bel-search-sqlite 0.4.0.beta1

checksums.yaml

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data/.gemspec

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+Gem::Specification.new do |spec|
+  spec.name                     = 'bel-search-sqlite'
+  spec.version                  = '0.4.0.beta1'
+  spec.summary                  = '''
+                                    Resource search plugin for bel.rb using Sqlite FTS.
+                                  '''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
+  spec.description              = '''
+                                    A resource search plugin for bel.rb that uses FTS tables in
+                                    Sqlite to search annotation and namespace values. Built to
+                                    run on MRI to take advantage of C extensions.
+                                  '''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
+  spec.license                  = 'Apache-2.0'
+  spec.authors                  = [
+                                    'Anthony Bargnesi',
+                                  ]
+  spec.email                    = [
+                                    'abargnesi@selventa.com',
+                                  ]
+  spec.files                    = [
+                                    Dir.glob('lib/**/*.{rb,erb}'),
+                                    __FILE__,
+                                    'CHANGELOG.md',
+                                    'LICENSE',
+                                    'INSTALL.md',
+                                    'README.md',
+                                  ].flatten!
+  spec.executables              = Dir.glob('bin/*').map(&File.method(:basename))
+  spec.homepage                 = 'https://github.com/OpenBEL/bel.rb-search-plugin'
+  spec.rdoc_options             = [
+                                    '--title', 'BEL Resource Search - Sqlite',
+                                    '--main', 'README.md',
+                                    '--line-numbers',
+                                    'CHANGELOG.md',
+                                    'LICENSE',
+                                    'INSTALL.md',
+                                    'README.md',
+                                  ]
+
+  spec.platform                 = 'ruby'
+  spec.required_ruby_version    = '>= 2.0.0'
+  spec.add_runtime_dependency     'sequel',  '4.28.0'
+  spec.add_runtime_dependency     'sqlite3', '1.3.11'
+  spec.post_install_message     = %Q{
+******************************
+*  bel-search-sqlite plugin  *
+******************************
+Thank you for installing the bel-search-sqlite plugin to bel.rb.
+
+This plugin is built to run on Ruby and uses sqlite3 + C
+extensions to access a SQLite database for full-text search of
+annotation and namespace values.
+
+To verify the bel-search-sqlite plugin can be used by bel.rb
+execute the bel.rb command:
+
+    bel plugins --list
+
+To access this within bel.rb execute the following ruby code:
+
+    require 'bel'
+    search_plugin = BEL::Resource::Search.plugins[:sqlite]
+    search_plugin.create_search(
+      :database => 'resources.db'
+    )
+
+}
+end
+# vim: ft=ruby ts=2 sw=2:
+# encoding: utf-8

data/CHANGELOG.md

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+# Change Log
+All notable changes to bel-search-sqlite will be documented in this file. The curated log begins at changes to version 0.1.0.
+
+This project adheres to [Semantic Versioning](http://semver.org/).
+
+## [0.1.0][0.1.0] - 2015-11-19
+### Fixed
+### Changed
+### Added

data/INSTALL.md

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+Install
+=======
+
+This library requires [Ruby](https://www.ruby-lang.org) (**>= 2.0.0**).  See [how to install ruby](https://github.com/OpenBEL/bel.rb-search-sqlite/blob/master/INSTALL_RUBY.md).
+
+Install from [RubyGems.org](http://rubygems.org/gems/bel-search-sqlite)
+
+```bash
+    gem install bel-search-sqlite
+```
+
+Build from master branch
+
+1. Obtain source for master branch.
+  - `git clone git@github.com:OpenBEL/bel.rb-search-sqlite.git`
+
+2. Build
+  - `gem build bel-search-sqlite.gemspec`
+  - `gem install bel-search-sqlite-[VERSION].gem`

data/LICENSE

@@ -0,0 +1,191 @@
+Apache License
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+http://www.apache.org/licenses/
+
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+
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+
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data/README.md

