +0,0 @@
-#!/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

@@ -1,13 +0,0 @@
-#!/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

@@ -1,13 +0,0 @@
-#!/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

@@ -1,30 +0,0 @@
-#!/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

@@ -1,13 +0,0 @@
-#!/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

@@ -1,18 +0,0 @@
-#!/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

@@ -1,98 +0,0 @@
-#!/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

data/lib/cli/auth.rb

@@ -1,122 +0,0 @@
-#!/usr/bin/env ruby
-# -*- coding: utf-8 -*-
-
-require 'readline'
-require 'io/console'
-
-require_relative  '../errors'
-require_relative  '../credentials'
-require_relative  '../client'
-
-module SolveBio::Auth
-
-    def ask_for_credentials(email=nil)
-        while true
-            email ||= Readline.readline('Email address: ', true)
-            print 'Password (typing will be hidden): '
-            password = STDIN.noecho(&:gets).chomp
-            puts
-            # FIXME: validate email address?
-            if email and password
-                return email, password
-            else
-                # FIXME: could say which one is needed.
-                print 'Email and password are both required.'
-                return nil, nil
-            end
-        end
-    end
-
-    def send_install_report
-        require 'socket';
-        data = {
-            :hostname              => Socket.gethostname(),
-            :ruby_version          => SolveBio::RUBY_VERSION,
-            :ruby_implementation   => SolveBio::RUBY_IMPLEMENTATION,
-            # :platform              => platform(),
-            :architecture          => SolveBio::ARCHITECTURE,
-            # :processor             => processor(),
-        }
-        SolveBio::Client.client
-            .request('post', '/v1/reports/install',
-                     {:params => data}) rescue nil
-    end
-
-
-    include SolveBio::Credentials
-
-    module_function
-
-    #
-    # Prompt user for login information (email/password).
-    # Email and password are used to get the user's auth_token key.
-    #
-    def login(email=nil)
-        delete_credentials
-
-        email, password = ask_for_credentials email unless
-            email and password
-        data = {
-            :email    => email,
-            :password => password
-        }
-
-        # FIXME: begin/rescue is a direct translation of the Python
-        # code.  Not sure if it's valid here, or what the equivalent
-        # is.
-        begin
-            response = SolveBio::Client.client
-                .request 'post', '/v1/auth/token', {:payload => data}
-        rescue SolveBio::Error => e
-            puts "Login failed: #{e.to_s}"
-            return false
-        else
-            save_credentials(email.downcase, response['token'])
-            # reset the default client's auth token
-            SolveBio::Client.client.api_key = response['token']
-            send_install_report
-            puts 'You are now logged-in.'
-            return true
-        end
-    end
-
-    def logout
-        if get_credentials()
-            delete_credentials()
-            SolveBio::Client.client.api_key = nil
-            puts 'You have been logged out.'
-            return true
-        else
-            puts 'You are not logged-in.'
-            return false
-        end
-    end
-
-    def whoami
-        creds = get_credentials()
-        if creds
-            puts creds[0]
-            return creds[0]
-        else
-            puts 'You are not logged-in.'
-            return nil
-        end
-    end
-
-end # SolveBio::Auth
-
-# Demo code
-if __FILE__ == $0
-    include SolveBio::Auth
-    case ARGV[0]
-    when 'password'
-        email, password = ask_for_credentials
-        puts email, password
-    when 'login'
-        login
-    when 'logout'
-        logout
-    when 'whoami'
-        whoami
-    end
-end