ontologies_api_client 0.0.5 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -8,12 +8,15 @@
 
 Configuration is provided by calling the <code>config</code> method
 
-    LinkedData::Client.config do |config|
-      config.rest_url   = "http://stagedata.bioontology.org"
-      config.apikey     = "your_apikey"
-      config.links_attr = "links"
-      config.cache      = false
-    end
+```ruby
+require 'ontologies_api_client'
+LinkedData::Client.config do |config|
+  config.rest_url   = "http://stagedata.bioontology.org"
+  config.apikey     = "your_apikey"
+  config.links_attr = "links"
+  config.cache      = false
+end
+```
 
 ## Usage
 
@@ -28,36 +31,82 @@ There are multiple ways to retrieve individual or groups of resources.
 
 To retrieve a single record by id:
 
-    Category.find("http://data.bioontology.org/categories/all_organisms")
+```ruby
+Category.find("http://data.bioontology.org/categories/all_organisms")
+```
 
 ***Where***
 
 To retrieve all records that match a particular an in-code filter. The code is a block that should return a
 boolean that indicates whether or not the item should be included in the results.
 
-    categories = Category.where do |ont|
-      ont.name.include?("health")
-    end
+```ruby
+categories = Category.where do |ont|
+  ont.name.include?("health")
+end
+```
 
 ***Find By***
 
 You can use shortcut methods to find by particular attribute/value pairs
 (attributes are named in the method and multiple can be provided by connecting them with 'and').
 
-    categories = Category.find_by_parentCategory("http://data.bioontology.org/categories/anatomy")
+```ruby
+categories = Category.find_by_parentCategory("http://data.bioontology.org/categories/anatomy")
+```
+
+## Create / Update / Delete
+
+Creates are done via HTTP POST, update via HTTP PATCH, and deletes using HTTP DELETE.
+
+### Create
+
+```ruby
+ontology_values = {
+  acronym: "MY_ONT",
+  name: "My Ontology",
+  administeredBy: [http://data.bioontology.org/users/my_user]
+}
+ontology = LinkedData::Client::Models::Ontology.new(values: ontology_values)
+response = ontology.save
+puts ontology_saved.errors
+```
+
+### Update
+
+```ruby
+new_values = {
+  administeredBy: [http://data.bioontology.org/users/my_other_user]
+}
+ontology = LinkedData::Client::Models::Ontology.find_by_acronym("MY_ONT")
+ontology.update_from_params(params[:ontology])
+response = ontology.update
+puts response.errors
+```
+
+### Delete
+
+```ruby
+ontology = LinkedData::Client::Models::Ontology.find_by_acronym("MY_ONT")
+response = ontology.delete
+```
 
 ## Hypermedia Navigation
 
 All resources have a collection of hypermedia links, available by calling the 'links' method.
 These links can be navigated by calling the 'explore' method and chaining the link:
 
-    ontology = Category.find("http://data.bioontology.org/categories/all_organisms")
-    classes = ontology.explore.classes
+```ruby
+ontology = Category.find("http://data.bioontology.org/categories/all_organisms")
+classes = ontology.explore.classes
+```
 
 Links may contain a [URI template](http://tools.ietf.org/html/rfc6570). In this case, the template can be
 populated by passing in ordered values for the template tokens:
 
-    cls = ontology.explore.single_class("http://my.class.id/class1")
+```ruby
+cls = ontology.explore.single_class("http://my.class.id/class1")
+```
 
 ## Defining Resources
 
@@ -67,10 +116,12 @@ providing attribute names that we want to retreive for each media type.
 
 For example:
 
-    class Category < LinkedData::Client::Base
-      include LinkedData::Client::Collection
-      @media_type = "http://data.bioontology.org/metadata/Category"
-    end
+```ruby
+class Category < LinkedData::Client::Base
+  include LinkedData::Client::Collection
+  @media_type = "http://data.bioontology.org/metadata/Category"
+end
+```
 
 ### Collections
 
@@ -89,14 +140,14 @@ For questions please email [support@bioontology.org](support@bioontology.org.)
 
 ## License
 
-Copyright (c) 2013, The Board of Trustees of Leland Stanford Junior University All rights reserved.
+Copyright (c) 2014, The Board of Trustees of Leland Stanford Junior University All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-    Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-    Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 
 THIS SOFTWARE IS PROVIDED BY THE BOARD OF TRUSTEES OF LELAND STANFORD JUNIOR UNIVERSITY ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL The Board of Trustees of Leland Stanford Junior University OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of The Board of Trustees of Leland Stanford Junior University.
+The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of The Board of Trustees of Leland Stanford Junior University.

data/lib/ontologies_api_client/collection.rb

@@ -56,6 +56,13 @@ module LinkedData
           entry_point(@media_type, params)
         end
 
+        ##
+        # Get all resources from the base collection for a resource as a hash with resource ids as the keys
+        def all_to_hash(*args)
+          all = all(*args)
+          Hash[all.map {|e| [e.id, e]}]
+        end
+
         ##
         # Find certain resources from the collection by passing a block that filters results
         def where(params = {}, &block)

data/lib/ontologies_api_client/http.rb

@@ -55,15 +55,17 @@ module LinkedData
         raw = options[:raw] || false # return the unparsed body of the request
         params = params.delete_if {|k,v| v == nil || v.to_s.empty?}
         params[:ncbo_cache_buster] = Time.now.to_f if raw # raw requests don't get cached to ensure body is available
+        invalidate_cache = params.delete(:invalidate_cache) || false
 
         begin
           puts "Getting: #{path} with #{params}" if $DEBUG
           begin
             response = conn.get do |req|
               req.url path
-              req.params = params
+              req.params = params.dup
               req.options[:timeout] = 60
               req.headers.merge(headers)
+              req.headers[:invalidate_cache] = invalidate_cache
             end
           rescue Exception => e
             params = Faraday::Utils.build_query(params)

data/lib/ontologies_api_client/link_explorer.rb

@@ -1,4 +1,4 @@
-require 'cgi'
+require 'uri'
 require_relative 'http'
 
 module LinkedData
@@ -61,7 +61,7 @@ module LinkedData
         values = values.dup
         values = [values] unless values.is_a?(Array)
         return url.gsub(/(\{.*?\})/) do
-          CGI.escape(values.shift)
+          URI.escape(values.shift, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))
         end
       end
 

data/lib/ontologies_api_client/middleware/faraday-object-cache.rb

@@ -4,13 +4,15 @@ require 'lz4-ruby'
 require_relative '../http'
 
 module Faraday
-  ##
-  # This middleware causes Faraday to return
-
   class ObjectCacheResponse < Faraday::Response
     attr_accessor :parsed_body
   end
 
+  ##
+  # This middleware causes Faraday to return an actual object instead of a response
+  # This is done so that the object is cached instead of the unparsed json body.
+  # Otherwise, we have to re-parse the json on every cache hit, which is extrememly costly
+  # when compared to unmarshaling an object.
   class ObjectCache < Faraday::Middleware
     def initialize(app, *arguments)
       super(app)
@@ -26,11 +28,21 @@ module Faraday
     end
 
     def call(env)
+      invalidate_cache = env[:request_headers].delete(:invalidate_cache)
+
       # Add if newer than last modified statement to headers
       request_key = cache_key_for(create_request(env))
       last_modified_key = "LM::#{request_key}"
       last_retrieved_key = "LR::#{request_key}"
 
+      # If we invalidate the cache, then it forces a clean request
+      if invalidate_cache
+        cache_delete(request_key)
+        cache_delete(last_modified_key)
+        cache_delete(last_retrieved_key)
+        env[:request_headers]["Cache-Control"] = "no-cache"
+      end
+
       # If we made the last request within the expiry
       if cache_exist?(last_retrieved_key) && cache_exist?(request_key)
         puts "DEBUG not expired #{env[:url].to_s}" if $CACHE_DEBUG
@@ -171,6 +183,9 @@ module Faraday
       obj
     end
 
+    def cache_delete(key)
+      @store.delete(key)
+    end
 
     # Internal: Generates a String key for a given request object.
     # The request object is folded into a sorted Array (since we can't count

data/lib/ontologies_api_client/models/class.rb

@@ -1,11 +1,10 @@
-require "cgi"
+require "uri"
 require_relative "../base"
 
 module LinkedData
   module Client
     module Models
       class Class < LinkedData::Client::Base
-        require 'cgi'
         HTTP = LinkedData::Client::HTTP
         @media_type = "http://www.w3.org/2002/07/owl#Class"
         @include_attrs = "prefLabel,definition,synonym,obsolete,childrenCount"
@@ -41,12 +40,12 @@ module LinkedData
         def purl
           return "" if self.links.nil?
           ont = self.explore.ontology
-          "#{LinkedData::Client.settings.purl_prefix}/#{ont.acronym}/#{CGI.escape(self.id)}"
+          "#{LinkedData::Client.settings.purl_prefix}/#{ont.acronym}?conceptid=#{URI.escape(self.id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}"
         end
 
         def self.find(id, ontology, params = {})
           ontology = HTTP.get(ontology, params)
-          ontology.explore.class(CGI.escape(id))
+          ontology.explore.class(URI.escape(id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")))
         end
 
         def self.search(*args)

data/lib/ontologies_api_client/models/mapping.rb

@@ -1,4 +1,4 @@
-require "cgi"
+require "uri"
 require_relative "../base"
 
 module LinkedData
@@ -11,11 +11,11 @@ module LinkedData
         @media_type = "http://data.bioontology.org/metadata/Mapping"
 
         def self.find(id, params = {})
-          HTTP.get(mappings_url_prefix + CGI.escape(id), params)
+          HTTP.get(mappings_url_prefix + URI.escape(id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")), params)
         end
 
         def delete
-          HTTP.delete(mappings_url_prefix + CGI.escape(self.id))
+          HTTP.delete(mappings_url_prefix + URI.escape(self.id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")))
         end
 
         private

data/lib/ontologies_api_client/models/ontology.rb

@@ -24,7 +24,7 @@ module LinkedData
         end
 
         def viewing_restricted?
-          private? && licensed?
+          private? || licensed?
         end
 
         def view?
@@ -39,28 +39,37 @@ module LinkedData
           end
         end
 
+        def access?(user)
+          return true if !viewing_restricted?
+          return false if user.nil?
+          return true if user.admin?
+          return self.full_acl.any? {|u| u == user.id}
+        end
+
         def admin?(user)
           return false if user.nil?
           return true if user.admin?
           return administeredBy.any? {|u| u == user.id}
         end
 
+        def invalidate_cache
+          self.class.all(invalidate_cache: true)
+          self.class.all(invalidate_cache: true, include_views: true)
+          HTTP.get(self.id, invalidate_cache: true) if self.id
+        end
+
+        # ACL with administrators
+        def full_acl
+          ((self.acl || []) + self.administeredBy).uniq
+        end
+
         # For use with select lists, always includes the admin by default
         def acl_select
           select_opts = []
-          return select_opts if self.acl.nil? or self.acl.empty?
-
-          if self.acl.nil? || self.acl.empty?
-            self.administeredBy.each do |userId|
-              select_opts << [User.get(userId).username, userId]
-            end
-          else
-            self.acl.each do |userId|
-              select_opts << [User.get(userId).username, userId]
-            end
+          self.full_acl.each do |userId|
+            select_opts << [User.get(userId).username, userId]
           end
-
-          (select_opts + self.administeredBy).uniq
+          select_opts
         end
 
         ##

data/lib/ontologies_api_client/read_write.rb

@@ -6,14 +6,17 @@ module LinkedData
       HTTP = LinkedData::Client::HTTP
 
       def save
-        # Create via post
-        HTTP.post(self.class.collection_path, self.to_hash)
+        resp = HTTP.post(self.class.collection_path, self.to_hash)
+        invalidate_cache()
+        resp
       end
 
       def update(options = {})
         values = options[:values] || changed_values()
         return if values.empty?
-        HTTP.patch(self.id, values)
+        resp = HTTP.patch(self.id, values)
+        invalidate_cache()
+        resp
       end
 
       def update_from_params(params)
@@ -46,7 +49,9 @@ module LinkedData
       end
 
       def delete
-        HTTP.delete(self.id)
+        resp = HTTP.delete(self.id)
+        invalidate_cache()
+        resp
       end
 
       private
@@ -75,6 +80,11 @@ module LinkedData
         return current_value.eql?(new_value) rescue current_value == new_value
       end
 
+      def invalidate_cache
+        self.class.all(invalidate_cache: true)
+        HTTP.get(self.id, invalidate_cache: true) if self.id
+      end
+
     end
   end
 end

data/ontologies_api_client.gemspec

@@ -10,13 +10,13 @@ Gem::Specification.new do |gem|
   gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
   gem.name          = "ontologies_api_client"
   gem.require_paths = ["lib"]
-  gem.version       = "0.0.5"
+  gem.version       = "0.0.6"
 
-  gem.add_dependency('multi_json')
-  gem.add_dependency('oj', '<= 2.0.14')
-  gem.add_dependency('faraday')
-  gem.add_dependency('excon')
-  gem.add_dependency('lz4-ruby')
+  gem.add_dependency('multi_json', '~> 1.8')
+  gem.add_dependency('oj', '~> 2.0')
+  gem.add_dependency('faraday', '~> 0.8')
+  gem.add_dependency('excon', '~> 0.29')
+  gem.add_dependency('lz4-ruby', '~> 0.1')
   gem.add_dependency('activesupport', '<= 3.0')
 
   # gem.executables = %w()

metadata

@@ -1,97 +1,97 @@
 --- !ruby/object:Gem::Specification
 name: ontologies_api_client
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
 platform: ruby
 authors:
 - Paul R Alexander
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-14 00:00:00.000000000 Z
+date: 2014-06-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: multi_json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: oj
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - <=
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.14
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - <=
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.14
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: faraday
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.8'
 - !ruby/object:Gem::Dependency
   name: excon
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.29'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.29'
 - !ruby/object:Gem::Dependency
   name: lz4-ruby
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.1'
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - <=
+    - - "<="
       - !ruby/object:Gem::Version
         version: '3.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - <=
+    - - "<="
       - !ruby/object:Gem::Version
         version: '3.0'
 description: Models and serializers for ontologies and related artifacts backed by
@@ -102,7 +102,7 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".gitignore"
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -146,17 +146,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: This library can be used for interacting with a 4store instance that stores