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+sqlite3 resource search
+=======================
+
+This implements a Resource Search plugin for [bel.rb](http://github.com/OpenBEL/bel.rb) backed by a [Sqlite3](http://sqlite.org/) database. The database utilizes Sqlite's FTS tables to provide full-text query over BEL Resource concepts.
+
+Features
+--------
+
+- Plugs in to bel.rb as a Resource Search API implementation.
+- Efficient full-text searching.
+
+Todo
+----
+
+- Implement sqlite3 database creation as an executable. Currently code to build the sqlite3 FTS database exists at [rdf-misc](https://github.com/OpenBEL/rdf-misc).
+
+How can I use this?
+------------------
+
+bel.rb provides an [approach to plugins](https://github.com/OpenBEL/bel.rb/wiki/Plugins-in-bel.rb) that is meant to be uncomplicated. The following steps will get you started:
+
+- Build gem with `gem build .gemspec` and install with `gem install bel-search-sqlite-1.0.0.gem`.
+- on JRuby, build gem with `gem build .gemspec-java` and install with `gem install bel-search-sqlite-1.0.0-java.gem`.
+- Now you have this plugin installed and ready for use in bel.rb!
+- With bel.rb installed run the command `bel plugins` to list available plugins.
+
+```bash
+$ bin/bel plugins
+Resource Search plugins
+-----------------------
+
+ Name:        Resource search on sqlite FTS
+ Description: A resource search implementation using sqlite FTS capabilities.
+```
+
+- To create the search implementation in Ruby try:
+
+```ruby
+search_plugin = BEL::Resource::Search.plugins[:sqlite]
+
+search_plugin.create_search(:database_file => 'resources.db')
+```
+
+- Enjoy FTS goodness with Sqlite!

data/lib/bel/resource/search/plugins/sqlite.rb

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+require 'bel'
+
+module BEL::Resource::Search::Plugins
+
+  module Sqlite
+
+    extend BEL::Resource::Search::ClassMethods
+
+    NAME        = 'Resource search on sqlite FTS'
+    DESCRIPTION = 'A resource search implementation using sqlite FTS capabilities.'
+
+    # @see BEL::Resource::Search::ClassMethods#create_search
+    def self.create_search(options = {})
+      database_file = options[:database_file]
+      unless database_file
+        raise ArgumentError.new(':database_file option must be provided')
+      end
+
+      # database abstraction
+      require 'sequel'
+      # Resource search implementation
+      require_relative 'sqlite/sqlite3'
+
+      case RUBY_ENGINE
+      when "jruby"
+        require 'jdbc/sqlite3'
+        Sqlite3FTS.new(Sequel.connect("jdbc:sqlite:#{database_file}"))
+      when "ruby", "rbx"
+        require 'sqlite3'
+        Sqlite3FTS.new(Sequel.connect("sqlite://#{database_file}"))
+      else
+        raise RuntimeError.new("Unsupported ruby engine: #{RUBY_ENGINE}")
+      end
+    end
+
+    def self.name
+      NAME
+    end
+
+    def self.description
+      DESCRIPTION
+    end
+  end
+end

data/lib/bel/resource/search/plugins/sqlite/sqlite3.rb

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+require 'bel'
+require 'erb'
+require 'pathname'
+require 'sequel'
+
+module BEL::Resource::Search::Plugins
+  module Sqlite
+
+    class Sqlite3FTS
+      include BEL::Resource::Search
+      include BEL::Resource::Search::API
+
+      QUERY_TEMPLATE = ERB.new(
+        File.read(Pathname(File.dirname(__FILE__)) + 'sqlite3_template.erb'),
+        nil,
+        '>'
+      )
+      PREPARED_STATEMENTS = {}
+
+      def initialize(db)
+        @db = db
+      end
+
+      # @see BEL::Resource::Search::API#search
+      def search(query_expression, concept_type = nil, scheme_uri = nil, species = nil, options = {})
+        # required SQL parameters
+        match = query_expression.encode('UTF-8')
+        start = (options.delete(:start) ||  0).to_i
+        size  = options.delete(:size)   || -1
+        if size.to_i.zero?
+          fail ArgumentError.new(":size is zero")
+        end
+
+        # optional SQL parameters
+        options = {
+          :concept_type => (concept_type ? concept_type.to_s.encode('UTF-8') : nil),
+          :scheme_uri   => (scheme_uri ? scheme_uri.to_s.encode('UTF-8') : nil),
+          :species      => (species ? species.to_s.encode('UTF-8') : nil),
+        }
+        options.keep_if { |key, value| value != nil }
+
+        query   = QUERY_TEMPLATE.result(binding)
+        enum    = @db.fetch(query, :match => match, :start => start, :size => size)
+
+        if enum.respond_to? :lazy
+          enum = enum.lazy
+        end
+
+        enum.map { |row|
+          row_hash = row.to_hash
+          row_hash[:alt_labels] = (row_hash[:alt_labels] || '').split('|')
+          SearchResult.new(row_hash)
+        }
+      end
+    end
+  end
+end

data/lib/bel/resource/search/plugins/sqlite/sqlite3_template.erb

@@ -0,0 +1,18 @@
+SELECT
+  distinct uri, scheme_uri, species, identifier, pref_label, title, alt_labels,
+  snippet(concepts_fts, '<<', '>>', '...', -1) AS snippet
+FROM
+  concepts_fts
+WHERE
+  concepts_fts MATCH :match
+<% [:concept_type, :scheme_type, :scheme_uri, :species].each do |column| %>
+  <% if options[column] %>
+
+  AND <%= column %> = <%= ":#{column}" %>
+
+  <% end %>
+<% end %>
+ORDER BY
+  length(pref_label) ASC
+LIMIT  :size
+OFFSET :start

metadata

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+--- !ruby/object:Gem::Specification
+name: bel-search-sqlite
+version: !ruby/object:Gem::Version
+  version: 0.4.0.beta1
+platform: ruby
+authors:
+- Anthony Bargnesi
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-12-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: sequel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 4.28.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 4.28.0
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.3.11
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.3.11
+description: " A resource search plugin for bel.rb that uses FTS tables in Sqlite
+  to search annotation and namespace values. Built to run on MRI to take advantage
+  of C extensions. "
+email:
+- abargnesi@selventa.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gemspec"
+- CHANGELOG.md
+- INSTALL.md
+- LICENSE
+- README.md
+- lib/bel/resource/search/plugins/sqlite.rb
+- lib/bel/resource/search/plugins/sqlite/sqlite3.rb
+- lib/bel/resource/search/plugins/sqlite/sqlite3_template.erb
+homepage: https://github.com/OpenBEL/bel.rb-search-plugin
+licenses:
+- Apache-2.0
+metadata: {}
+post_install_message: |2+
+
+  ******************************
+  *  bel-search-sqlite plugin  *
+  ******************************
+  Thank you for installing the bel-search-sqlite plugin to bel.rb.
+
+  This plugin is built to run on Ruby and uses sqlite3 + C
+  extensions to access a SQLite database for full-text search of
+  annotation and namespace values.
+
+  To verify the bel-search-sqlite plugin can be used by bel.rb
+  execute the bel.rb command:
+
+      bel plugins --list
+
+  To access this within bel.rb execute the following ruby code:
+
+      require 'bel'
+      search_plugin = BEL::Resource::Search.plugins[:sqlite]
+      search_plugin.create_search(
+        :database => 'resources.db'
+      )
+
+rdoc_options:
+- "--title"
+- BEL Resource Search - Sqlite
+- "--main"
+- README.md
+- "--line-numbers"
+- CHANGELOG.md
+- LICENSE
+- INSTALL.md
+- README.md
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.0.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">"
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5.1
+signing_key: 
+specification_version: 4
+summary: Resource search plugin for bel.rb using Sqlite FTS.
+test_files: []
+has_rdoc: